Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012549.1 Corchorus capsularis cultivar CVL-1 contig12570, 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: 4202
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Found at i:410 original size:23 final size:23
Alignment explanation
Indices: 378--424 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
368 CAATTATAAA
378 GGAGTCTTTCTGTCGAAAATCAT
1 GGAGTCTTTCTGTCGAAAATCAT
*
401 GGAGTTTTTCTGTCGAAAATCAT
1 GGAGTCTTTCTGTCGAAAATCAT
424 G
1 G
425 CGAAATTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (23 bp):
GGAGTCTTTCTGTCGAAAATCAT
Found at i:1706 original size:647 final size:642
Alignment explanation
Indices: 465--3865 Score: 3314
Period size: 647 Copynumber: 5.3 Consensus size: 642
455 TTTAACCCCG
* * * *
465 AATTTTTTTT-TTGAAATATTTGCCACAATATTCAGACAAAATATATGATTCAACGCCAAAAAGA
1 AATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
* * * *
529 TTGACGAACTTTTCACACCTCTA-TTTCGTTTTCCCATTTTTTTCCTAAAAAATTTCTAATGAAA
66 TTGACGAGCTTTTCACACCTCTACTATCGTTTTTCCATTTTTTT-CTAAAAAATTTCTAATTAAA
* *
593 TAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAACGCGGTTGAGTTTGTTGAAT
130 TAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGTTGAGTTTGATGAAT
* *
658 ATTGATATTTTAAAGAGTCTTCACGCCAAAAATTATGCAAAATTGAGCTAGGGCTCCGGCACGCG
195 ATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAACTGAGCTAGGGCTCCGGCACGCG
*
723 TTTTTTGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAACTGACCCG
260 TTTTTTGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTA-AATCTT-CAAAAACTGACCCG
*
788 AAATGTTTTTCCACAATTTTTTGCCACAATACTAAGAAAAAATTATATGATTCAACGCCAAAAAA
323 AAATGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATTCAACGCCAAAAAA
* **
853 TTGAAGGGGTTTTCACGCTTCTAATATCGTTTTACCATTTTTATTCCAATTTATTTCTAATTAAA
388 TTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCA-TTTTATTTGAATTTATTTCTAATTAAA
* *
918 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATCTGGCTGTGATTTTGTTA
452 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGTGATTTTGTTA
* * *
983 GATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATACGAAACTGAGCCGGAACCCCG
517 GATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTGAGCCGGGATCCCG
*
1048 AAACGCGTTTTTAGCCCCAAAACCGTCATGGTTAGTACACGATTT-CTAAAAACTGAGTCGA
582 AAACGCGTTTTTAGCCCCAAAACCGTCATGGTTAGTACACGATTTGCTAAAAACTGA-CCGA
* *
1109 AATTTTTTTTTTCCTGAAATATTTGCCACAATATTCAGGAAAAATATATAATTCAACGCCAAAAA
1 AA--TTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAA
*
1174 GATTGACGAGCTTTCCACACCTCTACT-TCGTTTTTCCATTTTTTTCCTAAAAAATTTCTAATTA
64 GATTGACGAGCTTTTCACACCTCTACTATCGTTTTTCCATTTTTTT-CTAAAAAATTTCTAATTA
*
1238 AATAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATGTCTAATGCGGTTGAGTTTGATGA
128 AATAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGTTGAGTTTGATGA
* *
1303 ATATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAATTGAGCTAGGGCTCTGGCACG
193 ATATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAACTGAGCTAGGGCTCCGGCACG
1368 CGTTTTTTGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATCTTGCAAAAACTGACC
258 CGTTTTTTGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTA-AATCTT-CAAAAACTGACC
*
1433 CGAAATGTTTTTCCTCAATTTTTTTCCACAATACTAAGAAAAAATTATATGATTCAACGCCAAAA
