Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008092.1 Corchorus capsularis cultivar CVL-1 contig08113, 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: 4300
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:698 original size:365 final size:364
Alignment explanation
Indices: 1--824 Score: 1341
Period size: 365 Copynumber: 2.3 Consensus size: 364
*
1 ATCACGGTTTTTAGCTAAAAACGCGTTC-TGGGCCCTGGCACAGTTTTGCATGATTTTTGGGGCC
1 ATCACGGTTTTTAGCTAAAAACGCGTTCTTGGGCCCTGGCACAGTTTTGCATGATTTTTGGCGCC
*
65 AACACTCCTTGAAATATCTATATTCATCTAACTATTTAAAAAAAATCTGTATTCATCTAACAAAA
66 AACACTCCTTGAAATATCTATATTCATCTAACTATTTAAAAAAAATCTATATTCATCTAACAAAA
*
130 TTGCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCTGAATCTTGTTTCGATTTAATTA
131 TTGCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCTGAATCTTGTTTCAATTTAATTA
* *
195 GAATTTGATTTAGAAAAAAAAATATGAAAAACAATATTAGAAGCGAGAAAAGCCCTCCTATCTTT
196 GAATTTAATTCAGAAAAAAAAATATGAAAAACAATATTAGAAGCGAGAAAAGCCCTCCTATCTTT
** *
260 TTGGCGTTGAATTATATATTTTTTATACGTATTGTAGCTAAAAATTGAGGGAAAATCTTTCGGGT
261 TTGGCAATGAATTATATATTTTTTATACGTATTGTAGCTAAAAATTGAGGGAAAATCTTTCAGGT
*
325 TAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
326 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
**
364 ATCACGGTTTTTAGCTAAAAACGCGTTCTTGGGCCCTGGCACAGTTTTGCATGATTTTTGTTGCC
1 ATCACGGTTTTTAGCTAAAAACGCGTTCTTGGGCCCTGGCACAGTTTTGCATGATTTTTGGCGCC
429 AACACTCCTTGAAATATCTATATTCATCTAACTATTTTAAAAAAAAATCTATATTCATCTAACAA
66 AACACTCCTTGAAATATCTATATTCATCTAACTA-TTT-AAAAAAAATCTATATTCATCTAACAA
* * *
494 AATTGTAGCAACATTTCATTTAAGGATTTGTTTTTAAGTGTATCTTAATCTTGTTTCAATTTAAT
129 AATTGCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCTGAATCTTGTTTCAATTTAAT
*
559 TAGAATTTAATTCAG-AAAAAAAATGTGAAAAACAATATTAGAAGCGAGAAAAGCCCTCCTATCT
194 TAGAATTTAATTCAGAAAAAAAAATATGAAAAACAATATTAGAAGCGAGAAAAGCCCTCCTATCT
* * *
623 TTTTGGCAATGAATTATATATTTTTTATACGTATTGTGGCTATAAATTTAGGGAAAATCTTTCAG
259 TTTTGGCAATGAATTATATATTTTTTATACGTATTGTAGCTAAAAATTGAGGGAAAATCTTTCAG
*
688 GTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACC
324 GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
* * ** * * *
729 ATTACGATTTTCGGCTAAAAACGCATTCTCTGGCCCCAT--CTCAGTTTTGCATGATTTTTGGCG
1 ATCACGGTTTTTAGCTAAAAACGCGTTCT-TGGGCCC-TGGCACAGTTTTGCATGATTTTTGGCG
*
792 CTAACACTCCTTGAAATATCTATATTCATCTAA
64 CCAACACTCCTTGAAATATCTATATTCATCTAA
825 AATAATCTCA
Statistics
Matches: 428, Mismatches: 28, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
363 28 0.07
364 68 0.16
365 226 0.53
366 105 0.25
