CAF (Common Assembly Format) - Version 2 Specification

CAF is a text format for describing sequence assemblies. It is acedb-compliant and is an extension of the ace-file format used earlier, but with support for base quality measures and a more extensive description of the Sequence data.

[Genome Research Limited]

Information
Attributes
User guide
Example file
ACeDB model
FTP downloads

Information

CAF is intended to be sufficently comprehensive that any assembly engine/editor such as Phrap, Consed, Gap, Acembly, FAK etc can derive all the information it needs from the CAF file without reading any other data, (except for trace information which is still held in SCF files). The eventual aim is to be able to freely convert between CAF and any other format so that different assembly programs can be combined. This aim is still some way off because of incompatibilities between these programs. Currently it is possible to convert to and from Phrap, FAK, and into GAP (the reverse is possible with some loss of information).

CAF Version 2 supports some additional tags (Insert_size, Ligation_no) for reads. More importantly, it has support for describing partially-assembled groups of contigs. The basic idea is that an Is_assembly Sequence object is an ordered set of Is_group Contig Group objects, listed by the Group_order tag. In turn, each Contig group is an ordered set of contigs listed by the Contig_order tag. It is thus easy to manipulate groups if contigs (eg that are believed to be adjacent) without having to use absolute coordinates.

In CAF files, Comments are any text preceded by //

CAF supports three object types, Sequence, DNA and BaseQuality. The Sequence type is the most complex. All base coordinates start at position 1 (NOT 0). These are the important Sequence attributes (others are available in the CAF acedb model but are not currently used by any processing module).

Sequence

Sequence : "Name"                       // Name of the Sequence
Is_read | Is_contig | Is_group | Is_assembly        // Type 
Padded | Unpadded                       // State
ProcessStatus "State" "Text"            // Reads only: Asp pass or failure, with reason. 
                                        // "State" can be:
                                        //   PASS, 
                                        //   SVEC (completely seq vector), 
                                        //   QUAL,(poor trace quality),
                                        //   CONT (contaminant, eg E.coli)
Asped "Date"                            // Reads only: Date processed
Dye Dye_terminator | Dye_primer         // Reads only: Chemistry
SCF_File "Filename"                     // Reads only: Name of SCF file containing trace data
Primer Unknown_primer | Universal_primer | Custom "Oligo"  // Reads only: primer type,
                                        //  including oligo sequence if Custom
Template "Template"                     // Reads only: Template name
Insert_size x1 x2                       // Predicted range [x1,x2] of insert size
Ligation_no "Text"                      // THe Ligation number (ie library identifier) for the read
Strand   Forward | Reverse              // Reads only: forward or reverse strand
Seq_vec   "Type" x1 x2 "Text"           // Sequencing vector from position x1 to position x2 inclusive
                                        // "Type" is redundant, set to SVEC by default. 
Clone_vec "Type" x1 x2 "Text"           // Cloning vector from position x1 to position x2 inclusive
                                        // "Type" is redundant, set to CVEC by default. 
Clipping  "Type" x1 x2 "Text"           // Clipping from position x1 to position x2 inclusive
GoldenPath "Read" x1 x2                 // Contigs only: Phrap Golden path: 
                                        // Use "Read" between contig coords x1, x2 inclusive
Tag "Type" x1 x2 "Text"                 // General Tag on interval [x1,x2] (used in GAP)
Assembled_from "Read" s1 s2 r1 r2       // Contigs only: Alignment of Read to contig. 
                                        // Interval [r1, r2] in the read align with [s1,s2] in contig. 
                                        // If s1 > s2 then align the reverse complement of [r1,r2] with [s1,s2].
Align_to_SCF s1 s2 r1 r2                // Reads only: Alignment of Read to original SCF base-calls. 
                                        // Similar to Assembled_from
Group_order  Group p1                   // Assemblies only: defines Group to be at group position p1 within assembly
Contig_order Contig q1                  // Groups only: Defines Contig to be at relative position q1 within group

DNA

DNA : "Name"                            // Name of sequence
ACGTGCGG......                          // The sequence: Use ACGT, N for unknowns, - for pads.

BaseQuality

BaseQuality : "Name"                    // Name of sequence
0 12 13 90 ...                          // Base qualities. These must be positive integers 
                                        // between 0 and 99 inclusive. If the Base Quality is present 
                                        // in must be the same length as the DNA

Sequence State: Padded vs Unpadded

The alignement of a reading to the contig can be Padded or Unpadded. Padded means that gaps ("-") have been inserted where required in both contig and aligned readings so that there is a 1-1 correspondence between the aligned DNAs. In a Padded assembly there is exactly one Assembled_from line for each aligned read in a contig, and the DNA objects contain "-" padding characters.

In an unpadded alignment all the pads are removed from the DNA objects and there are multiple Assembled_from lines for each reading in a contig. However, Within each Assembled_from line there is a 1-1 correspondence between the (possibly reverse-complemented) read interval [r1,r2] and the contig interval [s1,s2].

Some applications (eg auto-edit, gap) required padded alignments. Others require unpadded. The programs caf_pad and caf_depad allow one to move transparently between padded and unpadded states, without loss of information (well, almost - columns of pads are removed). Note that in a padded alignment with BaseQuality information it is necessary to attach a quality value to each pad to keep the lengths equal. By convention this is 1, but this may change.

[Another sequence state not considered here is "Loose". A Loose aligment of a read to a contig just says that [r1,r2] in the read aligned somehow with [s1,s2] in the contig, possibly with the inclusion of gaps.]

Example:

Sequence : hh26e2.s1
Is_read
Unpadded
SCF_File hh26e2.s1SCF
Template hh26e2
Dye Dye_primer
Primer Universal_primer 
Strand Forward
ProcessStatus PASS
Align_to_SCF 1 171 1 171
Align_to_SCF 172 595 173 596
Tag DONE 119 119 "AUTO-EDIT: replaced C by t at 119 (double, isolated, strong)"
Tag DONE 145 145 "AUTO-EDIT: replaced N by t at 145 (double, compound, strong)"
Tag DONE 146 146 "AUTO-EDIT: replaced T by g at 146 (double, compound, strong)"
Tag DONE 171 171 "AUTO-EDIT: deleted G at 171  (double, isolated, strong)"
Tag DONE 193 193 "AUTO-EDIT: replaced A by c at 193 (double, isolated, strong)"
Seq_vec SVEC 1 24 "M13mp18"
Clipping QUAL 56 117
Clipping ECLIP 46 241

DNA : hg02b9.s1
CGCTGCAGGTCGACTCTAGAGGCTCCCCTGAGCCGCTGTGGATTGAGGAGGTGAGGCGTG
AGGAGGTGAGGAGTGAGAAGGTCAGGAGGGACGGAGGTGACGAGTGAGGAGGCGAGGTGA
GGCGTTAGGAGGTGGGGAAGTCAGGAGGTGAGTCAGGACCTGAGGAGTCAGGGGGTGAGG
AGTTAGGTGGTCAGGAGTCAGGAGGTGACGAGTTAGGAGGTGGGGCAAGTGAGGAGGTGA
GGAGTGAGGACATGACGAGTGAGTAGGTGAGGAGTCACGGGGGTCAGGAACGTGACAAGG
TTTCGACGTCCAATCCATCGTTCCAGGACCTTCCAGCTTGTGTCCTCTGACAGTGACCTC
ACCTGCCAGGTCTGGCCCTCCTGGCAGGCAAGAGGGCCGGCCGTGGGGGCGGTGGAGGGG
GTGGCCTCCCAGGGGTGAAGTCGGGGGTTGGGCTCCGACCGTCTGGCCACCGTTGGGGGT
GAGCCCGGTGGGAGTGTTGGGGGGG

BaseQuality : hg02b9.s1
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 15 0 0 0 0 0 
0 18 17 17 0 18 0 0 0 0 0 0 0 0 0 0 19 0 15 0 0 0 0 18 17 24 
22 18 21 18 18 0 15 15 21 23 21 0 0 0 0 0 21 0 0 0 16 19 23 21 
0 0 0 0 0 21 21 22 0 0 0 0 0 0 0 0 0 0 0 0 18 18 23 22 23 23 
15 15 17 0 23 15 21 22 21 21 21 25 19 23 19 30 18 18 18 27 21 
0 0 0 0 0 0 25 18 22 15 0 0 0 15 0 21 17 0 0 0 0 0 18 0 0 0 16 
16 21 16 0 0 0 0 0 16 16 0 0 0 0 0 0 15 15 0 0 15 15 0 0 0 0 
0 0 0 18 18 21 20 20 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 25 19 19 0 0 0 0 0 0 0 0 0 0 16 0 0 
0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0 0 0

This is a padded reading, with standard dye primer chemistry with universal primer. The base at position 172 in the SCF trace have been deleted, hence the Align_to_SCF maps read position 171 -> trace position 171, and read position 172 -> trace position 173.

Positions 1 to 31 are sequencing vector
Positions 56 to 117 are high quality, according to the base-quality 
measures Positions 46 to 241 align well with the contig consensus

The read has been autoedited (hence the deleted base) and tags attached to the edited bases.

The corresponding contig is:


Sequence : Contig3
Is_contig
Unpadded
Assembled_from hg82b3.s1 7635 7677 1 43
Assembled_from hg82b3.s1 7678 7697 45 64
Assembled_from hg82b3.s1 7698 7703 66 71
.
.
.
Assembled_from hg02b9.s1 7968 7878 1 91
Assembled_from hg02b9.s1 7877 7745 93 225
Assembled_from hg02b9.s1 7744 7694 227 277
Assembled_from hg02b9.s1 7693 7607 279 365
Assembled_from hg02b9.s1 7606 7603 367 370
Assembled_from hg02b9.s1 7601 7599 371 373
Assembled_from hg02b9.s1 7598 7584 375 389
Assembled_from hg02b9.s1 7583 7570 391 404
Assembled_from hg02b9.s1 7569 7470 406 505
.
.
.

So that reverse-complemented read hg02b9.s1 positions [1,505] align to [7470,7968] (This is the full Phrap alignment, ie not clipped back). The individual unpadded subsections align as indicated, eg [1,91] with [7878,7968].

After padding the alignment (with caf_pad) we have


Sequence : hg02b9.s1
Is_read
Padded
SCF_File hg02b9.s1SCF
Template hg02b9
Dye Dye_primer
Primer Universal_primer
ProcessStatus QUAL
Align_to_SCF 1 3 1 3
Align_to_SCF 5 20 4 19
Align_to_SCF 22 37 20 35
Align_to_SCF 39 46 36 43
Align_to_SCF 48 48 44 44
Align_to_SCF 51 74 45 68
Align_to_SCF 76 80 69 73
Align_to_SCF 82 94 74 86
Align_to_SCF 96 108 87 99
Align_to_SCF 110 121 100 111
Align_to_SCF 123 128 112 117
Align_to_SCF 130 199 118 187
Align_to_SCF 201 267 188 254
Align_to_SCF 269 274 255 260
Align_to_SCF 276 278 261 263
Align_to_SCF 280 281 264 265
Align_to_SCF 283 284 266 267
Align_to_SCF 286 290 268 272
Align_to_SCF 292 292 273 273
Align_to_SCF 294 308 274 288
Align_to_SCF 311 312 289 290
Align_to_SCF 314 317 291 294
Align_to_SCF 319 334 295 310
Align_to_SCF 336 336 311 311
Align_to_SCF 338 371 312 345
Align_to_SCF 373 376 346 349
Align_to_SCF 378 398 350 370
Align_to_SCF 400 442 371 413
Align_to_SCF 444 444 414 414
Align_to_SCF 446 446 415 415
Align_to_SCF 448 468 416 436
Align_to_SCF 470 534 437 501
Align_to_SCF 536 539 502 505
Seq_vec SVEC 1 30 "M13mp18"
Clipping QUAL 2 537
DNA hg02b9.s1 539
Strand Forward
Clone 4B5
Asped 25-Mar-1996

DNA : hg02b9.s1
CGC-TGCAGGTCGACTCTAG-AGGCTCCCCTGAGCCG-CTGTGGAT-T--GAGGAGGTGA
GGCGTGAGGAGGTG-AGGAG-TGAGAAGGTCAGG-AGGGACGGAGGTG-ACGAGTGAGGA
G-GCGAGG-TGAGGCGTTAGGAGGTGGGGAAGTCAGGAGGTGAGTCAGGACCTGAGGAGT
CAGGGGGTGAGGAGTTAGG-TGGTCAGGAGTCAGGAGGTGACGAGTTAGGAGGTGGGGCA
AGTGAGGAGGTGAGGAGTGAGGACATG-ACGAGT-GAG-TA-GG-TGAGG-A-GTCACGG
GGGTCAGG--AA-CGTG-ACAAGGTTTCGACGTC-C-AATCCATCGTTCCAGGACCTTCC
AGCTTGTGTCC-TCTG-ACAGTGACCTCACCTGCCAGG-TCTGGCCCTCCTGGCAGGCAA
GAGGGCCGGCCGTGGGGGCGGT-G-G-AGGGGGTGGCCTCCCAGGGGT-GAAGTCGGGGG
TTGGGCTCCGACCGTCTGGCCACCGTTGGGGGTGAGCCCGGTGGGAGTGTTGGG-GGGG


BaseQuality : hg02b9.s1
0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 16 0 0 0 0 0 0 
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 17 0 0 0 0 0 0 
15 0 0 0 0 0 0 18 17 17 0 18 0 0 1 0 0 0 0 0 1 0 0 0 19 0 15 
0 0 0 0 18 17 24 1 22 18 21 18 18 0 15 15 21 23 21 0 0 1 0 0 
0 21 0 0 0 16 19 23 21 0 1 0 0 0 0 21 21 1 22 0 0 0 0 0 0 0 0 
0 0 0 0 18 18 23 22 23 23 15 15 17 0 23 15 21 22 21 21 21 25 
19 23 19 30 18 18 18 27 21 0 0 0 0 0 0 25 18 22 15 0 0 0 15 0 
21 17 0 0 0 0 0 18 0 0 0 16 16 21 16 1 0 0 0 0 0 16 16 0 0 0 
0 0 0 15 15 0 0 15 15 0 0 0 0 0 0 0 18 18 21 20 20 20 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 19 
19 1 0 0 0 0 0 0 1 0 0 0 1 0 16 1 0 0 1 0 0 15 0 0 1 0 1 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 1 0 1 0 1 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 1 0 0 0 0 0 0 0 0 0 0 
0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 1 0 0 0 0

Note how the Align_to_SCF is now much more complex since it has to take into account all the pads inserted into the dna. The DNA contains pads "-" and the BaseQuality data fake values "1" at each pad position. The alignment of the read to the contig is now much simpler however:


Sequence : Contig3
Is_contig
Padded
.
.
Assembled_from hg02b9.s1 8618 8080 1 539
.
.

So positions [1,539] in the padded (reverse-complemented) read align with [8080,8616] in the padded contig.

Attributes

Sequence Attributes

Sequence objects in the CAF file are used to represent both read and contigs (constructed during sequence assembly from reads).

Field	Description
Is_read	The sequence respresents a reading
Is_contig	The sequence respresents a set of aligned reads
Is_vector	The sequence respresents an artificial sequence

Attributes common to all Sequence objects

An assembly can be in either a padded or unpadded state. In the padded state, padding characters are added to the contig sequence and the reads so that the reads align with one another perfectly. In the unpadded state, the alignment between reads and the contig is described fully.

Field	Description
Padded	The sequence is padded
Unpadded	The sequence is unpadded

Features identified within sequences are annotated using one of the following four fields. In each case, Method is either the name of a program, or some generic name describing the method. We currently use the name of the GAP4 (Bonfield et al, 1996) tag id. The feature is considered to cover bases From through To in the Sequence. Comment is optional. If more than one word, the comment should be surrounded by double quotes.

Field	Attributes	Description
Clone_vec	Method From To Comment	Location of Cloning vector.
Seq_vec	Method From To Comment	Location of Sequencing vector.
Clipping	Method From To	High quality bases.
Tag	Method From To Comment	Some arbirary feature.

Attributes of reads only

Field	Attributes	Description
Sequencing_vector	Vector_name	The name of the sequencing vector used.
Template	Template_name	The name of the DNA template from which the sequence was determined.
Insert_size	From To	Minimum and maximum size estimate of insert of DNA template.
SCF_File	File_name	The name of the SCF file for this reading.
Base_caller	Base_caller_name	The name of the base calling software used to generate read.
Stolen	Comment	The read was not originally sequenced for the clone
Staden_id	Integer	The internal read number from the Staden GAP database (gap2caf).
Asped	Date	The date the read was sequenced/pre-processed.
ProcessStatus	Text	Preprocessing status (PASS or FAIL).
Align_to_SCF	ReadFrom ReadTo SCFFrom SCFTo	The alignment between the read and the original base calls

Information about the sequencing chemistry used to generate the read is included. One of the following must be specified.

Field	Description
Dye_primer	The read was sequenced using Dye primer chemistry
Dye_terminator	The read was sequenced using Dye terminator chemistry

Orientation of the read with respect to the template is specified by one of the following:

Field	Description
Forward	The read is on the Forward strand of the template
Reverse	The read is on the Reverse strand of the template

The location of the read with respect to the insert is specified by one of the following:

Field	Attributes	Description
Universal_primer		Either a forward or reverse universal primer was used.
Custom	Primer_name	A custom primer was used. The name is optional.

Attributes of contigs only

The alignment of the reading to the contig is described in lines:

Field	Attributes	Description
Assembled_from	ContigFrom ContigTo ReadFrom ReadTo	The alignment between the contig and the read

User guide

This document describes the functions and usage of the caftools suite of programs for manipulating CAF (Common Assembly Format) sequence assemblies. All the software was written by Simon Dear, Dave Hodgson and Richard Mott at the Sanger Institute.

Standard Interface programs

All the programs in this section act as filters on single CAF files and so can read and write CAF data on stdin and stdout:

program < input > output

or by the switches

program -caf input -out output

Other command-line options are available with individual applications. Boolean switches can be tuned off by prefixing them with "no", eg -clip and -noclip. Brief online help is available for most programs by typing

program -help

Some programs produce dignostics on stderr.

cafcat

usage: cafcat [-summary] [-sanitise] [-verbose] [-check] 
  -caf input | < input -out output | > output

Options:
  -reformat       switch               [ false ]
  -verbose        switch               [ false ]
  -check          switch               [ false ]
  -summary        switch               [ false ]
  -help           switch               [  ]
  -caf            Readable File        [  ]

Reads and writes a CAF assembly. Useful for consolidating a fragmented CAF file. The CAF database is also sanitised before being printed, ie contigs with no readings are removed, together with references in the Golden_path to non-existent readings.

If -summary is set then a summary of the assembly is written to stdout instead of the caf file.

If -check is set then the assembly is checked for consistency, but is not written to stdout. If -verbose is also set then errors are displayed to stderr. This is useful for checking whether an assembly is consistently padded/unpadded. The exit status is 0 if the assembly is consistent, non-zero if some kind of anomaly was detected. Note that sometimes the checking is too picky and will choke on legal but bizarre assemblies. -reformat is an obsolete switch used to convert ace-files to caf files.

caf_pad, caf_depad

caf_pad -caf input | < input -out output | > output

Pads an unpadded CAF assembly.

caf_depad -caf input |  < input -out output | > output

Depads a padded CAF assembly. These programs are almost inverses of each other except that columns consisting entrely of pads are deleted by caf_depad. If you are unsure of the pad-state of a CAF file it is safe to use these programs as they check the state before doing anything. Note however that if they encounter a problem (eg a contig containing reads in mixture of pad states) they will either leave the assembly untouched or exit with a non-zero error code.