321 CGAAATGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATTCAACGCCAAAA
*
1498 AATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCACTTTTATTTGAGTTTATTTCTAATTA
386 AATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCA-TTTTATTTGAATTTATTTCTAATTA
* * * *
1563 AATCGAAACAAGATTTAGATGCTTG-AAAAAGCAAATCCTTAAATCCAATGTGACGGTGATTTTG
450 AATCGAAACAAGATTCAGATGCTCGTAAAAA-CAAATCCTTAAATCCAATGTGGCTGTGATTTTG
* * * *
1627 TTAGATGAATATAGATATTTTAAGAAGTCTTTCTCCCAAAAATCATTCGAAACTGAGTCGGGATC
514 TTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTGAGCCGGGATC
* * * * * * *
1692 CCGAAACACGTTTTTAGCTCCAAAACTGTGATAGTTAGTACATGATTTCGGCTAAAAGCTGACC-
579 CCGAAACGCGTTTTTAGCCCCAAAACCGTCATGGTTAGTACACGATTT--GCTAAAAACTGACCG
1756 A
642 A
* * * * * *
1757 TAAATTTTTTTCCTGAAATTTTTGCAACAATACTCAGAAAAAATATATAATTAAACGCAAAAAAA
1 -AATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAG
* * * * **
1822 ATTGACG-GATTTTTA-ACGCTTCTAACTATCGTTTTTCCATTTTTCTATAATTAATTTCTAATT
65 ATTGACGAGCTTTTCACAC-C-TCT-ACTATCGTTTTTCCATTTTTTTCTAAAAAATTTCTAATT
* * * ** * * *
1885 AAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATAC-AATGTGGCTGTGATTTG
127 AAATAGAATCAAGATACAGATACCCGTAAAAA-ATGTCCCTATAT-CTAATGCGG-T-TGA----
* * * * * * *
1949 GTTAGATGAATATAGATA-TTTCAAGAAGTCTTTC-TGCCATAAATCATGCGAAACTGAGC-CGT
184 GTTTGATGAATATTGATATTTTAAAG-AGTC-TTCACGCCAAAAATCATGCAAAACTGAGCTAG-
* ** * **
2011 GGCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAGTACACGATTTCGG------C-T-
246 GGCTCCGGCACGCGTTTTTTG-CAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATCTTC
** * * * * *
2068 AAAAACTGAGTCGAAATTTTTATTTCCT-GATATATTTGCCACAATACTCAGAAAAAA-TATATA
310 AAAAACTGACCCGAAA-TGTT-TTTCCTCAAT-TTTTTGCCACAATACTAAGAAAAAATTATATG
* *** * * *
2131 ATTCAACACCAAAAAGATTGACTAGCTTTTCA-GACCTT-TACT-TCGTTTTTCCA-TTTATTTT
372 ATTCAACGCCAAAAA-ATTGAAGGGGTTTTCACG--CTTCTAATATCGTTTTCCCATTTTA-TTT
* *** * * * * * ** * * *
2192 CCTAAAAAATTTCTAATTAAATAGAATCAAGATACAGATACCCGTAAAAA-ATGTCCCTATATCT
433 --GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * * *
2256 AA--T-GCTGTTGA----GTTTGATGAATATTGATATTTTAA-AGAGTC-TTCACGCCAAAAATC
496 AATGTGGCTG-TGATTTTGTTAGATGAATATAGATATTTCAAGA-AGTCTTTC-TGCCAAAAATC
* * * * * * ** * * *
2312 ATGCAAAATTGAGCTAGGGATCCAG-CACGCGTTTTTTG-CAAAAAACTGTGATGGTTAGTACAT
558 ATGCGAAACTGAGC-CGGGATCCCGAAACGCGTTTTTAGCCCCAAAACCGTCATGGTTAGTACAC
2375 GATTTCGGCTACAATTTTGCAAAAACTGACCCGA
622 GATTT--G---C-----T--AAAAACTGA-CCGA
* * * * * *
2409 AA-TGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATTCAACGCCAAAAA-
1 AATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAA-TATATAATTCAACGCCAAAAAG
* * * * * * * *** *
2472 ATTGA-AAGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTTATTTTTAATTA
65 ATTGACGA-GCTTTTCACACCTCTACTATCGTTTTTCCATTTTT-TTCTAAAAAATTTCTAATTA
* * ** * ** * * * *
2536 AATCGAAACAAGATTTAGATGCTTGTAAAAGCAA-ATCCTTAAATCCAATGTGGCGG-TGATTTG
128 AATAGAATCAAGATACAGATACCCGTAAAA--AATGTCCCTATATCTAA--T-GCGGTTGA----
* * * * *
2599 GTTAGATGAATATAGATATTTT-AAGAAGTCTTTC-TGCCAAAAATCCTG-ACAAACTGAG-TCG
184 GTTTGATGAATATTGATATTTTAAAG-AGTC-TTCACGCCAAAAATCATGCA-AAACTGAGCTAG
* ** * ** * * * *
2660 GGACCCCGAAACGCGTTTTTAGCCCCAAAACTGAGATCGTTATTACACGATTTCGGCT-AA---T
246 GG-CTCCGGCACGCGTTTTTTG-CAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATCTT
