Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009190.1 Corchorus capsularis cultivar CVL-1 contig09211, 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: 6458
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Found at i:1688 original size:324 final size:321
Alignment explanation
Indices: 782--1882 Score: 1205
Period size: 324 Copynumber: 3.4 Consensus size: 321
772 CTCGGCTCAG
* * * * * * **
782 TTTTGCACGATTTTTGGCGTAAAGACTCCTTGAAATATTTTTATTCATCGAACTAAATACCAGCC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAGTATCTATATTCATCGAACCAAATGTCAGCC
* * *
847 ACATTCGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * ** * * *
912 TTCGAAAAAAAAAATT-CAAAAACGATATTAGAAGTATGAAAAACTCTTCAAACTTTTTGGTTTT
131 TTCG-GAAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAGAC-CTTCAATCTTTTTGGTGTT
* * * *
976 GAATTATATATTTTTTATGAGTATTGTAGTAAAAATTGAGAAAACAA-TTTTCGGGTCAATTTTT
194 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAA-AACTTTTCGGGTCAGTTTTT
** * * ** * * ** *
1040 AGCCGAAAAAGGGCACTAACCATCACGAATTTTGGCTCAAAACGCATTTCGGGCATTGAATCAG
258 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTCGAGCCCTGAATCAA
* * ** * *
1104 TTTTGCATGGTTTTTGGCATAAAGACTTCTTGATA-TATCTATATTCATCTTACCAAATCTAAGC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGA-AGTATCTATATTCATCGAACCAAATGTCAGC
* * * * * * *
1168 TACATTAGATTTAAGGAATTGTTTTTACGAGCATTTGAAT-TT-TATC---TCAA-T----A-T-
65 CACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * *
1221 ATT-AGAAATAAAATTGGAAAAATGGTATTAGAAACGTGAAAAGACCTTCAATCTTTTTGGTGTT
130 ATTCGGAAAAAAAATTGGAAAAATGATATTAGAAGCGTG-AAAGACCTTCAATCTTTTTGGTGTT
1285 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTT
194 GAATTATATATTTTTTCTGAGTATTGTGGC-AAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTT
* * * * **
1350 AACCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGCATTACAGAGCCCCGGGTCAA
258 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTC-GAGCCCTGAATCAA
* * * *
1415 TTTTGCAAGATTTTTAGCATAAAGACTTCTTGAAGTATCTATATTCATCTAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAGTATCTATATTCATCGAACCAAATGTCAGCC
* *
1480 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATGTTGTTTTGATTTAATTAGAAATTAA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* *
1545 TTCGGAAATAAAATTGGAAAAATGATA-TAGGAAGCGTGAAATGACCATCAATCTTTTTGGTGTT
131 TTCGGAAAAAAAATTGGAAAAATGATATTA-GAAGCGTGAAA-GACCTTCAATCTTTTTGGTGTT
* * *
1609 GAATTAAATATTTTTTCTTAGTATTGTGGCAAAATATTGAGAAAAAACCTTTCGGGTCAGTTTTT
194 GAATTATATATTTTTTCTGAGTATTGTGGCAAAA-ATTGAGAAAAAACTTTTCGGGTCAGTTTTT
* * * * *
1674 AGCTGAAGTCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGTCCTGACTCAA
258 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTC-GAGCCCTGAATCAA
* ** * * *
1739 TTTTGCATGATTTTGGGCGCAAAGACTCCTTGAAGTATCTATATTCAAT-GAACTAGATGTTAGC
1 TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAGTATCTATATTC-ATCGAACCAAATGTCAGC
* * *
1803 CAAATTGGATATAAGGATTTGCTTTTACGAGCA-CATGAATCTTGTTTCGATTTAATCAGAAATT
65 CACATTGGATATAAGGATTTGTTTTTACGAGCATC-TGAATCTTGTTTCGATTTAATTAGAAATT
1867 AATTCGGCAAAAAAAA
129 AATTCGG-AAAAAAAA
1883 AAGAGAAGAA
Statistics
Matches: 653, Mismatches: 100, Indels: 49
0.81 0.12 0.06
Matches are distributed among these distances:
308 9 0.01
309 62 0.09
310 79 0.12
311 99 0.15
312 3 0.00
313 2 0.00
316 4 0.01
317 4 0.01
320 3 0.00
321 3 0.00
322 86 0.13
323 14 0.02
324 276 0.42
325 9 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (321 bp):
TTTTGCATGATTTTTGGCATAAAGACTCCTTGAAGTATCTATATTCATCGAACCAAATGTCAGCC
ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCGGAAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAGACCTTCAATCTTTTTGGTGTTGA
ATTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGC
CGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTTCGAGCCCTGAATCAA
Found at i:2184 original size:572 final size:566
Alignment explanation
Indices: 1369--2499 Score: 1487
Period size: 572 Copynumber: 2.0 Consensus size: 566
1359 CGTGTATTAA
*
1369 CCATCACGGTTTTTGGCTAAAAACGCATTACAGAGCCCCGGGTCAATTTTGCAAGATTTTTAGCA
1 CCATCACGGTTTTTGGCTAAAAACGCATTACAGAGCCCCGCGTCAATTTTGCAAGATTTTTAGCA
* * *
1434 TAAAGACTTCTTGAAGTATCTATATTCATCTAACCAAATGTCAGCCACATTGGATATAAGGATTT
66 TAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGGATTT
* * * *
1499 GTTTTTACGAGCATCTGAATGTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGAA
131 GTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAATAAAATTGGAA
* * * * *
1564 AAATGATATAGGAAGCGTGAAATGACCATCAATCTTTTTGGTGTTGAATTAA-ATATTTTTTCTT
196 AAATGATATAGGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAA-TAATATATTTTCTC-T
* * * * *
1628 AG-TATTGTGGC-AAAATATTGAGAAAAAACCTTTCGGGTCAGTTTTTAGCTGAAGTCGTGTACT
259 AGATATTATGGCGAAAA-ATTGAGAAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACT
* * * * * *
1691 AACCATCAC-G-GTTTTTGGCTAAAAACGCGTTTCGGAGTCCTGACTCAATTTTGCATGAT-TTT
