Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1907
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4479
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Found at i:1511 original size:470 final size:474
Alignment explanation
Indices: 1--4479 Score: 6853
Period size: 470 Copynumber: 9.6 Consensus size: 474
* * *
1 GGAGGAGAATGTGTTTTATATTG-CTAATCATGAAAATGAGTGAAGATCCCTACTAGAATCCATG
1 GGAGGAGAATGTG-TTTATAGTGCCTAATCATG-AAATGAATGAAGATCCATACTAGAATCCATG
* *
65 TTTGTCTCATTTGAGGCGCGGGACTTAGGATTTTACACAAATTGGTGGGA-AAAAGCGTATCTTG
64 TTTGTCTCATTTGAGGCAC-GGACTTA-GATTTTACACAAATTGGT-GGACGAAAGCGTATCTTG
*
129 CGAAACCAAAGCATCAATATCATGTA-CCATAT-AGAAGACTATGTTTATGGTGCCCAAAATCCA
126 CGAAACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTG-CC-AAATACA
*
192 GAAAAGAAT-GGGATTAGT-AGAGTATTCTATGTTTGTCTTATTTAAAAGACAATTTTGATTCTA
189 GAAAAGAATGGGGATTAGTAAGAGTATTC-ATGTTTGTCTTATTTAAAAGACAACTTTGATTCTA
* * *
255 TCAATAATGGTGGGAAAGACAAGCTTCTCTTGCGACACCAAATCATCAATGTCATG-ATCCTAAT
253 TCAATAACGG-CGGAAAGACAAGCTTCTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAAT
319 GAAAGGAATGTG-TTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCAT
317 GAAAGGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCAT
* * **
383 GTCTCATTTAAAGTGC-AACATTGATTTTATGAAAAATAATGGCAAAGAAAAGATTTAAATGCAA
382 GTCTCATTTAAAGTGCAAACTTTGATTTTATGGAAAATAA-GGCAAAGAAAAGATTTCGATGCAA
*
447 AAGAAAACCATCAATATCTTGCAATCC--A
446 AAGAAAACCATCAATATCATGC-ATCCTGA
475 -GAGGAGAATGTG--TATAGTGCCTAATCATGAAATGAAAATGAAGATCCATACTAGAATCCATG
1 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATG--AATGAAGATCCATACTAGAATCCATG
* *
537 TTTGTCTCATTTGAGGC-CGGGACTTGGATTTTACACAAAATTGGTGGGGA-AAAAGCGTATCTT
64 TTTGTCTCATTTGAGGCAC-GGACTTAGATTTTACAC-AAATTGGT--GGACGAAAGCGTATCTT
600 GCGAAACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCC-AATACAG
125 GCGAAACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAG
*
664 AAAAAAGGGAATGGGGATT-GTAAGAGTA-TC-TG-TTGTCTTATTTAAAAGACAATTTTGATTC
190 --AAAA--GAATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAACTTTGATTC
* * *
725 TATCAATAATGG-TGAAAGACAAGCTTCTCTTGCGACACTAAAGCATCAATGTCATGTATCCTAA
251 TATCAATAACGGCGGAAAGACAAGCTTCTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAA
* *
789 TGAAAGGAATGTGTTTTTGTTTCCTAATCTTG-AAAGAATGGAGAAT-TTACGAGAATCAATGCA
316 TGAAAGGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCA
*
852 TGTCTCATTTAAAGTGGCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAGATTTC-AAGC-
381 TGTCTCATTTAAAGT-GCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAGATTTCGATGCA
915 AAAG-AAACCATCAATATCATGCATCCTGA
445 AAAGAAAACCATCAATATCATGCATCCTGA
944 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATG-ATG-AGATCCATACTAGAATCCCATGT
1 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAAT-CCATGT
*
1007 TTGTCTCATTTGAGGCGCGGACTTAGATTTTACACAAATTGGTGGACGAAAAGCGTATCTTTGCG
65 TTGTCTCATTTGAGGCACGGACTTAGATTTTACACAAATTGGTGGACG-AAAGCGTATC-TTGCG
* *
1072 AAACCAAAGCATCAATATCATGTATCC-CATAAGAAGACTATG-TTATGGTGCCAAATACAGAAC
128 AAACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAA
1135 AGAATGGGGATTAGTAAGAGTATTC-TGTTTGTCTTATTTTAAAAGACAA-TTTGATTCTATCAA
193 AGAATGGGGATTAGTAAGAGTATTCATGTTTGTCTTA-TTTAAAAGACAACTTTGATTCTATCAA
*
1198 TAACGGCGGAAAGACCAAGCTTTTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAATGAAA
257 TAACGGCGGAAAGA-CAAGCTTCTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAATGAAA
*
1263 -GAATGTGTTTTTGG-TCCTAATCTTGAAAAGAATGGAGACTGTTTAACAAGAATCAA-GCATGT
321 GGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTG-TT-ACGAGAATCAATGCATGT
*
1325 CTCATTTTAAAGTGCAAACTTTGATTTTAGGGAAAATAAGGCAAAGAAAAGA-TTC-ATGCAAAA
384 CTCA-TTTAAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAGATTTCGATGCAAAA
1388 GAAAACCATCAATATC-TGCATCCTGA
448 GAAAACCATCAATATCATGCATCCTGA
1414 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTT
1 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTT
1479 TGTCTCATTTGAGGCAAC-GACTTAGA-TTTACACAAATTGGTGGACGAAAGCGTA-CTTTGCGA
66 TGTCTCATTTGAGGC-ACGGACTTAGATTTTACACAAATTGGTGGACGAAAGCGTATC-TTGCGA
*
1541 AACCAAAGCATCAATATCATGTAT--ATATAAGAAGAGACTATGTTAATGGTGCCAAATACAGAA
129 AACCAAAGCATCAATATCATGTATCCATATAAG-A-AGACTATGTTTATGGTGCCAAATACAGAA
*
1604 AAG-ATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTT-AAAGACAACGTTGATTCTATCAA
192 AAGAATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAACTTTGATTCTATCAA
*
1667 TAACGGCGGAAAGACAAG---CTCTTGCGACACCAAAGCATCAATGTCGTGTATCCTATCCTAAT
257 TAACGGCGGAAAGACAAGCTTCTCTTGCGACACCAAAGCATCAATGTC----AT-GTATCCTAAT
* *
1729 GAAAGGAATGTGTTTGTGGTTCCTAATCTTGAAAA-AAAGGAGACTGTTACGAGAATCAATGCAT
317 GAAAGGAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCAT
1793 GTCTCATTTAAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAG-AAAGATTTCGATGCAAA
382 GTCTCATTTAAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAGATTTCGATGCAAA
1857 AGAAAACCATCAATATC-TGCATCCTGA
447 AGAAAACCATCAATATCATGCATCCTGA
1884 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATG-ATGAAGATCCATACTAGAATCCATGTT
1 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTT
* *
1948 TGTCTCATTTGAGGCGCGGACTTAGATTTTACACAAATTGGTGGGA-AAAAGCGTATCTTGCGAA
66 TGTCTCATTTGAGGCACGGACTTAGATTTTACACAAATTGGT-GGACGAAAGCGTATCTTGCGAA
*
2012 ACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATCCAGAAAAG
130 ACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAAG
* *
2077 AATGGGGATTAGTAAGAGTATTCTTGTTTGTCTTATTTAAAAGAC-ATTTTGATTCTATCAA-AA
195 AATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAACTTTGATTCTATCAATAA
* * *
2140 TGGTGGAAAGACAAGCTTCTCTTGCGACACTAAAGCATCAATGTCATGTATCCTAATGAAAGGAA
260 CGGCGGAAAGACAAGCTTCTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAATGAAAGGAA
2205 TGTG-TTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCATGTCTCATT
325 TGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCATGTCTCATT
*
2269 TAAAGTGCAAAC-TTGATTTTATGG-AAATAAGGCAAAGAAAAGAATTTCAATGGCAAAAGAAAA
390 TAAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAG-ATTTCGAT-GCAAAAGAAAA
2332 CCATCAATATCATGCATCCTGA
453 CCATCAATATCATGCATCCTGA
* * *
2354 GGAGGAGGAATGTGTTTATAGTGGCTAATCATG-AATGACTGAAGATCCATACTAGAATCCATTT