367 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (364 bp):
ATCACGGTTTTTAGCTAAAAACGCGTTCTTGGGCCCTGGCACAGTTTTGCATGATTTTTGGCGCC
AACACTCCTTGAAATATCTATATTCATCTAACTATTTAAAAAAAATCTATATTCATCTAACAAAA
TTGCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCTGAATCTTGTTTCAATTTAATTA
GAATTTAATTCAGAAAAAAAAATATGAAAAACAATATTAGAAGCGAGAAAAGCCCTCCTATCTTT
TTGGCAATGAATTATATATTTTTTATACGTATTGTAGCTAAAAATTGAGGGAAAATCTTTCAGGT
CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
Found at i:1082 original size:333 final size:325
Alignment explanation
Indices: 475--1698 Score: 1607
Period size: 322 Copynumber: 3.7 Consensus size: 325
465 TTAAAAAAAA
* * *
475 ATCTATATTCATCTAACAAAATTGT-AGCAACATTTCATTTAAGGATTTGTTTTTAAGTGTATCT
1 ATCTATATTCATCTAA-AAAAGTCTCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCT
* * *
539 TAATCTTGTTTCAATTTAATTAGAATTTAATTCAGAAAAAAAATGTGAAAAACAATATTAGAAGC
65 GAATCTTGTTTCGATTAAATTAGAATTTAATTC------AAAA---GAAAAACAATATTAGAAGC
* ** * *
604 GAGAAAAGCCCTCCT-ATCTTTTTGGCAATGAATTATATATTTTTTAT-ACGTATTGTGGCTATA
121 GAGAAAAGCCC-CCTAATATTTTTGGCGTTGAATTATATATTTTTTATGA-GAATTGTGGCTAAA
*
667 AATTTAGGGAAAATCTTTC-AGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCAT
184 AATTTAGGGAAAATCTTTCGA-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* * * * * *
731 TACGATTTTCGGCTAAAAACGCATTCTCTGGCCCCATCTCAGTTTTGCATGATTTTTGGCGCTAA
248 CACGGTTTTTGGCTAAAAACGCGTTCTCGGGCCCCACCTCAGTTTTGCATGATTTTTGGCGCTAA
796 CACTCCTTGAAAT
313 CACTCCTTGAAAT
809 ATCTATATTCATCTAAAATAA-TCTCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCT
1 ATCTATATTCATCTAAAA-AAGTCTCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCT
* *
873 GAATCTTGTTTCGATTTAATTAGAATTTAATTCTGAAAAAAATATGAAAAACAATATTAGAAGTG
65 GAATCTTGTTTCGATTAAATTAGAATTTAATTC------AAA-A-GAAAAACAATATTAGAAGCG
* * *
938 AGAAAAGCCCTCCT-ATCTTTTTGGCGTTGAATTATATATTTTTTAT-ACGTATTGTAGCTAAAA
122 AGAAAAGCCC-CCTAATATTTTTGGCGTTGAATTATATATTTTTTATGA-GAATTGTGGCTAAAA
*
1001 ATTTAAGGAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
185 ATTTAGGGAAAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
** * * *
1066 CGGTTTTTGGCTAAAAACGCGTTCTCGGGCCCTGCCACAGTTTTGCATGATCTTTGGCGCCAACA
250 CGGTTTTTGGCTAAAAACGCGTTCTCGGGCCCCACCTCAGTTTTGCATGATTTTTGGCGCTAACA
*
1131 CTCCTTGAAGT
315 CTCCTTGAAAT
* *
1142 ATCTATATTCATCTAAAAAAGTCTCAGAAACCTTTCATTTAAGGATTTGTTTTTAAGAGTATCTG
1 ATCTATATTCATCTAAAAAAGTCTCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCTG
* * * *
1207 AATCTTATTTCGATTAAATTTGAATTTAATTC---AGAAAAAAAATATTAGAAGCGGGAAAAGCC
