Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019705.1 Corchorus olitorius cultivar O-4 contig19738, whole genome shotgun sequence
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: 46717
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:680 original size:330 final size:330
Alignment explanation
Indices: 1--683 Score: 1050
Period size: 331 Copynumber: 2.1 Consensus size: 330
*
1 AATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTGGGGGTTGAATAGTACAGTT
1 AATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTGGGGGTTGAATAGTACAATT
*
66 TTTCTGAATATTGTGGCAAAAAATTAAGAAAAAACCTTTTGGGTAAGTTTTCGCCAAAATTTTAA
66 TTTCTGAATATTGTGGCAAAAAATTAAGAAAAAACCTTTTGGGTAAGTTTTCGCCAAAATTTCAA
* *
131 CCGAAATCGTGTATACATCACAGTTTTTGGCTAAAAACGCGATCTGGAGCCCCAGCTCAATTTTG
131 CCGAAATCGTGTATACATCACAGTTTTTGGCTAAAAACGCGATCCGGAGCCACAGCTCAATTTTG
* * **
196 CTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTAATCTAACCAAATTTTAGCCACAAT
196 CTTGATTTTTGGCACAAAGACTACTTCAAATATATATATTAATCTAACCAAAACTTAGCCACAAT
*
261 GGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATAAATTCGA
261 GGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGA
326 GAAAA
326 GAAAA
* *
331 AATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTTGGGGTTGAATAGTATAATT
1 AATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTGGGGGTTGAATAGTACAATT
* * * *
396 TTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAA-CTTTTCGGGTCAGTTTT-G-CAAAATTTCA
66 TTTCTGAATATTGTGGCAAAAAATTAAGAAAAAACCTTTT-GGGTAAGTTTTCGCCAAAATTTCA
* * * **
458 GCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAATGCGTTCCGGAGCCATGGCTCAAT
130 ACCGAAATCGTGTA-T-A-CATCACAGTTTTTGGCTAAAAACGCGATCCGGAGCCACAGCTCAAT
* * * *
523 TTTGCTTGATTTTTGGCACAAATACTACTTCAAATATATATTTTCATTTAACCAAAACTTAGCCA
192 TTTGCTTGATTTTTGGCACAAAGACTACTTCAAATATATATATTAATCTAACCAAAACTTAGCCA
* * *
588 CAATGGATTTAAGGATTTGTTTTTACGAGCATTTTAATCTTGTTTTGATTTAATTAAAAATAAAT
257 CAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAAT
653 TCGA-AAAA
322 TCGAGAAAA
*
661 AATGGAAAAACAATATTGGAAGC
1 AATGGAAAAACGATATTGGAAGC
684 CGAAATCATG
Statistics
Matches: 321, Mismatches: 28, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
328 22 0.07
329 7 0.02
330 130 0.40
331 162 0.50
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (330 bp):
AATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTGGGGGTTGAATAGTACAATT
TTTCTGAATATTGTGGCAAAAAATTAAGAAAAAACCTTTTGGGTAAGTTTTCGCCAAAATTTCAA
CCGAAATCGTGTATACATCACAGTTTTTGGCTAAAAACGCGATCCGGAGCCACAGCTCAATTTTG
CTTGATTTTTGGCACAAAGACTACTTCAAATATATATATTAATCTAACCAAAACTTAGCCACAAT
GGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGA
GAAAA
Found at i:1219 original size:557 final size:557
Alignment explanation
Indices: 154--1227 Score: 1216
Period size: 557 Copynumber: 1.9 Consensus size: 557
144 TACATCACAG
* * *
154 TTTTTGGCTAAAAACGCGATCTGGAGCCCCAGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTA
1 TTTTTGGCTAAAAACGCGATCTAGAGCCCCAGCTCAATTTTACATGATTTTTGGCGCAAAGACTA
** *** * *
219 CTTCAAATATCTATATTAATCTAACCAAATTTTAGCCACAATGGATTTAAGGATTTGTTTTTACG
66 CTTCAAATATCTATATTAATCTAAAAAAATCCCAGCCACAATAGATTTAAAGATTTGTTTTTACG
* *
284 AGCATCTGAATTTTGTTTCGATTTAATTAAAAATAAATTCGAGAAAAAATGGAAAAACGATATTG
131 AGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAGAAAAAATGGAAAAACGATATTA
* * ** * *
349 GAAGCGTGAAAAACCATTTTAATTTTTTGGGGTTGAATAGTATAATTTTTCTGAGTATTGTGGCA
196 GAAGCGTGAAAAACCACTTTAATTTATTGGCATTGAATAGTATAATTTTTATGACTATTGTGGCA
* * * *
414 AAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTGCAAAATTTCAGCCGAAATCGTGTATTAACCA
261 AAAAATTGAGGAAAAACTTTCCGGATCAGTTTTGCAAAATTTCAGCCGAAACCGTGTACTAACCA
* * * * *
479 TCACAGTTTTTGGCTAAAAATGCGTTCCGGAGCCATGGCTCAATTTTGCTTGATTTTTGGCACAA
326 TCACAGTTTTAGGCTAAAAACGCGTTCAGGAGCCACGGCTCAATTTTGCATGATTTTTGGCACAA
* * * * * *
544 ATACTACTTCAAATATATATTTTCATTTAACCAAAACTTAGCCACAATGGATTTAAGGATTTGTT
391 AGACTACCTCAAATATATATATTCATCTAACCAAAACTCAGCCACAATGGATCTAAGGATTTGTT
* ** * * * *
609 TTTACGAGCATTTTAATCTTGTTTTGATTTAATTAAAAATAAATTCGAAAAAAATGGAAAAACAA
456 TTTACGAACAACTGAATCTTGTTTCGATTTAATTAAAAATAAATTAGAAAAAAATAGAAAAACAA
674 TATTGGAAGCCGAAATCATGTACTAACCATCACTGTT
