[Bioperl-l] FW: problem parsing WU-blast output
Forrest Zhang
forrest_zhang at 163.com
Thu Oct 25 08:06:27 UTC 2007
Hi, Joe
My this script(wublast.pl) maybe is useful for you. You can get the
subsequence by using query range and hit range.
The script is below, and the file name is wublast.pl.
use strict;
use Bio::SearchIO;
die "Usage:perl wublast <File>\n"
unless @ARGV==1;
my $inputfile = $ARGV[0];
my $in = new Bio::SearchIO(-format => 'blast',
-file => $inputfile);
print "query","\t","hit","\t","total_length","\t",
"query_lenth","\t","hit_length","\t",
"percent_identity","\t","score","\t","evalue","\t","rank",
"\t","query range","\t","hit range","\n";
while( my $result = $in->next_result ) {
my $image=$result->query_name;
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
print $image,"\t",$hit->name,"\t",$hsp->length('total'),"\t",
$hsp->length('query'),"\t",$hsp->length('hit'),"\t",
$hsp->percent_identity,"\t",$hsp->score,"\t",$hsp->evalue,"\t",
$hsp->rank,"\t",$hsp->start('query'),",",$hsp->end('query'),"\t",
$hsp->start('hit'),",",$hsp->end('hit'),"\n";
}
}
}
Forrest Zhang
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph Fass
Sent: Thursday, October 25, 2007 5:43 AM
To: Dave Messina
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] problem parsing WU-blast output
Hi Dave,
here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.
Joe
***************code***************
#!/usr/bin/perl -w
use strict;
use Bio::SearchIO;
use Bio::SeqIO;
# note: processes only the first result (first query sequence) of the blast
report!
my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in = Bio::SearchIO->new(-file => $reportfile,
-format => 'blast');
# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;
# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
-format => 'fasta');
# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
# find hit ID in database file to fill in sequence and write corresponding
sequence to output file
my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
print "seq_id: " . $seq->id."\n";
# open database file
my $db = Bio::SeqIO->new(-file => $databasefile,
-format => 'fasta');
# now look through database sequences to pull out correct sequence for ID
from Blast hit
my $still_looking = 1;
do {
my $db_seq = $db->next_seq();
#print $seq->id() . " ... " . $db_seq->id() . "\n";
if ($seq->id() eq $db_seq->id()) {
$seq->seq($db_seq->seq);
$still_looking = 0;
} # if
} while ($still_looking);
# then write sequence (in fasta format) to output_file
$out->write_seq($seq);
print "found a sequence\n";
} # while
********************blast report*************************
BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]
Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.
Reference: Gish, W. (1996-2006) http://blast.wustl.edu
Notice: this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly. To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.
Query= 962_177_14574088_5489_46110_045.ab1
(676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA
Database: ../Cowpea1X/Cowpea_all_GSS_clean.fasta
260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done
Smallest
Sum
High
Expectation
Sequences producing High-scoring Segment Pairs: Score
E(N) N
962_177_14574088_5489_46110_045.ab1 3380 2.0e-147
1
962_191_14579666_5489_46288_070.ab1 2705 6.4e-117
1
962_307_14625348_5489_47135_029.ab1 2314 2.8e-99
1
962_370_14650238_5489_47797_032.ab1 2054 1.8e-87
1
962_400_14670294_5489_48184_096.ab1 2040 7.2e-87
1
962_79_14536329_16654_45346_033.ab1 1928 7.8e-82
1
962_187_14578095_5489_46263_022.ab1 1764 2.3e-74
1
962_309_14626130_16654_47155_078.ab1 1263 1.1e-51
1
962_45_14523164_5489_45006_087.ab1 1160 3.7e-47
1
962_394_14659720_16654_47971_045.ab1 1146 1.6e-46
1
962_61_14529390_16654_45210_020.ab1 1077 2.1e-43
1
962_177_14574088_16654_46114_045.ab1 955 7.5e-38
1
962_282_14615493_16654_46934_055.ab1 891 1.3e-34
1
962_248_14601477_16654_46676_055.ab1 687 1.0e-25
1
962_196_14581545_16654_48111_005.ab1 633 3.0e-23
1
>962_177_14574088_5489_46110_045.ab1
Length = 676
Plus Strand HSPs:
Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus
Query: 1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
Query: 61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
Query: 121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
Query: 181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
Query: 241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
Query: 301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
Query: 361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
Query: 421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
Query: 481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
Query: 541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
Query: 601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
Query: 661 CCCAACAATCCTACTT 676
||||||||||||||||
Sbjct: 661 CCCAACAATCCTACTT 676
>962_191_14579666_5489_46288_070.ab1
Length = 664
Plus Strand HSPs:
Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus
Query: 136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60
Query: 196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120
Query: 256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180
Query: 316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240
Query: 376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300
Query: 436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360
Query: 496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420
Query: 556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480
Query: 616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540
Query: 676 T 676
|
Sbjct: 541 T 541
>962_307_14625348_5489_47135_029.ab1
Length = 687
Minus Strand HSPs:
Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus
Query: 676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
||||||||||||||||||||||||||||| ||||||||||||| ||| ||||||||||
