Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1215
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: 6841
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Found at i:782 original size:388 final size:387
Alignment explanation
Indices: 40--801 Score: 1083
Period size: 392 Copynumber: 2.0 Consensus size: 387
30 AAGAAATCGA
* *
40 GGCTTGCCTTATTTAAATATGAACTTTGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATG
1 GGCTTGCCTTATTTAAAGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATG
*
105 CAAATAAAATCATCAATATCATTTATCCTAATGAGCAGAATGGTTTATAGTACCTAATCAAAATG
66 CAAAGAAAATCATCAATATCATTTATCCTAATGAGCAGAATGGTTTATAGTACCTAATCAAAATG
* * *
170 AACGAAGATCTTTACTAGAATCCATGTTTGTCTCATTTGAGGCACGAACTAGATTTAGAAAAATT
131 AACGAAGATCATTACAAGAATCCATGTTTGTCTCATTTGAGGCACGAACTAGATTTACAAAAATT
* * * *
235 GGTGGGAAAAATGCCTTTCTTGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTA
196 GGTAGGAAAAATGCCTTTCCTGCAAAACCAAAGCATCAATATGATCTATCCAAATGAGAAGACTA
* * *
300 TGTTTATGGTGTCTAATCTTGAAAAGAACAGGATTAGTATGAGTATTCATGTTTGTAATATTTAA
261 CGTTTATGGTGCCTAATCCTGAAAAGAACAGGATTAGTATGAGTATTCATGTTTGTAATATTTAA
365 GAGACAAACTTTGATTCTATCAAAAACGGTGCAAA-AAAAGCTTTTCTTGCAACCCCAAACGT
326 GAGACAAACTTTGATTCTATC-AAAACGGTGCAAAGAAAAGCTTTTCTTGCAACCCCAAACGT
*
427 GGCTTGCCTTATTTAAGGGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCAT
1 GGCTTGCCTTATTTAA-AGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCAT
* * **
492 GCAAAAGAAAATCATCAATATCA-TTATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACC
65 GC-AAAGAAAATCATCAATATCATTTATCCTAATGAGCAGAATG-GTTTATAGTACCTAAT---C
* * *
556 AAAA-GAATGAATATCATTACAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTA
125 AAAATGAACGAAGATCATTACAAGAATCCATGTTTGTCTCATTTGAGGCACGAAC-TAGA-TTTA
* * * *
620 CAAAAATTGGTAGGAAAAA-GCCTTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGA
188 CAAAAATTGGTAGGAAAAATGCCTTTCCTGCAAAACCAAAGCATCAATATGATCTATCCAAATGA
* **
684 GGAGACTACG-TTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGCT-TGAGTATTCATGTTTG
253 GAAGACTACGTTTATGGTGCCTAATCCTGAAAAGAA-CAGGATTAG-TATGAGTATTCATGTTTG
* * *
747 T-CT-TTTAAGAGACAAACTTTGATTTTATC-AAACGGTGGAAAGAAAAGCTTTTCTT
316 TAATATTTAAGAGACAAACTTTGATTCTATCAAAACGGTGCAAAGAAAAGCTTTTCTT
802 ACGACACCAA
Statistics
Matches: 333, Mismatches: 31, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
387 16 0.05
388 76 0.23
389 46 0.14
390 25 0.08
391 69 0.21
392 79 0.24
393 22 0.07
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (387 bp):
GGCTTGCCTTATTTAAAGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATG
CAAAGAAAATCATCAATATCATTTATCCTAATGAGCAGAATGGTTTATAGTACCTAATCAAAATG
AACGAAGATCATTACAAGAATCCATGTTTGTCTCATTTGAGGCACGAACTAGATTTACAAAAATT
GGTAGGAAAAATGCCTTTCCTGCAAAACCAAAGCATCAATATGATCTATCCAAATGAGAAGACTA
CGTTTATGGTGCCTAATCCTGAAAAGAACAGGATTAGTATGAGTATTCATGTTTGTAATATTTAA
GAGACAAACTTTGATTCTATCAAAACGGTGCAAAGAAAAGCTTTTCTTGCAACCCCAAACGT
Found at i:1661 original size:394 final size:394
Alignment explanation
Indices: 894--1667 Score: 1158
Period size: 394 Copynumber: 2.0 Consensus size: 394
884 CAAGAATCGA
* * *
894 GGCTTGCCTTATTTAAAATATGAACTTTGATTTTAAGGAAAATAGGGTAAAGAAAAGATTTTCAT
1 GGCTTGCCTTATTTAAAAGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCAT
* *
959 GCAAAATAAAATCATCAATATCATTTATCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACA
66 GCAAAAGAAAATCATCAATATCATATATCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACA
* * * *
1024 AAATGAACGAAGATCTTTACTAGGATCCATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTGA
131 AAATGAACGAAGATCATTACAAGAATCCATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTCA
* * * *
1089 AAAATTGGTGGGAAAAATGCCTTTCTTGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGA
196 AAAATTGGTAGGAAAAATGCCTTTCCTGCAAAACCAAAGCATCAATATGATCTATCCAAATGAGA
* * *
1154 AGACTATGTTTATGGTGTCTAATCTTGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTCA
261 AGACTACGTTTATGGTGCCTAATCCTGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTCA
1219 TATTTAAGAGACAAACTTTGATTCTATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAA
326 TATTTAAGAGACAAACTTTGATTCTATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAA
1284 ACGT
391 ACGT