521 TATTGGAAGCCGAAATCATGTACTAACCATCACTGTT
* * * * * *
711 TTTTTGGCTAACAACGCGTTCTAGTG-CCCGGCATCAGTTTTACATGATTTTTGGCGCCAAGACT
1 TTTTTGGCTAAAAACGCGATCTAGAGCCCCAGC-TCAATTTTACATGATTTTTGGCGCAAAGACT
* * * *
775 CCTTGAAATATCTATATTCATCTAAAAAAATCCCAGCCACATTAGATTTAAAGATTTGTTTTTAC
65 ACTTCAAATATCTATATTAATCTAAAAAAATCCCAGCCACAATAGATTTAAAGATTTGTTTTTAC
* * ** **
840 GAGTATCTGAATCTTGTTTCGATTTAATT-CAAATTTATTC-AGAAAAAATAGGAAGTACGATAT
130 GAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAGAAAAAAT-GGAAAAACGATAT
* * * * *
903 TAGAAGCGTGAAAAGCC-CTTTAGTCTTATTGGCATTGAATTA-TATATTTTTTATTACTATTTT
194 TAGAAGCGTGAAAAACCACTTTAAT-TTATTGGCATTGAA-TAGTATAATTTTTATGACTATTGT
* * * * *
966 GGCCAAAAATTGAGG-AAAA-TTCTCCCGGATCAATTTTTGCAAAATTTTAGTCGAAACCGTTTA
257 GGCAAAAAATTGAGGAAAAACTT-T-CCGGATC-AGTTTTGCAAAATTTCAGCCGAAACCGTGTA
** * * *
1029 CTAACCATCATGGTTTTAGGCT-AAAACGCATTTCAAGG-TCC-CGGCTCAGTTTTGCATGATTT
319 CTAACCATCACAGTTTTAGGCTAAAAACGC-GTTC-AGGAGCCACGGCTCAATTTTGCATGATTT
* * *** * ** * *
1091 TTGGCGTC-AAGACTCCCTGTGATATCTATATTCATCTAACCAAATGTCGGCCACATTGGATCTA
382 TTGGC-ACAAAGACTACCTCAAATATATATATTCATCTAACCAAAACTCAGCCACAATGGATCTA
* * *
1155 AGGATTTGTTTTTACGAACAACTGAATCTTGTTTCGATTTAATTAGAAATTAATTTATAAAAAAA
446 AGGATTTGTTTTTACGAACAACTGAATCTTGTTTCGATTTAATTA-AAAATAAATTAGAAAAAAA
1220 TAGAAAAA
510 TAGAAAAA
1228 ACGATATTAA
Statistics
Matches: 422, Mismatches: 84, Indels: 22
0.80 0.16 0.04
Matches are distributed among these distances:
554 2 0.00
555 19 0.05
556 195 0.46
557 204 0.48
558 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (557 bp):
TTTTTGGCTAAAAACGCGATCTAGAGCCCCAGCTCAATTTTACATGATTTTTGGCGCAAAGACTA
CTTCAAATATCTATATTAATCTAAAAAAATCCCAGCCACAATAGATTTAAAGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAGAAAAAATGGAAAAACGATATTA
GAAGCGTGAAAAACCACTTTAATTTATTGGCATTGAATAGTATAATTTTTATGACTATTGTGGCA
AAAAATTGAGGAAAAACTTTCCGGATCAGTTTTGCAAAATTTCAGCCGAAACCGTGTACTAACCA
TCACAGTTTTAGGCTAAAAACGCGTTCAGGAGCCACGGCTCAATTTTGCATGATTTTTGGCACAA
AGACTACCTCAAATATATATATTCATCTAACCAAAACTCAGCCACAATGGATCTAAGGATTTGTT
TTTACGAACAACTGAATCTTGTTTCGATTTAATTAAAAATAAATTAGAAAAAAATAGAAAAACAA
TATTGGAAGCCGAAATCATGTACTAACCATCACTGTT
Found at i:2134 original size:663 final size:660
Alignment explanation
Indices: 681--2897 Score: 2688
Period size: 663 Copynumber: 3.3 Consensus size: 660
671 CAATATTGGA
* * * * * ** *
681 AGCCGAAATCATGTACTAACCATCACTGTTTTTTTGGCTAACAACGCGTTCTAG-TGCCCGGCAT
1 AGCCTAAATCGTGTATTAACCATCACAG--TTTTTGGCTAAAAACGCGTTCCGGATCCCCGGC-T
* * * * * * * ** **
745 CAGTTTTACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAAAAAAATCCCA
63 CAATTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTTATCTAACCAAATCTTA
* * * * *
810 GCCACATTAGATTTAAAGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATT-CAAAT
128 GCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAAT
** ** * * * * **
874 TTATTCAGAAAAAATAGGAAGTACGATATTAGAAGCGTGAAAAGCC-CTTTAGTCTTATT-GGCA
193 AAATTC-GAAAAAAT-GGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAAT-TT-TTGGGGG
* * * * * * * ** *** *
937 TTGAATTA-TATATTTTTTATTACTATTTTGGCCAAAAATTGAGGAAAATTCTCCCGGATCAA-T
254 TTGAA-TAGTACAGTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAAACTTTTGGGT-AAGT
** * * * *
1000 TTTTGCAAAATTTTAGTCGAAACCGTT-TACTAACCATCATGGTTTTAGGCT-AAAACGC-ATTT
317 TTTTGCAAAATTTTAACCGAAATCGTTATA-TAACCATCATAGTTTTTGGCTAAAAACGCGATCT
** * * * * * *** *
1062 CAAGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGTC-AAGACTCCCTGTGATATCTATATTCAT
381 GGA-GCCCCGGCTCAATTTTGCTTGATTTTTGGC-ACAAAGACTCCTTAAAATATCTATATTAAT
* ** * * * *
1126 CTAACCAAATGTCGGCCACATTGGATCTAAGGATTTGTTTTTACGAACAACTGAATCTTGTTTCG
444 CTAACCAAATCTTAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
* * ** * *
1191 ATTTAATTAGAAATTAATTT-ATAAAAAAATAGAAAAAACGATATTAAAAACGTGAAAAACC-CT
509 ATTTAATTAAAAATAAATTTGA-AAAAAAATAG-AAAAACGATATTGGAAGCGTGAAAAACCATT
** * * * * * * *
1254 TTAATCTTTTTTGACGTTGAATTATATTTTTTTATTAGAATTTTGCCCAAAAATTGAGGAAAAAT
572 TTAATC--TTTTGGGGTTGAATAATATGTTTTTATAAGTATTGTGGCAAAAAATTGAGGAAAAA-
* * * * *
1319 CCTTCACGTCAATTTTTGTAAAATTTT
634 CTTTTAGGTCAGTTTTTGCAAAATTTT
* *
1346 AG-CTGAAATCGTGTAGTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGT-CCCGGCTC