* * * * *
2721 ----AACTAACCCGAAAT-TTTTTCCTGTAA-TTTTTGCCAAAATACTCAA-AAAAAA-AATATA
309 CAAAAACTGACCCGAAATGTTTTTCCT-CAATTTTTTGCCACAATACT-AAGAAAAAATTATATG
* ** *
2778 ATTCAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAAATATCGTATTT-CCATTTT-TTTA
372 ATTCAACGCCAAAAA-ATTGAAGGGGTTTTCACGCTTCT-AATATCGT-TTTCCCATTTTATTT-
* * * *
2841 TAATTAATTTCTAATTAAATAGAAACAAGATTCAGAAGCTCGTAAAAACAAATCCTTAAATCCAA
433 GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* *
2906 TGTGCCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCG
498 TGTGGCTGTGATTTTGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCG
* *
2971 AAATTGAGCCGTGG--CCCGGAAACGCGTTTTTAGCCCCAAAACCGTGATGG-T--T--A-G---
563 AAACTGAGCCG-GGATCCC-GAAACGCGTTTTTAGCCCCAAAACCGTCATGGTTAGTACACGATT
3025 -G----AAA-T------
626 TGCTAAAAACTGACCGA
* *
3030 --TTTTTTTTCCTGAAATATTTGACACAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGA
1 AATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
* * *
3093 TTGTCGAACTTTTCAGACCTCTACT-TCGTTTTTCCA-TTTTTTCGTAAAAAATTTCTAATTAAA
66 TTGACGAGCTTTTCACACCTCTACTATCGTTTTTCCATTTTTTTC-TAAAAAATTTCTAATTAAA
* *
3156 CAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGATGAGTTTGATGAAT
130 TAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGTTGAGTTTGATGAAT
* *
3221 ATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAAGTAAGCTAGGGCTCCGGCACGCG
195 ATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAACTGAGCTAGGGCTCCGGCACGCG
* * *
3286 TTTTTTGTAAAAAACTGTGATGGTTAGTACACGATTTCGGCTATAATTTTACAAAAAACTGACCC
260 TTTTTTGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTA-AATCTT-C-AAAAACTGACCC
* *
3351 GAAATGTTTTTCCTCAATTTTTTGCCACAATACTGAGAAAAAATTTTATGATTCAACGCCAAAAA
322 GAAATGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATTCAACGCCAAAAA
* *
3416 ATTAAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTTATTTCTAATTAA
387 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCA-TTTTATTTGAATTTATTTCTAATTAA
3481 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGTGATTTTGTT
451 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGTGATTTTGTT
* * * *
3546 AGATGAATATAGATAATTCAAGAAGTCTTTCTGCCATAAATCATGCGAAACTAAGCCGGG-GCTC
516 AGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTGAGCCGGGATC-C
*
3610 CGAAACGCGTTTTTAGCCCTAAAACCGTCATGGTTAGTACACGATTTCGGCTAAAAACTGACCCG
580 CGAAACGCGTTTTTAGCCCCAAAACCGTCATGGTTAGTACACGATTT--GCTAAAAACTGA-CCG
3675 A
642 A
* * *
3676 AATTTTTTTTCCTGAAACATTTGCCACAATACTCAGAAAAAATATATAATTCAACACTAAAAAGA
1 AATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
* * * * **
3741 TTGACG-GATTTTTA-ACGCTTCTAACTATCGTTTTTGCATTTTTGT-TAATTAATTTCTAATTA
66 TTGACGAGCTTTTCACAC-C-TCT-ACTATCGTTTTTCCATTTTTTTCTAAAAAATTTCTAATTA
* * ** * ** * *
3803 AATAGAATCAAGTTTCAGATACTTGTAAAAACAAGTCATTACATCTAATGCGATTGAGATTTG
128 AATAGAATCAAGATACAGATACCCGTAAAAA-ATGTCCCTATATCTAATGCGGTTGAG-TTTG
3866 GTTAGATGAA
Statistics
Matches: 2296, Mismatches: 305, Indels: 305
0.79 0.10 0.10
Matches are distributed among these distances:
610 32 0.01
611 57 0.02
612 10 0.00
614 4 0.00
615 5 0.00
616 2 0.00
617 13 0.01
618 38 0.02
619 30 0.01
620 51 0.02
621 30 0.01
622 213 0.09
623 23 0.01
625 1 0.00
627 1 0.00
628 2 0.00
629 3 0.00
634 1 0.00