66 AATCTTGTTTCGATTAAATTAGAATTTAATTCAAAAGAAAAACAATATTAGAAGCGAGAAAAGCC
* * * *
1269 CGCTAATATTTTTTGCGTTCAATTATATATTTTTTATGAGAATTGTGGCTAAAAATTGAGGGAAA
131 CCCTAATATTTTTGGCGTTGAATTATATATTTTTTATGAGAATTGTGGCTAAAAATTTAGGGAAA
* *
1334 ATCTTTCG-GATCAATTCTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTG
196 ATCTTTCGAG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
*
1398 CTAAAAACGCGTTCTCGGGCCCCAGCTCAGTTTTGCATGATTTTTGGCGCTAACACTCCTTGAAA
260 CTAAAAACGCGTTCTCGGGCCCCACCTCAGTTTTGCATGATTTTTGGCGCTAACACTCCTTGAAA
1463 T
325 T
1464 ATCTATATTCATCTAAAAAAAGTCTCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCT
1 ATCTATATTCATCT-AAAAAAGTCTCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCT
* * *
1529 GAATCTTGTTTGGATTAAATTTGAATTTAATTCAAAA-AAAAAC---ATTAGAAGCGGGAAAAGC
65 GAATCTTGTTTCGATTAAATTAGAATTTAATTCAAAAGAAAAACAATATTAGAAGCGAGAAAAGC
* * * * *
1590 CCGCTAATATTTTTTGCGTTGACTAATATATTTTTTATGAGAATTGTGGCTAAAAA-TTGGGGAA
130 CCCCTAATATTTTTGGCGTTGAATTATATATTTTTTATGAGAATTGTGGCTAAAAATTTAGGG-A
* * *
1654 AAATCTTTCGGGTCAATTTTTACAAAATTTTACCCGAAATCGTGT
194 AAATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
1699 TATATGAATA
Statistics
Matches: 814, Mismatches: 62, Indels: 40
0.89 0.07 0.04
Matches are distributed among these distances:
321 7 0.01
322 323 0.40
323 82 0.10
325 5 0.01
326 1 0.00
332 2 0.00
333 297 0.36
334 96 0.12
335 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (325 bp):
ATCTATATTCATCTAAAAAAGTCTCAGCAACATTTCATTTAAGGATTTGTTTTTAAGAGTATCTG
AATCTTGTTTCGATTAAATTAGAATTTAATTCAAAAGAAAAACAATATTAGAAGCGAGAAAAGCC
CCCTAATATTTTTGGCGTTGAATTATATATTTTTTATGAGAATTGTGGCTAAAAATTTAGGGAAA
ATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC
TAAAAACGCGTTCTCGGGCCCCACCTCAGTTTTGCATGATTTTTGGCGCTAACACTCCTTGAAAT
Found at i:1726 original size:21 final size:21
Alignment explanation
Indices: 1702--1741 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1692 ATCGTGTTAT
1702 ATGAATATAGATTGAATATAG
1 ATGAATATAGATTGAATATAG
1723 ATGAATATAGATTGAATAT
1 ATGAATATAGATTGAATAT
1742 GAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.35
Consensus pattern (21 bp):
ATGAATATAGATTGAATATAG
Found at i:1729 original size:10 final size:11
Alignment explanation
Indices: 1703--1741 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
1693 TCGTGTTATA
1703 TGAATATAGAT
1 TGAATATAGAT
1714 TGAATATAGA-
1 TGAATATAGAT
1724 TGAATATAGAT
1 TGAATATAGAT
1735 TGAATAT
1 TGAATAT
1742 GAATATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (11 bp):
TGAATATAGAT
Found at i:3274 original size:663 final size:662