The pad-state of a Sequence object is defined by the attribute Padded or Unpadded. If you have reason to suspect there is something wrong with an assembly you can check it with cafcat -check -verbose

caf2phrap

caf2phrap -caf input |  < input -fasta output [-fofn file] 
  [-clip|-noclip] [-high=0] [-low=0] -fasta fastafile 
  [-qual qualfile ] [-cafout caffile ]

Options:
  -high           integer              [ 0 ]
  -low            integer              [ 0 ]
  -mask           integer              [ 0 ]
  -fofn           Readable File        [  ]
  -contigs        switch               [ false ]
  -reads          switch               [ true ]
  -fasta          Writeable File       [  ]
  -qualfile       Writeable File       [  ]
  -qual           switch               [ true ]
  -clipping       text                 [ QUAL ]
  -svclip         switch               [ true ]
  -cvclip         switch               [ false ]
  -failures       switch               [ false ]
  -tag_mask       text                 [  ]
  -help           switch               [  ]
  -caf            Readable File        [  ]

Splits a CAF file into three output files suitable as inputs to Phrap. Given a file of read names, via the -fofn file switch, caf2phrap creates a fasta-format sequence file for those readings, a file of base quality measures (if they exist in the CAF input), and a CAF file corresponding to the entries in fofn which exist in the input. If -fofn is omitted or the corresponding file will not open then all the reads are processed.

The name of the fasta sequence file is defined by the -fasta output switch. If the switch -qual is true (which it is by default) then quality data are written out to the file specified by the -qualfile switch or derived by appending ".qual" to the file specified by -fasta If base_quality exists for a sequence then it is dumped out. If base-quality does not exist then it is faked from clipping data according to the [comma-separated list of] Clipping tags given by the -clipping switch, by default "QUAL". High quality regions are given quality "high" (1 by default), otherwise they are "low" (0 by default). If a sequence has no base quality or clipping tags then it is given the base quality 0 The output CAF file is named by -cafout if this argument is supplied.

If base-quality data for a sequence does not exist then it is faked, with upper-case nucleotides having the value set by -high (default 0) and lower-case by -low (default 0). All quality values less than -mask are set to 0.

If -svclip is set (on by default) then portions of sequence corresponding to sequencing vector (defined via the Seq_vec tags in the CAF file) are x-d out and the corresponding base quality measures set to 0.

If -cvclip is set (off by default) then portions of sequence corresponding to cloning vector (defined via the Clone_vec tags in the CAF file) are x-d out and the corresponding base quality measures set to 0.

If -tag_mask is present it must consist of a [comma-separated] list of Tag names. Portions of sequence corresponding to these Tag types are x-d out and the corresponding base quality measures set to 0. By default -tag_mask is empty

If -reads is set (on by default) then all Sequence objects that are readings are output.

If -contigs is set (off by default) then all Sequence objects that are contigs are output.

If -failures is set (off by default) then failed reads are output.

caf2phrap requires unpadded data.

cafmerge

cafmerge -caf1 input1 -caf2 input2  -out outfile |  > outfile

Merges the output of phrap2caf back with the CAF-file produced by caf2phrap, to generate a CAF file with the original unpadded DNA for the readings, suitable for further processing.

Sequence attributes in input1 are overwritten by the corresponding attributes in input2.

nd_clip

nd_clip [-clip type ] [-vector|-novector] [-fail|-nofail] 
  -caf input |  < input -out output |  > output

Options
  -clip           text                 [  ]
  -svector        switch               [ false ]
  -cvector        switch               [ false ]
  -fail           switch               [ true ]
  -warn           switch               [ false ]
  -logfile        Writeable File       [  ]
  -help           switch               [  ]
  -caf            Readable File        [  ]

Does clipping on assembled readings. If -clip type is set to a valid clip type (Corresponding to the CAF Clipping QUAL tag) then reads are clipped back accordingly. Eg if a reading is aligned to a contig between read positions 25 and 404, but its QUAL clip points are 45 to 500 then the read becomes aligned over 45 to 404.

A log file is written if -logfile defineds a writable file.

If -svector is set (on by default) then reads are also clipped for sequencing vector(as defined by Seq_vec tags) tags). E.g. if the previous reading has sequencing vector between 375 and 780 then the read is clipped to 45,375.

If -cvector is set (off by default) then reads are also clipped for cloning vector (as defined by Clone_vec tags) tags).

If -fail is set then reads with the Failure attribute set are deleted.

nd_clip requires unpadded data (but will depad on the fly if the input is padded).

ne_clip

ne_clip [-match=1] [-mismatch=20] [-gap=20] [-neutral=2] 
  [-original|-nooriginal] -caf input |
    < input -out output |  > output

Options:
  -bad            float                [ 0 ]
  -debug          text                 [  ]
  -logfile        Writeable File       [  ]
  -match          integer              [ 1 ]
  -mismatch       integer              [ -20 ]
  -gap            integer              [ -20 ]
  -neutral        integer              [ -2 ]
  -original       switch               [ false ]
  -extend         switch               [ true ]
  -help           switch               [  ]
  -caf            Readable File        [  ]

Clips back readings to where they best align with the contig consensus. If a region becomes single-stranded as a result then readings are extended out again appropriately.

The algorithm assumes the readings are already aligned to the consensus in a sensible fashion (as is the case with Phrap output) as far out as is possible. These alignments define "lax" clip points for the reads. Using strict mismatch and indel penalties the alignment of each read is re-scored, and the maximal matching segment determined, producing "strict" clip points. Then all reads are clipped back to their strict clip points. Regions which become zero- or single- stranded as a result are recovered by extending neighbouring reads back as far as required, up to their lax clip points. If -noextend is set then reads are NOT extended back.

The penalties for a match, mismatch and gap are set via the obvious switches. -neutral determines the penalty for matching to an N.

If -original is set then the contig sequence is used for alignment rather than the majority-vote consensus.

-bad controls the minimum percent identity a read must have with the consensus in order not be thrown out.

A log file is written if -logfile defineds a writable file.

ne_clip requires a padded assembly (but will pad on the fly).

np_edit, nd_edit

np_edit [-scf|-noscf] [-bad=85] [-logfile file] -caf input | 
  < input -out output |  > output

Options:

  -scf            switch               [ false ]
  -verbose        switch               [ false ]
  -bad            float                [ 85 ]
  -depth          integer              [ 4 ]
  -max_run        integer              [ 4 ]
  -max_stack      integer              [ 4 ]
  -dump           switch               [ false ]
  -scfcache       integer              [ 0 ]
  -stlouis        float                [ -1 ]
  -logfile        Writeable File       [  ]
  -help           switch               [  ]
  -caf            Readable File        [  ]
  -out            text                 [ stdout ]


nd_edit  -caf input |  < input -out output |  > output

Options:
  -verbose        switch               [ false ]
  -skip           switch               [ true ]
  -show_case      switch               [ true ]
  -help           switch               [  ]
  -caf            Readable File        [  ]
  -out            Writeable File       [  ]

np_edit proposes edits to the reads to generate a consensus. nd_edit disposes of the edits and creates tags indicating where an edit has been made. Normally np_edit pipes its output straight into nd_edit.

np_edit examines the alignment of reads to the consensus to find places of disagreement between aligned readings. It then examines the trace data in SCF files if available, to determine whether it is safe to make an edit. It currently will only edit down to the majority vote consensus, unless there is a tie when it will consider all consensuses. If -logfile is set then a logfile is created with explanantory info, including which reads were rejected and how many edits were made in each contig.

Trace data are used if the switch -scf is set. If the trace data are not in the current directory then the environment variable RAWDATA should be set to a colon-separated list of directories to search. The name of the SCF file corresponding to a reading is defined by the CAF Sequence attribute SCF_File.

np_edit throws out all readings with less than 85% identity (or to whatever -bad is set ) with the majority-vote consensus.

np_edit will not make an edit if it occurs as part of a horizontal run of edits longer than that defined by -max_run, or vertically more than -max_stack

The other options are probably not interesting.

Options for nd_edit (the disposer):

-skip (on by default) omits reads thrown out by np_edit as being misaligned. -show_case (on by default) down-cases edited bases in the consensus.

caf2gap, gap2caf

caf2gap -ace=input -project=PROJECT -version=version -caf=1

gap2caf -ace=output -project=PROJECT -version=version -caf=1

Convert CAF file to a GAP database and back. The transfer is lossy at the moment - alignment, tag and vector clip information is preserved, other data is lost.

Scripts

phrap2caf

phrap2caf  < acefile  > caffile

Is a perl program that massages the ace-file output of phrap into CAF format. The changes are mostly syntactical, except that reads which overhang the ends of contigs are trimmed back.

caf_phrap

caf_phrap -project project -fofn files -out outfile
   -tmp dir -clean -extend

caf_phrap is a perl script that runs Phrap on a CAF database and massages the output back into CAF format. It is assumed that the script is run from within the project directory. caf_phrap looks for the file ./CAF/caf.raw (see update_caf), and runs caf2phrap on this file to generate the phrap input files. Then Phrap is run and the results merged back by running phrap2caf and cafmerge. The contig base quality data are also appended to the output. The switch -fofn gives a file of read names to use. If this is omitted then all the reads in caf.raw are utilised. -tmp is the name of the temp directory to use for writing intermediate files. By default this is ./Phrap. If -clean is set then the temp files are deleted at the end.

update_caf


update_caf -clean

Updates the CAF database by searching the current directory for new experiment files (e.g. produced by Asp). The CAF database always resides in the file ./CAF/caf.raw. If this does not exist it is created. If it exists then any new exp files are converted to CAF format (by exp2caf) and appended to caf.raw. If -clean is set then the database is deleted and recreated. update_caf uses indir to determine what are the experiment files.

cafextend

cafextend  < input  > output

A perl script that looks for holes in the Phrap assembly and tries to extend readings to cover them using the Golden_path information.

phrap2gap

phrap2gap is a perl script that runs Phrap on a CAF database, then clips, autoedits and post-processes the result and finally generates a GAP database.

Example file


DNA : 22ak93c2.r1t
GTCGCnCATAAGATTACGAGATCTCGAGCTCGGTACCCTTCAAGCGATTCTCCTGCCTCA
GCCTCCCGAGTAGCTGGGATTATAGACTGTGCGTGCGCCACCATGCCTGGCTAATTTTTG
TATTTTTAGTAGGGATGGGGTTTCACCATGTTGGCCAAGCTGGTCTCGAGCTCCTGACCT
AGGATTACAGGCCTAAGCCACCGCACCCGGCATGATGGGTCTTTATTCTTCAAAGCAGGA
GGAAGGGATCCTAgAAAAACAGAGACAAGGCCAAACATGGTAgCTCACACCTGTAATCCC
AnCACTTTGGGAGGCCagTGCGGGTGAATCACGAAGTCAGGAGTTCAAGACCACCCTGGC
CAACATGGTGTAACACCTGCTCTCCTAAAATTAAACAAAATTTCATGGTTTGCGTGGGCC
GTCTTGTCTCATCACTTCACTCCTGAGGGCCGGCGCCGGAAAGATATCTTGATCTGCGGC
GCTCCGACCGTTTTCTTTAAACCTTACAACTCCCGACCTCCTCGCCTATCCTCCCTAAAT
CCTCGCCAGGCTCGCCTGCTTCAGCCACTCTTTCCTTCGCACCCTCCCCTCTCTTCAATA
TACTTCACCCGCCCATCCTTCACGCCGGCACGTATCCAATCTCTTCTTATCTTTCCGTAT
CCAAnTCCCTTCTCCCTCTGCCGCGACCTTCGCCATCCCTCTGCGCGTCCTCTTCC

BaseQuality : 22ak93c2.r1t
4 4 8 4 4 4 4 4 4 4 4 4 6 8 17 21 14 7 6 6 6 7 7 6 8 14 16 21 15 20 20
24 26 21 18 18 14 14 19 23 10 8 8 15 20 16 29 26 34 29 39 29 31 29 31
34 32 27 27 25 19 19 24 31 33 36 34 34 34 26 27 22 32 32 36 28 28 15
15 15 28 28 34 30 12 12 22 27 31 31 31 31 31 23 24 27 21 24 24 29 27
27 27 34 34 36 38 38 38 36 36 40 36 37 38 45 45 36 34 33 31 31 34 34
33 33 28 28 27 23 24 11 11 10 10 18 25 21 20 17 17 17 20 15 24 18 24
26 23 23 18 20 25 23 30 30 30 33 33 37 37 32 37 37 32 45 35 37 37 37
40 36 49 49 36 36 34 33 20 15 9 9 8 7 12 22 21 28 28 30 33 36 36 36 34
31 31 25 31 28 26 26 24 20 17 9 11 8 9 10 23 23 31 23 23 15 9 9 15 33
26 33 33 31 25 25 22 31 24 23 12 10 12 11 9 8 9 7 7 8 8 9 18 12 9 9 18
20 26 31 21 21 9 8 8 11 13 21 21 23 15 15 15 15 15 17 17 9 7 9 19 20
21 21 25 25 25 25 25 23 23 9 9 9 21 16 24 24 24 24 26 33 33 33 31 31
27 15 17 7 4 4 4 16 20 27 33 34 34 23 15 14 8 9 6 6 9 1 14 16 8 11 15
23 25 34 36 31 33 16 16 6 6 6 9 8 14 9 11 11 9 13 13 10 8 10 9 9 7 8
20 20 20 14 14 10 10 10 16 8 8 6 6 8 9 10 7 8 8 8 8 6 8 6 6 8 12 9 8 7
13 10 8 8 9 8 8 8 9 6 6 6 6 8 6 6 6 6 6 10 11 10 12 12 10 7 6 6 7 6 6
7 8 7 6 6 7 6 8 6 6 8 8 8 8 6 6 6 8 6 6 8 6 6 11 15 9 9 9 9 9 9 9 9 9
9 8 9 9 6 6 6 7 9 6 6 6 7 7 7 8 9 7 7 9 9 11 8 11 11 11 9 10 9 8 8 8
10 6 6 9 8 6 6 6 6 8 8 9 11 9 8 8 8 8 8 8 8 9 9 9 10 10 8 6 6 8 6 6 10
11 10 6 6 8 6 6 6 6 8 11 8 9 8 8 8 8 8 9 6 6 9 8 8 8 6 6 13 15 12 12 8
8 6 6 8 9 8 8 9 8 8 6 6 6 8 8 6 6 6 8 8 8 6 6 8 6 6 8 6 6 9 8 8 6 6 8
8 6 6 8 6 7 8 9 10 11 11 10 9 9 8 10 9 10 10 8 9 13 8 8 8 13 13 11 7 7
7 11 8 8 10 11 10 9 9 14 7 7 10 10 10 8 8 8 8 6 7 8 8 6 6 6 6 6 6 6 6
6 8 9 10 8 8 6 6 8 8 8 8 8 8 8 8 8 8 6 6 8 8 9 10 10 4 4 4 6 7 6 6 6 6
10 8 8 9 15 11 6 6 8 8 8 8 8 8 9 9 8 9 7 7 8 6 6 8 13 10 8 8 7 6 8 6 6
8 6 7 8 8 8 8 8 8 8 4


Sequence : 22ak93c2.r1t
Is_read
Padded
Staden_id 11
Clipping QUAL 39 331
Align_to_SCF 1 43 1 43
Align_to_SCF 44 317 45 318
Align_to_SCF 319 716 319 716
SCF_File 22ak93c2.r1tSCF
Primer Universal_primer
Strand Reverse
Dye Dye_terminator
Template 22ak93c2
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 38 "M13mp18"
Tag ALUS 43 180
Tag DONE 43 43 "AUTO-EDIT: deleted C at 43  (terminator, isolated, strong)"
Tag DONE 254 254 "AUTO-EDIT: replaced T by g at 254 (terminator, isolated, strong)"
Tag ALUS 269 402
Tag DONE 283 283 "AUTO-EDIT: replaced T by g at 283 (terminated, isolated, strong)"
Tag AMBG 298 302 "AUTOEDIT: Check this edit cluster!"
Tag DONE 317 317 "AUTO-EDIT: replaced C by a at 317 (terminated, compound, strong)"
Tag DONE 318 318 "AUTO-EDIT: inserted g at 318  (terminated, compound, strong)"

DNA : 22ak93c1.r1ta
GGGGGGATGATACAATTCGAGCTCGGTACCTTCAAGCGATTCTCCTGCCTCAGCCTCCCG
AGTAGCTGGGATTATAAACTGTGCGTGCGCCACCATGCCTGGCTAATTTTTGTATTTTTA
GTAGGGATGGGGTTTCACCATGTTGGCCAaGCTGGTCTCGAGCTCCTGACCTAGGATtAC
AGGCCTAaGCCACCGCACCCGGCATGATGGGTCTTTATTCTTCAAAGCAgGAGGAAGGGA
TCCTAGAAAAACAGAGACAAgGCCAAACATGGTAGCTCACACCTGTAATCCCAGCACTTT
GGGAgGCCAgTGCGGGTGAATCACgAAGTCAGGAGTTCAAGACCATCCTGGCCAACATGG
TGTAACACCGTCTCTCCTAGGATAAACCGAAATCACCTGGGTGTCCTGGCAAGTGCCTGT
CATCCCTGACCACTTGGAAAGCTGAGCCGAATCCTTATCCCnGAAAGTAAGGTTACGTGA
ACCCACATCAAACCACTGCGCTCCAGCCCAAAACATCGTGTTATACTCTGTCGCGACATT
GATGCCCAAAAAACAGGACCGCTATTGGGAGACACTCCCGGGTAATTGGGATTGAGGAGG
TTAAAGAAAACTCTTGATCTGAGAAAAAAGACCCTATCCTGGCGAGAAAACCACATGTGG
ACCACACCGCTTCACTTTGTCTAAGCAAAAAACGCCCCACTTGAAGATGACCCCCCCAGC
TGAAATCTTCCATTAATCCCCGAACATAAAGGTTTAACCCAAAATTTCCTGTTAGACCGC
CTTCTGAAGTTTCTAAAATTCTATGGGTAGGGACAAAAGTCCCTCGTTGAATTTCTAGGA
TACTTCCAAATATCCCCCACCTCTCCCCTGGGATCCCGATAGCTTTCTTGTCCCTAAAAA
AAACTTTGTTCAAACGGAGAAACCACACCCGGGGAAAATTCCCCTTTTCTTGGGGTTTAG
GTTTCTTTAAATAAATGCTGGGCACCAATCCTCAAATGAGTTCTTACCCAATCCCATATG
TTTTTAATCCTCAACAACAACCTTATTTCCTTAAGAGACCTCTCCTCGGAAATCATTTCA
AAACAAAAAAAACACTTAAGCCTTGGGTCTTTGGGACCCCCCAAAAAAAAAACATAAAGG
GGTGGCACCGTATACGCCTTGCCCATCTTTCTAGTGGAAGATAACGAAACGGTAGCTGGG
GCCAACCAGGCATCAGTGGGGGATACCGCTAAATGTTGGGGAACACCCAAAAACCCATCT
GCAGGCACCGCGAATGCGGAAAAGCGCACGCTATCACAAATGGTATATGGGCACC