**
1288 GGCTTGCCTTATTTAAGGGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCAT
1 GGCTTGCCTTATTTAAAAGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCAT
* * ** *
1353 GCAAAAGAAAATCATCAATATCATATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACC
66 GCAAAAGAAAATCATCAATATCATATATCCTAATGAGCAGAATGTGTTTATAGTACCTAATCA-C
* * *
1418 AAAA-GAATGAATATCATTACAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTA
130 AAAATGAACGAAGATCATTACAAGAATCCATGTTTGTCTCATTTGAGGCACGAACTTAGACTTT-
* * * *
1482 CAAAAATTGGTAGGAAAAA-GCCTTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGA
194 CAAAAATTGGTAGGAAAAATGCCTTTCCTGCAAAACCAAAGCATCAATATGATCTATCCAAATGA
* ** *
1546 GGAGACTACG-TTATGGTGCCTAATCCTGAAAAGAATGGGGATTAGTTTGAGTATTCATGTTTGT
259 GAAGACTACGTTTATGGTGCCTAATCCTGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGT
* * * *
1610 CGTATTTAAGAGACAAACTTTGATTTTATCCAAAACGGTGGAAAGAAAAGCTTTTCTT
324 CATATTTAAGAGACAAACTTTGATTCTATCAAAAACGGTGCAAA-AAAAGCTTTTCTT
1668 ACGACACCAA
Statistics
Matches: 339, Mismatches: 38, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
393 89 0.26
394 228 0.67
395 22 0.06
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (394 bp):
GGCTTGCCTTATTTAAAAGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCAT
GCAAAAGAAAATCATCAATATCATATATCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACA
AAATGAACGAAGATCATTACAAGAATCCATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTCA
AAAATTGGTAGGAAAAATGCCTTTCCTGCAAAACCAAAGCATCAATATGATCTATCCAAATGAGA
AGACTACGTTTATGGTGCCTAATCCTGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTCA
TATTTAAGAGACAAACTTTGATTCTATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAA
ACGT
Found at i:1887 original size:158 final size:156
Alignment explanation
Indices: 1288--1887 Score: 372
Period size: 158 Copynumber: 3.8 Consensus size: 156
1278 CCCCAAACGT
* * *
1288 GGCTTGCCTTATTTAAGGGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCAT
1 GGCTTGCCTTATTTAAGAGACGAACTTTGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCAT
* * * * ** * **
1353 GCAAAAGAAAATCATCAATATCATATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACC
66 GCAAAACAAAAGCATCAATATCATGTATCCTAATGAGGAGAATGTG-TTATAGTACCTAATCATG
* *
1418 AAAAGAATGAATAT-CATTACAAGAATCCA
130 AAAAGAATGGAGATGC--TACAAGAAT-CA
* * * * * ** * * * * * **
1447 TGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACA--AAAAT-TGG-TAGGAAAAAGCCTTTC
1 GGCTTGCCTTATTTAAGAGACGAACTTTGATTTTA-AGGAAAATAGGGCAAAG-AAAAGATTTTC
* * * * * * ** * * *
1508 CTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGCCTAATCCT
64 ATGCAAAACAAAAGCATCAATATCATGTATCCTAATGAGGAGAATGTGTTATAGTACCTAATCAT
* *** *
1573 GAAAAGAATGGGGATTAG-TTTGAGTATTCA
129 GAAAAGAATGGAGA-T-GCTACAAG-AATCA
* * * * * *** * * * *
1603 TGTTTGTCGTATTTAAGAGACAAACTTTGATTTTATCCAAAA-CGGTGGAAAGAAAAGCTTTTCT
1 GGCTTGCCTTATTTAAGAGACGAACTTTGATTTTAAGGAAAATAGG-GCAAAGAAAAGATTTTCA
* * * * * * * * * *
1667 TACGACACCAAAGCATCAATATCATGCATCCTAATGAAG-GAATGTGTTTTGGCATCCAAATCAT
65 TGCAAAACAAAAGCATCAATATCATGTATCCTAATGAGGAGAATGTGTTATAGTA-CCTAATCAT
1731 GAAAAGAATGGAGACTGCTACAAGAATCGA
129 GAAAAGAATGGAGA-TGCTACAAGAATC-A
*
1761 GGCTTGCCTTATTTAA-AGGATGAACTTTGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCA
1 GGCTTGCCTTATTTAAGA-GACGAACTTTGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCA
* * * *
1825 TGCAAAATAAAATCATCAATATCATTTATCCTAATGAGCAGAATGTGTTATAGTACCTAATCA
65 TGCAAAACAAAAGCATCAATATCATGTATCCTAATGAGGAGAATGTGTTATAGTACCTAATCA
1888 CAAAAATGAA
Statistics
Matches: 322, Mismatches: 102, Indels: 35
0.70 0.22 0.08
Matches are distributed among these distances:
156 56 0.17
157 69 0.21
158 156 0.48
159 40 0.12
160 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (156 bp):
GGCTTGCCTTATTTAAGAGACGAACTTTGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCAT
GCAAAACAAAAGCATCAATATCATGTATCCTAATGAGGAGAATGTGTTATAGTACCTAATCATGA
AAAGAATGGAGATGCTACAAGAATCA
Found at i:1961 original size:867 final size:868
Alignment explanation
Indices: 1--6841 Score: 12588
Period size: 867 Copynumber: 7.9 Consensus size: 868
1 CAAATCATGAAAAGAATGGAGACTGCTACAAGAAATCGAGGCTTGCCTTATTT-AAATATGAACT
1 CAAATCATGAAAAGAATGGAGACTGCTACAAG-AATCGAGGCTTGCCTTATTTAAAATATGAACT