1 GGAGGA-GAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGT
*
2418 TTGTCCTCA-TTGAGGCAC-GACTTAGATTTTAACACCAATTGGTGGGACGAAAGCGTATC-TGC
65 TTGT-CTCATTTGAGGCACGGACTTAGATTTT-ACACAAATTGGT-GGACGAAAGCGTATCTTGC
*
2480 GAAACC-AAGCATCAATATCATGTTATCCGTATAAGAAGACTATGTTTA--G-GCCAAATACAGA
127 GAAACCAAAGCATCAATATCATG-TATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGA
*
2541 AAAGAATGGGGATTAGTAAGAGTATTCAT-TTTGTCTTATTTAAAAGACAACGTTGATTCTATCA
191 AAAGAATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAACTTTGATTCTATCA
* *
2605 ATAACGGCGGAAA-ACAAGCTTTTCTTGCGACACCAAAGCATCAATGTCGTGTATCCTAATGAAA
256 ATAACGGCGGAAAGACAAGCTTCTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAATGAAA
* *
2669 GGAATGTGTTTTTGGTTCCTAA-CTATGAAAAGAATGGAGACT-TTAACAAGAATCAATGCATAT
321 GGAATGTGTTTTTGGTTCCTAATCT-TGAAAAGAATGGAGACTGTT-ACGAGAATCAATGCATGT
*
2732 CTCA-TTAAA-TGCAAACTTTGATTTTATGGAAAATAAGGCAAAG-AAAGATTTCATCATGCAAA
384 CTCATTTAAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAGATTTC--GATGCAAA
2794 AG-AAACCATC---AT-A-GCATCCTGA
447 AGAAAACCATCAATATCATGCATCCTGA
*
2816 GGAGGAGAAGGTGTTTATAGTGCCTAATCATGAAATG-A--AAGATCCATACTAGAATCCAT-TT
1 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTT
*
2877 TGTCTCCTTTGAGGGCACGGACTTAGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCG-
66 TGTCTCATTTGA-GGCACGGACTTAGATTTTACACAAATTGGT-GGACGAAAGCGTATCTTGCGA
*
2941 AACCAAAGCATCAATATCATGTATCCGTATAAGAAGACTATGTTTATGGTGCC-AATACAGAAAA
129 AACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAG--AA
*
3005 AAGAATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAACGTTGATTCTATCAA
192 AAGAATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAACTTTGATTCTATCAA
3070 TAACGGCGGAAAGACAAGCTT-TCTTGCGACACCAAAGCATCAATGTCATGTATCCTAATGAAAG
257 TAACGGCGGAAAGACAAGCTTCTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAATGAAAG
* *
3134 GAATGTGTTTTT--TTCCTAATCTTGAAAAGAATGGAGACT-TTACAAGAATCAATGCATATCTC
322 GAATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCATGTCTC
*
3196 ATTTAAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAGATTTCAATGCAAAAGAAA
387 ATTTAAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAGATTTCGATGCAAAAGAAA
3261 ACCATCAATATCATGCATCCTGA
452 ACCATCAATATCATGCATCCTGA
3284 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTT
1 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTT
*
3349 TGTCTCATTTGAGGCACGGACTTAGATTTTACACAAATTGGTGGGGCGAAAGCGTATCTTGCGAA
66 TGTCTCATTTGAGGCACGGACTTAGATTTTACACAAATTGGT-GGACGAAAGCGTATCTTGCGAA
*
3414 ACCAAAGCATCAATATCATGTATCCGTATAAGAAGACTATG-TTATGGTGCCAAA-ATCAGAAAA
130 ACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATA-CAGAAAA
3477 GAATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAA--TTGATTCTATCAAT-
194 GAATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAACTTTGATTCTATCAATA
*
3539 --GGTGGAAAGACAAGCTTCTCTTGCGACACCAAAGCA-CAATGTCATGTATCCTAATGAAAGGA
259 ACGGCGGAAAGACAAGCTTCTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAATGAAAGGA
3601 ATGTG--TTTGGTTCCTAATCTTGAAAAGAATGGAGACTG-TACGAGAATCAATGCATGTCTCAT
324 ATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCATGTCTCAT
3663 TTAAAGTGCAAAC-TTGATTTTATGG-AAATAAGGCAAAGAAAAGATTTCGATGCAAAAGAAAAC
389 TTAAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAGATTTCGATGCAAAAGAAAAC
*
3726 CATCAATATCTTGCATCCTGA
454 CATCAATATCATGCATCCTGA
*
3747 GGAGGAGAATGTG-TTATAGTGCCTAATCATGAAATGAGTGAAGA-CTCATACTAGAATCCATGT
1 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATC-CATACTAGAATCCATGT
* * *
3810 TTGTCTCGTTTGAGGCGCGGACTTAGATTTTACACAAATTGGTGGGA-AAAAGCGTATCTTGCGA
65 TTGTCTCATTTGAGGCACGGACTTAGATTTTACACAAATTGGT-GGACGAAAGCGTATCTTGCGA
3874 AACCAAAGCATCAATATCATGTATCCATATAAGAAGAC-ATGTTTATGGTGCCAAATACAGAAAA
129 AACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAA
*
3938 GAATGGGGATTAGTAAGAGTATTCATGTTTGTC-TATTTAAAAGACAATTTTGATTCTATCAATA
194 GAATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAACTTTGATTCTATCAATA
* *
4002 ATGGTGGAAAGACAAGCTTCTCTTGCGACACC-AAGCATCAATGTCATGTATCCTAATGAAAGGA
259 ACGGCGGAAAGACAAGCTTCTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAATGAAAGGA
*
4066 A--TGTTTTTGGTTCCTAATCTTGAAAAAAATGGAGACTGTTACGAGAATCAATGCATGTCTCAT
324 ATGTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCATGTCTCAT
4129 TTAAAGTGCAAAC-TTGATTTTATGGAAAA-ATAGGCAAAGAAAAGATTTCGATGCAAAAGAAAA
389 TTAAAGTGCAAACTTTGATTTTATGGAAAATA-AGGCAAAGAAAAGATTTCGATGCAAAAGAAAA
4192 CCATCAATATC-TGCATCCTGA
453 CCATCAATATCATGCATCCTGA
4213 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATG-ATGAAGATCCATACTAGAATCCATGTT
1 GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTT
4277 TGTCTCATTTGAGGCACGGACTTAGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCGAA
66 TGTCTCATTTGAGGCACGGACTTAGATTTTACACAAATTGGT-GGACGAAAGCGTATCTTGCGAA
*
4342 ACCAAAGCATCAATATCATGTATCC-TATAAGAAGACTATGTTTATGGTGCC-CA-ACA-AAAAG
130 ACCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAAG
*
4403 AATGGGGATTAGTAAGAGTATTCTTGTTTGTCTTATTTTAAAAG---ACTTTGATTCTATCAATA
195 AATGGGGATTAGTAAGAGTATTCATGTTTGTCTTA-TTTAAAAGACAACTTTGATTCTATCAATA
*
4465 ACGGTGGAAAGACAA
259 ACGGCGGAAAGACAA
Statistics
Matches: 3758, Mismatches: 102, Indels: 301
0.90 0.02 0.07
Matches are distributed among these distances:
457 3 0.00
458 9 0.00
459 82 0.02
460 49 0.01
461 161 0.04
462 168 0.04
463 181 0.05
464 177 0.05
465 246 0.07
466 204 0.05
467 260 0.07
468 443 0.12
469 405 0.11
470 557 0.15
471 416 0.11
472 305 0.08
473 52 0.01
474 20 0.01
475 8 0.00
476 12 0.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (474 bp):
GGAGGAGAATGTGTTTATAGTGCCTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTT
TGTCTCATTTGAGGCACGGACTTAGATTTTACACAAATTGGTGGACGAAAGCGTATCTTGCGAAA
CCAAAGCATCAATATCATGTATCCATATAAGAAGACTATGTTTATGGTGCCAAATACAGAAAAGA
ATGGGGATTAGTAAGAGTATTCATGTTTGTCTTATTTAAAAGACAACTTTGATTCTATCAATAAC
GGCGGAAAGACAAGCTTCTCTTGCGACACCAAAGCATCAATGTCATGTATCCTAATGAAAGGAAT
GTGTTTTTGGTTCCTAATCTTGAAAAGAATGGAGACTGTTACGAGAATCAATGCATGTCTCATTT
AAAGTGCAAACTTTGATTTTATGGAAAATAAGGCAAAGAAAAGATTTCGATGCAAAAGAAAACCA
TCAATATCATGCATCCTGA
Found at i:2063 original size:156 final size:155
Alignment explanation
Indices: 24--4407 Score: 1384
Period size: 156 Copynumber: 28.1 Consensus size: 155