BaseQuality : 22ak93c1.r1ta
8 10 8 9 16 9 9 9 11 8 8 9 10 11 11 10 19 24 26 24 26 22 21 17 13 16
11 11 10 10 14 14 19 22 24 26 32 32 33 29 29 29 27 27 27 27 27 32 32
25 27 20 25 19 32 27 29 32 32 32 34 34 21 23 12 14 14 27 32 32 29 28
27 34 31 34 34 34 37 34 32 32 30 30 28 28 28 30 30 33 33 33 30 30 34
34 34 37 40 38 37 34 32 34 32 37 32 37 37 28 28 28 33 33 33 33 32 30
30 29 28 21 23 14 12 30 32 45 45 41 41 30 25 22 33 33 34 23 21 18 12
12 11 13 27 27 23 23 11 11 9 10 11 18 18 30 15 20 12 11 10 20 12 14 14
32 32 33 28 28 18 23 18 12 12 20 12 16 13 18 14 15 12 32 23 21 10 10 9
9 10 16 18 21 9 9 9 18 21 14 14 12 10 14 14 23 27 24 19 19 24 28 30 29
29 34 34 29 25 17 12 12 16 14 14 23 10 10 10 11 15 21 24 18 25 11 11
15 32 28 34 34 29 32 32 37 37 34 34 31 28 28 25 22 17 14 11 10 10 8 8
9 14 8 8 12 17 18 15 13 18 17 17 10 10 10 22 16 24 30 24 28 27 32 19
12 12 12 30 21 17 9 9 9 9 17 16 24 24 23 20 12 12 7 7 7 14 13 10 10 10
23 23 22 15 17 18 24 24 15 17 11 10 8 8 8 13 20 25 17 17 17 20 20 18
10 11 12 12 11 25 10 12 12 9 8 8 8 8 8 12 14 9 9 9 9 10 10 8 8 11 9 9
9 14 20 20 19 15 15 15 15 11 11 6 6 9 8 10 12 12 15 15 10 9 10 11 7 7
9 11 14 11 11 10 11 9 14 14 23 19 18 14 12 10 10 10 10 10 16 11 11 9 8
8 9 8 11 11 9 8 8 10 9 12 13 9 9 8 8 8 8 8 6 6 11 6 6 8 11 9 9 9 6 6
12 9 9 6 6 8 11 9 8 6 7 9 9 7 8 4 4 4 6 8 6 6 8 8 6 6 8 6 8 12 12 14
10 9 10 11 9 8 7 7 7 7 10 8 8 6 6 8 6 6 8 10 8 6 6 10 8 10 9 10 10 9 8
8 6 6 6 6 8 8 8 9 9 9 9 7 7 9 9 10 10 10 13 12 9 9 9 9 7 8 8 8 9 8 8 9
9 9 8 6 6 8 6 6 6 7 7 9 9 10 8 8 7 7 7 9 10 10 8 6 6 6 6 6 10 10 8 6 6
8 8 8 7 9 7 10 7 11 8 8 8 8 9 9 9 8 8 6 6 10 11 16 8 7 7 7 6 8 6 6 8
10 11 9 9 9 7 7 8 7 7 7 7 7 8 11 9 16 16 24 22 15 9 8 13 13 12 12 9 9
9 9 9 7 7 7 7 7 7 7 8 7 7 7 6 9 11 9 8 8 9 9 9 7 9 10 14 12 9 9 8 8 6
6 6 6 8 6 6 8 6 6 6 6 6 9 8 10 10 9 10 10 13 10 11 6 7 11 6 6 8 6 6 6
6 6 6 9 9 7 7 8 8 8 8 8 9 8 9 13 11 8 6 6 6 9 9 8 8 8 8 8 8 8 11 8 7
10 12 7 7 9 8 6 6 8 8 7 7 10 8 8 7 7 7 8 8 8 8 7 7 7 7 7 10 9 10 12 10
7 7 6 9 6 6 6 6 7 9 7 7 4 10 9 7 6 8 6 6 8 6 6 9 6 7 7 10 10 10 10 13
13 8 9 8 8 8 6 7 10 11 10 9 8 6 6 6 6 6 8 8 7 9 7 7 7 7 7 7 7 10 10 10
8 8 8 7 7 8 8 8 8 6 6 7 7 7 9 8 6 8 6 6 6 8 8 8 7 9 9 12 15 9 8 7 9 8
8 9 8 8 6 8 12 11 7 7 7 7 7 7 9 11 11 9 9 9 10 9 9 9 8 8 8 8 8 7 7 12
13 13 15 11 11 7 7 7 9 11 10 12 6 6 6 6 8 7 7 7 8 10 10 10 10 13 9 12
11 11 6 6 6 6 8 8 6 7 7 12 10 13 9 8 7 7 10 7 7 15 17 15 12 17 20 15
13 15 6 6 6 6 8 8 6 6 6 7 7 7 10 7 7 10 11 8 8 5 5 8 8 12 12 8 10 6 6
6 6 8 8 7 7 7 12 10 7 7 9 7 7 9 9 8 9 10 10 8 8 9 11 9 8 9 9 11 11 9 9
8 6 8 6 6 6 6 6 6 6 6 8 8 8 8 12 6 6 6 6 8 6 7 7 6 8 6 6 8 8 10 11 10
12 7 8 8 9 12 6 6 6 6 6 6 6 6 8 9 9 9 9 9 8 7 8 7 7 7 8 7 7 7 7 9 9 9
9 6 6 6 6 14 8 8 8 8 8 6 6 7 7 7 11 9 7 6 6 6 6 10 6 6 6 8 8 7 8 7 7 6
7 7 8 8 12 13 15 15 21 9 10 9 8 8 10 6 6 6 6 4 4 4 8 8 8 7 6 6 6 6 6 6
6 6 6 6 6 9 9 9 6 6 6 10 6 10 15 20 12 9 8 6 6 6 6 6 8 8 6 6 6 6 8 12
13 12 10 9 8 11 8 10 9 7 7 4 4 6 6 8 4 4 4 6 8 6 6 6 8 8 13 10 8 9 9 9
7 7 9 10 8 8 6 6 6 6 6 6 10 11 10 10 10 7 7 8 6 6 8 6 6 8 10 13 8 11 8
11 10 6 6 6 7 11 14 11 11 6 6 8 8 8 9 9 9 9 7 7 10 10 6 6 6 6 6 6 8 8
8 7 7 7 8 8 11 11 11 7 6 8 6 6 8 8 6 6 10 10 13 8 8 6 6 6 8 9 9 6 6 9
9 8 8 6 6 8 6 6 8 8 4


Sequence : 22ak93c1.r1ta
Is_read
Padded
Staden_id 12
Clipping QUAL 31 335
Align_to_SCF 1 1315 1 1315
SCF_File 22ak93c1.r1taSCF
Primer Universal_primer
Strand Reverse
Dye Dye_terminator
Template 22ak93c1
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 30 "M13mp18"
Tag ALUS 31 172
Tag DONE 150 150 "AUTO-EDIT: replaced T by a at 150 (terminator, isolated, strong)"
Tag DONE 178 178 "AUTO-EDIT: replaced G by t at 178 (terminator, isolated, strong)"
Tag DONE 188 188 "AUTO-EDIT: replaced T by a at 188 (terminator, isolated, strong)"
Tag DONE 230 230 "AUTO-EDIT: replaced T by g at 230 (terminator, isolated, strong)"
Tag DONE 261 261 "AUTO-EDIT: replaced C by g at 261 (terminated, isolated, strong)"
Tag ALUS 262 446
Tag DONE 305 305 "AUTO-EDIT: replaced T by g at 305 (terminated, isolated, strong)"
Tag DONE 310 310 "AUTO-EDIT: inserted g at 310  (terminated, compound, strong)"
Tag DONE 325 325 "AUTO-EDIT: replaced A by g at 325 (terminated, isolated, strong)"

DNA : 22am91h5.r1t
GGGnnATAGATACGATCCGAGCTCGGTACCCATGTTGGCCAAGCTGGTCTCGAGCTCCTG
ACCTAGGATTACAGGCCTAAGCCACCGCACCCGGCATGATGGGTCTTTATTCTTCAAAGC
AGGAGGAAGGGATCCTAGAAAAACAGAGACAAGGCCAAACATGGTAGCTCACACCTGTAA
TCCCAGCACTTTGGGAGGCCAGTGCGGGTGAATCACGAAGTCAGGAGTTCAAGACCAGCC
TGGCCAACATGGTGAAACACCGTCTCTACTAAAATAAAAAGAAATTAGCTGGGTGTCGTG
GCAGGTGCCTGTAATCCCAGCCACTTGGGAAGCTGAGGCAGGAGAATCGCTTGAACCCGG
GAGGTGGAGGTTGCAnTGAGCCGAGATCACGCGACTGCACTCCAGCCCAACCAATAATGT
GAGACTCTGTCTCGAnAAnnnAAAGCnGAAAACAGACnnCTAGTACnGTACTTAACGGGG
TAATTATAATAATTAAATGAAAAAAATAnCTGTGAGGTGATTGATATAnTGCTGTTGCTA
AATACAACTAACATTTTAATATACCGGTGGAGTGTTTCTAATCTGAnAATCCAAATTAGA
AATGCTCACAGTCTGAAACTTTTTGAGCACCAACTAATGTTCAAAGAATTGCTATGGACC
ATATGGGTGGTTGATTTT

BaseQuality : 22am91h5.r1t
4 8 4 4 4 4 4 7 10 9 10 15 10 7 7 10 10 9 19 20 33 34 34 34 36 36 33
33 31 33 33 32 31 31 26 26 27 23 30 26 26 26 26 34 34 38 38 38 37 45
45 37 37 37 37 45 45 45 45 37 37 37 45 45 32 18 10 21 18 28 29 33 33
33 33 45 45 42 42 37 33 33 33 36 33 33 30 30 30 30 32 36 33 33 33 33
33 33 37 37 45 45 37 37 37 33 33 35 35 35 35 43 35 42 42 35 35 34 34
34 29 29 22 27 27 27 37 27 37 45 33 30 30 37 28 32 32 10 10 21 32 32
34 27 23 12 11 9 9 9 18 21 28 31 33 30 30 30 30 34 34 34 34 31 33 34
34 33 31 33 33 33 33 33 33 45 45 40 37 37 37 33 33 30 30 30 30 33 30
33 26 26 26 25 23 18 14 12 20 23 27 25 21 21 21 28 28 30 31 31 31 31
32 21 21 12 6 6 9 9 14 17 19 17 10 16 13 8 8 11 13 9 13 12 14 14 21 23
26 34 36 34 31 22 24 20 28 28 33 27 28 25 27 24 34 32 23 12 12 12 23
23 33 28 34 34 37 32 32 15 11 11 32 32 40 37 38 18 11 9 9 18 25 45 34
28 28 9 9 20 29 45 38 34 23 23 10 23 23 33 33 33 21 21 13 25 25 25 29
27 33 30 33 33 34 33 30 30 19 19 30 30 30 26 26 30 27 27 23 19 15 24
27 28 21 9 9 9 19 14 12 10 12 12 13 17 28 18 19 21 24 24 25 24 24 24
24 18 18 13 18 8 8 8 10 10 10 7 7 7 8 8 12 15 4 4 4 25 18 21 17 15 16
14 9 9 17 14 17 9 17 8 8 10 10 10 11 17 17 22 24 23 24 24 19 13 10 8
15 15 10 9 9 9 16 12 12 14 19 18 26 24 22 22 24 25 21 24 24 32 19 20 9
9 4 4 4 4 4 4 4 4 17 16 16 4 4 4 7 10 8 7 6 13 8 8 4 4 4 4 8 8 7 7 7 4
4 4 17 23 12 9 8 7 7 8 7 10 10 8 6 6 6 6 6 10 10 7 7 7 7 9 7 8 10 7 7
8 6 6 8 8 8 9 10 7 12 4 4 4 9 9 7 6 6 7 6 6 10 9 7 8 10 7 7 7 9 4 4 4
14 8 8 9 7 6 6 8 8 8 7 7 6 6 9 7 7 10 13 8 9 8 8 8 14 7 7 7 7 9 8 12
12 4 4 4 7 7 7 7 8 8 8 7 7 7 7 7 7 8 10 8 6 6 6 4 4 4 8 12 9 9 17 9 7
7 7 7 6 6 6 6 8 10 6 6 6 8 6 6 6 6 6 6 6 6 6 6 6 6 6 13 11 9 8 7 8 7 7
7 8 7 9 8 7 6 6 4 6 6 8 7 7 7 6 8 6 6 8 7 7 9 9 10 11 7 6 6 6 6 6 12 9
8 8 12 11 10 8 7 7 4 4 4 7 7 8 4
 

Sequence : 22am91h5.r1t
Is_read
Padded
Staden_id 20
Clipping QUAL 32 361
Align_to_SCF 1 678 1 678
SCF_File 22am91h5.r1tSCF
Primer Universal_primer
Strand Reverse
Dye Dye_terminator
Template 22am91h5
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 31 "M13mp18"
Tag ALUS 153 443

DNA : 22aq40a8.s1
AAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCACAGAGACAAGGCCAAACATGG
TAGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAGTGCGGGTGAATCACGAGGTCAG
GAGTTCAAGACCAGCCTGGCCAACATGGTGAA-CACCGTCTCTACTAAAATAAAAAGAAA
TTAGCTGGGTGTCGTGGCAGGTGCTtGTAATCCCAGCCACTTGGGAAGCTGAGGCAGGAG
AATCGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACGCGACTGCACTCCA
GCCCAACCAATAGTGTGAGACTCTGTCTCGAAAAAAAAAAAGCAGAGACAAGACAACTAG
TACAGTACTTACAGGGTTATTATGATGATTAnATGAGAGAATAGCTGTGAGGTGATTGAT
ATAGTGCTGTGCTTAAATACAACTATCAATTTTATTATACGGGGTTGAGTGTTTCCAATC
TGAAAATCCCAAATTTGGAATGCTCTACGGTCTGAAACCTTTTTTGAGCACCGACCTAAA

BaseQuality : 22aq40a8.s1
7 9 10 11 11 23 27 25 25 9 9 9 12 14 23 27 24 21 21 16 22 22 22 24 23
23 23 30 30 30 30 30 32 34 31 31 34 34 28 28 28 30 30 30 28 28 28 34
34 34 34 34 34 37 34 34 34 34 34 34 37 37 37 37 37 37 37 32 34 29 29
29 45 38 40 40 37 37 32 37 37 37 37 37 37 37 37 37 40 40 40 40 40 37
30 30 32 22 22 22 32 32 41 45 45 41 41 45 30 32 27 32 32 40 37 37 40
37 37 45 45 45 40 40 37 37 37 37 37 37 37 37 40 37 37 37 31 32 28 28
28 32 32 37 34 37 38 38 38 27 27 11 1 11 10 21 27 34 34 37 37 34 34 45
45 45 38 37 37 37 37 37 37 34 34 34 34 33 30 30 28 28 28 28 28 30 37
37 37 37 33 36 36 31 31 31 24 24 24 24 21 21 17 12 4 4 4 14 17 26 25
25 31 34 34 31 31 31 33 31 31 34 35 37 37 32 32 34 34 30 31 31 34 30
33 30 30 30 33 33 30 30 23 22 22 32 32 40 34 36 34 31 26 28 26 24 16 9
9 9 8 15 22 22 25 25 31 31 30 30 28 30 30 30 30 28 28 28 30 30 30 30
30 37 32 27 23 18 18 27 27 34 34 31 33 30 30 28 28 28 28 28 30 34 33
33 33 33 30 26 26 23 23 23 30 37 36 32 32 24 23 21 20 28 31 29 30 22
21 18 13 15 23 26 34 34 36 33 30 30 30 30 25 25 25 26 23 26 25 24 24
25 27 25 22 14 15 12 12 12 21 21 25 25 22 21 21 24 19 19 14 16 11 13
14 20 27 30 28 28 28 30 33 34 34 23 23 16 7 7 4 4 4 18 17 21 23 21 17
11 13 18 18 18 20 18 18 11 14 7 7 7 15 20 18 11 10 15 23 18 16 10 8 8
13 17 18 14 14 14 13 13 14 17 18 13 13 9 9 9 14 12 18 18 11 11 5 5 5 6
6 6 8 12 10 13 15 11 11 11 8 6 6 6 6 6 8 6 6 8 8 8 7 7 9 9 8 8 19 8 8
14 8 8 6 6 11 9 9 8 14 6 6 7 7 8 6 7 6 6 9 9 10 15 14 12 7 7 7 7 13 15
22 22 19 14 9 8 8 8 12 15 19 7 6 10 9 8 6 7 9 9 10 10 8 8 7 7 4 4


Sequence : 22aq40a8.s1
Is_read
Padded
Staden_id 3
Clipping QUAL 39 388
Align_to_SCF 1 152 1 152
Align_to_SCF 154 540 153 539
SCF_File 22aq40a8.s1SCF
Primer Universal_primer
Strand Forward
Dye Dye_primer
Template 22aq40a8
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 38 "M13mp18"
Tag ALUS 49 339
Tag DONE 206 206 "AUTO-EDIT: replaced N by t at 206 (terminated, compound, strong)"

DNA : 22an02b10.s1t
CGTGCCTGCAGGTCGACTCTAGAGGATCCCCCCTGTAATCCCAGCACTTTGGGAGGCCAg
TGCGGGTGAATCACgATGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACACCG
TCTCTACTAAAATAAAAAGAAATTAGCTGGGTGTCgTGGCAGGTGCCTGTAATCCCAGCC
ACTTGGGAAGCTGAgGCAGGAGAATCGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCC
GAgATCACGCGACTGCACTCCAGCCCAACCAATAGTGTGAGACTCTGTCTCGAAAAAAAA
AAAGCAGAGACAAGACAACTAGTACAGTACTTACaGGGTTATTATGATGATTAAATGAGA
gAATAGCTGTGAgGTGATTGATATAGTGCTGTGCTTAATACAAACTATCATTTTATTATA
CGGGTTGAGTGTATCTAATCTGAAAATCCAAAATCAGAAATGCGCTACAGTCTGAAACTT
TTTTGAGCACCGACCTAATGTTCCAAGGAAGTGCTTATCGGAGCACCATGGGTCGGTACA
CATTTGGGTCGGGAATATnCCACCAGTGAGTACCATAAAATGCCAATATCCCCTCCCACC
CCCAACA