65 TTGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGC-AAATAAAATCATCAATATCATTT
65 TTGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTT
*
129 ATCCTAATGAGCAGAATG-GTTTATAGTACCTAAT--CAAAATGAACGAAGATCTTTACTAGAAT
130 ATCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGAT
191 CCATGTTTGTCTCATTTGAGGCACGAAC-TAGA-TTTAGAAAAATTGGTGGGAAAAATGCCTTTC
195 CCATGTTTGTCTCATTTGAGGCACGAACTTAGACTTT-GAAAAATTGGTGGGAAAAATGCCTTTC
254 TTGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCT
259 TTGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCT
319 TGAAAAGAACA-GGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTCT
324 TGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTCT
383 ATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGAT
389 ATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGAT
448 GAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATAT
454 GAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATAT
513 CAT-TATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCATTACA
519 CATATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCATTACA
577 AGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAAAGCC
584 AGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAAAGCC
642 TTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGCCTAA
649 TTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGCCTAA
707 TCCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTC-T-TTTAAGAGACAAACTTTGAT
714 TCCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACTTTGAT
770 TTTAT-C-AAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCATCCT
779 TTTATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCATCCT
833 AATGAATGGAA--TGTTTTGGCATC
844 AATGAATGGAATGTGTTTTGGCATC
856 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAATATGAACTT
1 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAATATGAACTT
*
921 TGATTTTAAGGAAAATAGGGTAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
66 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
986 TCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGATC
131 TCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGATC
1051 CATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTGAAAAATTGGTGGGAAAAATGCCTTTCTT
196 CATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTGAAAAATTGGTGGGAAAAATGCCTTTCTT
1116 GCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCTTG
261 GCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCTTG
*
1181 AAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTCATATTTAAGAGACAAACTTTGATTCTAT
326 AAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTCTAT
1246 CAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGATGA
391 CAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGATGA
1311 ACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATATCA
456 ACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATATCA
1376 TATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCATTACAAG
521 TATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCATTACAAG
1441 AATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAAAGCCTT
586 AATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAAAGCCTT
1506 TCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGCCTAATC
651 TCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGCCTAATC
*
1571 CTGAAAAGAATGGGGATTAGTTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACTTTGATTT
716 CTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACTTTGATTT
1636 TATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCATCCTAA
781 TATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCATCCTAA
1701 TGAA-GGAATGTGTTTTGGCATC
846 TGAATGGAATGTGTTTTGGCATC
**
1723 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAGGATGAACTT
1 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAATATGAACTT
1788 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
66 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
1853 TCCTAATGAGCAGAATGTG-TTATAGTACCTAATCACAAAAATGAACGAAGATCTTTACTAGGAT
131 TCCTAATGAGCAGAATGTGTTTATAGTACCTAATCAC-AAAATGAACGAAGATCTTTACTAGGAT
1917 CCATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTGAAAAATTGGTGGGAAAAATGCCTTTCT