323 AACCATCACAGTGTTTTTGGCTAAAAACGCGTTCCAGAGCCCCGACTCAATATTGCAAGATATTT
* * * * *
1753 GGGCGCAAAGACTCCTTGAAGTATCT-ATATTCAAT-GAACTAGATGTTAGCCAAATTGGATATA
388 -GGCGCAAAGACTCCTTGAAATAT-TAATATTC-ATCGAACCAAATCTCAGCCAAATTGGATATA
*
1816 AGGATTTGCTTTTACGAGCACATGAATCTTGTTTCGATTTAATCAGAAATTAATTCGGCAAAAAA
450 AGGATTTGCTTTTACGAGCACATCAATCTTGTTTCGATTTAATCAGAAATTAATTCGG---AAAA
1881 AAAAGAGAAGAAAAAACAATATTAGAAGCGTGAACAA-CCCGTCAATCTTTTTAACCAAC
512 AAAA-AG--G-AAAAACAATATTAGAAGCGTGAA-AAGCCCGTCAATCTTTTTAACCAAC
* * * * * * *
1940 CCATCACGGTTTTTGGTTAAAAATGCATTCCGGATCCCCGACG-CAATTTTGCATGATTTTTTTG
1 CCATCACGGTTTTTGGCTAAAAACGCATTACAGAGCCCCG-CGTCAATTTTGCAAGA-TTTTTAG
* *
2004 CATAAAGACTCCTTGAAATATCTATATTCAT-TGAACCAAATCTCAGTCATATTGGATATAAGGA
64 CATAAAGACTCCTTGAAATATCTATATTCATCT-AACCAAATCTCAGCCACATTGGATATAAGGA
* *
2068 TTTGTTTTTTCGAGCATCTCAATCTT-TTGTCGATTTAATTATAAATTAATTCAGAAATAAAATT
128 TTTGTTTTTACGAGCATCTCAATCTTGTT-TCGATTTAATTAGAAATTAATTCAGAAATAAAATT
2132 GGAAAAATGATATTA-GAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTC
192 GGAAAAATGATA-TAGGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTC
*
2196 TCTAGATATTATGGCGAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTA
256 TCTAGATATTATGGCGAAAAATTGAGAAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTA
* * *
2261 CTAACCATCACAGTTTTTTTGGCTAAAAACGTGTTCCAGAGCCCCGTCTCAATATTGCAAGATAT
321 CTAACCATCACAGTGTTTTTGGCTAAAAACGCGTTCCAGAGCCCCGACTCAATATTGCAAGATAT
*
2326 TTGGCGCAAAGACTCCTTGAAATATTAATATTCATCGAACCAAATCTCAGCCATATTGGATATAA
386 TTGGCGCAAAGACTCCTTGAAATATTAATATTCATCGAACCAAATCTCAGCCAAATTGGATATAA
* * * * * * * * *
2391 GGATTTGTTTTTTCGAGCATATCAGTTTTGTTTCGATTTTATTAGATATTAATTCGGGAAAAAAA
451 GGATTTGCTTTTACGAGCACATCAATCTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAAA
* *
2456 TGGAAAAACAATATTAGAATCGTGAAAAGCCCGTCAATCTTTTT
516 AGGAAAAACAATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTT
2500 GGCATTGAAT
Statistics
Matches: 489, Mismatches: 57, Indels: 32
0.85 0.10 0.06
Matches are distributed among these distances:
566 2 0.00
567 37 0.08
568 1 0.00
570 1 0.00
571 63 0.13
572 232 0.47
573 10 0.02
574 140 0.29
575 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (566 bp):
CCATCACGGTTTTTGGCTAAAAACGCATTACAGAGCCCCGCGTCAATTTTGCAAGATTTTTAGCA
TAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGGATTT
GTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAATAAAATTGGAA
AAATGATATAGGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTCTAG
ATATTATGGCGAAAAATTGAGAAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACTAAC
CATCACAGTGTTTTTGGCTAAAAACGCGTTCCAGAGCCCCGACTCAATATTGCAAGATATTTGGC
GCAAAGACTCCTTGAAATATTAATATTCATCGAACCAAATCTCAGCCAAATTGGATATAAGGATT
TGCTTTTACGAGCACATCAATCTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAAAAGGAA
AAACAATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTAACCAAC
Found at i:3183 original size:640 final size:648
Alignment explanation
Indices: 1940--3384 Score: 1879
Period size: 640 Copynumber: 2.2 Consensus size: 648
1930 TTTAACCAAC
* * * * * *
1940 CCATCACGG-TTTTTGGTTAAAAATGCATTCCGGATCCCCGACGCAATTTTGCATGATTTTTTTG
1 CCATAACGGTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGA-TTTTTTG
* *
2004 CATAAAGACTCCTTGAAATATCTATATTCATTGAACCAAATCTCAGTCATATTGGATATAAGGAT
65 CGTAAAGACTCCTTGAAATATCTATATTCA-TCAACCAAATCTCAGTCATATTGGATATAAGGAT
*
2069 TTGTTTTTTCGAGCATCTCAATCTTTTGTCGATTTAATTATAAATTAATTCAGAAATAAAATTGG
129 TTGTTTTTTCGAGCATCTCAATCTTTTGTCGATTTAATTAGAAATTAATTCAGAAATAAAATTGG
*
2134 AAAAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTCT
194 AAAAATGAAATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAAT-ATATATTTTCTCT
* *
2199 AGATATTATGGCGAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACTA
258 AGATATTATGGCAAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATAGTGTACTA
* **
2264 ACCATCACAGTTTTTTTGGCTAAAAACGTGTTCCAGAGCCCCGTCTCAATATTGCAAGATATTTG
323 ACCATCACAGTGTTTTTGGCTAAAAACGTGTTCCAGAGCCCCAACTCAATATTGCAAGATATTTG
* * *
2329 GCGCAAAGACTCCTTGAAATATTAATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGA
388 ACGCAAAGACTCCTTGAAATATTAATATTCATCGAACCAAATATCAGCCACATTGGATATAAGGA
* * * * * *
2394 TTTGTTTTTTCGAGCATATCAGTTTTGTTTCGATTTTATTAGATATTAATTCGGGAAAAAAATGG
453 TTTGTTTTTACGAGCATATAAATCTTGTTTCGATTTAATTAGATAATAATTCGGGAAAAAAATGG
* * * * * ** *
2459 AAAAACAATATTAGAATCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTCTATATTTTTTAT
518 AAAAACAATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCATTGAATAATATATTTTCTAT
** *
2524 GAGTATTGTGACAAAAAATTGA-GATAAAATTTTTCGGGTCAGTTTTTAGCCGAAATAGTGTACT
583 GAGTATTGTGACAAAAAATTGAGGA-AAAACATTTCGGGACAGTTTTTAGCCGAAATAGTGTACT
2588 -A
647 AA
* ** * * * * *
2589 CCA-ATATGG-TTTTTGGCTAAAAACGTGTTTCGTAGCTCGGACTCAATTTTGCATGATTTTTGG
1 CCATA-ACGGTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTTG
* * * *