14 TTTTATATTG
* * ** * * * *
24 CTAATCATGAAAATGAGTGAAGATCCCTACTAGAATCCATGTTTGTCTCATTTGAGGCGCGGGAC
1 CTAATCATGAAAA-GAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAGCGC--AAC
* *
89 TTAGGATTTTACACAAATTGGTGGGAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGT
63 TT-TGATTTTACA-AAATTGGTGGAAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGT
*
154 A-CC--ATATAGAAGACTATGTTTATGGTGCC
126 ATCCTGATA-AGAAGAATATGTTTATGGTG-C
* * * * *
183 CAAAATCCA-GAAAAGAATGG-GAT-TAGTA-GAGTATTCTATGTTTGTCTTATTTAAAAG-ACA
1 C-TAAT-CATGAAAAGAATGGAGATCTA-TACGAG-AATCCATGTTTGTCTCATTT-AAAGCGCA
* * * * * * *
243 ATTTTGATTCTATCAATAA-TGGTGGGAAAGACAAGCTTCTCTTGCGACACCAAATCATCAATGT
61 ACTTTGATTTTA-CAA-AATTGGT-GGAAA-A-AAGCGTATCTTGCGAAACCAAAGCATCAATAT
* * * *
307 CATG-ATCCTAATGAA-AGGAATGTGTTT-TGGTTC
121 CATGTATCCTGAT-AAGAAGAATATGTTTATGGTGC
* * * ** * *
340 CTAATCTTGAAAAGAATGGAGA-CTGTTACGAGAATCAATGCATGTCTCATTTAAAGTGCAACAT
1 CTAATCATGAAAAGAATGGAGATCT-ATACGAGAATCCATGTTTGTCTCATTTAAAGCGCAACTT
* * ** * * * ** * *
404 TGATTTTATGAAAAATAATGGCAAAGAAA-AG-ATTTAAATGCAAAAGAAAACCATCAATATCTT
65 TGATTTTA-CAAAATTGGTGG-AAA-AAAGCGTATCT---TGCGAAACCAAAGCATCAATATCAT
* * * * *
467 GCAATCC--A-GAGGAG-A-ATGTGTATAGTGC
124 G-TATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * * **
495 CTAATCATGAAATGAAAATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCCGGGAC
1 CTAATCATGAAA--AGAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAG-CGCAAC
* *
560 TTGGATTTTACACAAAATTGGTGGGGAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATG
63 TTTGATTTT--ACAAAATTGGT-GGAAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATG
*
625 TATCCAT-ATAAGAAGACTATGTTTATGGTGC
125 TATCC-TGATAAGAAGAATATGTTTATGGTGC
* * * * * *
656 C-AATACA-GAAAAAAGGGAATGGGGAT-TGTAAGAGTAT-C-TG-TTGTCTTATTTAAAAG-AC
1 CTAAT-CATG--AAAA--GAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTT-AAAGCGC
* * * * * * *
714 AATTTTGATTCTATCAATAA-TGGT-GAAAGACAAGCTTCTCTTGCGACACTAAAGCATCAATGT
60 AACTTTGATTTTA-CAA-AATTGGTGGAAA-A-AAGCGTATCTTGCGAAACCAAAGCATCAATAT
* * * * * *
777 CATGTATCCTAATGAA-AGGAATGTGTTTTTGTTTC
121 CATGTATCCTGAT-AAGAAGAATATGTTTATGGTGC
* * ** *
812 CTAATCTTG-AAAGAATGGAGAAT-T-TACGAGAATCAATGCATGTCTCATTTAAAGTGGCAAAC
1 CTAATCATGAAAAGAATGGAG-ATCTATACGAGAATCCATGTTTGTCTCATTTAAAG-CGC-AAC
* * ** * * ** * *
874 TTTGATTTTATGGAAAATAAGG-CAAAGAAAAG-ATTTCAAGC-AAA-GAAACCATCAATATCAT
63 TTTGATTTTA--CAAAAT-TGGTGGAA-AAAAGCGTATCTTGCGAAACCAAAGCATCAATATCAT
* ** * * *
935 GCATCCTGAGGAGGAGAATGTGTTTATAGTGC
124 GTATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * *
967 CTAATCATGAAATG-AT-GAGATCCATACTAGAATCCCATGTTTGTCTCATTTGAGGCGCGGACT
1 CTAATCATGAAAAGAATGGAGATCTATACGAGAAT-CCATGTTTGTCTCATTTAAAGCGC-AACT
* *
1030 TAGATTTTACACAAATTGGTGGACGAAAAGCGTATCTTTGCGAAACCAAAGCATCAATATCATGT
64 TTGATTTTACA-AAATTGGTGGA-AAAAAGCGTATC-TTGCGAAACCAAAGCATCAATATCATGT
* *
1095 ATCC-CATAAGAAGACTATG-TTATGGTGC
126 ATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * * * *
1123 CAAATACA-GAACAGAATGGGGAT-TAGTAAGAGTATTC-TGTTTGTCTTATTTTAAAAG-ACAA
1 CTAAT-CATGAAAAGAATGGAGATCTA-TACGAGAATCCATGTTTGTCTCA-TTT-AAAGCGCAA