195 CCATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTGAAAAATTGGTGGGAAAAATGCCTTTCT
1982 TGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCTT
260 TGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCTT
*
2047 GAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTCATATTTAAGAGACAAACTTTGATTCTA
325 GAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTCTA
2112 TCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGATG
390 TCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGATG
2177 AACTTTGATTGTAAGG-AAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATATC
455 AACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATATC
2241 ATATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCATTACAA
520 ATATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCATTACAA
2306 GAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAAAGCCT
585 GAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAAAGCCT
2371 TTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTATATGAGGAGACTACGTTATGGTGCCTAA
650 TTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTA-ATGAGGAGACTACGTTATGGTGCCTAA
* *
2436 TTCTTGAAAAGAATGGGGATTAGTTTGAGTATTCAATG--T-TCG----T-A-A-ACAAACTTTG
714 -TCCTGAAAAGAATGGGGATTAGCTTGAGTATTC-ATGTTTGTCGTATTTAAGAGACAAACTTTG
2491 ATTTTATCGCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCAT
777 ATTTTATC-CAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCAT
*
2556 CCTAATGAA-GGGATGTGTTTTGGCATC
841 CCTAATGAATGGAATGTGTTTTGGCATC
*
2583 CAAATCATGAAAAGAATGGAGA-TGCTACAAGAATCGAGGCTTGCCTTATTTAAAGTATGAACTT
1 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAATATGAACTT
*
2647 TGATTTTAAGGAAAATAGGG-TAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
66 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
2711 TCCTAATGAGCAGAATGTGTTTATAGTAACCTAATCACAAAATGAACGAAGATCTTTACTAGGAT
131 TCCTAATGAGCAGAATGTGTTTATAGT-ACCTAATCACAAAATGAACGAAGATCTTTACTAGGAT
2776 CCA-GTTTGTCTCATTTGAGGCACGAACTTAGACTTTTGAAAAATTGGTGGGAAAAATGCCTTTC
195 CCATGTTTGTCTCATTTGAGGCACGAACTTAGAC-TTTGAAAAATTGGTGGGAAAAATGCCTTTC
*
2840 -TGC-AAACCAAAAGCCTCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATC
259 TTGCAAAACC-AAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATC
2903 TTGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTC
323 TTGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTC
2968 TATC-AAAACGGTGCAAAAAAAGCTTTTCTTGCAA-CCCAAACGTGGCTTGCCTTATTTAAGGGA
388 TATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGA
3031 TGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAG-AAATCATCAATA
453 TGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATA
3095 TCATATATCCTATTGAGGAGAATGTGTTTATAGTGGTCTAATGACCAAAAGAA-GAATATCATTA
518 TCATATATCCTATTGAGGAGAATGTGTTTATAGT-GTCTAATGACCAAAAGAATGAATATCATTA
3159 CAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAAAA
582 CAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGG-AAAAA
3224 GCC-TTCCTGCGAAACCAAAGCGTCAATATGATGTATCC-AATGAGGAGACTACGTTATGGTGCC
646 GCCTTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGCC
3287 TAATCCTGAAAAGAATGGGGATTAGCTTGAGTATTCATG-TTGTCGTATTTAAGAG-CAAACTTT
711 TAATCCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACTTT
3350 GATTTTATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCAT
776 GATTTTATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCAT
*
3415 CCTAATGAA-GGAAATGTATTTTGGCATC
841 CCTAATGAATGG-AATGTGTTTTGGCATC
* * **
3443 CAAATCAT-TAAAGAATGGAGACTGCTAGAAG-ATCGAGGCTTGCCTTATTTAAAGGATGAACTT
1 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAATATGAACTT
3506 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCA-TTA
66 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
3570 TCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGATC
131 TCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGAT-
3635 CCACTGTTTGTCTCATTTGAGGCACGAACTTAGACTTTTGAAAAATTGGTGGGAAAAATGCCTTT
195 CCA-TGTTTGTCTCATTTGAGGCACGAACTTAGAC-TTTGAAAAATTGGTGGGAAAAATGCCTTT
3700 CTTGC-AAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATC
258 CTTGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATC
3764 TTGAAAAGAACAGGGATTAGTATGAGTATTCATG-TTGTAATATTTAAGAGACAAACTTTGATTC