BaseQuality : 22an02b10.s1t
7 7 9 12 10 15 16 17 13 13 21 18 23 17 28 28 37 37 37 33 26 26 17 19
12 21 25 36 45 45 34 34 34 34 34 37 37 37 37 37 32 25 9 9 13 17 17 14
18 18 21 29 32 19 18 18 18 21 9 9 9 23 19 30 30 37 29 37 37 32 34 23
20 13 13 10 13 22 32 21 17 17 23 18 10 10 10 12 13 9 9 14 23 29 28 22
22 32 33 37 34 34 34 34 34 34 34 30 37 32 37 37 41 34 33 33 33 21 21
14 14 14 24 28 41 37 32 32 21 21 21 25 30 30 37 30 37 30 30 30 32 36
28 27 17 27 27 37 32 37 36 37 25 23 10 10 10 32 21 23 10 15 10 23 23
36 32 32 34 34 34 37 37 25 25 13 9 9 21 25 25 32 32 32 41 32 28 28 11
22 22 32 32 13 13 10 11 9 10 10 12 12 14 32 32 29 22 22 21 21 17 21 27
41 41 41 28 27 32 27 27 29 37 32 34 17 15 14 28 23 25 20 9 9 9 25 10
12 12 14 13 10 10 9 16 13 23 23 14 14 22 25 34 28 28 22 28 28 28 19 18
10 10 11 19 21 28 28 28 30 30 30 23 18 10 10 28 32 32 34 28 28 28 28
28 31 34 34 25 25 12 19 11 14 14 25 21 24 24 18 18 18 22 23 13 11 10
10 10 10 14 13 10 9 9 7 8 14 17 16 10 10 13 16 15 18 18 18 18 14 15 12
12 9 12 9 12 12 13 9 14 10 18 19 14 9 13 11 18 14 15 15 16 20 19 18 14
9 8 8 6 6 6 11 9 9 14 17 20 12 13 6 6 8 8 11 10 21 23 15 14 13 13 14
21 27 28 32 29 34 28 27 23 14 10 10 12 17 15 13 11 11 11 18 28 33 24
18 14 12 17 12 12 18 22 19 19 24 28 20 21 19 19 20 17 17 26 25 20 9 14
7 7 7 15 21 33 27 27 18 20 19 15 15 20 18 14 14 8 8 9 9 9 7 7 7 7 7 8
9 9 12 7 7 9 11 10 11 13 13 11 7 7 8 15 17 26 25 25 27 25 24 21 19 20
18 13 13 14 9 9 14 18 17 12 15 16 21 20 18 8 7 6 6 6 13 20 25 18 11 14
9 9 9 11 11 12 12 15 15 18 10 10 8 8 10 10 9 9 9 16 11 7 7 6 6 8 4 4 4
4 4 6 10 10 13 13 12 6 6 6 6 12 15 12 11 11 4 4 4 6 6 6 6 6 8 6 6 6 8
6 8 11 13 8 8 6 6 6 6 9 16 9 13 13 17 14 13 9 7 7 12 8 8 8 9 9 9 9 9 9
8 8 8 10 9 7


Sequence : 22an02b10.s1t
Is_read
Padded
Staden_id 21
Clipping QUAL 32 446
Align_to_SCF 1 607 1 607
SCF_File 22an02b10.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22an02b10
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 31 "M13mp18"
Tag ALUS 32 301
Tag DONE 60 60 "AUTO-EDIT: inserted g at 60  (terminated, compound, strong)"
Tag DONE 75 75 "AUTO-EDIT: replaced A by g at 75 (terminated, isolated, strong)"
Tag DONE 156 156 "AUTO-EDIT: replaced C by g at 156 (terminated, isolated, strong)"
Tag DONE 195 195 "AUTO-EDIT: replaced A by g at 195 (terminated, isolated, strong)"
Tag DONE 243 243 "AUTO-EDIT: replaced T by g at 243 (terminated, isolated, strong)"
Tag DONE 335 335 "AUTO-EDIT: replaced T by a at 335 (all_stranded, isolated, strong)"
Tag DONE 361 361 "AUTO-EDIT: replaced C by g at 361 (terminated, isolated, strong)"
Tag DONE 373 373 "AUTO-EDIT: replaced C by g at 373 (terminated, isolated, strong)"

DNA : 22ak67d6.r1t
CGCGCCCCTCnGACTCCGGCCCTAnCACGGTACCCACTTTGGGAGGCCAGTGCGGGTGAA
TCACGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACACCGTCTCTACTAA
AATAAAAAGAAATTAGCTGGGTGTCGTGGCAGGTGCCTGTAATCCCAGCCACTTGGGAAG
CTGAgGCAGGAGAATCGCTTGAACCCGGGAgGTGGAGGTTGCAGTGAGCCGAGATCACGC
GACTGCACTCCAGCCCAACCAATAGTGTGAGACTCTGTCTCGAAAAAAAAAAAGCAGAGA
TCAGATCACTAGTACAGTACTTACGGGCTTATTATGATGATTAAATGAGAGAATACCTGT
GAGGTGATTGATATATTGCTGTGCTTAATACAnACTATCATTTTATTATACGGGTCGAGT
GTTTCTAATCTGACAATCCAAATTAGAAATGCTCTACAGTCTGAAACCTTTTTGAGCACC
CACCTACTGTTCAAAGGACGTGCTTATTGGAGCATTATGGGTTGTAACATTTTTGGGTTG
GGAATTTTCACCCATTAGTACTATAAATGCCATTTTCCAAAAAATCTGAATCTAAAATTT
CTGGTCCTACCAGCATTTGCTAGGGATCCCACCCGTCTTCTTCCTTACCTGTTTAAGTCT
TATAAATC

BaseQuality : 22ak67d6.r1t
6 6 6 4 8 11 15 8 4 4 4 4 8 6 6 9 7 8 9 8 4 4 4 4 4 4 10 9 9 21 19 33
30 33 30 30 30 28 28 28 23 23 20 11 11 16 12 13 17 21 25 28 33 33 33
38 34 34 34 33 30 22 22 12 14 21 10 12 21 21 16 14 11 13 13 14 21 21
21 19 15 18 23 23 25 30 28 33 38 38 33 33 30 30 30 30 30 30 30 37 37
45 45 33 33 33 33 33 33 40 42 49 42 40 40 40 34 34 31 35 34 35 37 42
42 37 32 19 9 9 11 23 19 28 30 30 28 38 45 37 37 37 32 32 24 34 34 30
30 26 21 20 11 27 27 40 34 30 30 28 30 30 30 23 18 17 9 9 18 16 16 24
24 24 23 21 18 11 11 18 25 25 16 9 7 9 15 11 8 7 9 7 7 8 16 16 27 28
25 20 16 10 10 9 13 8 8 7 12 4 4 4 14 6 6 6 7 9 6 7 7 7 7 16 10 20 15
13 11 9 9 8 8 8 15 8 10 10 17 14 9 9 19 15 15 7 7 12 20 19 25 25 22 18
17 7 9 12 20 21 25 21 21 20 22 28 32 30 25 25 12 12 18 32 32 36 49 49
33 33 24 20 13 12 16 18 20 14 25 23 25 19 12 11 8 8 4 4 4 4 4 8 8 6 4
6 8 15 17 21 19 15 8 8 8 8 10 7 7 13 9 7 11 14 6 6 4 4 4 6 12 8 13 17
21 18 19 19 20 18 18 15 10 15 14 13 14 8 8 8 9 8 8 10 10 8 8 15 17 17
17 17 14 13 19 17 16 12 10 14 15 17 15 14 8 8 7 7 15 19 18 12 11 16 12
15 11 10 13 13 11 4 4 4 10 12 12 18 12 14 9 10 9 10 21 22 18 14 6 6 6
6 6 8 4 4 4 8 8 7 8 7 9 14 7 8 7 10 16 31 17 14 4 4 4 10 11 8 10 13 17
13 8 8 9 8 8 12 12 14 14 7 7 7 7 7 7 7 8 9 13 11 10 7 10 7 6 6 10 8 8
23 23 12 7 7 7 7 7 10 10 18 6 6 6 6 6 6 7 7 7 6 6 6 7 6 6 4 4 4 4 8 11
18 15 23 11 9 8 7 7 7 7 7 7 8 15 18 8 10 10 12 8 6 8 6 6 6 7 7 12 10
12 18 11 12 10 19 19 15 15 10 10 9 7 11 7 8 9 10 7 7 6 6 6 6 4 6 7 7 7
7 9 9 9 13 13 9 7 7 7 9 7 7 7 6 6 6 6 8 8 9 8 11 8 7 6 6 6 6 9 7 8 7 7
6 8 6 6 9 10 12 10 13 12 6 6 6 6 6 7 6 6 7 7 7 11 13 11 9 8 6 6 8 6 6
8 12 14 8 8 8 6 13 8 8 8 6 7 8 7 8 9 8 10 6 6 10 11 17 20 16 11 11 7 6
8 8 9 8 6 12 10 7 7 8 8 4


Sequence : 22ak67d6.r1t
Is_read
Padded
Staden_id 19
Clipping QUAL 30 292
Align_to_SCF 1 668 1 668
SCF_File 22ak67d6.r1tSCF
Primer Universal_primer
Strand Reverse
Dye Dye_terminator
Template 22ak67d6
Clone bK216E10
Sequencing_vector "m13mp18"
Tag ALUS 35 291
Tag DONE 185 185 "AUTO-EDIT: replaced C by g at 185 (terminated, isolated, strong)"
Tag DONE 211 211 "AUTO-EDIT: replaced T by g at 211 (terminated, isolated, strong)"

DNA : 22ak64b1.s1t
TGGGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCTGAAACACCGTCTCTACTAAA
ATAAAAAGAAATTAGCTGGGTGTCGTGGCAGGTGCCTGTAATCCCAGCCACTTGGGAAGC
TGAGGCAGGAGAATCGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAgATCACGCG
ACTGCACTCCAGCCCAACCAATAGTGTGAGACTCTGTCTCGAAAAAAAAAAAGCAGAGAC
AAGAcCACTAGTACAGTACTTACAGGGTtATTATGATGATTAAATGAGAGAATAGCTGTG
AGGTGATTGATATAGTGCTGTGCTTAATACAAACTATCATTTTATTATACGGGTTGAGTG
TTTCTAATCTGAaAATCCAAAATTAGAAATGCTCTACAGTCTGAAACTTTTTTGAGCACC
GACCTAAATGTTCAAAGGGAGGTGCTTAATTGGAGCATTATGGGTTGTTAGATCTTTGGG
TTGGGAATATTCAACC

BaseQuality : 22ak64b1.s1t
4 4 8 11 13 20 16 16 16 19 24 32 31 37 37 35 34 29 32 18 32 24 33 33
37 37 37 23 32 11 10 21 17 37 34 34 45 45 45 45 32 29 26 26 28 30 30
33 45 45 49 49 45 43 45 45 45 45 45 37 45 45 45 45 45 45 45 37 37 37
38 32 40 37 41 37 45 32 45 45 44 37 45 30 45 45 33 33 33 33 33 22 37
37 45 45 45 40 37 34 37 37 33 32 32 33 33 33 33 40 40 40 42 40 42 37
37 37 45 45 45 45 45 35 34 34 28 28 18 21 17 17 27 38 38 45 34 34 34
34 34 34 34 34 34 34 34 34 34 34 34 37 34 34 33 33 33 33 28 31 31 36
34 31 36 36 34 33 20 14 8 8 8 8 14 23 27 31 36 33 36 38 30 30 28 28 28
30 30 27 30 30 30 30 33 33 23 21 18 18 17 20 32 37 37 45 45 45 45 34
34 34 45 45 45 44 45 37 45 45 45 37 40 37 37 33 40 44 40 40 36 31 31
28 25 22 27 14 14 8 9 10 8 7 8 7 12 18 18 23 15 9 9 15 15 20 20 25 28
25 21 21 18 18 8 9 8 6 6 8 11 14 28 28 28 30 30 30 30 31 30 31 25 22
22 27 15 15 15 16 13 17 25 25 30 25 27 28 31 24 24 19 24 29 33 27 31
31 31 31 28 27 22 14 15 27 32 40 37 36 36 36 33 33 34 33 27 13 14 7 7
8 18 23 32 32 23 20 20 33 30 27 27 21 14 14 18 21 18 21 15 15 17 11 11
16 24 23 30 23 14 10 13 14 15 10 8 9 16 16 28 4 4 4 10 11 12 9 8 10 14
20 18 19 19 19 10 10 12 15 25 23 26 26 28 18 14 14 16 20 15 14 12 12
12 21 23 25 24 21 17 17 14 21 20 19 12 9 9 8 9 8 10 7 6 9 8 7 8 9 7 7
7 6 6 8 7 8 6 6 6 6 6 13 11 6 6 6 8 10 11 8 9 9 10 10 15 10 11 12 16
13 10 9 7 7 7 7 9 10 8 8 7 6 6 6 6 6 14 10 7 7 7 9 9 10 11 16 16 7 6 4
4 4 8 4


Sequence : 22ak64b1.s1t
Is_read
Padded
Staden_id 8
Clipping QUAL 40 416
Align_to_SCF 1 496 1 496
SCF_File 22ak64b1.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ak64b1
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 39 "M13mp"
Tag CONF 44 44 "AUTOEDIT: possible compression"
Tag CONF 96 96 "AUTOEDIT: possible compression"
Tag DONE 172 172 "AUTO-EDIT: replaced A by g at 172 (terminated, isolated, strong)"
Tag DONE 245 245 "AUTO-EDIT: replaced A by c at 245 (all_stranded, compound, strong)"
Tag AMBG 246 246 "AUTOEDIT: Check this edit stack (conflict & possible misassembly))!"
Tag DONE 269 269 "AUTO-EDIT: replaced C by t at 269 (all_stranded, isolated, strong)"
Tag DONE 373 373 "AUTO-EDIT: replaced N by a at 373 (terminated, isolated, strong)"

DNA : 22ak81h10.s1t
GTGGCATGCCTGCAGGTCAACTCTAAAAGATCCCCTGAAACACCGTCTCTACTAAAATAA
AAAGAAATTAGCTGGGTGTCGTGGCAGGTGCCTGTAATCCCAgCCACTTGGGAAGCTGAG
GCAGGAGAATCGCTTGAACCCGGGAgGTGGAgGTTGCAGTGAGCCGAGATCACGCGACTG
CACTCCAGCCCAAcCAATAGTGTGAGACTCTGTCTCGAaaAAaAAAAAGCAgAGACaAGA
CCACTAGTACAGTACTTACAGGGTTATTATGATGATTAAaTGAGAGAATAGCTGTGAGGT
GATTGATATAGTGCTGTGCTTAATACaAACTATCATTTTATTATACGGGTTGAGTGTTTC
TAATCTGAAAATCCaaAATTAGAAATGCTCTACAGTCTGAAACTTTtTTGAGCACCGACC
TACTGTGCACAGGAAGTGCTTATTGGAGCATGATGGGTTGTTACATATTTGGGTTGGGAA
TATTCACCCAGTAAGTACTATAAAATGCAAATATTCCAACAAG

BaseQuality : 22ak81h10.s1t
6 6 6 6 6 8 9 16 11 13 21 20 22 22 22 15 14 9 9 9 9 15 18 15 9 9 9 9 9
15 23 36 36 36 36 34 38 40 30 28 28 28 30 32 37 37 36 38 37 44 45 45
49 49 45 45 37 37 38 45 45 45 38 37 37 38 38 37 37 34 34 34 32 32 38
45 49 45 45 45 45 37 33 33 27 27 18 18 30 32 36 36 36 36 36 36 36 34
32 21 18 4 4 4 18 17 27 28 33 36 36 36 49 36 36 36 34 34 45 27 27 30
25 27 12 20 20 34 34 38 37 37 34 34 25 25 18 18 21 29 38 45 21 28 14
14 14 27 21 34 18 17 17 32 27 25 22 13 13 10 18 15 32 32 32 37 28 22
22 21 14 10 10 11 23 22 28 20 14 14 8 8 11 20 20 16 12 16 16 28 21 19
10 10 10 19 18 20 20 14 14 32 32 34 32 25 18 18 18 18 27 32 32 24 24
23 23 14 10 10 10 9 9 10 11 12 12 12 12 17 11 11 11 10 8 6 6 8 8 10 16
16 16 11 14 10 9 9 9 17 11 11 11 14 15 22 18 14 14 11 11 15 27 22 19
23 27 30 28 22 18 16 11 10 10 11 9 10 11 11 12 15 20 27 27 23 21 14 10
10 10 10 14 22 25 22 14 14 22 32 38 34 34 34 31 24 18 14 12 9 10 10 23
18 24 16 16 18 18 18 19 18 17 21 18 18 12 14 21 27 37 34 34 28 28 34
27 27 28 31 20 18 11 9 9 12 11 11 27 15 15 20 23 26 14 8 8 8 8 14 16
23 19 19 28 31 31 31 25 18 11 11 18 10 10 10 10 11 12 16 16 21 23 12
12 13 23 13 13 19 11 10 10 10 10 10 18 21 28 16 19 29 32 19 19 8 8 8
10 10 18 18 22 21 16 18 22 21 11 11 14 14 15 14 18 7 7 7 7 7 7 14 18
10 10 9 9 14 15 15 23 20 22 19 19 21 16 11 11 9 8 8 9 9 18 14 11 9 9
15 8 9 10 8 9 8 8 8 14 14 25 27 16 9 8 14 8 9 17 13 18 15 8 8 7 7 7 7
6 6 6 6 6 4 4 4 8 9 10 17 11 15 12 17 9 9 10 7 7 7 10 11 10 7 7 7 6 6
8 6 6 8 4


Sequence : 22ak81h10.s1t
Is_read
Padded
Staden_id 5
Clipping QUAL 36 418
Align_to_SCF 1 523 1 523
SCF_File 22ak81h10.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ak81h10
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 35 "M13mp1"
Tag ALUS 36 216
Tag DONE 103 103 "AUTO-EDIT: replaced N by g at 103 (terminated, isolated, strong)"
Tag DONE 146 146 "AUTO-EDIT: replaced T by g at 146 (terminated, isolated, strong)"
Tag DONE 152 152 "AUTO-EDIT: replaced A by g at 152 (terminated, isolated, strong)"
Tag DONE 194 194 "AUTO-EDIT: replaced G by c at 194 (all_stranded, isolated, strong)"
Tag DONE 219 219 "AUTO-EDIT: replaced G by a at 219 (all_stranded, compound, strong)"
Tag DONE 220 220 "AUTO-EDIT: replaced C by a at 220 (all_stranded, compound, strong)"
Tag DONE 223 223 "AUTO-EDIT: replaced G by a at 223 (all_stranded, isolated, strong)"
Tag DONE 232 232 "AUTO-EDIT: replaced C by g at 232 (all_stranded, isolated, strong)"
Tag DONE 237 237 "AUTO-EDIT: replaced G by a at 237 (all_stranded, isolated, strong)"
Tag DONE 280 280 "AUTO-EDIT: replaced G by a at 280 (terminated, isolated, strong)"
Tag DONE 327 327 "AUTO-EDIT: replaced G by a at 327 (terminated, isolated, strong)"
Tag DONE 375 375 "AUTO-EDIT: replaced T by a at 375 (terminated, compound, strong)"
Tag DONE 376 376 "AUTO-EDIT: replaced C by a at 376 (terminated, compound, strong)"
Tag DONE 407 407 "AUTO-EDIT: replaced C by t at 407 (terminated, isolated, strong)"