1 AGCCT-AAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGA-TCCCCGGCTC
* *
1409 AATTTTGCTTGATTTTTGGTGCAAAGTCTACTTCAAATATCTATATTTATCTAACCAAATCTTAG
64 AATTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTTATCTAACCAAATCTTAG
* *
1474 TCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATA
129 CCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATA
*
1539 AATTTGGAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTGGGGGTTG
194 AA-TTCG-AAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTGGGGGTTG
*
1604 AATAGTACAGTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAAACTTTTGGGTAAGTTTTTG
257 AATAGTACAGTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAAACTTTTGGGTAAGTTTTTG
*
1669 CAAAATTTTAACCGAAATCGTTATATAACCATCACAGTTTTTGGCTAAAAACGCGATCTGGAGCC
322 CAAAATTTTAACCGAAATCGTTATATAACCATCATAGTTTTTGGCTAAAAACGCGATCTGGAGCC
*
1734 CCGGCTCAATTTTGCTTGATTTTTGGCACAAAGACTCCTTAAAATATCTATATTTATCTAACCAA
387 CCGGCTCAATTTTGCTTGATTTTTGGCACAAAGACTCCTTAAAATATCTATATTAATCTAACCAA
* *
1799 ATCTTAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATT
452 ATCTTAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
*
1864 AAAAATAAATTTGAAAAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTC
517 AAAAATAAATTTGAAAAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTT
* * *
1929 GGGGTTGAATAATATGGTTTTTATAAGTATTGGGGCAAAAAATTGAGGGAAAACTTTTGGGTCAG
582 GGGGTTGAATAATAT-GTTTTTATAAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTAGGTCAG
* *
1994 TTTTTGCAATATTTA
646 TTTTTGCAAAATTTT
* * * ** *
2009 AGCCTAAATCGTGTATTAACCATCATAGTTTTTTGCTAAAAACGCATTTTGGATCCCCGACTCAA
1 AGCCTAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGATCCCCGGCTCAA
* * * * *
2074 TTTTGCTTGATTGTTGGCGCAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCTTATCT
66 TTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTTATCTAACCAAATCTTAGCC
* *
2139 ACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGAATTAATTAAAAATAAA
131 ACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAA
*
2204 TTCAAGAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCATTCTAATTTTTGGGGGTTGAA
196 TTC--GAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTGGGGGTTGAA
*
2269 TAGTACAG-TTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACCTTTTGGGTAAGTTTTTGCA
259 TAGTACAGTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAAACTTTTGGGTAAGTTTTTGCA
*
2333 AAATTTTAACCGAAATCGTGTAT-TAACCATCATAGTTTTTGGCTAAAAACGAGATCTGGAGCCC
324 AAATTTTAACCGAAATCGT-TATATAACCATCATAGTTTTTGGCTAAAAACGCGATCTGGAGCCC
** * * *
2397 CAACTCAATTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTAATCTAACCAAA
388 CGGCTCAATTTTGCTTGATTTTTGGCACAAAGACTCCTTAAAATATCTATATTAATCTAACCAAA
* *
2462 TCTTAGCCACAATGGATATAAGGATTTGTTTTTACGAGAATCTGAATTTTGTTTCGATTTAATTA
453 TCTTAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT-
* * * * *
2527 AAAAATAAATTCGAGAAAAAATCGTAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTT
517 AAAAATAAATTTGAAAAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTT
* * * * *
2592 GGGGCTGAATAGTATAGTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCTGGTCA
582 GGGGTTGAATAATAT-GTTTTTATAAGTATTGTGGCAAAAAATTGAGGAAAAACTTTT-AGGTCA
2657 GTTTTTGCAAAATTTT
645 GTTTTTGCAAAATTTT
* * *
2673 AGCCGAAATCGTGTATTAA-CATCACAGTTTTTGGCTAAAAATGCGTTCCGGAGCCCCGGCTCAA
1 AGCCTAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGATCCCCGGCTCAA
* *
2737 TTTTGCTTGATTTTTGGTGCAAAGACTACTTCAAATATATAT-TTTCATCTAACCAAATCTTAGC
66 TTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTT-ATCTAACCAAATCTTAGC
* * *
2801 CACAATGGATTTAAGGATTTGTTTTTACGAGCATTTTAATCTTGTTTTGATTTAATTAAAAATAA
130 CACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAA
*
2866 ATTCGAAAAAATGGAAGAACGATATTGGAAGC
195 ATTCGAAAAAATGGAAAAACGATATTGGAAGC
2898 CGAATTCATG
Statistics
Matches: 1352, Mismatches: 175, Indels: 54
0.86 0.11 0.03
Matches are distributed among these distances:
661 27 0.02
662 237 0.18
663 673 0.50
664 223 0.16
665 187 0.14
666 5 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (660 bp):
AGCCTAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGATCCCCGGCTCAA
TTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTTATCTAACCAAATCTTAGCC
ACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAA
TTCGAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTGGGGGTTGAATA
GTACAGTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAAACTTTTGGGTAAGTTTTTGCAAA
ATTTTAACCGAAATCGTTATATAACCATCATAGTTTTTGGCTAAAAACGCGATCTGGAGCCCCGG
CTCAATTTTGCTTGATTTTTGGCACAAAGACTCCTTAAAATATCTATATTAATCTAACCAAATCT
TAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAA
ATAAATTTGAAAAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTTGGGG
TTGAATAATATGTTTTTATAAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTAGGTCAGTTTTT
GCAAAATTTT
Found at i:2147 original size:331 final size:331
Alignment explanation
Indices: 680--2897 Score: 2511
Period size: 332 Copynumber: 6.7 Consensus size: 331
670 ACAATATTGG
* * * * * * *
680 AAGCCGAAATCATGTACTAACCATCACTGTTTTTTTGGCTAACAACGCGTTCTAGTG-CCCGGCA
1 AAGCCGAAATCGTGTATTAACCATCACAG--TTTTTGGCTAAAAACGCATTCTGGAGCCCCGGC-
* * * * * * ** **
744 TCAGTTTTACATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAAAAAAATCCC
63 TCAATTTTGCTTGATTTTTGGCGCAAAGACTCCTTCAAATATCTATATTTATCTAACCAAATCTT
* * * * *
809 AGCCACATTAGATTTAAAGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATT-CAAA
128 AGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAA
** * * ** * * * * *
873 TTTA-TTCAGAAAAAATAGGAAGTACGATATTAGAAGCGTGAAAAGCC-CTTTAGTCTTATTGGC
193 TAAATTTGAAAAAAAATA-GAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTT-TTGGG
* * * * * * * * *** * *
936 ATTGAATTATATATTTTTTATTACTATTTTGGCCAAAAATTGAGGAAAATTCTCCCGGATCAATT
256 GTTGAATAATATAGTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAA-ACTTTTGGGTCAGTT
1001 TTTGCAAAATTT
320 TTTGCAAAATTT
* * * * * ** * ** *
1013 TAGTCGAAACCGTTTACTAACCATCATGGTTTTAGGCT-AAAACGCATT-TCAAGGTCCCGGCTC
1 AAGCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCATTCTGGA-GCCCCGGCTC
* * * *** * * **
1076 AGTTTTGCATGATTTTTGGCGTC-AAGACTCCCTGTGATATCTATATTCATCTAACCAAATGTCG
65 AATTTTGCTTGATTTTTGGCG-CAAAGACTCCTTCAAATATCTATATTTATCTAACCAAATCTTA
* * * * *
1140 GCCACATTGGATCTAAGGATTTGTTTTTACGAACAACTGAATCTTGTTTCGATTTAATTAGAAAT
129 GCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAAT
* ** * * *
1205 TAATTT-ATAAAAAAATAGAAAAAACGATATTAAAAACGTGAAAAACC-CTTTAATCTTTTTTGA
194 AAATTTGA-AAAAAAATAG-AAAAACGATATTGGAAGCGTGAAAAACCATTTTAATC--TTTTGG
* * * * * * * * * *** *
1268 CGTTGAATTATAT-TTTTTTATTAGAATTTTGCCCAAAAATTGAGGAAAAATCCTTCACGTCAAT
255 GGTTGAATAATATAGTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAA-CTTTTGGGTCAGT
*
1332 TTTTGTAAAATTT
319 TTTTGCAAAATTT
* * * * * * *
1345 TAGCTGAAATCGTGTAGTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCA
1 AAGCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCATTCTGGAGCCCCGGCTCA
* * * *
1410 ATTTTGCTTGATTTTTGGTGCAAAGTCTACTTCAAATATCTATATTTATCTAACCAAATCTTAGT
66 ATTTTGCTTGATTTTTGGCGCAAAGACTCCTTCAAATATCTATATTTATCTAACCAAATCTTAGC
*
1475 CACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATAA
131 CACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAA
* *
1540 ATTTGGAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAAT-TTTTGGGGGTTG
196 ATTTGAAAAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTT-GGGGTTG
* * * * *
1604 AATAGTACAGTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAAAAAACTTTTGGGTAAGTTTTTG
260 AATAATATAGTTTTTATGAGTATTGTGGCAAAAAATTGAGG-AAAAACTTTTGGGTCAGTTTTTG
1669 CAAAATTTT
324 CAAAA-TTT
1678 AA-CCGAAATCGT-TATATAACCATCACAGTTTTTGGCTAAAAACGCGA-TCTGGAGCCCCGGCT
1 AAGCCGAAATCGTGTAT-TAACCATCACAGTTTTTGGCTAAAAACGC-ATTCTGGAGCCCCGGCT
* *
1740 CAATTTTGCTTGATTTTTGGCACAAAGACTCCTTAAAATATCTATATTTATCTAACCAAATCTTA
64 CAATTTTGCTTGATTTTTGGCGCAAAGACTCCTTCAAATATCTATATTTATCTAACCAAATCTTA
*
1805 GCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAAT
129 GCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAAT
*
1870 AAATTTGAAAAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTCGGGGTT
194 AAATTTGAAAAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTTGGGGTT
* * * *
1935 GAATAATATGGTTTTTATAAGTATTGGGGCAAAAAATTGAGGGAAAACTTTTGGGTCAGTTTTTG
259 GAATAATATAGTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTGGGTCAGTTTTTG
*