Alignment explanation
Indices: 1832--4298 Score: 2016
Period size: 663 Copynumber: 3.8 Consensus size: 662
1822 TTTTGAAATA
* * ** *
1832 GTTATATGAATATAGATATTTCAAGGAGTGTTGGCGCCAAAAATCATTCAAAACTGAA-TCAGGG
1 GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGAAAAACT-AAGTCGGGG
* * * * * * *
1896 CCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGT-TAGTACACGATTTCGGCTAAAATTTGGCA
65 CCAGGAACGAGTTTTTAGCCAAAAACTGTGAGGGTAT-GTACACGATTTCGGCTAAAATTTTGTA
* *
1960 AAAATTGACCCGAAAGATTTTCCCTCCATTTTTAGCCAACAATAACGT-AT-AAAAATATATAAT
129 AAAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCC-ACAAT-AC-TCATAAAAAATATATAAT
* * *
2023 TCAATGCCAAAAAGA-TAGGAGGGCTTTTCTCGCTTTTAATATTGTTTTTCATATTTTTTTTCTG
191 TCAACGCCAAAAAGATTA-GAGGGCTTTTCCCGCTTCTAATATTGTTTTTC-T-TTTTTTTTCTG
* * * ** *
2087 AGTT-AATTTATAACTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATCTT-GTTGAATT
253 AATTAAATTCA-AATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATCTTAAATGAAAT
* **
2150 GTTTCTAAGATTTTGTTAGATGAATATAGATATTTCAAGCAACGCGTTTTTAACCAAAAATCATG
317 GTTGCTAAGATTTTGTTAGATGAATATAGATATTTCAAGCAACGCGTTTAGAACCAAAAATCATG
* * *
2215 AAAAACTATGCCGGGGCCAAGGAACGCGTTTTTAACCAAAAATTGTGAGGGTATGTACATGATTT
382 AAAAACTA-GCCGGAGCCAAGGAACGCGTTTTTAACCAAAAATCGTGAGGGTATGTACACGATTT
*
2280 CGGCTAAAATTTTGCAAAAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCAAAATAATCATA
446 CGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTCCCTCAATTTTTAGCCAAAATAATCATA
* * * * * * *
2345 AAAAATATATGATTCAACTCCTAAAAGATTGGAGGGATTTTCCCGCATCTAATCTTGTTTTTCTT
511 AAAAATATATGATGCAACGCCAAAAAGATAGGAGGGATTTTCCCGCATCTAATATTATTTTTCAT
* * *
2410 ATTTTTTTAATTAATTTCCAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATACTCA
576 ATTTTTTTAATTAATTTACAACTAAATCGAAACAAGATTCAGATACTCTTAAAAACAAATACTCA
2475 ATTCAAATCTTACCGAGATTTT
641 ATTCAAATCTTACCGAGATTTT
* * * * * *
2497 GTTAGATGAACATAGATATTTCAAGGAGTTTTGCCACCAAAAATCATGAAAAAATGAG-CTGGGG
1 GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGAAAAACTAAGTC-GGGG
* ** ** *
2561 TCCAGGAACGAGTTTTTAGCCAAAAACTGTGTGCTTACATACATGATTTCGGCTAAAATTTTGTA
65 -CCAGGAACGAGTTTTTAGCCAAAAACTGTGAGGGTATGTACACGATTTCGGCTAAAATTTTGTA
* *
2626 AAAATTGAACTGAAAGATTTTCCCTCAATTTTTAGCCACAATTCTCATAAAAAATATATAATTCA
129 AAAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCA
* * *
2691 ACGCAAAAAATATTAGCGGGCTTTTCCCGCTTCTAATATTGTTTTTCTTTTTTTTTCTGAATTAA
194 ACGCCAAAAAGATTAGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCTTTTTTTTTCTGAATTAA
* *
2756 ATTCAAATTTAATCGAAACAAGATTCAGATACTCTTAAAAACAAATCCTTAAATGAAATGTTGCT