DNA : 22ak66c6.s1t
nCGTGGCTGCCTGCAGGTCGACTCTAGAGGATCCCCACCGTCTCTACTAAAATAAAAAGA
AATTAGCTGGGTGTCGTGGCAGGTGCCTGTAATCCCAGCCACTTGGGAAGCTGAGGCAGG
AGAATCGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACGCGACTGCACTC
CAGCCCAACCAATAGTGTGAGACTCTGTCTCGAAAAAAAAAAAGCAGAGACAAGACAACT
AGTACAGTACTTACAGGGTTATTATGATGATTAAATGAGAGAATAGCTGTGAGGTGATTG
ATATAGTGCTGTGCTTAATACAAACTATCATTTTATTATACGGGTTGAGTGTTTCTAATC
TGAAAATCCAAAATTAGAAATGCTCTACAGTCTGAAACTTTTTTGAGCACCGACCTAATG
TTCAAAGGAAGTGCTTATTGGAGCATTATGGGTTGTTAGATTTTTGGGTTGGGAATATTC
AACCAGTAAGTACTATAAAATGCAAATATTCCAAAAAAAATCTGAAATCTGAAACATtTC
TGGTCCTAAGCAAGCATnTTGCAAAGGGATACGCAACCTGTAGTACGTCCTTTATCATTG
TnTCAAGTAGTTAATATATTGTGGTACAGATTCTGAGGTGGTATAnCAnATTCGATTGTA
TTATT

BaseQuality : 22ak66c6.s1t
4 4 8 4 6 10 13 21 24 25 33 33 33 30 27 21 15 27 19 30 30 33 33 30 21
21 10 9 17 11 27 27 37 38 33 35 35 35 35 44 45 45 38 37 37 45 45 45 43
43 43 45 45 45 45 45 45 45 21 21 23 30 30 34 37 37 38 45 32 45 37 41
37 45 30 45 45 34 34 34 32 29 22 32 32 45 45 45 33 28 28 37 37 34 34
34 35 34 34 34 34 34 34 37 37 40 41 37 34 37 37 37 32 24 22 27 29 25
27 20 21 21 21 27 45 41 40 40 40 42 34 34 37 41 45 51 45 45 37 30 37
41 41 37 36 28 30 30 30 22 33 33 35 33 33 41 51 51 45 39 39 39 30 28
33 34 34 39 34 41 34 34 41 33 33 39 39 39 33 33 33 30 33 33 33 30 29
19 19 24 25 32 33 45 36 36 36 36 41 41 30 30 30 37 37 43 51 51 51 51
45 37 37 30 37 37 37 51 51 51 51 51 37 37 28 28 10 10 10 13 10 10 10 9
9 9 21 21 28 37 37 37 33 33 33 33 33 33 34 34 34 33 33 33 33 21 25 25
22 22 29 29 33 33 33 33 31 31 27 28 17 23 23 28 26 24 32 10 10 10 15
15 26 32 32 37 45 45 32 45 33 26 24 32 37 37 35 34 37 35 37 34 37 37
40 37 37 45 45 38 38 45 45 40 37 37 37 34 30 30 28 28 28 30 37 37 34
34 34 34 34 33 31 31 25 21 19 22 21 25 30 32 32 30 22 22 25 28 24 25
26 17 17 23 27 27 33 31 31 34 38 38 38 38 34 26 17 15 8 8 11 16 25 31
32 33 29 26 32 29 33 34 34 34 36 33 34 34 31 27 31 34 38 45 45 36 37
37 37 36 36 38 34 32 28 25 22 22 21 17 18 29 29 23 23 22 27 25 20 18
11 11 15 15 16 23 21 17 19 24 24 24 31 31 31 33 33 33 31 33 33 29 29
29 29 29 31 31 31 23 24 19 12 10 16 10 10 20 10 10 13 15 30 23 29 23
28 18 10 10 16 21 18 19 19 24 24 12 11 9 9 10 21 23 31 31 33 28 28 14
17 17 28 21 30 24 30 28 22 26 23 19 10 10 12 23 22 23 19 12 10 9 9 10
19 24 29 30 34 34 34 34 34 29 25 25 32 26 31 31 32 20 17 15 12 12 4 4
4 17 23 33 30 24 18 13 18 16 12 16 8 9 9 19 15 15 4 4 4 7 11 6 6 6 7 8
9 17 12 13 19 23 25 13 13 13 19 21 29 32 30 26 20 20 12 9 9 8 9 8 8 15
24 17 15 8 8 9 17 16 4 4 4 8 8 13 15 23 14 9 8 8 10 10 17 23 21 17 12
13 22 20 19 15 11 11 9 8 8 8 8 8 8 10 9 9 7 8 8 10 12 10 10 12 4 4 4 4
4 4 10 10 10 10 10 9 8 8 7 8 9 11 9 9 4


Sequence : 22ak66c6.s1t
Is_read
Padded
Staden_id 18
Clipping QUAL 37 548
Align_to_SCF 1 665 1 665
SCF_File 22ak66c6.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ak66c6
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 36 "M13mp"
Tag ALUS 38 221
Tag DONE 538 538 "AUTO-EDIT: replaced N by t at 538 (terminated, isolated, strong)"

DNA : 22ak93c1.s1lt
TTTCTTTGGGGGCAATCTTGATGCTAGCGTCGTTCAAGATGATCCACACCCAGCTCACTG
TTTTATTCTCTCCAATAATCCTAAGCAAGCTCTCAAAATATAAATATGCTTTTTAATAAT
ACAATCGAATTTGCTATACCACCTCAGAATCTGTACCACAATATATTAACTACTTAAAAC
AATGATAAAGAACGTACTACAGGTTGCGTATCCCTTTGCAAAATGCTTGCTTAGGACCAG
AAATGTTTCAGATTTCAGATTTTTTTTGGAATATTTGCATTTTATAGTACTTACTGGTTG
AATATTCCCAACCCAAAAATCTAACAACCCATAATGCTCCAATAAGCACTTCCTTTGAAC
ATTAGGTCGGTGCTCAAAAAAGTTTCAGACTGTAGAGCATTTCTAATTTTGGATTTTCAG
ATTAGAAACACTCAACCCGTATAATAAAATGATAGTTTGTATTAAGCACAGCACTATATC
AATCACCTCACAGCTATTCTCTCATTTAATCATCATAATAACCCTGTAAGTACTGTACTA
gTTGTCTTGTCTCTGCTTTTTTTTTTTCgAgACAGAGTCTCACACTATTGGTTGGGCTGG
AATGCAnTCGCGTGATCTCGGCTCACTGGCAACCTCCACCTCCCGGGG

BaseQuality : 22ak93c1.s1lt
4 4 4 4 4 4 4 4 9 6 4 8 15 11 4 6 4 12 8 9 10 12 11 8 8 6 7 8 14 14 9
4 4 8 8 8 8 8 4 6 8 11 9 10 8 9 9 11 10 9 9 9 9 9 9 16 16 32 23 29 21
27 27 22 22 20 28 32 37 37 34 31 30 28 28 24 29 29 34 34 38 32 32 18
22 18 22 22 28 29 37 37 37 37 35 35 34 34 35 34 37 37 37 37 37 37 34
37 37 37 37 32 32 28 28 31 30 30 30 23 23 23 28 27 21 32 13 13 16 24
32 34 31 30 28 28 28 28 28 34 34 34 34 33 25 16 9 9 10 23 32 33 41 37
34 28 30 30 30 28 28 22 27 25 32 25 30 27 22 24 22 22 28 25 24 30 30
30 30 30 30 24 28 13 10 10 23 20 18 9 9 9 18 23 30 30 30 28 24 19 25
11 11 12 27 31 34 30 30 30 30 37 45 51 41 39 28 28 28 25 25 24 30 34
39 39 39 39 39 39 36 31 13 10 9 10 10 23 23 9 9 13 23 31 31 14 14 31
31 13 9 9 9 23 23 23 13 9 9 9 31 31 41 51 36 31 14 13 31 19 30 31 31
22 34 25 33 33 33 30 24 29 30 18 24 24 11 11 24 24 33 39 34 34 30 30
34 22 22 14 19 18 23 23 17 31 24 37 33 33 33 33 33 28 34 18 18 27 34
34 38 27 20 20 24 24 30 30 39 34 34 30 22 22 24 33 33 33 33 28 24 24
22 30 22 24 24 33 33 33 39 51 51 41 32 27 17 25 17 31 31 34 19 15 10
10 31 14 27 21 30 30 24 24 30 34 39 39 41 36 34 30 30 30 34 31 16 9 9
10 20 19 16 11 9 9 9 13 23 22 28 28 37 33 33 33 28 32 18 13 10 20 18
10 32 21 31 23 14 9 9 9 16 11 9 9 10 20 25 33 30 30 28 32 28 28 37 35
35 34 34 34 34 34 37 40 37 33 32 25 12 10 10 16 16 28 32 32 34 30 28
28 29 31 33 32 28 30 30 25 21 16 19 19 19 27 19 14 14 22 22 28 25 29
29 29 30 30 23 23 21 18 14 21 17 24 19 32 32 37 37 31 30 30 28 31 30
34 34 28 28 28 28 31 31 30 28 28 28 30 30 25 32 10 10 10 23 23 27 17
17 22 17 23 23 23 24 20 17 4 4 4 14 16 24 22 19 18 13 19 9 12 14 25 25
33 32 29 40 38 49 49 49 34 34 17 14 8 7 7 9 9 10 8 7 7 9 10 15 17 18
22 24 18 18 18 22 20 24 24 28 18 19 18 19 21 24 25 14 12 8 8 9 14 12 4
4 4 17 17 17 14 9 9 9 12 21 21 18 12 10 13 10 11 9 12 12 8 7 8 8 9 10
9 15 10 8 9 10 10 21 21 28 27 18 14 7 7


Sequence : 22ak93c1.s1lt
Is_read
Padded
Staden_id 1
Clipping QUAL 56 598
Align_to_SCF 1 648 1 648
SCF_File 22ak93c1.s1ltSCF
Primer Universal_primer
Strand Forward
Dye Dye_primer
Template 22ak93c1
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 47 "M13mp18"
Tag DONE 541 541 "AUTO-EDIT: replaced N by g at 541 (all_stranded, isolated, strong)"
Tag ALUS 559 647
Tag DONE 569 569 "AUTO-EDIT: replaced A by g at 569 (all_stranded, isolated, strong)"
Tag DONE 571 571 "AUTO-EDIT: replaced A by g at 571 (all_stranded, isolated, strong)"

DNA : 22ak64e2.s1t
GTAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTTTGCAAAATGCTTGCTTA
GGACCAGAAATGTTTCAGATTTCAGATTTTTTTTGGAATATTTGCATTTTATAGTACTTA
CTGGTTGAATATTCCCAACCCAAAAATCTAACAACCCATAATGCTCCAATAAGCACTTCC
TTTGAACATTAGGTCGGTGCTCAAAAAAGTTTCAGACTGTAGAGCATTTCTAATTTTGGA
TTTTCAGATTAGAAACACTCAACCCGTATAATAAAATGATAGTTTGTATTAAGCACAGCA
CTATATCAATCACCTCACAGCTATTCTCTCATTTAATCATCATAATAACCCTGTAAGTAC
TGTACTAGTTGTCTTGTCTCTGCTTTTTTTTTTTCGAGACAGAGTCTCACACTATTGGTT
GGACTGGAGTGCAATTCnCCTGAATTCGGCTCACGGCAACTTCAACCTCCCGGGTTCAAG
TGAATCTCCTC

BaseQuality : 22ak64e2.s1t
4 4 8 10 12 15 18 18 28 30 30 30 30 26 37 34 30 30 22 22 20 23 16 11
11 18 23 23 23 28 9 9 10 9 21 12 32 34 45 45 45 45 38 30 30 30 30 30
28 34 30 33 33 33 33 33 43 45 45 32 18 10 11 11 25 23 10 10 22 32 38
37 27 27 27 23 20 9 9 10 23 25 25 21 9 9 10 29 32 45 45 45 45 45 45 37
37 37 38 45 37 41 28 29 28 28 28 28 34 34 33 33 33 28 28 34 33 34 34
34 34 34 34 45 37 37 29 37 37 45 45 45 45 42 37 34 35 35 35 34 34 34
34 34 37 37 37 45 45 35 35 35 35 35 35 35 37 37 37 37 45 37 42 42 33
30 30 33 33 33 40 34 34 34 34 34 34 40 40 40 37 37 37 34 34 34 34 34
31 31 27 28 19 21 19 28 28 30 32 34 34 31 31 31 33 39 27 20 7 7 8 8 14
15 11 11 17 28 23 28 17 9 9 11 23 27 33 33 40 40 40 40 40 40 40 37 32
32 31 31 28 37 30 33 25 21 13 13 14 26 22 11 11 21 21 30 33 31 31 33
37 37 37 45 49 45 40 40 40 40 40 45 40 40 40 40 40 31 29 29 32 27 37
37 45 45 45 40 37 37 37 37 37 33 34 33 33 30 30 34 34 36 36 36 30 30
28 28 28 27 38 38 36 31 33 32 27 20 20 20 28 32 33 24 24 29 36 34 30
33 30 26 26 26 30 30 26 37 36 34 33 30 31 31 28 27 27 25 24 29 33 27
27 31 31 31 31 33 36 38 38 32 32 21 13 13 16 19 19 24 25 33 30 33 33
33 38 39 40 44 40 40 36 33 37 40 40 40 40 49 40 36 33 31 26 23 23 21
18 20 14 12 11 14 17 25 31 33 33 33 36 30 30 30 30 30 28 28 20 15 14 4
4 4 12 9 9 4 4 4 7 8 7 7 7 7 4 4 4 7 8 10 7 6 9 9 9 7 7 11 17 19 9 8 7
7 8 7 8 9 7 6 10 6 7 6 6 7 7 8 8 8 12 13 8 8 8 8 10 10 9 8 7 6 6 8 13
7 7 7 7


Sequence : 22ak64e2.s1t
Is_read
Padded
Staden_id 14
Clipping QUAL 41 420
Align_to_SCF 1 491 1 491
SCF_File 22ak64e2.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ak64e2
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 40 "M13mp"

DNA : 22ak70f10.s1t
TTGGCTGCCTGCAGGTCGACTCTAGAGGATCCCCCAGGGTTATTATGATGATTAAATGAG
AGAATAGCTGTGAGGTGATTGATATAGTGCTGTGCTTAATACAAACTATCATTTTATTAT
ACGGGTTGAGTGTTTCTAATCTGAAAATCCAAAATTAGAAATGCTCTACAGTCTGAAACT
TTTTTGAGCACCGACCTAATGTTCAAAGGAAGTGCTTATTGGAGCATTATGGGTTGTTAG
ATTTTTGGGTTGGGAATATTCAACCAGTAAGTACTATAAAATGCAAATATTCCAAAAAAA
ATCTGAAATCTGAAACATTTCTGGTCCTAAGCAAGCATTTTGCAAAGGGATACGCAACCT
GTAGTACGTTCTTTATCATTGTTTTAAGTAGTTAATATATTGTGGTACAGATTCTGAGGT
GGTATAGCAAATTCGATTGTATTATTAAAAAGCATATTTATATTTTGAGAGCTTGCTTAG
GATTATTGGAGAGAATAAAACAGTGAAGCTTTGGTGTTATGAGGGAATnTTAGATAGAAA
AGTGCAGTnTTTCAGTTCATGCTCTnTCATTTnTTACTCCCTCCGGTTAAAGCTGAAGCT
CAACAAAGATATAGTGATCTCTGTGGGCATTATAATCCTGTCCC

BaseQuality : 22ak70f10.s1t
4 4 6 8 8 9 19 23 33 33 34 33 27 21 18 27 18 27 27 34 34 31 27 23 13
11 19 16 31 31 37 45 45 34 34 31 31 22 31 25 31 37 45 45 45 45 37 37
37 37 37 37 45 37 37 37 45 38 29 27 27 32 32 37 45 33 37 37 45 37 45
45 37 37 37 40 40 40 37 45 37 37 34 33 33 34 34 34 37 33 40 37 37 37
33 33 33 33 33 33 33 33 33 32 33 41 41 35 35 35 40 40 36 36 36 34 33
33 37 37 37 37 37 41 45 30 30 41 41 37 28 45 18 18 29 35 37 37 37 37
41 41 51 51 51 51 51 33 33 33 33 33 33 45 45 45 41 39 39 51 51 41 45
45 45 45 35 33 33 33 33 33 40 51 51 51 51 51 51 51 51 51 43 45 39 34
30 30 33 33 33 33 45 45 38 38 38 38 33 30 29 14 15 27 27 30 33 51 51
41 41 37 34 37 37 37 40 40 40 37 45 51 33 33 33 33 33 33 37 37 31 45
33 25 22 27 21 28 33 28 28 33 41 37 45 41 33 45 33 22 22 33 33 34 44
44 45 45 33 33 33 33 33 30 34 34 34 34 37 37 29 34 37 33 33 33 33 33
33 34 40 33 33 33 30 30 30 37 37 37 30 30 33 30 33 33 49 49 45 45 45
45 45 45 44 38 38 38 44 38 45 45 49 40 40 35 35 35 35 38 37 40 37 37
34 34 34 34 34 34 34 36 36 36 34 36 33 31 31 36 33 28 28 27 23 19 17
17 23 23 23 33 27 28 28 28 30 33 40 40 31 31 17 20 20 28 32 25 17 17
32 27 37 37 36 33 33 33 33 32 36 34 28 30 32 31 31 14 18 10 9 9 19 21
30 31 38 38 38 37 37 31 34 34 36 31 30 31 31 31 31 33 33 33 39 30 25
24 24 29 33 33 34 33 33 23 23 12 23 23 30 33 33 37 37 37 38 40 37 34
33 37 36 33 33 33 33 33 33 36 28 28 22 24 24 24 21 29 33 33 33 34 33
33 33 33 33 33 33 33 33 27 28 28 31 31 23 27 19 15 11 20 21 33 33 31
31 31 31 31 26 28 24 24 24 29 24 29 29 33 27 31 27 30 36 29 18 20 12
17 9 9 9 19 19 15 8 8 13 15 14 8 9 9 9 10 12 4 4 4 9 10 11 12 24 26 18
13 13 11 11 13 10 16 14 13 12 4 4 4 17 11 7 7 8 7 8 8 8 20 20 26 16 14
4 4 4 8 8 10 18 4 4 4 8 8 21 11 13 10 8 10 6 6 6 6 6 8 9 12 14 17 11
14 14 8 8 8 7 9 7 8 8 12 9 9 8 8 7 10 10 12 10 9 8 16 9 8 8 8 7 6 6 8
6 6 6 6 6 6 6 9 12 7 7 8 8 7 7 7 12 8 7 7


Sequence : 22ak70f10.s1t
Is_read
Padded
Staden_id 2
Clipping QUAL 35 508
Align_to_SCF 1 644 1 644
SCF_File 22ak70f10.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ak70f10
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 34 "M13mp1"
Seq_vec SVEC 584 644 "M13mp1"