2652 CGTAAAGACTCCTTGAAGTATCTATATTCATCAACCAAATGTCAGCCACATTGGATATAAGGATT
65 CGTAAAGACTCCTTGAAATATCTATATTCATCAACCAAATCTCAGTCATATTGGATATAAGGATT
* * * *
2717 TGTTTTTACGAGCATCTGAAT-TTTT-T-TATTTAATTAGAAATTAATTCGGAAATAAAATTGGA
130 TGTTTTTTCGAGCATCTCAATCTTTTGTCGATTTAATTAGAAATTAATTCAGAAATAAAATTGGA
* *
2779 AAAATGAAATTAGAAGCGTGAAAAGACCATCAATATTTTTGGTGTTGAAT-TATATTTT-T-TAC
195 AAAATGAAATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATATATATTTTCTCTA-
* * ** * *
2841 GAGTATTGTGGCAAAAAATTGA-GATAAATTTTTCGGGTCAGTTTTTTGCTCGAAATAGTGTACT
259 GA-TATTATGGCAAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGC-CGAAATAGTGTACT
* * * ** * *
2905 AACCATTAC-G-GTTTTTGGTTAAAAACACGT-TTCC-GAGCCCCAACTCAATTTTTTATGATTT
322 AACCATCACAGTGTTTTTGGCT-AAAA-ACGTGTTCCAGAGCCCCAACTCAATATTGCAAGATAT
* *
2966 TTGACGCAAAGACTCCTT-AAAGTATGT-ATATTCATCTAACCAAATATCAGCTACATTGGATAT
385 TTGACGCAAAGACTCCTTGAAA-TAT-TAATATTCATCGAACCAAATATCAGCCACATTGGATAT
* *
3029 AAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGATTTAATTAGA-AGATAATTC-GGAAAT
448 AAGGATTTGTTTTTACGAGCATATAAATCTTGTTTCGATTTAATTAGATA-ATAATTCGGGAAA-
** *
3092 AAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATA
511 AAAA-TGGAAAAACAATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCATTGAATAATATA
* * *
3157 TTTTCTCTGAGTATTGTGGC-AAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATC
575 TTTTCTATGAGTATTGTGACAAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATA
3221 GTGTACTAA
640 GTGTACTAA
3230 CCATAACGGTTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTTG
1 CCATAACGG-TTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTTG
* * *
3295 CGTAAAGACTCTTTGAAATATCTATATTCATCGAACCAAATCTTAGTCATATTCGATATAAGGAT
65 CGTAAAGACTCCTTGAAATATCTATATTCATC-AACCAAATCTCAGTCATATTGGATATAAGGAT
3360 TTGTTTTTTCGAGCATCTCAATCTT
129 TTGTTTTTTCGAGCATCTCAATCTT
3385 GTGTTTGTTG
Statistics
Matches: 686, Mismatches: 92, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
639 9 0.01
640 177 0.26
641 111 0.16
642 51 0.07
643 77 0.11
644 127 0.19
645 3 0.00
646 4 0.01
647 50 0.07
648 34 0.05
649 43 0.06
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (648 bp):
CCATAACGGTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTTGC
GTAAAGACTCCTTGAAATATCTATATTCATCAACCAAATCTCAGTCATATTGGATATAAGGATTT
GTTTTTTCGAGCATCTCAATCTTTTGTCGATTTAATTAGAAATTAATTCAGAAATAAAATTGGAA
AAATGAAATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATATATATTTTCTCTAGA
TATTATGGCAAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATAGTGTACTAACC
ATCACAGTGTTTTTGGCTAAAAACGTGTTCCAGAGCCCCAACTCAATATTGCAAGATATTTGACG
CAAAGACTCCTTGAAATATTAATATTCATCGAACCAAATATCAGCCACATTGGATATAAGGATTT
GTTTTTACGAGCATATAAATCTTGTTTCGATTTAATTAGATAATAATTCGGGAAAAAAATGGAAA
AACAATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCATTGAATAATATATTTTCTATGAG
TATTGTGACAAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATAGTGTACTAA
Found at i:3363 original size:325 final size:323
Alignment explanation
Indices: 1940--3391 Score: 1788
Period size: 325 Copynumber: 4.5 Consensus size: 323
1930 TTTAACCAAC
* * * * * * *
1940 CCATCACGGTTTTTGGTTAAAAATGCATTCCGGATCCCCGACGCAATTTTGCATGATTTTTTTGC
1 CCATAACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGA-TTTTTTGC
* * *
2005 ATAAAGACTCCTTGAAATATCTATATTCATTGAACCAAATCTCAGTCATATTGGATATAAGGATT
65 GTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATT
* * *
2070 TGTTTTTTCGAGCATCTCAATCTT-TTGTCGATTTAATTATAAATTAATTCAGAAATAAAATTGG
130 TGTTTTTTCGAGCATCTCAATCTTGTT-TTGATTTAATTAGAAATTAATTCGGAAATAAAATTGG
2134 AAAAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTCT
194 AAAAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTCT
* * *
2199 -AGATATTATGGCGAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACT
259 GAG-TATTGTGGCAAAAAATTGA-GAAAAACATTTCGGGACAGTTTTTAGCCGAAATAGTGTACT
2263 AA
322 AA
* * * * * * * * * *
2265 CCATCACAGTTTTTTTGGCTAAAAACGTGTTCCAGAGCCCCGTCTCAATATTGCAAGATATTTGG
1 CCATAAC-G-GTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGATTTTTTG
*
2330 CGCAAAGACTCCTTGAAATAT-TAATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGA
64 CGTAAAGACTCCTTGAAATATCT-ATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGA
* * * * * *
2394 TTTGTTTTTTCGAGCATATCAGTTTTGTTTCGATTTTATTAGATATTAATTCGGGAAA-AAAA-T
128 TTTGTTTTTTCGAGCATCTCAATCTTGTTTTGATTTAATTAGAAATTAATTC-GGAAATAAAATT
** * * * * * * ** *
2457 GGAAAAACAATATTAGAATCGTGAAAAGCCCGTCAATCTTTTTGGCATTGAATTCTATATTTTTT
192 GGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCT
* * ** *
2522 ATGAGTATTGTGACAAAAAATTGAGATAAAATTTTTCGGGTCAGTTTTTAGCCGAAATAGTGTAC
257 CTGAGTATTGTGGCAAAAAATTGAGA-AAAACATTTCGGGACAGTTTTTAGCCGAAATAGTGTAC
2587 T-A
321 TAA
* * * * * *
2589 CCA-ATATGGTTTTTGGCTAAAAACGTGTTTCGTAGCTCGGACTCAATTTTGCATGATTTTTGGC
1 CCATA-ACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGATTTTTTGC
* * *