323 TTGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTC
3828 TATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAA-CCCAAACGTGGCTTGCCTTATTTAAGGGA
388 TATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGG-
*
3892 ATGAACTTTGATTAT-AGGAAAATAGGGCAAAGAAAAAGATTTTCATGC-AAAGAAAATCATCAA
452 ATGAACTTTGATTGTAAGGAAAATAGGGCAAAG-AAAAGATTTTCATGCAAAAGAAAATCATCAA
3955 TATTCATATATCCTATTGAGGAGAATGTGTTTATAGGTGTCTAATGACCAAAAGAATGAATATCA
516 TA-TCATATATCCTATTGAGGAGAATGTGTTTATA-GTGTCTAATGACCAAAAGAATGAATATCA
*
4020 TTACAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACATAAAAATTGGTAGAA
579 TTACAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTAC--AAAAATTGGTAGGA
4085 AAAAGCCTTTCCTGCGAAACCAAAGCGTC-ATATGATGTATCCTAATGAGGAGACTACGTTATGG
642 AAAAGCCTTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGG
4149 TGCCTAATCCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAA
707 TGCCTAATCCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAA
4214 CTTTGATTTTATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACC-AAGCATCAATATCAT
772 CTTTGATTTTATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCAT
4278 GCATCCTAATGAATGGAATGTGTTTTGGCATC
837 GCATCCTAATGAATGGAATGTGTTTTGGCATC
*
4310 CAAATCATGAAAA-AATGGAGACTGCTACAATAAATCGAGGCTTGCCTTATTTAAAATATGAACT
1 CAAATCATGAAAAGAATGGAGACTGCTACAA-GAATCGAGGCTTGCCTTATTTAAAATATGAACT
* *
4374 TTGATTTT-AGGAAAAATAGCCGTAAAGAAAAGATTTTCATGCAAAATAAAATCATC-ATATCAT
65 TTGATTTTAAGG-AAAATAG-GGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCAT
*
4437 TTATCCTAATGAGCAGAATGTATTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGG
128 TTATCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGG
4502 AAT-CACTGTTTGTCTCATTTGAGGCACGAACTTAGACTTTTGAAAAATTGGT-GGAAAAATGCC
193 -ATCCA-TGTTTGTCTCATTTGAGGCACGAACTTAGAC-TTTGAAAAATTGGTGGGAAAAATGCC
4565 TTTCTTGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAA-ACTATGTTTATGGTGTCTA
255 TTTCTTGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTA
*
4629 ATC-TGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATCTTTAAGAGAC-AACTTTGA
320 ATCTTGAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGA
4692 TTCTATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAG
385 TTCTATCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAG
4757 GGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCA
450 GGATGAACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCA
4822 ATATC--ATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCAT
515 ATATCATATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCAT
4885 TACAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAA
580 TACAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAA
4950 AGCCTTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGC
645 AGCCTTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGC
5015 CTAATCCTGAAAAGAAT-GGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACTT
710 CTAATCCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACTT
5079 TGATTTTATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCA
775 TGATTTTATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCA
5144 TCCTAATGAATGGAATGTGTTTTGGCATC
840 TCCTAATGAATGGAATGTGTTTTGGCATC
5173 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAATATGAACTT
1 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAATATGAACTT
5238 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
66 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
5303 TCCTAATGAGCAGAA--TGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGATC
131 TCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGATC
5366 CATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTAGAAAAATTGGTGGGAAAAATGCCTTTCT
196 CATGTTTGTCTCATTTGAGGCACGAACTTAGACTTT-GAAAAATTGGTGGGAAAAATGCCTTTCT
5431 TGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCTT
260 TGCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCTT
*
5496 GAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTCATATTTAAGAGACAAACTTTGATTCTA
325 GAAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTCTA
5561 TCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGATG
390 TCAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGATG
5626 AACATTGTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAAT
455 AAC--T-TTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAAT
5691 ATCATATTTATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCAT
517 ATCATA--TATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCAT
5756 TACAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAA
580 TACAAGAATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGG-AAA
5821 AAGCCTTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTG
644 AAGCCTTTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTG
5886 CCTAATCCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCG---TTAAGAGACAAACT
709 CCTAATCCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACT
5948 TTGATTTTATCCAAAACGGTGGAAAGAAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATG
774 TTGATTTTATCCAAAACGGTGGAAAG-AAAAGCTTTTCTTACGACACCAAAGCATCAATATCATG
*
6013 CATCCTAATGAAGGGAATGTGTTTTGGCATC
838 CATCCTAATGAATGGAATGTGTTTTGGCATC
6044 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTT-AAATATGAACTT
1 CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAATATGAACTT
6108 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
66 TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
6173 TCCTAATGAGCAGAA--TGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGATC
131 TCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGATC
6236 CATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTGAAAAATTGGTGGGAAAAATGCCTTTCTT
196 CATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTGAAAAATTGGTGGGAAAAATGCCTTTCTT
6301 GCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCTTG
261 GCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCTTG
6366 AAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTCTAT
326 AAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTCTAT
6431 CAAAAACGGTGC-AAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGATGA
391 CAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGATGA
6495 ACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATATCA
456 ACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATATCA
6560 TATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCATTACAAG
521 TATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCATTACAAG
6625 AATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTAC-AAAATTGGTAGGAAAAAAGCCT
586 AATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGG-AAAAAGCCT
6689 TTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGCCTAAT
650 TTCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGCCTAAT
6754 CCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACTTTGATT
715 CCTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACTTTGATT
6819 TTATCCAAAACGGTGGAAAGAAA
780 TTATCCAAAACGGTGGAAAGAAA
Statistics
Matches: 5849, Mismatches: 44, Indels: 177
0.96 0.01 0.03
Matches are distributed among these distances:
852 3 0.00
853 32 0.01
854 50 0.01
855 84 0.01
856 239 0.04
857 110 0.02
858 254 0.04
859 368 0.06
860 387 0.07
861 518 0.09
862 602 0.10
863 393 0.07
864 266 0.05
865 158 0.03
866 397 0.07
867 743 0.13
868 267 0.05
869 309 0.05
870 314 0.05
871 240 0.04
872 86 0.01
873 29 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (868 bp):
CAAATCATGAAAAGAATGGAGACTGCTACAAGAATCGAGGCTTGCCTTATTTAAAATATGAACTT
TGATTTTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAATAAAATCATCAATATCATTTA
TCCTAATGAGCAGAATGTGTTTATAGTACCTAATCACAAAATGAACGAAGATCTTTACTAGGATC
CATGTTTGTCTCATTTGAGGCACGAACTTAGACTTTGAAAAATTGGTGGGAAAAATGCCTTTCTT
GCAAAACCAAAGCATCATTATGATCTATTCAAATGAGAAGACTATGTTTATGGTGTCTAATCTTG
AAAAGAACAGGGATTAGTATGAGTATTCATGTTTGTAATATTTAAGAGACAAACTTTGATTCTAT
CAAAAACGGTGCAAAAAAAGCTTTTCTTGCAACCCCAAACGTGGCTTGCCTTATTTAAGGGATGA
ACTTTGATTGTAAGGAAAATAGGGCAAAGAAAAGATTTTCATGCAAAAGAAAATCATCAATATCA
TATATCCTATTGAGGAGAATGTGTTTATAGTGTCTAATGACCAAAAGAATGAATATCATTACAAG
AATCCATGTTTGTCTCATTTGAGTCACGAACTTAGACTTTACAAAAATTGGTAGGAAAAAGCCTT
TCCTGCGAAACCAAAGCGTCAATATGATGTATCCTAATGAGGAGACTACGTTATGGTGCCTAATC
CTGAAAAGAATGGGGATTAGCTTGAGTATTCATGTTTGTCGTATTTAAGAGACAAACTTTGATTT
TATCCAAAACGGTGGAAAGAAAAGCTTTTCTTACGACACCAAAGCATCAATATCATGCATCCTAA
TGAATGGAATGTGTTTTGGCATC
Done.