* * * * * * *
1184 -TTTGATTCTATCAATAA-CGGCGGAAAGACCAAGCTTTTCTTGCGACACCAAAGCATCAATGTC
62 CTTTGATTTTA-CAA-AATTGGTGGAAA-A--AAGCGTATCTTGCGAAACCAAAGCATCAATATC
* * * *
1247 ATGTATCCTAATGA-AAGAATGTGTTTTTGGT-C
122 ATGTATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * ** *
1279 CTAATCTTGAAAAGAATGGAGACTGTTTAACAAGAAT-CAAGCATGTCTCATTTTAAAGTGCAAA
1 CTAATCATGAAAAGAATGGAGA-TCTAT-ACGAGAATCCATGTTTGTCTCA-TTTAAAGCGC-AA
* ** * * * * ** *
1343 CTTTGATTTTAGGGAAAATAAG-GCAAAGAAA-AG-ATTCATGCAAAAGAAAACCATCAATATC-
62 CTTTGATTTTA--CAAAATTGGTGGAAA-AAAGCGTA-TCTTGCGAAACCAAAGCATCAATATCA
* ** * * *
1404 TGCATCCTGAGGAGGAGAATGTGTTTATAGTGC
123 TGTATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * * * *
1437 CTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCAACGACTT
1 CTAATCATGAAAAGAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAGC-GCAACTT
* **
1502 AGA-TTTACACAAATTGGTGGACGAAAGCGTA-CTTTGCGAAACCAAAGCATCAATATCATGTAT
65 TGATTTTACA-AAATTGGTGGAAAAAAGCGTATC-TTGCGAAACCAAAGCATCAATATCATGTAT
* *
1565 -AT-ATAAGAAGAGACTATGTTAATGGTGC
128 CCTGATAAGAAGA-A-TATGTTTATGGTGC
* * * * * * * *
1593 CAAATACA-GAAAAG-ATGGGGAT-TAGTAAGAGTATTCATGTTTGTCTTATTTAAAG-ACAACG
1 CTAAT-CATGAAAAGAATGGAGATCTA-TACGAGAATCCATGTTTGTCTCATTTAAAGCGCAACT
* * * * * *
1654 TTGATTCTATCAATAA-CGGCGGAAAGACAAGC---TCTTGCGACACCAAAGCATCAATGTCGTG
64 TTGATTTTA-CAA-AATTGGTGGAAA-A-AAGCGTATCTTGCGAAACCAAAGCATCAATATCATG
* * *
1715 TATCCT-ATCCTAATGAAAGGAATGTGTTTGTGGTTC
125 TATCCTGA---TAA-G-AA-GAATATGTTTATGGTGC
* * * * ** *
1751 CTAATCTTGAAAA-AAAGGAGA-CTGTTACGAGAATCAATGCATGTCTCATTTAAAGTGCAAACT
1 CTAATCATGAAAAGAATGGAGATCT-ATACGAGAATCCATGTTTGTCTCATTTAAAGCGC-AACT
* ** * * * * * ** *
1814 TTGATTTTATGGAAAATAAG-GCAAAGAAAG-ATTTCGATGCAAAAGAAAACCATCAATATC-TG
64 TTGATTTTA--CAAAATTGGTGGAAA-AAAGCGTATC-TTGCGAAACCAAAGCATCAATATCATG
* ** * * *
1876 CATCCTGAGGAGGAGAATGTGTTTATAGTGC
125 TATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * * *
1907 CTAATCATGAAATG-ATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCGCGGACTT
1 CTAATCATGAAAAGAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAGCGC-AACTT
* *
1971 AGATTTTACACAAATTGGTGGGAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTATC
65 TGATTTTACA-AAATTGGTGGAAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTATC
*
2036 CAT-ATAAGAAGACTATGTTTATGGTGC
129 C-TGATAAGAAGAATATGTTTATGGTGC
* * * * * * * * *
2063 CAAATCCA-GAAAAGAATGGGGAT-TAGTAAGAGTATTCTTGTTTGTCTTATTTAAA-AG-ACAT
1 CTAAT-CATGAAAAGAATGGAGATCTA-TACGAGAATCCATGTTTGTCTCATTTAAAGCGCA-AC
* * * * * *
2124 TTTGATTCTATCAAAA-TGGTGGAAAGACAAGCTTCTCTTGCGACACTAAAGCATCAATGTCATG
63 TTTGATTTTA-CAAAATTGGTGGAAA-A-AAGCGTATCTTGCGAAACCAAAGCATCAATATCATG
* * * *
2188 TATCCTAATGAA-AGGAATGTGTTT-TGGTTC
125 TATCCTGAT-AAGAAGAATATGTTTATGGTGC
* * * ** *
2218 CTAATCTTGAAAAGAATGGAGA-CTGTTACGAGAATCAATGCATGTCTCATTTAAAGTGCAAAC-
1 CTAATCATGAAAAGAATGGAGATCT-ATACGAGAATCCATGTTTGTCTCATTTAAAGCGC-AACT
** * ** ** * * * ** *
2281 TTGATTTTATGGAAATAAGG-CAAAGAAAAGAATTTCAATGGCAAAAGAAAACCATCAATATCAT
64 TTGATTTTA-CAAAAT-TGGTGGAA-AAAAGCGTATC--TTGCGAAACCAAAGCATCAATATCAT