2000 CAATATTT
324 CAAAATTT
* * * * * *
2008 AAGCCTAAATCGTGTATTAACCATCATAGTTTTTTGCTAAAAACGCATTTTGGATCCCCGACTCA
1 AAGCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCATTCTGGAGCCCCGGCTCA
* * *
2073 ATTTTGCTTGATTGTTGGCGCAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCTTATC
66 ATTTTGCTTGATTTTTGGCGCAAAGACTCCTTCAAATATCTATATTTATCTAACCAAATCTTAGC
* * *
2138 TACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGAATTAATTAAAAATAA
131 CACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAA
* * *
2203 A-TTCAAGAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCATTCTAAT-TTTTGGGGGTT
196 ATTTGAA-AAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTT-GGGGTT
* * * *
2266 GAATAGTACAG-TTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACCTTTTGGGTAAGTTTTT
259 GAATAATATAGTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAA-CTTTTGGGTCAGTTTTT
2330 GCAAAATTTT
323 GCAAAA-TTT
* * **
2340 AA-CCGAAATCGTGTATTAACCATCATAGTTTTTGGCTAAAAACG-AGATCTGGAGCCCCAACTC
1 AAGCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCA-TTCTGGAGCCCCGGCTC
* *
2403 AATTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTAATCTAACCAAATCTTAG
65 AATTTTGCTTGATTTTTGGCGCAAAGACTCCTTCAAATATCTATATTTATCTAACCAAATCTTAG
* * *
2468 CCACAATGGATATAAGGATTTGTTTTTACGAGAATCTGAATTTTGTTTCGATTTAATTAAAAAAT
130 CCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT-AAAAAT
* * * * * *
2533 AAATTCGAGAAAAAATCGTAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTTGGGGCT
194 AAATTTGAAAAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTTGGGGTT
* * *
2598 GAATAGTATAGTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCTGGTCAGTTTTT
259 GAATAATATAGTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTT-GGGTCAGTTTTT
2663 GCAAAATTT
323 GCAAAATTT
* * * *
2672 TAGCCGAAATCGTGTATTAA-CATCACAGTTTTTGGCTAAAAATGCGTTCCGGAGCCCCGGCTCA
1 AAGCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCATTCTGGAGCCCCGGCTCA
* * *
2736 ATTTTGCTTGATTTTTGGTGCAAAGACTACTTCAAATATATAT-TTTCATCTAACCAAATCTTAG
66 ATTTTGCTTGATTTTTGGCGCAAAGACTCCTTCAAATATCTATATTT-ATCTAACCAAATCTTAG
* * *
2800 CCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTTAATCTTGTTTTGATTTAATTAAAAATA
130 CCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATA
* * *
2865 AATTCG--AAAAAATGGAAGAACGATATTGGAAGC
195 AATTTGAAAAAAAATAGAAAAACGATATTGGAAGC
2898 CGAATTCATG
Statistics
Matches: 1639, Mismatches: 208, Indels: 80
0.85 0.11 0.04
Matches are distributed among these distances:
329 25 0.02
330 166 0.10
331 493 0.30
332 683 0.42
333 269 0.16
334 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (331 bp):
AAGCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCATTCTGGAGCCCCGGCTCA
ATTTTGCTTGATTTTTGGCGCAAAGACTCCTTCAAATATCTATATTTATCTAACCAAATCTTAGC
CACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAA
ATTTGAAAAAAAATAGAAAAACGATATTGGAAGCGTGAAAAACCATTTTAATCTTTTGGGGTTGA
ATAATATAGTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTGGGTCAGTTTTTGCA
AAATTT
Found at i:3101 original size:225 final size:226
Alignment explanation
Indices: 2700--3123 Score: 525
Period size: 225 Copynumber: 1.9 Consensus size: 226
2690 AACATCACAG
* * * * *
2700 TTTTTGGCTAAAAATGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGTGCAAAGACTA
1 TTTTTGGCTAAAAACGCGTTCCAGAGCCCCGGCTCAATTTTACATGATTTTTGGCGCAAAGACTA
* * * ** ** *
2765 CTTCAAATATATATTTTCATCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTTACG
66 CTTAAAATATATATATTCATCTAACAAAATCCCAGCCACAATAAATTTAAAGATTTGTTTTTACG
* * * *
2830 AGCATTTTAATCTTGTTTTGATTTAATTAAAAATAAATTCGAAAAAAT-GGAAGA-ACGATATTG
131 AGCATCTGAATCTTGTTTAGATTTAATTAAAAATAAATTCGAAAAAATAGGAA-ATACGATATTA
2893 GAAGCCGAATTCATGTACTAACCATCACTGTT
195 GAAGCCGAATTCATGTACTAACCATCACTGTT
* * * * *
2925 TTTTTGGCTAACAACGCGTTCTAGTG-CCCGGCATCAGTTTTACATGATTTTTGGCGCCAAGACT
1 TTTTTGGCTAAAAACGCGTTCCAGAGCCCCGGC-TCAATTTTACATGATTTTTGGCGCAAAGACT
* * *
2989 CCTTAAAATATCTATATTCATCTAA-AAAGATCCCAGCCACATTAAATTTAAAGATTTGTTTTTA
65 ACTTAAAATATATATATTCATCTAACAAA-ATCCCAGCCACAATAAATTTAAAGATTTGTTTTTA
* **
3053 CGAGCATCTGAATCTTGTTTAGATTTAATT-CAAATTTATTCAGAAAAAATAGGAAATACGATAT
129 CGAGCATCTGAATCTTGTTTAGATTTAATTAAAAATAAATTC-GAAAAAATAGGAAATACGATAT