259 ATTCAAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAAT-CTTAAATGAAATGTTGCT
* * * ** *
2821 GAGACTTTT-TTAGATGAATATAGATATTTCAAG-GA-GTG-TTAGCGCCAAAAATCATGCAAAA
323 AAGA-TTTTGTTAGATGAATATAGATATTTCAAGCAACGCGTTTAGAACCAAAAATCATGAAAAA
* * * *
2882 CT-GACCTGGAGCC-TGAGAACGCGTTTTTATCCGAAAATCGTGATGGT-TAGTACACGATTTCG
387 CTAG-CC-GGAGCCAAG-GAACGCGTTTTTAACCAAAAATCGTGAGGGTAT-GTACACGATTTCG
* * *
2944 GCTAAAATTTTGCAAAAATTGACCCGAAATATTTTCCCTCAATTTTTAGCCACAATACGT-ATAA
448 GCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTCCCTCAATTTTTAGCCAAAATA-ATCATAA
* * *
3008 AAAATATA-GAATGCAACGCCAAAAAGATAGGAGGGCTTTTCTCGCTTCTAATATTATTTTTCAT
512 AAAATATATG-ATGCAACGCCAAAAAGATAGGAGGGATTTTCCCGCATCTAATATTATTTTTCAT
* *
3072 ATTTTTTTCTGAGTTAATTTATAACTAAATCGAAACAAGATTCAGATACTCTTAAAAACAAAT-C
576 A-TTTTTT-T-AATTAATTTACAACTAAATCGAAACAAGATTCAGATACTCTTAAAAACAAATAC
** * * *
3136 -CTGTTGAATTGTT-CCTGAGATTTT
638 TCAATTCAAATCTTACC-GAGATTTT
* *
3160 GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCAGGAAAAACTAAGTCGGGGC
1 GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGAAAAACTAAGTCGGGGC
* * *
3225 CAAGGAACGTGTTTTTAACCAAAAATTGTGAGGGTATGTACACGATTTCGGCTAAAATTTTGTAA
66 C-AGGAACGAGTTTTTAGCCAAAAACTGTGAGGGTATGTACACGATTTCGGCTAAAATTTTGTAA
* * **
3290 AAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCAAAATAATCATAAAAAATATATGGTTCAA
130 AAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAA
* * * * *
3355 CGCCTAAAAGATTGGAGGGATTTTCCCGCTTCTAATATTGTTTTTCTTATTTTTT-T-AATTAAT
195 CGCCAAAAAGATTAGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCTTTTTTTTTCTGAATTAAA
* * * * *
3418 TTCCAATTAAATCCAAATAAGATTCAGATACTCTTAAAAACAAATACTTAATTAAAAT-TTTC-A
260 TTCAAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAAT-CTTAAATGAAATGTTGCTA
** * ** * * ** * ** ***** *
3481 AGGAGTTTTGCCACCAAAAATCAT-GAAAATTT-GAGC-TGGGGTCCAGGAACCCGTTTTTA-GC
324 A-GA-TTTTGTTA-GATGAAT-ATAG-ATATTTCAAGCAACGCGTTTA-GAACCAAAAATCATG-
* * * * * *** * **
3542 CAAAAA--A-TCGTGAGCTAA-CATACACG-ATTTCGGCTAAAAT--T-----T-TGTA-AAAAT
382 -AAAAACTAGCCG-GAGCCAAGGA-ACGCGTTTTTAACCAAAAATCGTGAGGGTATGTACACGAT
* * * * * **
3593 TGAC-CCGAAAGA-TTT-------TT--CCTC---A-ATTTT--T---------AGCCACAATTC
444 T-TCGGCTAAA-ATTTTGCAAAAATTGACC-CGAAAGATTTTCCCTCAATTTTTAGCCAAAATAA
* * * * * * *
3632 TCATAAAAAAATATATAATTCAACGCAAAAAATATTAGCG-GGCA-TTTCCCGCTTCTAATATTG
506 TCAT-AAAAAATATATGATGCAACGCCAAAAAGA-TAG-GAGGGATTTTCCCGCATCTAATATTA
* * * * *
3695 TTTTTCTTTTTTTTTCTGAATTAAATT-CAAATTTAATCGAAACAAGATTCAGATACTCTTAAAA