Sbjct: 72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131
Query: 617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
|| | | | || |||| || |||||||||||||||||| | |||||| | ||
Sbjct: 132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184
Query: 564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
|| || |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct: 185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240
Query: 504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300
Query: 444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360
Query: 384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
||||| ||||||||||||||||||||||||| || | | |||||||||||||||||
Sbjct: 361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420
Query: 332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
|||| | ||||||| ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct: 421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478
Query: 272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538
Query: 212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
|||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct: 539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598
Query: 152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
|||||||||||||| ||| ||||||||||||||||||| |||| ||| |||||||||
Sbjct: 599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658
Query: 95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
|||||| |||||| |||||| || |||
Sbjct: 659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687
>962_370_14650238_5489_47797_032.ab1
Length = 581
Plus Strand HSPs:
Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus
Query: 1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
|||| |||||||||||||||||||| ||||||||||||||| | | ||||| |||||||
Sbjct: 74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130
Query: 61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
| |||||||| || |||||| |||||| ||||||||||||||| ||| ||||||| |
Sbjct: 131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190
Query: 119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct: 191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250
Query: 178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310
Query: 238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct: 311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370
Query: 298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
||||||||||||||| |||||| |||| | ||||||||||||||||||||| | ||
Sbjct: 371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428
Query: 353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
| ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct: 429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488
Query: 410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct: 489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548
Query: 470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
||||||||| |||||| | || ||||||||||||
Sbjct: 549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581
>962_400_14670294_5489_48184_096.ab1
Length = 641
Plus Strand HSPs:
Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus
Query: 123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct: 1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60
Query: 183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120
Query: 243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
|||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct: 121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180
Query: 303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
|||||||||| |||||| | | | | ||||| ||| ||| || || | | | || |
Sbjct: 181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239
Query: 355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct: 240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299
Query: 415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
|||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359
Query: 475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct: 360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419
Query: 535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
| |||||||||||||||||| ||||| || || | | | ||| | ||
Sbjct: 420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476
Query: 594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
| | || | || | | | |||||||||| ||| ||||||||||||| |||||
Sbjct: 477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534
Query: 653 CACAGAAGCCCAACAATCCTACTT 676
||||||||||||||||||||||||
Sbjct: 535 CACAGAAGCCCAACAATCCTACTT 558
>962_79_14536329_16654_45346_033.ab1
Length = 675
Plus Strand HSPs:
Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus
Query: 77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
|||| || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct: 6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65
Query: 133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
| ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct: 66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125
Query: 193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct: 126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185
Query: 253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
|| | || |||||||||||||| ||||| |||||||||| |||||||||| |||||||
Sbjct: 186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245
Query: 313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
| || | || || | | ||| | |||||||||| || || || ||||| ||
Sbjct: 246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302
Query: 365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
|||||||||||| | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct: 303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362
Query: 425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct: 363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422