638 3 0.00
639 1 0.00
640 33 0.01
641 55 0.02
642 8 0.00
643 2 0.00
644 4 0.00
645 10 0.00
646 41 0.02
647 786 0.34
648 209 0.09
649 117 0.05
650 274 0.12
651 47 0.02
652 7 0.00
653 6 0.00
654 69 0.03
655 74 0.03
656 34 0.01
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (642 bp):
AATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
TTGACGAGCTTTTCACACCTCTACTATCGTTTTTCCATTTTTTTCTAAAAAATTTCTAATTAAAT
AGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGTTGAGTTTGATGAATA
TTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAACTGAGCTAGGGCTCCGGCACGCGT
TTTTTGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATCTTCAAAAACTGACCCGAAA
TGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATTCAACGCCAAAAAATTG
AAGGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTATTTGAATTTATTTCTAATTAAATCGA
AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGTGATTTTGTTAGATG
AATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTGAGCCGGGATCCCGAAAC
GCGTTTTTAGCCCCAAAACCGTCATGGTTAGTACACGATTTGCTAAAAACTGACCGA
Found at i:2397 original size:973 final size:966
Alignment explanation
Indices: 776--3992 Score: 4728
Period size: 973 Copynumber: 3.3 Consensus size: 966
766 CAATTTTGCA
* ** * * * *
776 AAAACTGACCCGAAATGTTTTTCCACAATTTTTTGCCACAATACTAAGAAAAAATTATATGATTC
1 AAAACTGACCCGAAATTTTTTTCCTGAAATTTTTGCAACAATACTCAGAAAAAA-TATATAATTC
* * ** * * *
841 AACGCCAAAAAATTGAAGGGGTTTTCACGCTTCTAA-TATCGTTTTACCATTTTTATTCCAATTT
65 AACGCAAAAAAATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTTATT--AATTA
* * * *
905 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATCTGGC
128 ATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* *
970 TGTGATTTTGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATACGAAACTG
193 TGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTG
* *
1035 AGCCG-GAACCCCGAAACGCGTTTTTAGCCCCAAAACCGTCATGGTTAGTACACGATTT--CTAA
258 AGCCGTG-GCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAGTACACGATTTGGCTAA
*
1097 AAACTGAGTCGAAATTTTTTTTTTCCTGAAATATTTGCCACAATATTCAGGAAAAATATATAATT
322 AAACTGAGTCGAAA--TTTTTTTTCCTGAAATATTTGCCACAATATTCAGAAAAAATATATAATT
* *
1162 CAACGCCAAAAAGATTGACGAGCTTTCCACACCTCTACTTCGTTTTTCCATTTTTTTCCTAAAAA
385 CAACGCCAAAAAGATTGACGAGCTTTTCAGACCTCTACTTCGTTTTTCCATTTTTTTCCTAAAAA
*
1227 ATTTCTAATTAAATAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATGTCTAATGCGGTT
450 ATTTCTAATTAAATAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGTT
1292 GAGTTTGATGAATATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAATTGAGCTAGG
515 GAGTTTGATGAATATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAATTGAGCTAGG
* * *
1357 GCTCTGGCACGCGTTTTTTGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATCTTGC
580 GCTCCGGCACGCGTTTTTTGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTACAATTTTGC
*
1422 AAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTTCCACAATACTAAGAAAAAATTATATGATT
645 AAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATT
* * *
1487 CAACGCCAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCACTTTTATTTGAGTTT
710 CAACGCCAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTT
*
1552 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGAAAAAGCAAATCCTTAAATCCAATGTGAC