* * * * * * *
2345 GCATCCTGAGGAGGAGGAATGTGTTTATAGTGG
124 GTATCCTGA-TAAGAAGAATATGTTTATGGTGC
* * * * * * * * * *
2378 CTAATCATG-AATGACTGAAGATCCATACTAGAATCCATTTTTGTCCTCA-TTGAGGCACGACTT
1 CTAATCATGAAAAGAATGGAGATCTATACGAGAATCCATGTTTGT-CTCATTTAAAGCGCAACTT
* * **
2441 AGATTTTAACACCAATTGGTGGGACGAAAGCGTATC-TGCGAAACC-AAGCATCAATATCATGTT
65 TGATTTT-ACA-AAATTGGT-GGAAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATG-T
*
2504 ATCC-GTATAAGAAGACTATGTTTA--G-GC
126 ATCCTG-ATAAGAAGAATATGTTTATGGTGC
* * * * * * *
2531 CAAATACA-GAAAAGAATGGGGAT-TAGTAAGAGTATTCAT-TTTGTCTTATTTAAAAG-ACAAC
1 CTAAT-CATGAAAAGAATGGAGATCTA-TACGAGAATCCATGTTTGTCTCATTT-AAAGCGCAAC
* * * * * * * * *
2592 GTTGATTCTATCAATAA-CGGCGGAAAACAAGCTTTTCTTGCGACACCAAAGCATCAATGTCGTG
63 TTTGATTTTA-CAA-AATTGGTGGAAAA-AAGCGTATCTTGCGAAACCAAAGCATCAATATCATG
* * * * *
2656 TATCCTAATGAA-AGGAATGTGTTTTTGGTTC
125 TATCCTGAT-AAGAAGAATATGTTTATGGTGC
* * * ** * *
2687 CTAA-CTATGAAAAGAATGGAGA-CTTTAACAAGAATCAATGCATATCTCA-TTAAATGC-AAAC
1 CTAATC-ATGAAAAGAATGGAGATCTAT-ACGAGAATCCATGTTTGTCTCATTTAAA-GCGCAAC
* ** * ** * ** *
2748 TTTGATTTTATGGAAAATAAG-GCAAAGAAAGATTTCATCATGC-AAAAGAAACCATC---AT-A
63 TTTGATTTTA--CAAAATTGGTGGAAA-AAAG-CGT-ATCTTGCGAAACCAAAGCATCAATATCA
* ** * ** *
2807 -GCATCCTGAGGAGGAGAAGGTGTTTATAGTGC
123 TGTATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * *
2839 CTAATCATGAAATGAA---AGATCCATACTAGAATCCAT-TTTGTCTCCTTT-GAGGGCACGGAC
1 CTAATCATGAAAAGAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAGCGCA---AC
* **
2899 TTAGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCG-AACCAAAGCATCAATATCATGT
63 TTTGATTTTACA-AAATTGGT-GGAAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGT
*
2963 ATCC-GTATAAGAAGACTATGTTTATGGTGC
126 ATCCTG-ATAAGAAGAATATGTTTATGGTGC
* * * * * *
2993 C-AATACA-GAAAAAAGAATGGGGAT-TAGTAAGAGTATTCATGTTTGTCTTATTTAAAAG-ACA
1 CTAAT-CATG--AAAAGAATGGAGATCTA-TACGAGAATCCATGTTTGTCTCATTT-AAAGCGCA
* * * * * * *
3054 ACGTTGATTCTATCAATAA-CGGCGGAAAGACAAGC-TTTCTTGCGACACCAAAGCATCAATGTC
61 ACTTTGATTTTA-CAA-AATTGGTGGAAA-A-AAGCGTATCTTGCGAAACCAAAGCATCAATATC
* * * * *
3117 ATGTATCCTAATGAA-AGGAATGTGTTT-T-TTTC
122 ATGTATCCTGAT-AAGAAGAATATGTTTATGGTGC
* * * * ** * *
3149 CTAATCTTGAAAAGAATGGAGA-CTTTACAAGAATCAATGCATATCTCATTTAAAGTGCAAACTT
1 CTAATCATGAAAAGAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAGCGC-AACTT
* * ** * * * * ** *
3213 TGATTTTATGGAAAATAAGG-CAAAGAAAAG-ATTTCAATGCAAAAGAAAACCATCAATATCATG
65 TGATTTTA--CAAAAT-TGGTGGAA-AAAAGCGTATC-TTGCGAAACCAAAGCATCAATATCATG
* ** * * *
3276 CATCCTGAGGAGGAGAATGTGTTTATAGTGC
125 TATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * * * *
3307 CTAATCATGAAATGAATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCACGGACTT
1 CTAATCATGAAAAGAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAGCGC-AACTT
* ***
3372 AGATTTTACACAAATTGGTGGGGCGAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTAT
65 TGATTTTACA-AAATTGGT-GGAAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTAT
*
3437 CC-GTATAAGAAGACTATG-TTATGGTGC
128 CCTG-ATAAGAAGAATATGTTTATGGTGC
* * * * * * *