Query: 485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
| | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct: 423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482
Query: 545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
|||||||||| ||||||| ||||| | ||||| | |||||||| || |||||||||
Sbjct: 483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539
Query: 605 TTTCTCTCTAAAT 617
|||||||||||||
Sbjct: 540 TTTCTCTCTAAAT 552
Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus
Query: 220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
||| ||| |||| || | || || ||| || | | | || || | ||||
Sbjct: 159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214
Query: 279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
|||| | | |||| ||| | | ||||| ||| | || || ||||
Sbjct: 215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271
Query: 338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
||| || | | || || || ||||| |||||||||||||| | || || ||||
Sbjct: 272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330
Query: 393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
|||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct: 331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390
Query: 453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct: 391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450
Query: 513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
|||||||||||||| |||||||||||||||| |||||||||| ||||||| ||||| |
Sbjct: 451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508
Query: 573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
||||| | |||||||| || ||||||||| ||||||||||||| | | || || |
Sbjct: 509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567
Query: 626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
|| ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct: 568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618
>962_187_14578095_5489_46263_022.ab1
Length = 590
Plus Strand HSPs:
Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus
Query: 1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
||||||||||||||||||||||||| ||||||||||||||| | ||||||| |||||||
Sbjct: 144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200
Query: 61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
| |||||||| || ||||| |||||| ||||||||||||||| ||| ||||||| |
Sbjct: 201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260
Query: 119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct: 261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320
Query: 178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380
Query: 238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct: 381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440
Query: 298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
||||||||||||||| |||||| |||| ||| ||||||||||| ||| ||||| | |
Sbjct: 441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497
Query: 352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
| | |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557
Query: 408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
||||||||||||| |||||||||||||||||||
Sbjct: 558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590
>962_309_14626130_16654_47155_078.ab1
Length = 531
Plus Strand HSPs:
Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus
Query: 365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
|||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct: 1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60
Query: 425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct: 61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120
Query: 485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct: 121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180
Query: 545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
|||||||||| ||||| | | ||| | ||||||||| ||||||||||||||| |||
Sbjct: 181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238
Query: 605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct: 239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297
Query: 665 ACAATCCTACTT 676
|||||||||||
Sbjct: 298 GCAATCCTACTT 309
>962_45_14523164_5489_45006_087.ab1
Length = 697
Plus Strand HSPs:
Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus
Query: 327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
| | | ||| | |||||||||| || || || ||||| ||||||||||||||
Sbjct: 13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72
Query: 380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
| || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct: 73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132
Query: 440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct: 133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192
Query: 500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
||||||||||||||||||||||||||| |||||||||||||||| |||||||||| |||
Sbjct: 193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252
Query: 560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
|||| ||||| | ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct: 253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309
Query: 619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
| | | || ||| ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct: 310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369
Query: 673 ACTT 676
||||
Sbjct: 370 ACTT 373
>962_394_14659720_16654_47971_045.ab1
Length = 708
Minus Strand HSPs:
Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus
Query: 676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
||||||||||||||||||||||||||||| ||||||||||||| ||| ||||||||||
Sbjct: 374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433
Query: 617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
|| | | ||| || ||| || | | || |||| | | | || || ||||
Sbjct: 434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490