2653 GTAAAGACTCCTTGAAGTATCTATATTCATC-AACCAAATGTCAGCCACATTGGATATAAGGATT
65 GTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATT
* *
2717 TGTTTTTACGAGCATCTGAAT-TT-TTTT-ATTTAATTAGAAATTAATTCGGAAATAAAATTGGA
130 TGTTTTTTCGAGCATCTCAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGA
* * * *
2779 AAAATGAAATTAGAAGCGTGAAAAGACCATCAATATTTTTGGTGTTGAAT--TATATTTTTTAC-
195 AAAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCT-CT
* ** * *
2841 GAGTATTGTGGCAAAAAATTGAGATAAATTTTTCGGGTCAGTTTTTTGCTCGAAATAGTGTACTA
259 GAGTATTGTGGCAAAAAATTGAGAAAAACATTTCGGGACAGTTTTTAGC-CGAAATAGTGTACTA
2906 A
323 A
* * * * * **
2907 CCATTACGGTTTTTGGTTAAAAACACGTTTCCGAGCCCCAACTCAATTTTTTATGA-TTTTTGAC
1 CCATAACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGATTTTTTG-C
* * * * * *
2971 GCAAAGACTCCTT-AAAGTATGTATATTCATCTAACCAAATATCAGCTACATTGGATATAAGGAT
65 GTAAAGACTCCTTGAAA-TATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGAT
* *
3035 TTGTTTTTACGAGCATCTAAATCTTGTTTTGATTTAATTAGAAGA-TAATTCGGAAATAAAATTG
129 TTGTTTTTTCGAGCATCTCAATCTTGTTTTGATTTAATTAGAA-ATTAATTCGGAAATAAAATTG
3099 GAAAAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTC
193 GAAAAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTC
*
3164 TGAGTATTGTGGC-AAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACT
258 TGAGTATTGTGGCAAAAAATTGA-GAAAAACATTTCGGGACAGTTTTTAGCCGAAATAGTGTACT
3228 AA
322 AA
* *
3230 CCATAACGGTTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTTG
1 CCATAACGG--TTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGATTTTTTG
* * * *
3295 CGTAAAGACTCTTTGAAATATCTATATTCATCGAACCAAATCTTAGTCATATTCGATATAAGGAT
64 CGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGAT
3360 TTGTTTTTTCGAGCATCTCAATCTTGTGTTTG
129 TTGTTTTTTCGAGCATCTCAATCTTGT-TTTG
3392 TTGGAGTTGT
Statistics
Matches: 967, Mismatches: 129, Indels: 61
0.84 0.11 0.05
Matches are distributed among these distances:
316 23 0.02
317 59 0.06
318 92 0.10
319 99 0.10
320 4 0.00
321 52 0.05
322 153 0.16
323 36 0.04
324 50 0.05
325 230 0.24
326 126 0.13
327 43 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (323 bp):
CCATAACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGATTTTTTGCG
TAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTT
GTTTTTTCGAGCATCTCAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGAA
AAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTCTGA
GTATTGTGGCAAAAAATTGAGAAAAACATTTCGGGACAGTTTTTAGCCGAAATAGTGTACTAA
Found at i:3925 original size:579 final size:577
Alignment explanation
Indices: 2845--3965 Score: 1917
Period size: 579 Copynumber: 1.9 Consensus size: 577
2835 TTTTACGAGT
* * * *
2845 ATTGTGGCAAAAAATTGAGATAAATTTTTCGGGTCAGTTTTTTGCTCGAAATAGTGTACTAACCA
1 ATTGTGGCAAAAAATTGAAATAAATTTTTCGAGTCACTTTTTAGCTCGAAATAGTGTACTAACCA
* * **
2910 TTACGGTTTTTGGTTAAAAACACGTTTCCGAGCCCCAACTCAATTTTTTATGATTTTTGACGCAA
66 TCACGGTTTTTGGCTAAAAACACGTTTCCGAGCCCCAACTCAATTTTGCATGATTTTTGACGCAA
* *
2975 AGACTCCTTAAAGTATGTATATTCATCTAACCAAATATCAGCTACATTGGATATAAGGATTTGTT
131 AGACTCCTTAAAGTATCTATATTCATCTAACCAAATATCAGCCACATTGGATATAAGGATTTGTT
3040 TTTACGAGCATCTAAATCTTGTTTTGATTTAATTAGAAGATAATTCGGAAATAAAATTGGAAAAA
196 TTTACGAGCATCTAAATCTTGTTTTGATTTAATTAGAAGATAATTCGGAAATAAAATTGGAAAAA
*
3105 TGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTCTGAGTA
261 TGATAATAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTCTGAGTA
3170 TTGTGGCAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACTAACCATA
326 TTGTGGCAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACTAACCATA
3235 ACGGTTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTTGCGTAA
391 ACGGTTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTTGCGTAA
* *
3300 AGACTCTTTGAAATATCTATATTCATCGAACCAAATCTTAGTCATATTCGATATAAGGATTTGTT
456 AGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCATATTCGATATAAGGATTTGTT
*
3365 TTTTCGAGCATCTCAATCTTGTGTTTGTTGGAGTTGTATTATATATTTTTTATCAAC
521 TTTACGAGCATCTCAATCTTGTGTTTGTTGGAGTTGTATTATATATTTTTTATCAAC
*
3422 ATTGTGGCAAAAAATTGAAATAAAATTTTTCGAGTCACTTTTTAGC-CGAAATTGTGTACTAACC
1 ATTGTGGCAAAAAATTGAAAT-AAATTTTTCGAGTCACTTTTTAGCTCGAAATAGTGTACTAACC
** * ** * *
3486 ATCACGGTTTTAT-GCTAAAAACGTGTTTCGGAGCCCGGACTCAATTTTGCATGATTTTTGGCGT
65 ATCACGGTTTT-TGGCTAAAAACACGTTTCCGAGCCCCAACTCAATTTTGCATGATTTTTGACGC
* * *
3550 AAAGACTCCTTGAAGTATCTATATTCATC-AATCAAATGTCAGCCACATTGGATATAAGGATTTG
129 AAAGACTCCTTAAAGTATCTATATTCATCTAACCAAATATCAGCCACATTGGATATAAGGATTTG
*
3614 TTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAA-ATTAATTCGGAAATAAAATTGGAA
194 TTTTTACGAGCATCTAAATCTTGTTTTGATTTAATTAGAAGA-TAATTCGGAAATAAAATTGGAA
3678 AAATGATAATAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATATTTTCTCT
258 AAATGATAATAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAAT-A-ATATATTTTCTCT
3743 GAGTATTGTGGCAAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACTA
321 GAGTATTGTGGC-AAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACTA
*
3808 ACCATCACGGTTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTT
385 ACCATAACGGTTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTT
3873 GCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCATATTCGATATAAGGA
450 GCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCATATTCGATATAAGGA
3938 TTTGTTTTTACGAGCATCTCAATCTTGT
515 TTTGTTTTTACGAGCATCTCAATCTTGT
3966 TTCGATTTAA
Statistics
Matches: 511, Mismatches: 27, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
575 1 0.00
576 141 0.28
577 116 0.23
578 47 0.09
579 206 0.40
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (577 bp):
ATTGTGGCAAAAAATTGAAATAAATTTTTCGAGTCACTTTTTAGCTCGAAATAGTGTACTAACCA
TCACGGTTTTTGGCTAAAAACACGTTTCCGAGCCCCAACTCAATTTTGCATGATTTTTGACGCAA
AGACTCCTTAAAGTATCTATATTCATCTAACCAAATATCAGCCACATTGGATATAAGGATTTGTT
TTTACGAGCATCTAAATCTTGTTTTGATTTAATTAGAAGATAATTCGGAAATAAAATTGGAAAAA
TGATAATAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATTTTCTCTGAGTA
TTGTGGCAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACTAACCATA
ACGGTTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTTGCGTAA
AGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCATATTCGATATAAGGATTTGTT
TTTACGAGCATCTCAATCTTGTGTTTGTTGGAGTTGTATTATATATTTTTTATCAAC
Found at i:4632 original size:325 final size:322
Alignment explanation
Indices: 3404--5089 Score: 2178
Period size: 325 Copynumber: 5.2 Consensus size: 322
3394 GGAGTTGTAT
** * * * *
3404 TATATATTTTTTATCAACATTGTGGCAAAAAATTGAAATAAAATTTTTCGAGTCACTTTTTAGCC
1 TATATATTTTTT-T-AGTATTGTGGCAAAAAATTGAAAAAAAACTTTTCGGGTCAGTTTTTAGCC
* *
3469 GAAATTGTGTACTAACCATCACGGTTTTAT-GCTAAAAACGTGTTTCGGAGCCCGGACTCAATTT
64 GAAATCGTGTACTAACCATCACGGTTTT-TGGCTAAAAACGCGTTTCGGAGCCC-GACTCAATTT
* * *
3533 TGCATGATTTTTGGCGTAAAGACTCCTTGAAGTATCTATATTCATC-AATCAAATGTCAGCCACA
127 TGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACA
*
3597 TTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTC
192 TTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC
* *
3662 GGAAATAAAATTGGAAAAATGATAATAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAAT
257 GGAAATAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTTTT-GGCGTTGAAT
*
3727 AA
321 TA
* ** * *
3729 TATATATTTTCTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCC
1 TATATATTTT-T-TTAGTATTGTGGCAAAAAATTGAAAAAAAACTTTTCGGGTCAGTTTTTAGCC
* *
3794 GAAATCGTGTACTAACCATCACGGTTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATT
64 GAAATCGTGTACTAACCATCACGG--TTTTTGGCTAAAAACGCGTTTCGGAG-CCCGACTCAATT
* * *
3859 TTGCATGATTTTTTGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCAT
126 TTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCAC
* *
3924 ATTCGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAA-TAGAAATTAATT
191 ATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
* *
3988 CGGAAATAAAATTGGAAAAATGATATTAGAAACGTGAAAAGACCATCAATCTCTTTGGTGTTGAA
256 CGGAAATAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCT-TTTGGCGTTGAA
4053 TTA
320 TTA
* * * * * *
4056 TATAT-TTTTTCTGAGTATTGTGTCAAAAAATTGAGGAAAAACCATTTCGGGACAGTTTTTAGCC
1 TATATATTTTT-TTAGTATTGTGGCAAAAAATTGA-AAAAAAACTTTTCGGGTCAGTTTTTAGCC
* * *
4120 GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGTG-TTCCGAGTACC-AGCTCAATTT
64 GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAG-CCCGA-CTCAATTT
* * * *
4183 TGCAAGATTTTTGGCGCAAAGACTCCTTGAAATAT-TCATATTCATCGAACCAAATCTTAGGCAC
127 TGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCT-ATATTCATCGAACCAAATCTCAGCCAC
* * *
4247 ATTGGATATATGGATTTGTTTTTACGAGCATTTGAATCTTGTTTTGATTTAATTAGAAATTAATT
191 ATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
* * *
4312 CGGAAATAAAATTGGAAAAATGATTTTAGAAGCGTGAAAAGACCATCAATCTCTTCGCTGTTGAA
256 CGGAAATAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTTTTGGC-GTTGAA
4377 TTA
320 TTA
4380 TATATATATTTTTTAGTATTGTGGCAAAAAATTGAAAAAAAACTTTTCGGGTCAGTTTTTAGCCG
1 TATATAT-TTTTTTAGTATTGTGGCAAAAAATTGAAAAAAAACTTTTCGGGTCAGTTTTTAGCCG
4445 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAG-CCGTAACTCAATTTT
65 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCG--ACTCAATTTT
* * * * *
4509 GCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATTGAACCAAATGTTAGCCAAAT
128 GCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAT
** * *
4574 TGGATATAAATATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAATCAGAAATTAATTCG
193 TGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG
* * * * * * **
4639 GCAAAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAA-ACCCGTCAATCTTTTTGGCAATGAA
258 G-AAATAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGA-CCATCAATC-TTTTGGCGTTGAA
4703 TTA
320 TTA
* * * * *
4706 TATATGTTTTCTGAGTATTGTGGCAGAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCG
1 TATATATTTTTTTAGTATTGTGGCAAAAAATTGA-AAAAAAACTTTTCGGGTCAGTTTTTAGCCG
* * * *
4771 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACACATTCCGGAGCCCCGACCCAATTTTG
65 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAG-CCCGACTCAATTTTG
* * * * *
4836 TATGATTTTTTGCGTAAAGACTCCTTGAAATTTCTATATTCATCGAACCAAATCTCAGTCATATT
129 CATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATT
** * * *
4901 CAATATAAGGATTTATTTTTTA-GAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCA
194 GGATATAAGGATTT-GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG
* * *
4965 GAAATAAAATTGGAAAAAAT-ATATTAGAAGCGTGAACATACCATCAATATTTTGGGCGTTGAA-
258 GAAATAAAATTGG-AAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTTTT-GGCGTTGAAT
5028 TA
321 TA
**
5030 -ATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACATTTT-GGGAT-AGTTTTT
1 TATATATTTTTT-T-AGTATTGTGGCAAAAAATTGAAAAAAAAC-TTTTCGGG-TCAGTTTTT
5090 GGCTAAAAAC
Statistics
Matches: 1199, Mismatches: 128, Indels: 69
0.86 0.09 0.05
Matches are distributed among these distances:
322 2 0.00
323 132 0.11
324 179 0.15
325 341 0.28
326 311 0.26
327 163 0.14
328 71 0.06
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (322 bp):
TATATATTTTTTTAGTATTGTGGCAAAAAATTGAAAAAAAACTTTTCGGGTCAGTTTTTAGCCGA
AATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCGACTCAATTTTGCA
TGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGG
ATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAA
ATAAAATTGGAAAAATGATATTAGAAGCGTGAAAAGACCATCAATCTTTTGGCGTTGAATTA
Found at i:4972 original size:651 final size:650
Alignment explanation
Indices: 3422--6458 Score: 3617
Period size: 652 Copynumber: 4.7 Consensus size: 650
3412 TTTTATCAAC
* * * * *
3422 ATTGTGGCAAAAAATTGA-AATAAAATTTTTCGAGTCACTTTTTAGCCGAAATTGTGTACTAACC
1 ATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
* *
3486 ATCACGGTTTTAT-GCTAAAAACGTGTTTCGGAGCCCGGACTCAATTTTGCATGATTTTTGGCGT
66 ATCACGGTTTT-TGGCTAAAAACGTGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGT
* * * *
3550 AAAGACTCCTTGAAGTATCTATATTCATC-AATCAAATGTCAGCCACATTGGATATAAGGATTTG
130 AAAGACTCCTTGAAATTTCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTG
3614 TTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGAAA
195 TTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGAAA
*
3679 AATGATAATAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATATTTTCTCTG
260 AATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATATTTT-TCTG
* *
3744 AGTATTGTGGCAAAAAATTGAGGAAAAACATTTCGGGACAGTTTTTAGCCGAAATCGTGTACTAA
324 AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAA
* *
3809 CCATCACGGTTTTTTTGGCTAAAAACGCATTTCGGAGCCCCGACCCAATTTTGCATGATTTTTTG
389 CCATCACGG-TTTTTTGGCTAAAAACGCATTTCGGAGCCCCAACCCAATTTTGCATGATTTTTGG
* * * *
3874 CGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCATATTCGATATAAGGAT
453 CGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCAAATTCGATATAAAGAT
* * * *
3939 TTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATAGAAATTAATTCGGAAATAAAATTGGA
518 TTGTTTTTACGAGCATATCAATCTTGTTTCGATTTAATAGAAATTAATTCGGAAAAAAAAATGAA
* *** *
4004 AAAATGATATTAGAAACGTGAAAAGACCATCAATCTCTTTGGTGTTGAATTATATATTTTTTCTG
583 AAAACGATATTAGAAACGTGAAAAGACCATCAATCTCTTTGGCAATGAATTATATATGTTTTCTG
4069 AGT
648 AGT
* ** *
4072 ATTGTGTCAAAAAATTGAGGAAAAACCA-TTTCGGGACAGTTTTTAGCCGAAATCGTGTACTAAC
1 ATTGTGGCAAAAAATTGA-GAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAC
** *
4136 CATCACGGTTTTTGGCTAAAAACGTGTTCC-GAGTACC-AGCTCAATTTTGCAAGATTTTTGGCG
65 CATCACGGTTTTTGGCTAAAAACGTGTTCCGGAGCCCCGA-CTCAATTTTGCATGATTTTTGGCG
* * * *
4199 CAAAGACTCCTTGAAATATTC-ATATTCATCGAACCAAATCTTAGGCACATTGGATATATGGATT
129 TAAAGACTCCTTGAAAT-TTCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATT
*
4263 TGTTTTTACGAGCATTTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGA
193 TGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGA
* * * *
4328 AAAATGATTTTAGAAGCGTGAAAAGACCATCAATCTCTT-CGCTGTTGAATTATATATATATTTT
258 AAAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGC-GTTGAA-TA-ATATATATTTT
**
4392 T-T-AGTATTGTGGCAAAAAATTGAAAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTA
320 TCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTA
* ** *
4455 CTAACCATCACGG-TTTTTGGCTAAAAACGCGTTTCGGAGCCGTAACTCAATTTTGCATGATTTT
385 CTAACCATCACGGTTTTTTGGCTAAAAACGCATTTCGGAGCCCCAACCCAATTTTGCATGATTTT
* * * *
4519 TGGCGCAAAGACTCCTTGAAATATCTATATTCATTGAACCAAATGTTAGCCAAATTGGATATAAA
450 TGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCAAATTCGATATAAA
* *
4584 TATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAATCAGAAATTAATTCGGCAAAAAAAA
515 GATTTGTTTTTACGAGCATATCAATCTTGTTTCGATTTAAT-AGAAATTAATTCGG-AAAAAAAA
* *
4649 ATGAAAAAACGATATTA-AAAGCGTGAAAA-ACCCGTCAATCTTTTTGGCAATGAATTATATATG
578 ATGAAAAAACGATATTAGAAA-CGTGAAAAGA-CCATCAATCTCTTTGGCAATGAATTATATATG
4712 TTTTCTGAGT
641 TTTTCTGAGT
*