3464 CAAAATCA-GAAAAGAATGGGGAT-TAGTAAGAGTATTCATGTTTGTCTTATTTAAAAG-ACAA-
1 C-TAATCATGAAAAGAATGGAGATCTA-TACGAGAATCCATGTTTGTCTCATTT-AAAGCGCAAC
* * * * *
3525 -TTGATTCTATC--AA-TGGTGGAAAGACAAGCTTCTCTTGCGACACCAAAGCA-CAATGTCATG
63 TTTGATTTTA-CAAAATTGGTGGAAA-A-AAGCGTATCTTGCGAAACCAAAGCATCAATATCATG
* * * *
3585 TATCCTAATGA-AAGGA-ATGTGTT-TGGTTC
125 TATCCTGATAAGAAGAATATGT-TTATGGTGC
* * * ** *
3614 CTAATCTTGAAAAGAATGGAGA-CTGTACGAGAATCAATGCATGTCTCATTTAAAGTGCAAAC-T
1 CTAATCATGAAAAGAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAGCGC-AACTT
** * ** * * * * ** * * *
3677 TGATTTTATGGAAATAAGG-CAAAGAAAAG-ATTTCGATGCAAAAGAAAACCATCAATATCTTGC
65 TGATTTTA-CAAAAT-TGGTGGAA-AAAAGCGTATC-TTGCGAAACCAAAGCATCAATATCATGT
** * * *
3740 ATCCTGAGGAGGAGAATGTG-TTATAGTGC
126 ATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * * * *
3769 CTAATCATGAAATGAGTGAAGA-CTCATACTAGAATCCATGTTTGTCTCGTTTGAGGCGCGGACT
1 CTAATCATGAAAAGAATGGAGATCT-ATACGAGAATCCATGTTTGTCTCATTTAAAGCGC-AACT
* *
3833 TAGATTTTACACAAATTGGTGGGAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTAT
64 TTGATTTTACA-AAATTGGTGGAAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTAT
*
3898 CCAT-ATAAGAAG-ACATGTTTATGGTGC
128 CC-TGATAAGAAGAATATGTTTATGGTGC
* * * * * * *
3925 CAAATACA-GAAAAGAATGGGGAT-TAGTAAGAGTATTCATGTTTGTCT-ATTTAAAAG-ACAAT
1 CTAAT-CATGAAAAGAATGGAGATCTA-TACGAGAATCCATGTTTGTCTCATTT-AAAGCGCAAC
* * * * *
3986 TTTGATTCTATCAATAA-TGGTGGAAAGACAAGCTTCTCTTGCGACACC-AAGCATCAATGTCAT
63 TTTGATTTTA-CAA-AATTGGTGGAAA-A-AAGCGTATCTTGCGAAACCAAAGCATCAATATCAT
* * * * *
4049 GTATCCTAATGA-AAGGA-ATGTTTTTGGTTC
124 GTATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * ** *
4079 CTAATCTTGAAAAAAATGGAGA-CTGTTACGAGAATCAATGCATGTCTCATTTAAAGTGCAAAC-
1 CTAATCATGAAAAGAATGGAGATCT-ATACGAGAATCCATGTTTGTCTCATTTAAAGCGC-AACT
* * ** * * * * ** *
4142 TTGATTTTATGGAAAAATAGG-CAAAGAAAAG-ATTTCGATGCAAAAGAAAACCATCAATATC-T
64 TTGATTTTA---CAAAATTGGTGGAA-AAAAGCGTATC-TTGCGAAACCAAAGCATCAATATCAT
* ** * * *
4204 GCATCCTGAGGAGGAGAATGTGTTTATAGTGC
124 GTATCCTGATAAGAAGAATATGTTTATGGTGC
* * * * * * * *
4236 CTAATCATGAAATG-ATGAAGATCCATACTAGAATCCATGTTTGTCTCATTTGAGGCACGGACTT
1 CTAATCATGAAAAGAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAGCGC-AACTT
* **
4300 AGATTTTACACAAATTGGTGGGACGAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTAT
65 TGATTTTACA-AAATTGGT-GGAAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTAT
*
4365 CCT-ATAAGAAGACTATGTTTATGGTGC
128 CCTGATAAGAAGAATATGTTTATGGTGC
*
4392 CCAA-CA--AAAAGAATGG
1 CTAATCATGAAAAGAATGG
4408 GGATTAGTAA
Statistics
Matches: 3003, Mismatches: 893, Indels: 663
0.66 0.20 0.15
Matches are distributed among these distances:
147 1 0.00
148 11 0.00
149 58 0.02
150 35 0.01
151 53 0.02
152 91 0.03
153 126 0.04
154 259 0.09
155 426 0.14
156 790 0.26
157 462 0.15
158 379 0.13
159 152 0.05
160 91 0.03
161 41 0.01
162 28 0.01
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (155 bp):
CTAATCATGAAAAGAATGGAGATCTATACGAGAATCCATGTTTGTCTCATTTAAAGCGCAACTTT
GATTTTACAAAATTGGTGGAAAAAAGCGTATCTTGCGAAACCAAAGCATCAATATCATGTATCCT
GATAAGAAGAATATGTTTATGGTGC
Done.