3117 TAGAAGC
193 TAGAAGC
3124 GTGAAAAGCC
Statistics
Matches: 166, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
224 16 0.10
225 133 0.80
226 17 0.10
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (226 bp):
TTTTTGGCTAAAAACGCGTTCCAGAGCCCCGGCTCAATTTTACATGATTTTTGGCGCAAAGACTA
CTTAAAATATATATATTCATCTAACAAAATCCCAGCCACAATAAATTTAAAGATTTGTTTTTACG
AGCATCTGAATCTTGTTTAGATTTAATTAAAAATAAATTCGAAAAAATAGGAAATACGATATTAG
AAGCCGAATTCATGTACTAACCATCACTGTT
Found at i:3410 original size:555 final size:556
Alignment explanation
Indices: 2412--3412 Score: 1212
Period size: 555 Copynumber: 1.8 Consensus size: 556
2402 CAATTTTGCT
* * ** **
2412 TGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTAATCTAACCAAATCTTAGCCACAATGG
1 TGATTTTTGGCGCAAAGACTACTTAAAATATCTATATTAATCTAACAAAATCCCAGCCACAATAA
* * *
2477 ATATAAGGATTTGTTTTTACGAGAATCTGAATTTTGTTTCGATTTAATTAAAAAATAAATTCGAG
66 ATATAAAGATTTGTTTTTACGAGAATCTGAATCTTGTTTAGATTTAATT-AAAAATAAATTCGAG
* * * * **
2542 AAAAAATCGTAAAACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTTGGGGCTGAATAGTAT
130 AAAAAATAGGAAAACGATATTAGAAGCGTGAAAAACCACTTTAATTTTTTGGCACTGAATAGTAT
* * * * *
2607 AGTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCTGGTCAGTTTTTGCAAAATTT
195 AGTTTTTATGACTATTGTGGCAAAAAATTGAGGAAAAACTTTCCGGGTCAATTTTTGCAAAATTT
* * * ** *
2672 TAGCCGAAATCGTGTATTAACATCACAGTTTTTGGCTAAAAATGCGTTCCGGAGCCCCGGCTCAA
260 TAGCCGAAACCGTGTACTAACATCACAGTTTTTGGCTAAAAACGCGTTCAAGAGCCCCAGCTCAA
* * * * *
2737 TTTTGCTTGATTTTTGGTGCAAAGACTACTTCAAATATATATTTTCATCTAACCAAATCTTAGCC
325 TTTTGCATGATTTTTGCTGCAAAGACTACCTCAAATATATATATTCATCTAACCAAATCTCAGCC
* * ** * *
2802 ACAATGGATTTAAGGATTTGTTTTTACGAGCATTTTAATCTTGTTTTGATTTAATTAAAAATAAA
390 ACAATGGATCTAAGGATTTGTTTTTACGAACAACTGAATCTTGTTTCGATTTAATTAAAAATAAA
2867 TTCGAAAAAATGGAAGAACGATATTGGAAGCCGAATTCATGTACTAACCATCACTGTTTTTTTGG
455 TTCGAAAAAATGGAAGAACGATATTGGAAGCCGAATTCATGTACTAACCATCACTGTTTTTTTGG
2932 CTAACAACGCGTTCTAGTGCCCGGCATCAGTTTTACA
520 CTAACAACGCGTTCTAGTGCCCGGCATCAGTTTTACA
* * * *
2969 TGATTTTTGGCGCCAAGACTCCTTAAAATATCTATATTCATCTAA-AAAGATCCCAGCCACATTA
1 TGATTTTTGGCGCAAAGACTACTTAAAATATCTATATTAATCTAACAAA-ATCCCAGCCACAATA
* * * **
3033 AATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTAGATTTAATT-CAAATTTATTC-AG
65 AATATAAAGATTTGTTTTTACGAGAATCTGAATCTTGTTTAGATTTAATTAAAAATAAATTCGAG
* * *
3096 AAAAAATAGGAAATACGATATTAGAAGCGTGAAAAGCC-CTTTAGTCTTTTTGGCATTGAATTA-
130 AAAAAATAGGAAA-ACGATATTAGAAGCGTGAAAAACCACTTTAAT-TTTTTGGCACTGAA-TAG
* * * *
3159 TATATTTTTTATTACTATTTTGGCCAAAAATTGAGG-AAAA-TTCTCCCGGGTCAATTTTTGCAA
192 TATAGTTTTTATGACTATTGTGGCAAAAAATTGAGGAAAAACTT-T-CCGGGTCAATTTTTGCAA
* * ** * *
3222 AATTTTAGTCGAAACCGTTTACTAACCATCATGGTTTTTGGCT-AAAACGCATTTCAAG-GTCCC
255 AATTTTAGCCGAAACCGTGTACTAA-CATCACAGTTTTTGGCTAAAAACGC-GTTCAAGAGCCCC
* * * * *** *
3285 AGCTCAGTTTTGCATGATTTTTGTCTTC-AAGGCTCCCTGTGATATCTATATTCATCTAACCAAA
318 AGCTCAATTTTGCATGATTTTTG-CTGCAAAGACTACCTCAAATATATATATTCATCTAACCAAA
* * *
3349 TGTCGGCCACATTGGATCTAAGGATTTGTTTTTACGAACAACTGAATCTTGTTTCGATTTAATT
382 TCTCAGCCACAATGGATCTAAGGATTTGTTTTTACGAACAACTGAATCTTGTTTCGATTTAATT
3413 TGAAATTAAT
Statistics
Matches: 365, Mismatches: 70, Indels: 20
0.80 0.15 0.04
Matches are distributed among these distances:
553 2 0.01
554 23 0.06
555 219 0.60
556 25 0.07
557 96 0.26
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (556 bp):
TGATTTTTGGCGCAAAGACTACTTAAAATATCTATATTAATCTAACAAAATCCCAGCCACAATAA
ATATAAAGATTTGTTTTTACGAGAATCTGAATCTTGTTTAGATTTAATTAAAAATAAATTCGAGA
AAAAATAGGAAAACGATATTAGAAGCGTGAAAAACCACTTTAATTTTTTGGCACTGAATAGTATA
GTTTTTATGACTATTGTGGCAAAAAATTGAGGAAAAACTTTCCGGGTCAATTTTTGCAAAATTTT
AGCCGAAACCGTGTACTAACATCACAGTTTTTGGCTAAAAACGCGTTCAAGAGCCCCAGCTCAAT
TTTGCATGATTTTTGCTGCAAAGACTACCTCAAATATATATATTCATCTAACCAAATCTCAGCCA
CAATGGATCTAAGGATTTGTTTTTACGAACAACTGAATCTTGTTTCGATTTAATTAAAAATAAAT
TCGAAAAAATGGAAGAACGATATTGGAAGCCGAATTCATGTACTAACCATCACTGTTTTTTTGGC
TAACAACGCGTTCTAGTGCCCGGCATCAGTTTTACA
Found at i:4040 original size:335 final size:333
Alignment explanation
Indices: 2957--4162 Score: 1338
Period size: 335 Copynumber: 3.6 Consensus size: 333
2947 AGTGCCCGGC
* * *
2957 ATCAGTTTTACATGATTTTTGGCGCCAAGACTCCTTAAAATATCTATATTCATCTAAAAAGATC-