4722 ATTGTGGCAGAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
1 ATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
*** * * *
4787 ATCACGGTTTTTGGCTAAAAACACATTCCGGAGCCCCGACCCAATTTTGTATGATTTTTTGCGTA
66 ATCACGGTTTTTGGCTAAAAACGTGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGTA
* * ** *
4852 AAGACTCCTTGAAATTTCTATATTCATCGAACCAAATCTCAGTCATATTCAATATAAGGATTTAT
131 AAGACTCCTTGAAATTTCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTT-G
* * *
4917 TTTTTA-GAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAATAAAATTGGAAA
195 TTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGG-AA
* *
4981 AAAT-ATATTAGAAGCGTGAACATACCATCAATATTTTGGGCGTTGAATAATATAT-TTTTTCTG
259 AAATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATATTTTTCTG
5044 AGTATTGTGGCAAAAAATTGAGGAAAAA----------CA--TTTT----G-----G-G------
324 AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAA
* * * ** *
5081 --AT-A--G-TTTTTGGCTAAAAACGCGTTCCGGAGCACTGACTCAATTTTGCATGATTTTTGGC
389 CCATCACGGTTTTTTGGCTAAAAACGCATTTCGGAGCCCCAACCCAATTTTGCATGATTTTTGGC
* * * * * *
5140 GCAAAGACTCCTTGAAATAT-TCATATTCATCAAACTAAATCTCAGCCATATTGGATATAAGGAA
454 GCAAAGACTCCTTGAAATATCT-ATATTCATCGAACCAAATCTCAGCCAAATTCGATATAAAGAT
* * * * * * *
5204 TTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTTATTATATATTAATTCGG----GAAAATGG
518 TTGTTTTTACGAGCATATCAATCTTGTTTCGA-TTTAATAGAAATTAATTCGGAAAAAAAAATGA
* * * * * *
5265 AAAAACGATATTAGAAGA-GTGAAAAGCCCGTAAATCTTTTTGG-AGTTGAATTATATATTTTTT
582 AAAAACGATATTAGAA-ACGTGAAAAGACCATCAATCTCTTTGGCA-ATGAATTATATATGTTTT
* * **
5328 ATCAAC
645 CTGAGT
* * * * *
5334 ATTGTGGCAAAAATTTGA-AATAAAATTTTTCGGGTCACTTTTTAGCCGAAATTGTGTACTAACC
1 ATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
* * * * * *
5398 ATCACGGTTTTTGGTTAAAAACGTGTTTCGGAGCCCGGACTCAATCTTGCATAAATTTTGGCGTA
66 ATCACGGTTTTTGGCTAAAAACGTGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGTA
* * *
5463 AAGACTCCTTGAAGTATCTATATTCATC-AACCAAATGTCAGCCACATTGGATATAAGGATTTGT
131 AAGACTCCTTGAAATTTCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGT
5527 TTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGAAAA
196 TTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGAAAA
* ** * *
5592 ATGATATTAGAAGCGTGAAAAGACCATCAATCTCTTT-GTTGTTGAAT--TATATATTTTTTTTA
261 ATGATATTAGAAGCGTGAAAAGACCATCAATAT-TTTGGGCGTTGAATAATATATATTTTTCTGA
*
5654 GTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAC
325 GTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAC
* * * * *
5719 CATCACGG-TTTTTGTCTAAAAACGCGTTTCGAAGCCCTAACTCAATTTTGCATGATTTTTGGCG
390 CATCACGGTTTTTTGGCTAAAAACGCATTTCGGAGCCCCAACCCAATTTTGCATGATTTTTGGCG
* * ** * * * * * *
5783 CAAAGACTACTTGAAATATCTATATTCATTGATGCAAATGTTAGGGCAAGTTGGATATAAGGATT
455 CAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCA-GCCAAATTCGATATAAAGATT
* * * * *
5848 TGTTTTTACGAGCATCTGAATCTTGTTTCGGCGTTAATTAATCAGAAATTAATTCAGCAAAAAAA
519 TGTTTTTACGAGCATATCAATCTTGTTT---CG--ATTTAAT-AGAAATTAATTCGGAAAAAAAA
** * * **
5913 ATGAAAAAGTGATATTA-AAAGCGTGAAAA-ACTCGTCAATCTTTTTGGCGTTGAATTATATATG
578 ATGAAAAAACGATATTAGAAA-CGTGAAAAGAC-CATCAATCTCTTTGGCAATGAATTATATATG
*
5976 TTTTGTGAGT
641 TTTTCTGAGT
* * * *
5986 ATTGTGGCAAAAAATTGAG-AAAAAACTTTTCGGGTCAGATTTTAGCCGAAATCGTATATTAACC
1 ATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
* ** * * *
6050 TTCACGGTTTTTGGCTAAAAACGCATTCCCGAGCCCCGACTCAATTTTGCAAGATTTTTGTCGTA
66 ATCACGGTTTTTGGCTAAAAACGTGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGTA
*** * * * *
6115 AAGACTCCTTGAAGGATCTATATTCATCTAACCTAATGTCAACCACATTGGATATAAGGATTTGT
131 AAGACTCCTTGAAATTTCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGT
* *
6180 TTTTTCGAGCATCTGAATCTTGTTTT-AATTAATTAGAAATTAATTCGGAAATAAAATTGGAAAA
196 TTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGAAAA
* * * *
6244 ATGATATTTGAAGCGTGAAAAGACCGTCAATCTCTTT--GCTGTTGAATTATATATATTTTT-T-
261 ATGATATTAGAAGCGTGAAAAGACCATCAATAT-TTTGGGC-GTTGAATAATATATATTTTTCTG
* * * * *
6305 AGTATTGTGGCAAAAAATTCAGAAAAAACTTTGCGGGTCAGTTTTTAACCGAAATTGTGTACTAA
324 AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAA
* * * * *
6370 CCATCACGG-TTTTCGGCTAAAAACGCGTTTCGGAGCCCTAACTCAATTTTGCATGATTTTTGGG
389 CCATCACGGTTTTTTGGCTAAAAACGCATTTCGGAGCCCCAACCCAATTTTGCATGATTTTTGGC
*
6434 GCAAACACTCCTTGAAATATCTATA
454 GCAAAGACTCCTTGAAATATCTATA
Statistics
Matches: 2067, Mismatches: 234, Indels: 170
0.84 0.09 0.07
Matches are distributed among these distances:
608 5 0.00
609 45 0.02
610 116 0.06
611 125 0.06
612 75 0.04
613 2 0.00
614 1 0.00
616 1 0.00
617 146 0.07
618 5 0.00
619 3 0.00
620 2 0.00
621 4 0.00
625 1 0.00
628 1 0.00
629 1 0.00
630 1 0.00
631 1 0.00
634 1 0.00
638 4 0.00
639 2 0.00
640 3 0.00
642 85 0.04
643 44 0.02
646 2 0.00
647 4 0.00
648 157 0.08
649 33 0.02
650 316 0.15
651 362 0.18
652 437 0.21
653 71 0.03
654 11 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (650 bp):
ATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
ATCACGGTTTTTGGCTAAAAACGTGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGTA
AAGACTCCTTGAAATTTCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGT
TTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGAAAA
ATGATATTAGAAGCGTGAAAAGACCATCAATATTTTGGGCGTTGAATAATATATATTTTTCTGAG
TATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
ATCACGGTTTTTTGGCTAAAAACGCATTTCGGAGCCCCAACCCAATTTTGCATGATTTTTGGCGC
AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCAAATTCGATATAAAGATTTG
TTTTTACGAGCATATCAATCTTGTTTCGATTTAATAGAAATTAATTCGGAAAAAAAAATGAAAAA
ACGATATTAGAAACGTGAAAAGACCATCAATCTCTTTGGCAATGAATTATATATGTTTTCTGAGT
Found at i:6390 original size:322 final size:320
Alignment explanation
Indices: 5084--6458 Score: 1737
Period size: 322 Copynumber: 4.3 Consensus size: 320
5074 TTTTGGGATA
*
5084 GTTTTTGGCTAAAAACGCGTTCCGGAGCACTGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
1 GTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
* * * * *
5149 CCTTGAAATAT-TCATATTCATCAAACTAAATCTCAGCCATATTGGATATAAGGAATTGTTTTTT
66 CCTTGAAATATCT-ATATTCATC-AACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTA
* * * * * * * *
5213 CGAGCATCTCAATCTTGTTTCGATTTTATTATATATTAATTCGG---GAAAA-TGGAAAAACGAT
129 CGAGCATCTGAATCTTGTTT-TAATTAATTAGAAATTAATTCGGAAATAAAATTGGAAAAATGAT
* * * * ** **
5274 ATTAGAAGAGTGAAAAGCCCGTAAATCTTTTTGGAGTTGAATTATATATTTTTTATCAACATTGT
193 ATTAGAAGCGTGAAAAGACCGTCAATCTCTTTGCTGTTGAATTATATATTTTTT-T-AGTATTGT
* * * *
5339 GGCAAAAATTTGA-AATAAAATTTTTCGGGTCACTTTTTAGCCGAAATTGTGTACTAACCATCAC
256 GGCAAAAAATTGAGAA-AAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCAC
5403 G
320 G
* * * * * * * *
5404 GTTTTTGGTTAAAAACGTGTTTCGGAGCCCGGACTCAATCTTGCATAAATTTTGGCGTAAAGACT
1 GTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
*
5469 CCTTGAAGTATCTATATTCATCAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACG
66 CCTTGAAATATCTATATTCATCAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACG
*
5534 AGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAATAAAATTGGAAAAATGATAT
131 AGCATCTGAATCTTGTTTT-AATTAATTAGAAATTAATTCGGAAATAAAATTGGAAAAATGATAT
* *
5599 TAGAAGCGTGAAAAGACCATCAATCTCTTTGTTGTTGAATTATATATTTTTTTTAGTATTGTGGC
195 TAGAAGCGTGAAAAGACCGTCAATCTCTTTGCTGTTGAATTATATA-TTTTTTTAGTATTGTGGC
5664 AAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACG
259 AAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACG
* * * *
5726 GTTTTTGTCTAAAAACGCGTTTCGAAGCCCTAACTCAATTTTGCATGATTTTTGGCGCAAAGACT
1 GTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
* * ** * *
5791 ACTTGAAATATCTATATTCATTGATGCAAATGTTAGGGCA-AGTTGGATATAAGGATTTGTTTTT
66 CCTTGAAATATCTATATTCA-TCAACCAAATGTCA-GCCACA-TTGGATATAAGGATTTGTTTTT
* * *
5855 ACGAGCATCTGAATCTTGTTTCGGCGTTAATTAATCAGAAATTAATTCAGCAAA-AAAAAT-GAA
128 ACGAGCATCTGAATCTTG-TT-----TTAATTAATTAGAAATTAATTC-GGAAATAAAATTGGAA
* *
5918 AAAGTGATATTAAAAGCGTGAAAA-ACTCGTCAATCTTTTTGGC-GTTGAATTATATATGTTTTG
186 AAA-TGATATTAGAAGCGTGAAAAGAC-CGTCAATCTCTTT-GCTGTTGAATTATATAT-TTTT-
* * * *
5981 TGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGATTTTAGCCGAAATCGTATATT
246 TTAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACT
*
6046 AACCTTCACG
311 AACCATCACG
* * * * * *
6056 GTTTTTGGCTAAAAACGCATTCCCGAGCCCCGACTCAATTTTGCAAGATTTTTGTCGTAAAGACT
1 GTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
** * * *
6121 CCTTGAAGGATCTATATTCATCTAACCTAATGTCAACCACATTGGATATAAGGATTTGTTTTTTC
66 CCTTGAAATATCTATATTCATC-AACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTAC
6186 GAGCATCTGAATCTTGTTTTAATTAATTAGAAATTAATTCGGAAATAAAATTGGAAAAATGATAT
130 GAGCATCTGAATCTTGTTTTAATTAATTAGAAATTAATTCGGAAATAAAATTGGAAAAATGATAT
*
6251 TTGAAGCGTGAAAAGACCGTCAATCTCTTTGCTGTTGAATTATATATATTTTTTAGTATTGTGGC
195 TAGAAGCGTGAAAAGACCGTCAATCTCTTTGCTGTTGAATTATATAT-TTTTTTAGTATTGTGGC
* * * *
6316 AAAAAATTCAGAAAAAACTTTGCGGGTCAGTTTTTAACCGAAATTGTGTACTAACCATCACG
259 AAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACG
* * * * *
6378 GTTTTCGGCTAAAAACGCGTTTCGGAGCCCTAACTCAATTTTGCATGATTTTTGGGGCAAACACT
1 GTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
6443 CCTTGAAATATCTATA
66 CCTTGAAATATCTATA
Statistics
Matches: 911, Mismatches: 115, Indels: 56
0.84 0.11 0.05
Matches are distributed among these distances:
319 74 0.08
320 75 0.08
321 1 0.00
322 281 0.31
323 140 0.15
324 57 0.06
325 2 0.00
328 11 0.01
329 112 0.12
330 158 0.17
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (320 bp):
GTTTTTGGCTAAAAACGCGTTCCGGAGCCCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
CCTTGAAATATCTATATTCATCAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTTAATTAATTAGAAATTAATTCGGAAATAAAATTGGAAAAATGATATT
AGAAGCGTGAAAAGACCGTCAATCTCTTTGCTGTTGAATTATATATTTTTTTAGTATTGTGGCAA
AAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACG
Done.