DNA : 22ak92c4.s1t
nGGGCGCTGCCTGCAGGTCGACTCTAnAGGATCCCCATTATACGGGTTGAGTGTTTCTAA
TCTGAAAATCCAAAATTAGAAATGCTCTACAGTCTGAAACTTTTTTGAGCACCGACCTAA
TGTTCAAAGGAAGTGCTTATTGGAGCATTATGGGTTGTTAGATTTTTGGGTTGGGAATAT
TCAACCAGTAAGTACTATAAAATGCAAATATTCCAAAAAAAATCTGAAATCTGAAACATT
TCTGGTCCTAAGCAAGCATTTTGCAAAGGGATACGCAACCTGTAGTACGTTCTTTATCAT
TGTTTTAAGTAGTTAATATATTGTGGTACAGATTCTGAGGTGGTATAGCAAATTCGATTG
TATTATTAAAAAGCATATTTATATTTTGAGAGCTTGCTTAGGATTATTGGAGAGAATAAA
ACAGTGAAGCTTTGGTGTTATGAGGGAATTTTAGATAGAAAAGTGCAGTTTTTCAGTTCA
TGCTCTTTCATTTC

BaseQuality : 22ak92c4.s1t
4 4 6 4 6 8 11 14 18 26 32 34 36 34 23 25 10 23 9 23 23 34 29 23 22 4
4 4 16 14 25 24 29 33 30 33 33 33 33 40 37 40 45 28 28 25 15 18 32 32
17 14 28 13 13 38 38 40 40 37 37 37 37 38 45 45 45 38 33 32 33 33 33
33 38 38 38 45 32 30 45 32 34 34 34 34 40 33 33 32 32 28 28 38 45 45
49 45 45 45 45 40 37 41 45 45 40 30 30 33 33 33 33 40 40 45 45 45 45
32 32 28 11 12 27 25 33 33 45 41 33 32 14 14 28 33 37 37 37 37 37 45
45 37 37 37 37 37 37 37 37 28 33 32 21 14 32 20 24 32 21 21 32 36 41
41 45 32 32 28 13 13 33 33 45 51 51 41 37 32 32 32 32 32 32 34 34 30
30 31 32 12 12 27 31 30 35 35 35 33 39 41 28 28 28 28 28 28 41 41 41
30 32 30 30 30 32 51 51 51 51 45 45 45 45 45 45 45 45 51 45 45 45 45
33 33 33 33 33 33 51 51 51 51 51 41 41 45 45 45 39 39 39 39 39 39 41
41 41 41 40 33 33 33 33 33 33 41 45 41 41 41 41 33 33 33 33 33 33 51
51 45 34 22 22 20 28 30 17 15 15 45 30 33 33 33 33 33 33 33 33 37 37
32 33 33 25 25 9 10 9 14 14 33 33 34 34 41 40 40 40 40 37 40 37 37 34
33 33 29 24 22 32 32 45 45 40 27 27 14 32 32 45 38 34 45 19 21 10 21
21 30 37 37 34 34 37 38 38 37 37 37 37 37 35 34 36 36 40 40 49 34 34
34 34 37 37 38 37 33 30 30 30 30 30 40 40 34 34 34 27 27 31 31 33 35
33 30 30 21 21 12 30 28 36 40 36 36 36 33 33 26 26 21 19 20 29 30 36
34 34 33 31 28 28 32 35 32 35 26 30 25 26 26 25 21 19 12 11 19 21 23
21 11 13 17 17 24 29 27 29 29 28 31 20 25 18 16 12 14 23 21 11 11 16
14 10 21 23 33 33 34 31 31 22 22 14 21 11 16 18 31 40 40 36 36 24 27
19 19 13 16 10 8

Sequence : 22ak92c4.s1t
Is_read
Padded
Staden_id 16
Clipping QUAL 37 490
Align_to_SCF 1 494 1 494
SCF_File 22ak92c4.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ak92c4
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 36 "M13mp1"

DNA : 22ap08f1.s1t
GAACTATCATnnnATATACGGGTTGAGTGTnTCTAATCTGAAAATCCAAAATTAGAAATG
CTCTACAGTCTGAAACTTTTTTGAGCACCGACCTAATGTTCAAAGGAAGTGCTTATTGGA
GCATTATGGGTTGTTAgATTTTTGGGTtGGGAATATTCAACCATTAAGCTACACACAATG
CAAATATCCCACAAACAATCTGAAATCTGAAACACTTCTGGTCCAAGCAAGCATCCGCAA
CGGATACGCAACCTGCACACGTTCTTATCATCGTTAACTCTnATATATGTGGACAAATCT
GACGTGGTACACACACTCATGTATATCACAACATATTACATTTGAAGCTGCTACGAATAT
GGAAGAATnnnnCCTGAACTTGGTGTATGACGAACTTAGATAGACAGTGACTCTTCAGTT
CAGCTCnTCATTTnTnnTCCCTCGGTTTTnCTAAnCnCnnCnnAAAAnnnnATCCnGTGG
GCATAAAnnCnGGTCCCACCGCCCCCnCCCCACAAAACCACACACTACCGACCTCCCAA

BaseQuality : 22ap08f1.s1t
7 9 10 13 14 16 21 15 14 4 4 4 4 4 11 11 20 26 28 28 30 30 30 25 25 20
25 23 28 4 4 4 18 18 18 21 24 31 33 34 33 34 34 40 30 31 30 24 24 24
31 27 30 31 30 23 32 32 37 36 38 34 33 24 18 15 10 8 8 18 25 32 33 34
31 31 33 29 21 12 9 7 8 11 13 18 22 25 25 33 33 32 29 22 27 24 25 16 9
9 19 21 20 14 16 10 12 12 11 11 18 23 21 19 19 10 10 10 20 9 9 13 18
18 20 21 18 17 14 16 9 9 9 10 10 10 9 9 21 25 22 18 18 14 20 21 13 13
21 17 26 25 23 20 15 10 12 16 17 15 10 11 8 8 8 8 6 4 4 4 8 10 8 8 6 6
8 13 15 21 21 15 11 9 12 11 7 6 6 6 6 6 6 10 6 6 6 6 10 14 10 10 9 12
9 11 10 14 9 13 10 10 12 9 9 15 17 20 16 17 21 25 10 8 10 10 7 7 10 9
7 8 14 7 7 8 10 8 6 6 6 8 8 10 11 14 8 9 11 19 17 13 9 9 9 8 8 10 9 8
8 8 9 8 11 11 10 8 8 8 8 6 6 8 10 8 7 6 4 8 4 4 4 7 7 11 10 12 9 12 10
10 10 11 6 6 9 9 14 8 7 7 7 7 12 16 11 6 6 6 6 6 6 6 6 6 8 13 9 8 8 15
12 10 9 8 8 8 8 7 9 12 8 6 6 8 4 6 6 7 11 13 13 7 8 9 7 7 12 12 10 9 4
4 4 6 7 7 12 14 7 7 12 6 6 6 7 4 4 4 4 4 4 8 8 14 12 13 16 16 16 10 11
16 14 12 7 6 6 4 4 4 8 7 7 7 12 7 7 8 11 4 4 4 4 4 6 6 6 6 6 6 6 6 6 4
4 8 6 6 12 12 12 9 8 4 4 4 6 11 6 9 4 4 4 4 4 4 9 9 9 15 9 9 6 6 6 8 4
4 4 9 9 4 4 4 4 4 4 4 4 4 4 4 9 9 4 4 4 4 4 4 11 12 4 4 4 8 8 15 9 6 8
9 9 9 4 4 4 4 4 4 7 10 6 8 15 8 8 4 6 14 15 17 18 4 4 4 14 8 6 6 8 8 9
13 9 9 9 7 7 7 7 8 8 6 6 8 6 6 6 8 6 6 8 8 8 8 4

Sequence : 22ap08f1.s1t
Is_read
Padded
Staden_id 17
Clipping QUAL 17 155
Align_to_SCF 1 539 1 539
SCF_File 22ap08f1.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ap08f1
Clone bK216E10
Sequencing_vector "m13mp18"
Tag DONE 137 137 "AUTO-EDIT: replaced T by g at 137 (terminated, isolated, strong)"
Tag DONE 148 148 "AUTO-EDIT: replaced A by t at 148 (terminated, isolated, strong)"

DNA : 22ai01c4.s1t
GGAACATGCTGCAGGTCGACTCTAGAGGATCCCCGCTCTACAGTCTGAAACTTTTTTGAG
CACCGACCTAATGTTCAAAGGAAGTGCTTATTGGAGCATTATGGGTTGTTAGATTTTTGG
GTTGGGAATATTCAACCAGTAAGTACTATAAAATGCAAATATTCCAAAAAAAATCTGAAA
TCTGAAACATTTCTGGTCCTAAGCAAGCATTTTGCAAAGGGATACGCAACCTGTAGTACG
TTCTTTATCATTGTTTTAAGTAGTTAATATATTGTGGTACAGATTCTGAGGTGGTATAGC
AAATTCGATTGTATTATTAAAAAGCATATTTATATTTTGAGAGCTTGCTTAGGATTATTG
GAGAGAATAAAACAGTGAAGCTTTGGTGTTATGAGGGAATTTTAGATAGAAAAGTGCAGT
TTTTCAGTTCATGCTCTTTCATTTTTTACTCCCTCAGGTTAAAGCT-GAAGCTCAACAAA
GATATAGTGATCTCTGTGGGCATTTATAATCTGGTCCAGAAGGCTCTCAAGCCTCCTCCA
ATAAAGCTCTATCGGGAAACAAATGAAACAGTGAAAACCAAGAACCGGAACTTTAATACA
AGTACAGGCGGTTTGCTTTCTGCTAGCGATACCAAAAGTCTCAGGTAGGTAAAAATGCTn
nTGTGTTA

BaseQuality : 22ai01c4.s1t
4 4 6 8 8 18 18 25 25 30 25 21 27 16 16 27 24 27 31 37 33 33 31 31 21
21 23 25 37 34 37 45 45 45 45 40 40 40 33 33 30 30 30 30 38 45 45 49
45 45 45 45 45 45 45 45 38 38 30 30 30 33 33 30 37 37 40 42 42 45 38
45 35 25 27 33 33 33 33 37 37 37 40 37 37 37 37 42 42 42 40 37 40 45
33 33 33 33 33 33 45 45 41 41 45 37 30 41 32 41 45 37 37 41 41 45 45
41 32 38 37 30 30 30 41 41 51 51 51 51 33 33 35 35 35 29 33 33 33 33
33 45 37 37 37 37 37 40 40 40 40 45 43 35 33 33 33 33 33 43 45 43 32
33 33 28 28 29 51 51 45 51 51 51 51 51 51 51 51 51 51 51 51 51 51 42
42 42 40 39 39 51 51 45 45 45 38 38 37 37 38 33 33 33 33 33 33 37 40
39 39 42 33 33 33 33 33 33 37 37 41 41 41 41 33 33 33 33 33 33 51 45
41 41 39 34 34 29 31 37 34 34 45 37 38 42 33 32 32 32 32 32 37 51 32
32 32 32 32 21 24 12 25 25 33 33 33 33 40 40 40 37 37 41 45 45 45 35
34 34 34 34 34 41 41 45 45 45 41 37 37 41 40 45 37 37 42 33 33 22 33
33 33 37 37 37 37 37 37 37 37 37 36 33 33 33 33 33 33 40 40 45 34 34
34 34 34 34 37 37 40 33 33 33 33 33 36 36 40 34 37 37 37 37 38 38 36
33 33 33 31 31 20 29 27 34 34 34 40 40 34 34 38 38 38 34 34 40 37 40
37 30 30 30 30 30 34 36 40 40 36 36 28 33 32 27 27 18 14 14 18 23 27
34 33 29 29 24 29 29 27 27 28 28 25 25 33 22 24 23 31 28 33 34 31 25
25 25 25 30 31 36 32 27 18 13 13 25 25 17 23 25 31 45 45 45 38 31 31
24 22 20 27 35 34 31 33 33 33 33 36 36 36 38 20 13 10 8 12 11 18 20 23
34 34 30 1 29 22 19 24 22 24 28 31 31 31 27 27 23 28 10 25 20 17 10 25
25 35 35 38 38 36 36 27 27 17 17 11 13 16 19 18 18 18 22 15 11 11 15
27 25 24 24 18 8 9 8 7 7 8 7 8 8 15 17 21 14 10 10 19 17 20 25 24 24
21 16 15 21 21 26 33 33 26 23 19 23 23 28 21 20 15 10 8 7 8 6 8 11 7
10 18 17 12 9 9 7 11 9 7 6 7 6 8 9 9 9 6 10 8 10 7 8 8 7 6 6 8 7 8 8
14 23 24 19 14 14 7 7 7 7 8 8 6 6 7 6 6 6 6 6 9 21 13 12 13 15 15 10
11 17 16 15 8 7 7 9 9 10 10 8 8 8 8 9 8 6 8 8 8 7 7 7 7 7 7 7 7 7 7 7
10 8 7 7 8 11 4 4 4 4 9 6 6 6 6 6


Sequence : 22ai01c4.s1t
Is_read
Padded
Staden_id 6
Clipping QUAL 35 553
Align_to_SCF 1 466 1 466
Align_to_SCF 468 668 467 667
SCF_File 22ai01c4.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ai01c4
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 34 "M13mp18"

DNA : 22ak93c1.s1t
nGGTGAAGCTTGCATGCCTGCAGGTCGACTCTAAAGGATCCCCACAcCAAAGCTTCACTG
TTTTATTCTCTCCAATAATCCTAAgCAAGCTCTCAAAATATAAATATGCTTTtTAATAAT
ACAATCGAATTTGCTATACCACCTCAGAATCTGTACCACAATATATTAACTACTTAAAAC
AATGATAAAGAACGTACTACAGGTTGCGTATCCCTTTGCAAAATGCTTGCTTAgGACCAG
AAATGTtTCAGATTTCAGATTTTTTTTGGAATATTTGCATTTTATAGTACTTACTGGTTG
AATATTCCCAACCCAAAaATCTAACAACCCATAATGCTCCAATAAGCACTTCCTTTGAAC
ATTATGTCGGTGCTCAAAAAAGTTTCAGACTGTAAAGCATTTCCTAATTTTGGATTTCCA
GAATAGAAACACTCAACCCGTATAATAAAATGATAATCTGTATTAAGCACAGCACTATAT
CAAGCACCTCACAGCTATTCTCTCATTTAATCATCATAATAACCCTGTAAGTACTGTACA
AGTGGTCTGGTCCCTGCTTTTATTTCTCCAAGAACGACTCTCACACTATTGGTTCGCCTG
GAGTGCnTCGCGTGATCCCCGCTCATGGCACCTCCACTCCCGGGTCCAAGCAATTCTCTT
GCTCAACTTCCAAGTGGTGGGATTAGGGCCCTGCCATAACCCACTTATTTCTTTTATTTT
AATAAAACGTTTCCCCATTTTGGCAGTGGGTTTTACCCTGACCCGTATTGCCCTTCCGGC
CCACGATTTGGGGGAACCAGTTGGGCCCCCCTTTGGGCCTCTCCTGTTCCGAGC

BaseQuality : 22ak93c1.s1t
4 4 4 4 8 8 12 20 25 31 33 33 30 30 30 31 31 35 35 34 27 23 12 11 25
11 14 14 28 32 20 14 6 6 6 6 8 16 16 25 28 15 15 13 17 9 10 9 16 16 18
18 18 25 27 30 26 20 21 19 10 10 14 23 25 30 30 37 37 37 34 31 28 30
22 18 29 18 22 18 15 11 21 12 15 15 22 24 28 37 37 37 37 32 27 10 10
13 18 20 25 25 23 23 24 32 33 40 40 38 32 18 18 18 27 27 28 37 37 21
21 15 15 12 22 32 23 23 30 30 45 45 37 37 32 32 23 22 22 22 27 28 31
26 23 12 12 18 32 38 37 37 37 37 34 34 30 30 30 30 30 30 34 34 37 37
37 34 34 31 31 31 28 27 24 22 22 22 30 30 33 30 30 32 26 24 15 15 9 7
7 14 10 10 9 14 11 12 10 11 6 7 9 8 17 24 26 28 26 28 28 35 34 34 30
26 26 26 28 28 31 31 33 33 31 23 20 15 13 15 18 14 6 6 8 13 13 19 9 7
7 16 10 10 15 10 8 8 12 10 9 9 18 13 14 17 11 7 7 13 21 23 28 21 20 19
19 22 25 27 31 32 32 28 28 25 25 25 25 25 25 31 30 19 19 13 13 13 27
28 33 33 33 33 33 36 33 31 24 21 14 15 18 24 27 31 25 28 30 30 28 23
23 21 17 14 8 9 9 25 25 33 25 25 28 30 30 30 22 21 20 20 22 25 28 34
28 21 16 15 10 14 17 25 25 12 12 12 12 12 20 10 14 16 21 17 13 11 9 12
11 7 6 6 6 8 14 8 8 6 6 11 23 21 28 28 31 31 34 23 10 7 7 7 7 7 9 8 8
14 16 20 20 16 10 7 7 7 14 7 9 14 10 9 14 9 19 22 27 25 13 13 18 14 17
23 16 9 8 9 7 7 7 7 9 8 8 13 16 21 19 15 15 10 10 15 11 18 25 23 21 21
21 32 25 28 25 28 17 20 10 7 7 11 6 7 6 6 7 9 8 6 6 6 6 6 8 7 7 9 13
11 13 13 20 21 18 15 10 10 9 9 8 8 8 9 9 13 16 16 14 14 14 25 10 11 6
6 6 6 7 10 14 9 13 20 8 7 7 8 11 10 13 12 12 13 16 14 15 15 13 13 10
12 7 8 9 14 11 12 12 9 10 8 8 8 10 20 12 9 9 12 6 6 6 6 8 9 6 6 6 6 7
6 6 8 16 18 18 9 6 6 6 13 7 7 7 8 9 9 7 7 7 7 7 6 6 6 6 6 6 6 6 7 8 8
10 9 8 8 6 7 8 4 4 4 4 4 10 7 7 9 9 8 8 4 4 4 4 4 4 8 4 9 9 12 9 8 6 6
6 9 11 7 7 7 7 7 9 11 11 9 6 6 6 10 8 8 7 10 10 14 25 16 10 7 7 7 7 10
10 8 8 7 7 7 8 6 6 6 6 8 11 12 7 6 13 6 7 7 7 8 7 7 7 8 8 10 8 6 6 6 4
4 8 8 10 13 22 24 24 20 14 8 6 6 6 6 6 10 15 15 10 9 6 6 10 8 7 7 9 9
13 13 10 11 11 11 8 7 7 6 14 6 7 8 6 6 7 7 7 7 7 7 12 7 8 10 10 13 14
9 8 8 8 11 9 7 7 7 8 8 11 10 12 11 11 10 10 12 12 17 13 9 8 9 6 6 6 6
6 12 8 8 8 8 9 8 8 9 8 7 7 7 9 9 8 8 6 6 8 8 11 12 8 6 8 6 6 6 6 6 7 8
9 11 12 12 6 6 8 7 8 8 13 7 7 7 6 8 8 8 8 8 8 6 6 8 4 6 4 4 4 4