Query: 562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
|| ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct: 491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546
Query: 502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606
Query: 442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct: 607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666
Query: 382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
||| |||||||||||||| |||||||||| | |
Sbjct: 667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699
>962_61_14529390_16654_45210_020.ab1
Length = 696
Plus Strand HSPs:
Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus
Query: 372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
||||| | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct: 1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60
Query: 432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
|||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct: 61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120
Query: 492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
|||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct: 121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180
Query: 552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
||| ||||||| ||||| | ||||| | |||||||| || ||||||||| |||||||
Sbjct: 181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237
Query: 612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
|||||| | | | | || ||| ||| ||||||||||| | |||||||||||||||||
Sbjct: 238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297
Query: 665 ACAATCCTACTT 676
||| ||||||||
Sbjct: 298 ACAGTCCTACTT 309
>962_177_14574088_16654_46114_045.ab1
Length = 625
Minus Strand HSPs:
Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus
Query: 676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494
Query: 616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554
Query: 556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614
Query: 496 TCGTTTTCATT 486
|||||||||||
Sbjct: 615 TCGTTTTCATT 625
>962_282_14615493_16654_46934_055.ab1
Length = 274
Minus Strand HSPs:
Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus
Query: 561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
||||| |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct: 68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127
Query: 501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
|||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187
Query: 441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct: 188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247
Query: 381 CTTTCCCTGTAATTAACAAATTGATTA 355
|| |||||| ||||||| | |||||||
Sbjct: 248 CTCTCCCTGCAATTAACGATTTGATTA 274
>962_248_14601477_16654_46676_055.ab1
Length = 566
Minus Strand HSPs:
Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus
Query: 333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
|||| | | | ||| ||||| | ||| |||||| ||| ||||||| | ||||||
Sbjct: 1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56
Query: 274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct: 57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116
Query: 214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
|||||||||| | ||| ||||||| ||| |||||| ||||||| || || || |||
Sbjct: 117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176
Query: 157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
| || | |||||| | || ||| |||| |||||| |||| || | || ||||||
Sbjct: 177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236
Query: 97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
|| |||||| | |||||| ||| || || |||
Sbjct: 237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269
>962_196_14581545_16654_48111_005.ab1
Length = 538
Minus Strand HSPs:
Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus
Query: 201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
||||||||||||||||||| | |||||||||||||| ||||||||||| || |||||||
Sbjct: 2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61
Query: 141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
||| ||| |||||||||||||||||| | ||||||||||||| ||| ||||| ||||
Sbjct: 62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121
Query: 84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
|| ||| | | ||||||| ||||| || ||||||| | | | ||||||||||| |
Sbjct: 122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172
Query: 24 AGGAGACAGAAAGTGATGCCAGGA 1
|||| ||||||| |||||||||||
Sbjct: 173 AGGAAACAGAAACTGATGCCAGGA 196
Parameters:
E=1e-20
evalues
echofilter
-o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n
ctxfactor=2.00
Query ----- As Used ----- ----- Computed
----
Strand MatID Matrix name Lambda K H Lambda K H
+1 0 +5,-4 0.192 0.182 0.357 same same same
Q=10,R=10 0.104 0.0151 0.0600 n/a n/a n/a
-1 0 +5,-4 0.192 0.182 0.357 same same same
Q=10,R=10 0.104 0.0151 0.0600 n/a n/a n/a
Query
Strand MatID Length Eff.Length E S W T X E2 S2
+1 0 676 676 9.9e-21 611 11 n/a 73 0.049 80
134 0.048 119
-1 0 676 676 9.9e-21 611 11 n/a 73 0.049 80
134 0.048 119
Statistics:
Database: ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
Title: ../Cowpea1X/Cowpea_all_GSS_clean.fasta
Posted: 2:44:50 PM PDT Oct 19, 2007
Created: 2:44:50 PM PDT Oct 19, 2007
Format: XDF-1
# of letters in database: 158,813,828
# of sequences in database: 260,642
# of database sequences satisfying E: 15
No. of states in DFA: 245 (490 KB)
Total size of DFA: 548 KB (2076 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Elapsed: 00:00:00
No. of threads or processors used: 2
Search cpu time: 1.19u 0.04s 1.23t Elapsed: 00:00:00
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Start: Fri Oct 19 14:51:16 2007 End: Fri Oct 19 14:51:16 2007
On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>
--
Joseph Fass
joseph.fass at gmail.com || joefass at hotmail.com
970.227.5928 (c) || 530.754.7978 (w)
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