1 ATCAGTTTTGCATGATTTTTGGCGACAAGACTCCTTAAAATATCTATATTCATCTAATAA-ATCT
* ** * *
3021 CCAGCCACATTAAATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTAGATTTAATTC-A
65 CAAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTCGA
* * * * *
3085 AATTTATTCAGAAAAAATAGGAAATACGATATTAGAAGCGTGAAAAGCCCTTTAGTCTTTTTGGC
130 AATTAATTC-GAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGAC
* * ** * * *
3150 ATTGAAT-TATATATTTTTTATTACT--ATTTTGGCCAAAAATTGAGG-AAAATTCTCCCGGGTC
194 GTTGAATATATATATTTTTTTTTTTTGAATTTTGCCCAAAAATTGAGGAAAAATTCT-TCAGGTC
* * *
3211 AATTTTTGCAAAATTTTAGTCGAAACCGTTTACTAACCATCATGGTTTTTGGCT-AAAACGCATT
258 AATTTTTGCAAAATTTTAGTCGAAATCGTATACTAA-CATCACGGTTTTTGGCTAAAAACGCATT
*
3275 TCAAGGTCCCAG-
322 TC-AGGACCCAGT
* * ** * * *** * *
3287 CTCAGTTTTGCATGATTTTTGTCTTCAAGGCTCCCTGTGATATCTATATTCATCTAACCAAATGT
1 ATCAGTTTTGCATGATTTTTGGCGACAAGACTCCTTAAAATATCTATATTCATCTAA-TAAATCT
* * * * *
3352 C-GGCCACATTGGATCTAAGGATTTGTTTTTACGAACAACTGAATCTTGTTTCGATTTAATTTGA
65 CAAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTCGA
* * * *
3416 AATTAATTTAGAAAAAAATAGAAAAAACGATATTAAAAACGTGAAAAGCCCTTCAATCTTTTTTG
130 AATTAA-TTCG-AAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATC-TTTTTG
* * * *
3481 ACGTTG-A-AT-TATA-TTTTTTTGTTAGAATTTTGCCCAAAAATTGAGAAAAAATTCTTCACGT
192 ACGTTGAATATATATATTTTTTTTTTTTGAATTTTGCCCAAAAATTGAGGAAAAATTCTTCAGGT
* *
3542 CAATTTTTGCAAAATTTTAG-CTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCG
257 CAATTTTTGCAAAATTTTAGTC-GAAATCGTATACTAA-CATCACGGTTTTTGGCTAAAAACGCA
* *
3606 TTTCAGCACCCAAT
320 TTTCAGGACCCAGT
* * ** * *
3620 ATCAATTTTGCATGATTTTTGACGACAAGGGTCCTCAAAATATCTATATTCATCTAAATAAATCA
1 ATCAGTTTTGCATGATTTTTGGCGACAAGACTCCTTAAAATATCTATATTCATCT-AATAAATCT
** * * *
3685 CAATTC-TATTGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAGTCGA
65 CAAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTCGA
* *
3749 AATTAATTCGTAAAAGAATA-G-AAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTCA
130 AATTAATTCG-AAAA-AATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGA
* *
3812 CGTTGAATTATATATATTTATATTTTTTTTTGAATTTTGCCCAAATATTGAGGAAAAATCCTTCA
193 CGTTGAA-TATATATA-TT-T-TTTTTTTTTGAATTTTGCCCAAAAATTGAGGAAAAATTCTTCA
* * * *
3877 GGTCAATTTTTGTAAAATTTTAGTCGAAATCGTATACT-A-ATCACGATTTATGGCTAAAAACGA
254 GGTCAATTTTTGCAAAATTTTAGTCGAAATCGTATACTAACATCACGGTTTTTGGCTAAAAACGC
*
3940 ATTTCAGGACCTAGT
319 ATTTCAGGACCCAGT
* *
3955 ATCAGTTTTGCATGATTTTTGGTGACAAGACTCCTTAAAACATCTATATTCATCTAATTAAATCT
1 ATCAGTTTTGCATGATTTTTGGCGACAAGACTCCTTAAAATATCTATATTCATCTAA-TAAATCT
* * * * *
4020 CAATCC-TATTGGACTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGTTTTAATTAGA
65 CAAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTCGA
*
4084 AATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTCAATCTTTTT-AG
130 AATTAATTC-GAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGA-
*
4148 CGATGAATCATATAT
193 CGTTGAAT-ATATAT
4163 TGTTATCTGT
Statistics
Matches: 734, Mismatches: 111, Indels: 56
0.81 0.12 0.06
Matches are distributed among these distances:
330 118 0.16
331 48 0.07
332 128 0.17
333 141 0.19
334 13 0.02
335 160 0.22
336 52 0.07
337 2 0.00
338 71 0.10
339 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (333 bp):
ATCAGTTTTGCATGATTTTTGGCGACAAGACTCCTTAAAATATCTATATTCATCTAATAAATCTC
AAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTCGAA
ATTAATTCGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGACGT
TGAATATATATATTTTTTTTTTTTGAATTTTGCCCAAAAATTGAGGAAAAATTCTTCAGGTCAAT
TTTTGCAAAATTTTAGTCGAAATCGTATACTAACATCACGGTTTTTGGCTAAAAACGCATTTCAG
GACCCAGT
Found at i:6093 original size:41 final size:39
Alignment explanation
Indices: 6036--6383 Score: 473
Period size: 40 Copynumber: 8.6 Consensus size: 39
6026 TGGCACATTC
*
6036 ACATTGAACTTGCCTTAATTCACAGTCAACTTTCCCAACTT
1 ACATTGAACTTGCCTT-ATTCACATTCAACTTTCCCAA-TT
* *
6077 ACATTGAACTTGCCTTATTCACATCCAATTTTCCCAACTT
1 ACATTGAACTTGCCTTATTCACATTCAACTTTCCCAA-TT
6117 ACATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATT
1 ACATTGAACTTGCCTT-ATTCACATTCAACTTTCCCAATT
* *
6157 GACATTGAACTTGCCTTAATTCACATTCAACTTTCCAAATA
1 -ACATTGAACTTGCCTT-ATTCACATTCAACTTTCCCAATT