Sequence : 22ak93c1.s1t
Is_read
Padded
Staden_id 10
Clipping QUAL 44 345
Align_to_SCF 1 834 1 834
SCF_File 22ak93c1.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ak93c1
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 43 "M13mp1"
Tag DONE 47 47 "AUTO-EDIT: replaced T by c at 47 (terminator, isolated, strong)"
Tag DONE 85 85 "AUTO-EDIT: replaced C by g at 85 (terminated, isolated, strong)"
Tag DONE 113 113 "AUTO-EDIT: replaced A by t at 113 (terminated, isolated, strong)"
Tag DONE 234 234 "AUTO-EDIT: replaced C by g at 234 (terminated, isolated, strong)"
Tag DONE 247 247 "AUTO-EDIT: replaced C by t at 247 (terminated, isolated, strong)"
Tag DONE 318 318 "AUTO-EDIT: replaced G by a at 318 (terminated, isolated, strong)"

DNA : 22ak65e10.s1t
TGAGGGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCTTAAAAAATAAATAAATAA
ATAAATTAGCTGGGTGTGATGTCACATGCCTGTGATCCCAGCTACTTGGGAGGCTGAGAC
AGAAGGATCGCTTGAGTCCAGGAGGTCAAGGCTGTAGCGAGTCATGTTCGCCCCACTGCA
CTCCAGCCTGGGCGACACAATGAGACCCTGTCTCAAAAACAACAACAACAAAAGGCATCT
CTACCTACCTGAGACCTCTTGGTATCGCTAGGCAGAAGCAAACCGCCTGTACTTGTATTA
AAGGTCCGGGTCTTGGTTTTCACTGGTTCATTTGTTTCCCGATAGAGCTTTATTGGAGGA
gGCTTGAGAGCCTTCTGGACCAGATTATaAATGCCCACAGAGATCACTATATCTTTGTTG
AGCTTC-AGCTTTAACCTGAGGGAGTAAAAAATGAAAGAGCATGAACTGAAAAACTGCAC
TTTTCTATCTAAAATTCCCTCATAACACCAAAGCTTCACTGTTTTATTCTCTCCAATAAT
CCTAAGCAAGCTCTCAAAATATAAATATGCTTTTTAATAATACAATCC

BaseQuality : 22ak65e10.s1t
4 4 8 8 9 9 14 15 31 31 28 28 28 30 30 33 33 33 30 22 20 12 22 12 18
18 30 31 27 23 32 10 10 14 12 32 32 37 45 45 45 45 45 38 34 29 29 29
29 29 29 29 32 32 30 34 34 34 34 35 34 34 32 35 29 27 32 32 32 37 45
32 45 37 37 37 24 24 32 32 19 22 11 21 21 31 31 34 45 45 45 28 30 30
37 40 34 33 33 28 28 28 37 45 41 41 41 41 45 41 27 27 33 37 37 32 27
20 20 20 30 20 20 21 24 17 38 32 30 42 37 37 37 30 28 13 12 18 25 21
24 14 25 25 22 28 17 28 28 18 32 36 36 32 32 21 32 32 31 31 27 27 21
32 32 27 13 13 32 33 38 45 36 34 30 30 21 21 23 23 23 23 30 33 33 37
34 41 36 41 37 37 34 29 29 19 30 30 40 37 37 36 37 25 25 26 26 30 45
41 51 37 33 30 28 28 33 20 18 20 20 20 20 26 20 20 18 21 21 31 31 28
32 14 18 20 29 33 34 45 45 40 40 40 37 37 37 37 37 32 45 30 23 23 32
32 37 34 35 34 34 34 34 37 37 37 37 45 37 37 32 27 23 14 12 12 14 17
19 27 27 28 30 37 45 45 45 45 37 37 37 42 42 40 37 37 34 33 33 40 31
26 28 25 27 31 34 34 34 31 27 27 27 31 27 31 23 23 18 18 18 25 25 31
35 31 30 27 25 27 35 33 32 30 21 21 21 23 23 27 26 21 20 16 16 17 18
30 30 36 36 36 34 34 36 34 26 15 12 6 6 6 12 11 23 23 26 17 17 21 32
35 35 40 33 33 33 38 33 27 23 23 12 12 18 18 19 10 8 8 17 19 34 33 34
31 34 31 31 22 22 19 18 27 27 32 22 25 24 32 32 34 34 34 37 34 30 33
27 27 27 31 32 27 27 18 1 12 12 11 15 15 17 27 28 28 34 34 30 25 18 13
19 15 15 25 21 29 26 34 24 28 25 27 21 20 23 24 24 26 29 30 26 27 22
29 27 33 34 34 36 38 38 38 34 31 30 24 24 24 31 33 35 35 29 33 33 31
31 28 28 29 26 22 14 8 9 9 9 14 9 13 18 21 21 27 23 18 15 21 21 25 33
33 31 31 21 21 24 27 29 25 19 19 19 25 27 27 34 34 34 14 9 7 7 9 18 23
27 23 19 19 23 24 21 18 8 8 9 21 20 31 24 20 13 11 16 24 32 32 25 18
13 13 20 20 26 21 27 21 20 13 17 15 21 12 12 18 15 15 15 15 8 8 7 10 8
4


Sequence : 22ak65e10.s1t
Is_read
Padded
Staden_id 4
Clipping QUAL 42 575
Align_to_SCF 1 426 1 426
Align_to_SCF 428 588 427 587
SCF_File 22ak65e10.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ak65e10
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 41 "M13mp"
Tag DONE 361 361 "AUTO-EDIT: replaced C by g at 361 (all_stranded, compound, strong)"
Tag DONE 389 389 "AUTO-EDIT: replaced C by a at 389 (terminated, isolated, strong)"

DNA : 22ak93c2.s1t
CTGGGAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCACTCATTTTCTGCCTGG
TGTTTATTCTCATCCAAATTCGTATACATGCTCGGTGTGAATGGTTACTCATTATAGTAT
ACAATCGACTTTCTCAAACGACCACACATGCTGAATATCTATACATGTGCTAGTTGGACC
TCTGATTATCAACGTGAGACTGGTGGCGTATCCCTTTGCAAAATGCTAACAAAAGACCAC
AAACGTGTCACATTTCAGAATTGCTTGGAATATTCGCGTGTATAGTACTTACTGGTTCAA
GGGTCCAAAACATACCTCTACACACCATCCTGATTCCCTGGGACACTTCCTTTGAACATC
ACGTCGGTGCTCAAAAAAGTGTCAGACTGTAGAGCATATCTGGTTTCGGAATGTCGAGAT
AGAAGGTCTCAAGCCGTATAAATAAACGAGAGTCTGTATCAAGCACTGCAGGAGAATCAT
AACCTCACAGCTATGCTCTCATGGAAACATCTCAATACACCTCGTAGTACTGTACTAATA
GTCATGTCGCTGCTTTTTGTTnCCGACAACCAATCTCACGGATTGGTTCGGCCGGTTTGC
ATCCCTGATTCCGATCATTGAAGGTCGAACTCCCGGTCCAAGCAATCTCCTGCCCCGGCT
CCAGATGACGGGATTCTTGCCTTTCAACACCCCGGCTAATTCATCCTCTCCCTCGACACC
GATTTCACGAAATGGGGGTCGGCCCCAACCCGAACATTTGTTTACTGGGTAAAACGGTTC
CCCAGTTACCCGTTGGCCCACTCCTGGGCCATTAATTGCCTC

BaseQuality : 22ak93c2.s1t
4 4 8 8 9 12 12 22 27 30 30 30 30 33 33 35 33 37 37 33 31 30 25 25 27
27 18 18 32 38 32 28 28 9 9 10 10 25 21 27 38 28 25 23 16 12 10 10 11
10 13 12 11 15 14 8 8 11 13 18 21 21 9 7 7 6 11 8 8 8 6 6 8 8 8 8 10 9
9 10 9 14 9 13 11 8 8 8 8 8 11 10 11 14 14 14 21 11 10 10 10 11 17 11
7 7 8 8 9 9 13 14 18 15 9 9 9 8 8 10 12 12 10 10 8 9 12 12 13 14 23 10
10 10 12 11 11 10 10 10 11 14 14 15 15 21 22 10 10 10 10 28 10 9 9 9
10 12 15 18 15 15 12 12 12 12 25 21 24 27 18 13 13 13 14 12 14 12 10
10 10 14 18 14 9 9 11 12 12 10 10 10 10 9 14 14 8 8 8 8 6 6 9 6 6 6 12
18 34 36 38 38 38 38 36 36 33 33 23 23 13 13 15 23 28 20 9 6 6 4 6 10
8 7 7 9 10 9 13 13 10 10 9 8 8 6 6 8 8 11 12 10 9 9 9 6 4 6 6 8 6 7 11
10 9 7 8 17 18 21 19 17 11 8 8 9 11 11 15 12 8 8 8 9 9 15 15 10 10 9
10 7 7 8 12 10 10 9 9 9 9 10 11 10 8 8 8 7 12 7 7 7 8 9 8 9 10 10 9 10
8 6 6 6 6 7 6 9 10 10 10 7 6 6 6 8 6 6 9 10 13 12 12 9 12 15 14 14 8 8
8 9 10 10 9 9 9 9 8 6 6 10 8 13 6 6 6 11 16 18 12 11 8 10 12 8 7 9 7 7
7 7 9 9 7 7 10 10 12 10 20 9 7 7 7 8 8 8 9 7 7 7 11 9 13 19 15 12 7 8
7 6 6 6 6 6 6 6 10 13 8 6 6 8 6 8 10 10 12 7 7 7 7 7 7 8 10 9 9 8 7 6
6 8 6 6 8 9 9 10 7 7 8 8 8 8 7 7 8 7 7 7 7 7 9 8 8 15 8 8 6 6 6 6 6 6
7 10 9 9 8 7 8 8 10 7 7 8 8 11 11 11 8 6 6 6 6 6 12 6 6 6 6 6 7 11 12
9 7 10 11 8 8 7 8 11 8 7 7 7 6 8 6 6 8 6 8 7 7 8 7 7 7 8 9 7 7 7 7 7 7
9 7 7 7 6 13 4 7 7 7 12 23 21 14 12 9 8 9 8 4 4 4 6 6 6 7 6 8 4 4 4 6
6 6 6 6 6 8 6 7 10 9 9 9 8 6 4 4 4 6 8 6 6 6 6 8 6 6 8 8 8 8 8 8 6 6 8
11 10 7 7 7 7 9 9 9 8 7 11 8 7 7 8 9 8 8 7 7 7 7 7 7 7 7 8 7 7 7 7 8 7
7 8 7 7 7 7 8 7 7 7 7 7 7 6 6 7 7 6 6 6 8 9 8 7 7 7 7 8 8 12 9 7 7 7 7
6 7 8 7 7 7 8 8 6 6 6 6 6 6 7 7 9 12 10 14 8 9 8 6 6 6 6 6 6 9 10 10 9
6 6 6 6 8 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 7 7 7 6 6 6 4 6 6 6 6 8 6
6 6 6 6 8 8 10 7 4 7 4 4 4 6 6 6 6 6 6 6 6 6 6 6 7 7 9 9 8 8 7 9 9 7 7
7 8 6 6 6 6 6 6 6 6 6 6 8 8 8 8 8 8 8 7 7 6 6 6 6 7 8 9 9 9 9 7 7 7 7
7 7 7 6 6 6 6

Sequence : 22ak93c2.s1t
Is_read
Padded
Staden_id 13
Clipping QUAL 44 45
Align_to_SCF 1 822 1 822
SCF_File 22ak93c2.s1tSCF
Primer Universal_primer
Strand Forward
Dye Dye_terminator
Template 22ak93c2
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 43 "M13mp1"

DNA : 22am84d9.s1
CAACCCGCACACCTGCACGTCGACTCTAGAGGATCCCCATAAATAAATAAATtAgCTGGG
TGTGATGTCACATGCCTGTgATCCCAGCTACTTGGGAgGCTGAGACAGAAGGATCGCTTG
AGTCCAGGAGGTCAAGGCTGTAGCGAGTCATGTTCGCCCCACTGCACTCCAGCCTGGGCG
ACACAATGAGACCCTGTCTCAAAAACAACAACAACAAAAGGCATCTCTACCTACCTGAGA
CCTCTTGGTATCGCTAGGCAGAAGCAAACCGCCTGTACTTGTATTAAAGGTCCGGGTCTT
GGTTTTCACTGGTTCATTTGTTTCCCGATAGAGCTTTATTGGAGGAGGCTTGAGAGCCTT
CTGGACCAGATTATAAATGCCCACAGAGATCACTATATCTTTGTTGAGCTTCAAGCTTTA
ACCTGAGGGCAGTAAAAAATGGAAGAGCATGAACTGGCAAAATGCACTTTTCTATCTAAA
ATTCC

BaseQuality : 22am84d9.s1
4 9 9 9 9 10 10 9 9 9 9 10 10 10 8 8 6 6 10 8 11 12 15 14 13 15 11 11
11 12 14 10 10 10 17 23 31 31 21 20 13 21 11 10 10 16 14 14 14 23 11
11 10 10 10 11 11 12 32 18 23 23 32 32 34 37 34 37 37 38 27 18 18 17
24 30 32 32 10 10 11 23 23 38 37 37 37 37 37 37 37 37 37 37 32 32 22
22 22 32 28 40 37 37 37 45 32 32 28 22 22 12 16 16 32 32 37 37 37 37
28 28 28 32 32 30 30 27 29 29 34 37 37 37 37 37 37 37 37 37 28 22 20
30 30 29 37 34 37 37 37 37 37 37 37 37 37 37 37 45 45 37 37 37 37 45
37 37 34 34 34 33 31 33 34 37 27 27 13 13 13 21 32 34 36 31 31 33 19
17 14 9 9 13 24 27 27 33 33 33 33 33 33 33 33 33 36 36 37 37 37 37 37
45 45 36 34 34 28 31 31 34 34 37 38 34 38 38 33 30 30 30 30 30 33 34
37 37 37 34 34 34 34 34 35 35 33 33 33 33 33 33 34 30 30 30 30 30 30
33 33 30 30 30 34 34 34 34 31 31 31 36 36 34 31 17 13 8 8 15 18 27 31
28 28 28 28 28 30 31 35 35 34 34 34 34 33 33 33 34 34 38 38 38 37 32
28 22 19 19 25 27 37 30 30 30 28 28 28 38 37 34 34 37 31 31 25 24 28
30 30 28 28 28 28 28 28 34 34 34 33 33 31 31 27 24 18 15 18 18 23 23
28 27 22 18 11 11 16 21 24 33 34 23 23 8 8 9 12 14 17 20 20 20 25 25
27 27 23 16 11 15 14 9 9 19 17 18 22 18 11 11 11 12 17 18 31 31 31 31
27 27 33 29 22 18 17 17 20 20 17 13 11 11 11 6 8 14 17 22 22 25 25 20
20 20 17 14 4 4 4 14 15 21 22 18 11 12 7 7 7 7 7 12 21 18 15 13 9 9 15
12 8 6 6 6 6 9 6 6 6 12 14 13 13 17 21 21 24 21 22 18 14 18 16 14 14
10 6 7 6 13 8 8 7


Sequence : 22am84d9.s1
Is_read
Padded
Staden_id 7
Clipping QUAL 39 427
Align_to_SCF 1 485 1 485
SCF_File 22am84d9.s1SCF
Primer Universal_primer
Strand Forward
Dye Dye_primer
Template 22am84d9
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 38 "M13mp18"
Tag ALUS 41 210
Tag DONE 53 53 "AUTO-EDIT: replaced C by t at 53 (all_stranded, isolated, strong)"
Tag DONE 55 55 "AUTO-EDIT: replaced C by g at 55 (all_stranded, isolated, strong)"
Tag DONE 80 80 "AUTO-EDIT: replaced C by g at 80 (all_stranded, isolated, strong)"
Tag DONE 98 98 "AUTO-EDIT: replaced C by g at 98 (all_stranded, isolated, strong)"
Tag AMBG 338 360 "AUTOEDIT: Check this edit cluster!"
Tag CONF 413 413 "AUTOEDIT: possible compression"

DNA : 22ak66f10.s1lt
CCCGCGGGGGAGGAGGGAnGGGGGGAGAGGAGnAnAAnnnnnnnnnnnnnAGCCCCAAnn
nAnnCCCTCTTnnnnnnnnAGACGGGGGGnGCCCTGGGnGnGCnTnnnnnnnnnnTTGGT
TGAGGTGnCGAGCAAATCTTGCATGCCTGtcCGTCTACTCtAGAGGATCCCACAAATGAA
CCAGTGAAAACCAAGACCCGGACCTTTAATACAAGTACAGGCGGTTTGCTTCTGCCTAGC
GATACCAAGAGGTCTCAGGTAGGTAGAGATGCCTTTTGTTGTTGTTGTTTTTGAGACAGG
GTCTCATTGTGTCGCCCAGGCTGGAGTGCAGTGGGGCGAACATGACTCGCTACAGCCTTG
ACCTCCTGGACTCAAGCGATCCTTCTGTCTCAGCCTCCCAAGTAGCTGGGATCACAGGCA
TGTGACATCACACCCAGCTAATTTATTTATTTATTTATTTTTTAAGAGACTGGATCGACT
GGGCACAGTGGCTCATGCCTGTAATCCCAnCACTTTGGGAGGCCGAGGCAGGTGGATTAC
CGAGGTCAGGAGTTCAAGACCAGCCTGACCAACATGGAGAAACCCCATCTCTACTAAAAA
TACAAAATGAGCTGGGCATGGTGGTGCATGCCTGTAATCCCAGCTACTCCGGAGGCTGAG
GCAnGAGAATCCCTTGAACCCGGGAGGCAAAAGTTGCGGTGAGCCGAAATCTCGCCATTG
CGCTCCAGCCTGGGCAACAAAAGCGTAACTCCGTCTCCnnnnnnnnAAAAAAAGAGACGG
TGTTTCGCTATGTTGCCTGGGCTGGGTGTCAAACTCCTGGGTCTTAAAGTAATCCCCCCC
TGCTTTGGGTTCCCCCAAATTGCTGGGGGTGGCTGGGATTCCCGAACTTTGGGGCCACTG
TTGCCCCAGCCGTTTTTTTGGTTTCGTTTTGGTTTTGGTTTTGTTTTAATAAAAAAATAA
AGGGTCTCACCTATGTT