775 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGAAAAAGCAAATCCTTAAATCCAATGTGGC
* *
1617 GGTGATTTTGTTAGATGAATATAGATATTTTAAGAAGTCTTTCTCCCAAAAATCATTCGAAACTG
840 GGTGATTTTGTTAGATGAATATAGATATTTTAAGAAGTCTTTCTGCCAAAAATCATACGAAACTG
* * *
1682 AGTCGGGATCCCGAAACACGTTTTTAGCTCCAAAACTGTGATAGTTAGTACATGATTTCGGCT
905 AGTCGGGACCCCGAAACGCGTTTTTAGC-CCAAAACTGTGATAGTTAGTACACGATTTCGGCT
** *
1745 AAAAGCTGACCATAAATTTTTTTCCTGAAATTTTTGCAACAATACTCAGAAAAAATATATAATTA
1 AAAA-CTGACCCGAAATTTTTTTCCTGAAATTTTTGCAACAATACTCAGAAAAAATATATAATTC
*
1810 AACGCAAAAAAAATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTTCTATAATTA
65 AACGC-AAAAAAATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTTAT-TAATTA
*
1875 ATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATACAATGTGGC
128 ATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGC
*
1940 TGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCATAAATCATGCGAAACTG
193 TGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTG
2005 AGCCGTGGCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
258 AGCCGTGGCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAGTACACGATTT-GGCTAA
* *
2070 AAACTGAGTCGAAATTTTTATTTCCTGATATATTTGCCACAATACTCAGAAAAAATATATAATTC
322 AAACTGAGTCGAAATTTTT-TTTCCTGAAATATTTGCCACAATATTCAGAAAAAATATATAATTC
* * *
2135 AACACCAAAAAGATTGACTAGCTTTTCAGACCTTTACTTCGTTTTTCCATTTATTTTCCTAAAAA
386 AACGCCAAAAAGATTGACGAGCTTTTCAGACCTCTACTTCGTTTTTCCATTT-TTTTCCTAAAAA
*
2200 ATTTCTAATTAAATAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCTGTT
450 ATTTCTAATTAAATAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGTT
2265 GAGTTTGATGAATATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAATTGAGCTAGG
515 GAGTTTGATGAATATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAATTGAGCTAGG
* * *
2330 GATCCAGCACGCGTTTTTTGCAAAAAACTGTGATGGTTAGTACATGATTTCGGCTACAATTTTGC
580 GCTCCGGCACGCGTTTTTTGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTACAATTTTGC
2395 AAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATT
645 AAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATT
*
2460 CAACGCCAAAAAATTGAAAGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTT
710 CAACGCCAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTT
* *
2525 ATTTTTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAGCAAATCCTTAAATCCAATGTGGC
775 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGAAAAAGCAAATCCTTAAATCCAATGTGGC
* *
2590 GGTGATTTGGTTAGATGAATATAGATATTTTAAGAAGTCTTTCTGCCAAAAATCCTGAC-AAACT
840 GGTGATTTTGTTAGATGAATATAGATATTTTAAGAAGTCTTTCTGCCAAAAATCAT-ACGAAACT
* * *
2654 GAGTCGGGACCCCGAAACGCGTTTTTAGCCCCAAAACTGAGATCGTTATTACACGATTTCGGCT
904 GAGTCGGGACCCCGAAACGCGTTTTTAG-CCCAAAACTGTGATAGTTAGTACACGATTTCGGCT
* * * *
2718 AATAACTAACCCGAAA-TTTTTTCCTGTAATTTTTGCCAA-AATACTCAAAAAAAAAATATAATT
1 AA-AACTGACCCGAAATTTTTTTCCTGAAATTTTTG-CAACAATACTCAGAAAAAATATATAATT
* * * *
2781 CAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAAATATCGTATTTCCATTTTTTTATAATT
64 CAACG-CAAAAAAATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTTAT-TAATT
2846 AATTTCTAATTAAATAGAAACAAGATTCAGA-AGCTCGTAAAAACAAATCCTTAAATCCAATGTG
127 AATTTCTAATTAAATAGAAACAAGATTCAGATA-CTCGTAAAAACAAATCCTTAAATCCAATGTG
* *
2910 CCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAAT
191 GCTGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAAC
*
2975 TGAGCCGTGGCCCGGAAACGCGTTTTTAGCCCCAAAACCGTGATGG-T--T-----A---GG---
256 TGAGCCGTGGCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAGTACACGATTTGGCTA
*
3026 --AA---A-T-----TTTTTTTTCCTGAAATATTTGACACAATATTCAGAAAAAATATATAATTC
321 AAAACTGAGTCGAAATTTTTTTTCCTGAAATATTTGCCACAATATTCAGAAAAAATATATAATTC
* * *
3080 AACGCCAAAAAGATTGTCGAACTTTTCAGACCTCTACTTCGTTTTTCCA-TTTTTTCGTAAAAAA
386 AACGCCAAAAAGATTGACGAGCTTTTCAGACCTCTACTTCGTTTTTCCATTTTTTTCCTAAAAAA
* *
3144 TTTCTAATTAAACAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGATG
451 TTTCTAATTAAATAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGTTG
* *
3209 AGTTTGATGAATATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAAGTAAGCTAGGG
516 AGTTTGATGAATATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAATTGAGCTAGGG
* * *
3274 CTCCGGCACGCGTTTTTTGTAAAAAACTGTGATGGTTAGTACACGATTTCGGCTATAATTTTACA
581 CTCCGGCACGCGTTTTTTGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTACAATTTTGC-
* *
3339 AAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTGAGAAAAAATTTTATGATT
645 AAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATT
*
3404 CAACGCCAAAAAATTAAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTT
710 CAACGCCAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTT
* *
3469 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-CAAATCCTTAAATCCAATGTGG
775 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTTG-AAAAAGCAAATCCTTAAATCCAATGTGG
* * * * *
3533 CTGTGATTTTGTTAGATGAATATAGATAATTCAAGAAGTCTTTCTGCCATAAATCATGCGAAACT
839 CGGTGATTTTGTTAGATGAATATAGATATTTTAAGAAGTCTTTCTGCCAAAAATCATACGAAACT
* * * * * * *
3598 AAGCCGGGGCTCCGAAACGCGTTTTTAGCCCTAAAACCGTCATGGTTAGTACACGATTTCGGCT
904 GAGTCGGGACCCCGAAACGCGTTTTTAGCCC-AAAACTGTGATAGTTAGTACACGATTTCGGCT
** *
3662 AAAAACTGACCCGAAATTTTTTTTCCTGAAACATTTGCCACAATACTCAGAAAAAATATATAATT
1 -AAAACTGACCCGAAA-TTTTTTTCCTGAAATTTTTGCAACAATACTCAGAAAAAATATATAATT
* * * *
3727 CAACACTAAAAAGATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTGCATTTTTGTTAATTA
64 CAACGC-AAAAAAATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTTATTAATTA
* * * * * * * * **
3792 ATTTCTAATTAAATAGAATCAAGTTTCAGATACTTGTAAAAACAAGTCATTACATCTAATGCGAT
128 ATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * * *
3857 TGAGATTTGGTTAGATGAATAGAGATATTTCAGGGAGTCTTTCTGCCAAAAATCATGCGAAACTC
193 TGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTG
* * * * * * * *
3922 AG--ATGGAACCCCGAAACACGTTTTTAACCCAAAAATCGTGAT-TTTAGTACACAATTTCGGCC
258 AGCCGTGG--CCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAGTACACGATTT-GGCT
3984 AAAAACTGA
320 AAAAACTGA
3993 TCTGAAACAA
Statistics
Matches: 2043, Mismatches: 157, Indels: 101
0.89 0.07 0.04
Matches are distributed among these distances:
943 202 0.10
944 302 0.15
945 245 0.12
946 96 0.05
947 1 0.00
951 1 0.00
952 2 0.00
955 2 0.00
956 2 0.00
960 2 0.00
961 2 0.00
964 2 0.00
969 18 0.01
970 248 0.12
971 26 0.01
972 356 0.17
973 532 0.26
974 4 0.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (966 bp):
AAAACTGACCCGAAATTTTTTTCCTGAAATTTTTGCAACAATACTCAGAAAAAATATATAATTCA
ACGCAAAAAAATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTTATTAATTAATT
TCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGT
GATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTGAGC
CGTGGCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAGTACACGATTTGGCTAAAAAC
TGAGTCGAAATTTTTTTTCCTGAAATATTTGCCACAATATTCAGAAAAAATATATAATTCAACGC
CAAAAAGATTGACGAGCTTTTCAGACCTCTACTTCGTTTTTCCATTTTTTTCCTAAAAAATTTCT
AATTAAATAGAATCAAGATACAGATACCCGTAAAAAATGTCCCTATATCTAATGCGGTTGAGTTT
GATGAATATTGATATTTTAAAGAGTCTTCACGCCAAAAATCATGCAAAATTGAGCTAGGGCTCCG
GCACGCGTTTTTTGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAAC
TGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATTATATGATTCAACGC
CAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTTATTTCT
AATTAAATCGAAACAAGATTTAGATGCTTGAAAAAGCAAATCCTTAAATCCAATGTGGCGGTGAT
TTTGTTAGATGAATATAGATATTTTAAGAAGTCTTTCTGCCAAAAATCATACGAAACTGAGTCGG
GACCCCGAAACGCGTTTTTAGCCCAAAACTGTGATAGTTAGTACACGATTTCGGCT
Found at i:3822 original size:323 final size:321
Alignment explanation
Indices: 3339--3992 Score: 781
Period size: 323 Copynumber: 2.0 Consensus size: 321
3329 TAATTTTACA
*** * * *
3339 AAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTGAGAAAAAATTTTATGATT
1 AAAAACTGACCCGAAATGTTTTTCCTCAAACATTTGCCACAATACTCAGAAAAAATTATATAATT
* * * *
3404 CAACGCCAAAAAATTAAAGGGGTTTTCACGCTTCTAATATCGTTTTCCCATTTTTATTCGAATTT
66 CAACACCAAAAAATTAAAGGAGTTTTAACGCTTCTAATATCGTTTTCCCATTTTTATTC-AATTA
* * * * *
3469 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
130 ATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCATTAAATCCAATGCGAC
* * * *
3534 TGTGATTTTGTTAGATGAATATAGATAATTCAAGAAGTCTTTCTGCCATAAATCATGCGAAACTA
195 TGAGATTTGGTTAGATGAATAGAGATAATTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTA
* ** * * * * * *
3599 AGCCGGGGCTCCGAAACGCGTTTTTAGCCCTAAAACCGTCATGGTTAGTACACGATTTCGGCT
260 AGACGGAACCCCGAAACACGTTTTTAACCCAAAAACCGTCAT-GTTAGTACACAATTTCGGCC
* *
3662 AAAAACTGACCCGAAATTTTTTTTCCTGAAACATTTGCCACAATACTCAGAAAAAA-TATATAAT
1 AAAAACTGACCCGAAA-TGTTTTTCCTCAAACATTTGCCACAATACTCAGAAAAAATTATATAAT
* * * * ** *
3726 TCAACACTAAAAAGATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTGCATTTTTGTT-AAT
65 TCAACACCAAAAA-ATTAAAGGAGTTTTAACGCTTCTAA-TATCGTTTTCCCATTTTTATTCAAT
* * * * * *
3790 TAATTTCTAATTAAATAGAATCAAGTTTCAGATACTTGTAAAAACAAGTCATTACATCTAATGCG
128 TAATTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCATTAAATCCAATGCG
* * * *
3855 ATTGAGATTTGGTTAGATGAATAGAGATATTTCAGGGAGTCTTTCTGCCAAAAATCATGCGAAAC
193 ACTGAGATTTGGTTAGATGAATAGAGATAATTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAAC
* * * * *
3920 TCAGATGGAACCCCGAAACACGTTTTTAACCCAAAAATCGTGATTTTAGTACACAATTTCGGCC
258 TAAGACGGAACCCCGAAACACGTTTTTAACCCAAAAACCGTCATGTTAGTACACAATTTCGGCC
3984 AAAAACTGA
1 AAAAACTGA
3993 TCTGAAACAA
Statistics
Matches: 276, Mismatches: 52, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
322 26 0.09
323 179 0.65
324 53 0.19
325 18 0.07
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (321 bp):
AAAAACTGACCCGAAATGTTTTTCCTCAAACATTTGCCACAATACTCAGAAAAAATTATATAATT
CAACACCAAAAAATTAAAGGAGTTTTAACGCTTCTAATATCGTTTTCCCATTTTTATTCAATTAA
TTTCTAATTAAATAGAAACAAGATTCAGATACTCGTAAAAACAAATCATTAAATCCAATGCGACT
GAGATTTGGTTAGATGAATAGAGATAATTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACTAA
GACGGAACCCCGAAACACGTTTTTAACCCAAAAACCGTCATGTTAGTACACAATTTCGGCC
Done.