* *
6198 ACATTGAACTTGCCTCATTCACATTCAACTTTCCCAAATA
1 ACATTGAACTTGCCTTATTCACATTCAACTTTCCC-AATT
*
6238 ACATTGAACTTGCCTTATTCACATTCAACTTTCCCAAATA
1 ACATTGAACTTGCCTTATTCACATTCAACTTTCCC-AATT
*
6278 ACATTGAACTTGCCTTATTCACATTCAAC-TTCCCTATT
1 ACATTGAACTTGCCTTATTCACATTCAACTTTCCCAATT
*
6316 GACATTGAACTTGCCTTGATTCACATTCAACTTTTCCAATT
1 -ACATTGAACTTGCCTT-ATTCACATTCAACTTTCCCAATT
* *
6357 GACATTGAACTTTCCTTCATTTACATT
1 -ACATTGAACTTGCCTT-ATTCACATT
6384 GGCCCTTAAT
Statistics
Matches: 283, Mismatches: 18, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
38 2 0.01
39 39 0.14
40 139 0.49
41 103 0.36
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (39 bp):
ACATTGAACTTGCCTTATTCACATTCAACTTTCCCAATT
Found at i:26279 original size:32 final size:32
Alignment explanation
Indices: 26233--26300 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
26223 TTTTGGGATG
* *
26233 TTTTGTCCCATGAACTT-TCCAAATTCATGACA
1 TTTTGCCCCATGAACTTCT-CAAATTCAAGACA
*
26265 TTTTGCCCCTTGAACTTCTCAAATTCAAGACA
1 TTTTGCCCCATGAACTTCTCAAATTCAAGACA
26297 TTTT
1 TTTT
26301 AGTTATTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (32 bp):
TTTTGCCCCATGAACTTCTCAAATTCAAGACA
Found at i:26388 original size:31 final size:32
Alignment explanation
Indices: 26316--26395 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
26306 TTCTTAACGG
26316 AGGGGGCAAATTGTCCTGAATTTGGAAAACTC
1 AGGGGGCAAATTGTCCTGAATTTGGAAAACTC
*
26348 AGGGGGCAAATTGTCCTGAATTTGGAAAGCTC
1 AGGGGGCAAATTGTCCTGAATTTGGAAAACTC
26380 A-GGGGCAAATTGTCCT
1 AGGGGGCAAATTGTCCT
26396 TGGATCCATA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 15 0.32
32 32 0.68
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (32 bp):
AGGGGGCAAATTGTCCTGAATTTGGAAAACTC
Found at i:33081 original size:31 final size:31
Alignment explanation
Indices: 32944--33081 Score: 125
Period size: 31 Copynumber: 4.5 Consensus size: 31
32934 TTCTTTTGTG
**
32944 CACGTGGCATGCCACATGTCACTTTTTGAAA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* ** *
32975 CACATGGCATGCCATGTGTCACTTTTGGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* * ***
33006 CACATGGCGTAATACATGTCA-TTTTTCGGTA
1 CACGTGGCATGCCACATGTCACTTTTT-GGTA
* * *
33037 CACGTGACGTGCCACATGTCGCTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
*
33068 CACGTGGTATGCCA
1 CACGTGGCATGCCA
33082 TGTCGGACAC
Statistics
Matches: 83, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
30 4 0.05
31 74 0.89
32 5 0.06
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (31 bp):
CACGTGGCATGCCACATGTCACTTTTTGGTA
Found at i:33474 original size:8 final size:7
Alignment explanation
Indices: 33457--33491 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
33447 AGAGAAAGAA
33457 TTTTTAT
1 TTTTTAT
33464 TTTTTATT
1 TTTTTA-T
33472 TTTTTAT
1 TTTTTAT
33479 TTTTTAT
1 TTTTTAT
33486 TTTTTA
1 TTTTTA
33492 GAAAAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:33477 original size:15 final size:15
Alignment explanation
Indices: 33457--33490 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
33447 AGAGAAAGAA
33457 TTTTTATTTTTTATT
1 TTTTTATTTTTTATT
33472 TTTTTATTTTTTATT
1 TTTTTATTTTTTATT
33487 TTTT
1 TTTT
33491 AGAAAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTATTTTTTATT
Found at i:42835 original size:50 final size:50
Alignment explanation
Indices: 42754--42853 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
42744 TAAAGCTCAT
* *
42754 ATTAGTATGCTTTAGCCTTGGTTTGCTATGATGATTTTATACTTAGCAAG
1 ATTAATATGCTTTAGCCTTGGTTTGCAATGATGATTTTATACTTAGCAAG
42804 ATTAATATGCTTTAGCCTTGGTTTGCAATGATGATTTTATACTTAGCAAG
1 ATTAATATGCTTTAGCCTTGGTTTGCAATGATGATTTTATACTTAGCAAG
42854 TTGGTCTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (50 bp):
ATTAATATGCTTTAGCCTTGGTTTGCAATGATGATTTTATACTTAGCAAG
Found at i:45686 original size:18 final size:18
Alignment explanation
Indices: 45663--45702 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
45653 AGGGAGGGGG
*
45663 AGAAGAAAATGAAGACGA
1 AGAAGAAAATGAAGAAGA
* *
45681 AGAAGAAGATGAGGAAGA
1 AGAAGAAAATGAAGAAGA
45699 AGAA
1 AGAA
45703 ATGGTCCCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.33, T:0.05
Consensus pattern (18 bp):
AGAAGAAAATGAAGAAGA
Done.