BaseQuality : 22ak66f10.s1lt
6 6 4 6 8 8 11 8 8 6 6 11 4 4 4 12 6 4 4 4 8 7 6 6 6 6 6 6 6 8 4 4 4 4
4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 7 7 6 6 6 8 4 4 4 4 4 4 4 4 6 4 6 6
8 4 4 4 4 4 4 4 4 4 4 4 4 6 6 6 6 6 6 4 4 4 6 6 4 4 8 12 4 4 4 4 4 4 4
4 4 4 4 4 4 4 4 4 4 4 4 6 6 4 4 4 4 4 4 8 6 4 4 4 4 4 4 15 17 8 4 4 6
9 21 21 30 28 30 33 33 21 18 8 8 8 10 15 23 21 26 26 19 14 7 7 8 8 10
18 21 18 10 9 9 18 14 24 24 29 32 34 37 34 36 32 32 30 30 30 34 38 44
45 37 37 34 27 27 15 15 23 32 40 40 37 37 34 45 45 45 45 45 42 25 25
25 26 26 20 23 28 30 33 33 33 34 34 34 34 37 45 45 45 45 49 49 49 49
49 45 45 43 38 38 37 37 40 37 37 34 27 27 12 10 18 14 32 27 27 27 29
29 12 18 10 15 10 21 10 14 10 19 19 41 45 45 45 45 45 40 40 34 37 37
45 45 45 45 45 45 45 45 45 40 51 37 37 25 22 18 27 22 25 25 29 29 28
33 33 40 37 37 37 37 37 37 34 37 37 42 35 32 30 30 37 38 45 45 30 30
30 33 31 33 32 37 45 45 45 32 30 30 37 33 37 37 40 37 37 37 37 37 37
37 37 37 37 34 34 34 37 45 45 45 45 45 45 45 45 49 45 45 45 45 33 33
29 29 33 33 33 33 33 37 40 45 45 45 45 45 45 45 35 35 35 35 35 40 38
45 45 45 37 37 32 22 14 14 14 32 45 45 45 38 37 31 28 27 30 28 27 22
27 27 31 31 34 31 28 28 27 31 33 33 33 33 33 33 32 28 28 30 34 37 37
35 35 35 37 37 33 33 33 33 33 33 31 31 30 30 33 31 31 36 33 33 33 34
25 25 10 10 10 19 19 34 34 34 34 31 31 34 34 36 38 30 30 26 23 30 31
34 32 45 37 37 37 37 33 33 40 40 40 36 33 31 31 31 33 33 23 22 4 4 4
18 23 32 34 36 36 32 28 21 21 21 29 20 28 25 24 18 25 21 27 27 32 32
34 31 31 34 37 37 37 37 32 32 10 21 10 25 28 32 29 34 28 31 27 27 28
22 22 27 29 32 32 37 37 37 37 37 37 37 37 35 34 34 34 31 27 27 19 19
30 34 37 38 34 34 34 34 34 40 38 38 38 38 37 37 37 35 35 32 28 28 28
30 30 30 33 30 30 22 22 22 32 32 35 35 34 34 35 35 34 37 37 38 30 24
24 24 24 24 31 38 38 32 27 27 27 35 25 18 12 9 9 11 21 23 18 12 6 6 8
8 8 9 10 17 10 14 8 9 8 7 4 4 4 16 14 14 12 15 8 8 11 15 14 25 25 25
28 33 33 33 21 29 7 7 7 8 8 7 8 9 9 8 11 24 22 31 25 23 23 15 13 10 7
9 9 8 8 12 7 7 7 16 11 18 14 25 25 22 19 16 17 14 8 9 10 13 15 27 28
31 23 22 14 14 13 15 15 23 21 8 8 6 6 6 6 9 18 20 28 22 22 20 17 14 9
4 4 4 4 4 4 4 4 4 4 16 10 13 20 23 23 12 9 9 9 17 10 9 7 8 6 6 8 4 4 7
12 13 14 7 8 8 8 8 8 18 21 16 9 10 9 7 9 7 9 8 10 7 7 7 12 9 9 7 7 8 8
6 6 8 8 8 6 8 6 6 6 6 7 6 11 6 8 6 6 6 6 6 8 9 9 8 9 12 8 8 8 7 8 8 7
8 6 6 6 9 8 6 6 6 10 13 11 7 9 7 7 7 7 7 8 9 7 7 9 9 7 4 4 4 7 11 7 7
9 8 7 6 6 6 6 6 8 8 10 9 8 8 6 6 6 6 7 6 6 4 4 4 4 8 6 8 13 16 20 8 8
7 7 7 7 7 7 7 8 12 8 8 6 6 6 6 6 6 6 6 6 6 9 8 8 6 6 6 8 6 9 14 9 9 8
9 7 6 6 8 6 6 8 7 6 6 8 6 6 7 7 7 7 7 7 8 8 4 4


Sequence : 22ak66f10.s1lt
Is_read
Padded
Staden_id 9
Clipping QUAL 140 640
Align_to_SCF 1 977 1 977
SCF_File 22ak66f10.s1ltSCF
Primer Universal_primer
Strand Forward
Dye Dye_primer
Template 22ak66f10
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 3 "M13mp18"
Tag DONE 150 150 "AUTO-EDIT: replaced C by t at 150 (all_stranded, compound, strong)"
Tag DONE 151 151 "AUTO-EDIT: replaced G by c at 151 (all_stranded, compound, strong)"
Tag DONE 161 161 "AUTO-EDIT: replaced A by t at 161 (all_stranded, compound, strong)"
Tag ALUS 283 462
Tag ALUS 477 767

DNA : 22ak70h4.r1t
TGCCGCCTTAGATTACAGCTCTACACGGTACCTCTATCGGGAAACAAATGAACCAgTGAA
AACCAAGACCCGGACCTTTAATACAAGTACAGGCGGTTTGCTTCTGCCTAGCGATACCAA
GAGGTCTCAGGTAGGTAGAGATGCCTTTTGTTGTTGTTGTTTTTGAGACAGGGTCTCATT
GTGTCGCCCAgGCTGGAGTGCAGTGGGGCGAACATGACTCGCTACAGCCTTGACCTCCTG
GACTCAAGCGATCCTTCTGTCTCAGCCTCCCAAGTAGCTGGGATCACAGGCATGTGACAT
CACACCCAGCTAATTTATTTATTTATTTATTTTTTAAGAGACTGGATCGACTGGGCACAG
TGGCTCATGCCTGTAATCCCACCACTTTGGGAGGCCGAGGCATGTGGATTACCGAGGTTC
GGAGTTCAAGACCAGCCTGACCCTTCTGGAGAAACCCCATCTCCACTTTAAATACCAAAT
GAAGCTGGGCCTGGTGGTGCCTGCCTGTAATCCCCCCTTCTCAGGATGCTGAAGCAGGAC
ATTCCTTGAACCCCGGAAGCACATGTTGCCGTGACCCAATATCCCCCCTTGTCCCTCACC
CCGGGCCACCAAACCTTATTCCCTCCCAAATAAAAAAAAAAAAAAACGGGTTCCCTTTTT
TGCCGGGGGGGGTTTCTACCCC

BaseQuality : 22ak70h4.r1t
4 4 4 4 4 8 6 6 8 8 12 6 7 11 13 12 6 6 6 6 6 6 9 10 10 10 21 21 26 31
27 27 13 14 11 11 11 12 19 20 27 18 18 23 23 16 10 10 14 28 18 18 11
11 9 9 9 10 10 10 21 21 27 23 18 10 9 9 14 18 32 31 37 34 28 28 22 19
19 27 24 21 18 17 9 9 12 19 24 28 30 30 30 33 33 30 30 37 40 40 45 37
41 41 44 44 45 32 42 37 32 32 32 32 37 31 31 33 21 21 11 10 22 18 32
24 27 27 27 27 11 14 10 23 12 23 9 10 10 18 11 25 25 34 45 37 37 34 34
34 34 34 34 34 33 33 33 34 34 34 34 33 34 28 31 25 21 23 21 21 13 13
15 15 17 23 21 26 26 31 28 32 23 23 12 22 25 21 19 9 8 8 17 21 23 23
20 18 17 27 23 21 27 30 38 38 28 28 17 17 13 18 19 27 25 25 28 28 28
28 25 31 26 26 18 15 13 9 9 15 19 23 25 31 36 36 36 36 36 36 36 36 24
19 12 13 18 24 31 31 29 29 31 29 29 33 36 40 44 36 33 34 34 37 36 36
45 45 34 30 28 28 28 22 32 24 22 22 32 32 36 37 27 27 14 25 25 29 23
22 19 17 19 19 24 25 27 24 18 18 16 16 16 24 22 30 30 28 28 30 27 27
23 20 22 25 25 25 21 22 21 16 14 19 17 17 19 20 17 11 11 11 11 12 24
24 22 20 34 17 17 23 23 31 34 27 27 17 13 15 27 27 34 31 31 24 22 19
16 16 15 32 23 27 18 9 9 9 13 9 14 20 22 21 21 19 17 14 8 6 6 8 8 9 11
14 8 7 11 15 14 9 9 9 12 8 10 6 8 8 6 4 4 4 14 15 23 21 13 13 11 13 11
11 6 8 8 6 6 6 7 6 6 6 6 7 6 6 11 15 17 27 20 17 17 13 21 13 14 4 4 8
6 6 6 6 8 6 8 11 7 8 8 10 10 19 24 16 16 9 9 12 7 7 8 8 8 8 6 6 11 15
11 10 9 9 11 14 15 11 8 7 7 7 7 12 9 10 10 8 8 14 10 10 18 21 21 18 16
10 9 11 9 9 14 10 10 8 8 9 8 8 12 14 10 10 11 11 10 9 8 7 7 7 7 4 4 4
12 10 14 10 8 14 6 6 6 7 6 6 6 6 6 10 8 9 7 7 7 9 14 15 10 10 10 10 9
8 13 8 4 4 4 4 4 6 6 12 6 6 10 8 8 8 6 9 12 7 6 6 6 8 8 9 7 7 7 8 9 8
8 6 6 6 6 6 4 6 6 6 6 7 8 8 6 6 8 8 8 8 9 9 8 10 11 9 8 8 8 8 6 6 11 9
9 10 9 12 8 6 6 6 10 12 10 10 8 8 8 7 10 13 8 13 19 18 13 6 6 6 6 8 6
7 12 7 7 10 10 7 7 7 7 7 7 9 13 6 10 7 7 12 11 7 6 6 6 6 8 8 8 4


Sequence : 22ak70h4.r1t
Is_read
Padded
Staden_id 15
Clipping QUAL 28 377
Align_to_SCF 1 682 1 682
SCF_File 22ak70h4.r1tSCF
Primer Universal_primer
Strand Reverse
Dye Dye_terminator
Template 22ak70h4
Clone bK216E10
Sequencing_vector "m13mp18"
Seq_vec SVEC 1 27 "M13mp18"
Tag DONE 56 56 "AUTO-EDIT: replaced C by g at 56 (all_stranded, isolated, strong)"
Tag ALUS 155 334
Tag DONE 191 191 "AUTO-EDIT: replaced T by g at 191 (all_stranded, isolated, strong)"
Tag ALUS 349 579

Sequence : Contig1
Is_contig
Padded
Assembled_from 22ak93c2.r1t 1 293 39 331
Assembled_from 22ak93c1.r1ta 1 305 31 335
Assembled_from 22am91h5.r1t 110 439 32 361
Assembled_from 22aq40a8.s1 221 570 39 388
Assembled_from 22an02b10.s1t 252 666 32 446
Assembled_from 22ak67d6.r1t 260 522 30 292
Assembled_from 22ak64b1.s1t 331 707 40 416
Assembled_from 22ak81h10.s1t 331 713 36 418
Assembled_from 22ak66c6.s1t 337 848 37 548
Assembled_from 22ak93c1.s1lt 1024 482 56 598
Assembled_from 22ak64e2.s1t 866 487 41 420
Assembled_from 22ak70f10.s1t 554 1027 35 508
Assembled_from 22ak92c4.s1t 635 1088 37 490
Assembled_from 22ap08f1.s1t 639 777 17 155
Assembled_from 22ai01c4.s1t 682 1200 35 553
Assembled_from 22ak93c1.s1t 1036 735 44 345
Assembled_from 22ak65e10.s1t 1499 966 42 575
Assembled_from 22ak93c2.s1t 1036 1035 44 45
Assembled_from 22am84d9.s1 1488 1100 39 427
Assembled_from 22ak66f10.s1lt 1174 1674 140 640
Assembled_from 22ak70h4.r1t 1190 1539 28 377

DNA : Contig1
TTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTATAnACTGTGCGTGCGC
CACCATGCCTGGCTAATTTTTGTATTTTTAGTAGGGATGGGGTTTCACCATGTTGGCCAA
GCTGGTCTCGAGCTCCTGACCTAGGATTACAGGCCTAAGCCACCGCACCCGGCATGATGG
GTCTTTATTCTTCAAAGCAGGAGGAAGGGATCCTAGAAAAACAGAGACAAGGCCAAACAT
GGTAGCTCACACCTGTAATnnnnnCACTTTGGGAGGCCAGTGCGGGTGAATCACGAnGTC
AGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAnCACCGTCTCTACTAAAATAAAAAGA
AATTAGCTGGGTGTCGTGGCAGGTGCnTGTAATCCCAGCCACTTGGGAAGCTGAGGCAGG
AGAATCGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACGCGACTGCACTC
CAGCCCAACCAATAGTGTGAGACTCTGTCTCGAAAAAAAAAAAGCAGAGACAAGACnACT
AGTACAGTACTTACAGGGTTATTATGATGATTAAATGAGAGAATAGCTGTGAGGTGATTG
ATATAGTGCTGTGCTTAATACAAACTATCATTTTATTATACGGGTTGAGTGTnTCTAATC
TGAAAATCCAAAATTAGAAATGCTCTACAGTCTGAAACTTTTTTGAGCACCGACCTAATG
TTCAAAGGAAGTGCTTATTGGAGCATTATGGGTTGTTAGATTTTTGGGTTGGGAATATTC
AACCAGTAAGTACTATAAAATGCAAATATTCCAAAAAAAATCTGAAATCTGAAACATTTC
TGGTCCTAAGCAAGCATTTTGCAAAGGGATACGCAACCTGTAGTACGTTCTTTATCATTG
TTTTAAGTAGTTAATATATTGTGGTACAGATTCTGAGGTGGTATAGCAAATTCGATTGTA
TTATTAAAAAGCATATTTATATTTTGAGAGCTTGCTTAGGATTATTGGAGAGAATAAAAC
AGTGAAGCTTTGGTGTTATGAGGGAATTTTAGATAGAAAAGTGCAGTTTTTCAGTTCATG
CTCTTTCATTTTTTACTCCCTCAGGTTAAAGCTnGAAGCTCAACAAAGATATAGTGATCT
CTGTGGGCATTTATAATCTGGTCCAGAAGGCTCTnnAnnCnnnTCCnnnnnnnCTnnAnn
nnnnnACAAATGAACCAGTGAAAACCAAGACCCGGACCTTTAATACAAGTACAGGCGGTT
TGCTTCTGCCTAGCGATACCAAGAGGTCTCAGGTAGGTAGAGATGCCTTTTGTTGTTGTT
GTTTTTGAGACAGGGTCTCATTGTGTCGCCCAGGCTGGAGTGCAGTGGGGCGAACATGAC
TCGCTACAGCCTTGACCTCCTGGACTCAAGCGATCCTTCTGTCTCAGCCTCCCAAGTAGC
TGGGATCACAGGCATGTGACATCACACCCAGCTAATTTATTTATTTATTTATTTTTTAAG
AGACTGGATCGACTGGGCACAGTGGCTCATGCCTGTAATCCCAnCACTTTGGGAGGCCGA
GGCAGGTGGATTACCGAGGTCAGGAGTTCAAGACCAGCCTGACCAACATGGAGAAACCCC
ATCTCTACTAAAAATACAAAATGAGCTGGGCATGGTGGTGCATGCCTGTAATCC

ACeDB model


// models.wrm - main file defining tree class structures
// This file is read only when starting a new database or when you select 
// "Read Models" or "Add Update File" from the main menu.
//
// all tags must appear in tags.wrm or systags.wrm
//
// Magic tag2 construct, such as Inside xxx ?AA
//  denotes a case where Inside and ?AA are read by the display code
// whereas the intermediate xxx is up to the schema designer
//
// @  is for Attach-Query

?Clone  Main_clone   // Clone for project
      // Contains default info on sequencing vector etc
        Subclone ?Clone XREF Subclone_of
  Subclone_info  Subclone_of ?Clone XREF Subclone
           Read ?Sequence XREF Template      // Reads from this clone
  Gel ?Motif  #Lane                    // Restriction map
  Stolen_reads ?Sequence XREF Stolen  // for neighbouring cosmids, not Main_clone
        Vector  Cloning_vector UNIQUE ?Sequence UNIQUE Int  // Int is cloning site position (default 1)
    Sequencing_vector UNIQUE ?Sequence UNIQUE Int  // Default sequencing vector; Int is cloning site position (default 1)
               
       
#Lane UNIQUE Bands UNIQUE Float REPEAT // In base pairs: if you prefer to minimise the ace format
             Band_Lengths  UNIQUE Float REPEAT // in mm: if you prefer to minimise the ace format
             Band Float Text    // if you wish to comment single band value

?Sequence DNA UNIQUE ?DNA UNIQUE Int  // Int is the length
          Position UNIQUE ?BasePosition UNIQUE Int
    Quality UNIQUE ?BaseQuality UNIQUE Int
    Type UNIQUE Is_read
          Is_contig
          Is_assembly
          Is_vector
    Padded_state UNIQUE Padded
                              Unpadded
    Structure  From Source UNIQUE ?Sequence XREF Subsequence
         Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int
    Assembly   Assembled_from ?Sequence XREF Assembled_into UNIQUE Int COORD UNIQUE Int COORD UNIQUE Int UNIQUE Int
               Assembled_into ?Sequence XREF Assembled_from
    // these two are the binding relationships reads <-> contigs - they are loose
    // the first two ints are the positions in the contig.  The next two are the left and right clip points
    // for the read with respect to this assembly.
    Sequencing_vector UNIQUE ?Sequence UNIQUE Int  // Int is cloning site.  Overrides default from Main_clone
    Library ?Library UNIQUE Text UNIQUE Text // Texts are ID, Accession_number
               // to be used for reads from EMBL etc.
    Properties    EST
      Stolen UNIQUE ?Clone XREF Stolen_reads
      Base_caller UNIQUE Text
      Staden_id UNIQUE Int
    ASP    Asped UNIQUE DateType
      ProcessStatus UNIQUE Text
    Features Tag ?Method Int COORD Int COORD Text
       Seq_vec ?Method Int COORD Int COORD Text
       Clone_vec ?Method Int COORD Int COORD Text
       Clipping ?Method Int COORD Int COORD
    Read  Template UNIQUE ?Clone XREF Read
    Dye UNIQUE Dye_primer
         Dye_terminator
    Strand UNIQUE Forward
            Reverse
    Primer UNIQUE Universal_primer
            Custom UNIQUE Text  // text may be the oligo - or should it be an object?
    Insert_size UNIQUE Int UNIQUE Int
    SCF_File UNIQUE Text
      // for acembly: absolute file name, or relative to $SCF_DATA, or to $ACEDB/SCF
    Align_to_SCF Int COORD UNIQUE Int COORD UNIQUE Int UNIQUE Int
      // tight alignment of current (edited) read to SCF file
    Homol DNA_homol ?Sequence XREF DNA_homol ?Method Float Int COORD UNIQUE Int COORD Int UNIQUE Int
          Feature ?Method Int COORD Int COORD UNIQUE Float UNIQUE Text
     // Float is score
     // Text is shown on select, and same Text are neighbours


?Method  Remark ?Text  // need this to enter Homol data, but caf does not need display info
        GAP_tag UNIQUE Text


// ?Motif to read in restriction enzymes

?Motif  Match_sequence  UNIQUE Text // idem for ace4
  Restriction_Enzyme  Isoschizomer ?Motif XREF Isoschizomer
                                Offset UNIQUE Int   
                                Cleavage UNIQUE Text  // will show the cleavage points ex: G_ACGT'C
                                Overhang UNIQUE Int
                                Company UNIQUE Text
        Remark Text
        Substrate UNIQUE DNA
                         Peptide

// tag type - name is 4-letter code

// ?Tag_type Colour #Colour
//    Description UNIQUE Text