568 TTTTTCATATTTTTT-T-AATTAATTTAC-AACTAAATCGAAACAAGATTCAGATACTCTTAAAA
* * * * * * *
3759 ACAAATCCTTAAATGAAATGTTGCTGAGACTTTT
630 ACAAATACTCAATTCAAATCTTACCGAGA-TTTT
* * * * * * *
3793 -TTAGATAAATATGGATATTTCAAGGAGTGTTAGCGCAAAAAATCATGCAAAACTGAGTC-GGGC
1 GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGAAAAACTAAGTCGGGGC
* * * * * *
3856 CCGAGAA-AACGTTTTTAGCCAAAAACCGTAATGAT-TAGTACACGATTTTCGGCTAAAATTTTG
66 CAG-GAACGA-GTTTTTAGCCAAAAACTGTGAGGGTAT-GTACACGA-TTTCGGCTAAAATTTTG
** * *
3919 TAAAAATTGAGCC-GAAAGATTTTTGCTGAATTTTTAGCCACAATTC-CAT-AAAAATATATAAT
127 TAAAAATTGA-CCTGAAAGATTTTCCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAAT
* * * * * *
3981 TCAACACCAAAAACATTAGCGGGCTTTTCCCGCTTCAAATATTTTTTTTCTTATTTTTTCTGAAT
191 TCAACGCCAAAAAGATTAGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCTTTTTTTTTCTGAAT
* * * *
4046 TAATTTCTAATTAAATCGAAACAATATTCAGATACTCTTAAAAACAAATCCTTAAATGAAATGTT
256 TAAATTCAAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAAT-CTTAAATGAAATGTT
* *
4111 GCTGAGATTTTGTTAGATGAATATAGATATTTCAAG-GA-GTC-TTGCT-G--CCAAAAATCATG
320 GCTAAGATTTTGTTAGATGAATATAGATATTTCAAGCAACG-CGTT--TAGAACCAAAAATCATG
* * * * * * *
4170 CAAAACTGAGTCAGG-GCCCAGGAACGCGTTTTTAGCCAAAAACCGTGATGAT-TAGTACACGAT
382 AAAAACT-AG-CCGGAGCCAAGGAACGCGTTTTTAACCAAAAATCGTGAGGGTAT-GTACACGAT
* *
4233 ATCGGCTAAAATTTTGCAAAAATTGA-CCGAAAAGATTTTTCCTCAATTATTT--CCAAAAATAA
444 TTCGGCTAAAATTTTGCAAAAATTGACCCG-AAAGATTTTCCCTCAATT-TTTAGCC-AAAATAA
4295 TCAT
506 TCAT
4299 TA
Statistics
Matches: 1429, Mismatches: 261, Indels: 226
0.75 0.14 0.12
Matches are distributed among these distances:
627 4 0.00
628 4 0.00
629 2 0.00
630 148 0.10
631 106 0.07
632 188 0.13
633 14 0.01
634 1 0.00
638 2 0.00
639 5 0.00
640 10 0.01
641 5 0.00
642 1 0.00
644 2 0.00
645 1 0.00
646 2 0.00
647 3 0.00
648 1 0.00
651 1 0.00
652 5 0.00
653 11 0.01
654 5 0.00
655 2 0.00
659 1 0.00
660 11 0.01
661 63 0.04
662 200 0.14
663 319 0.22
664 20 0.01
665 198 0.14
666 94 0.07
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (662 bp):
GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGAAAAACTAAGTCGGGGC
CAGGAACGAGTTTTTAGCCAAAAACTGTGAGGGTATGTACACGATTTCGGCTAAAATTTTGTAAA
AATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAAC
GCCAAAAAGATTAGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCTTTTTTTTTCTGAATTAAAT
TCAAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATCTTAAATGAAATGTTGCTAAG
ATTTTGTTAGATGAATATAGATATTTCAAGCAACGCGTTTAGAACCAAAAATCATGAAAAACTAG
CCGGAGCCAAGGAACGCGTTTTTAACCAAAAATCGTGAGGGTATGTACACGATTTCGGCTAAAAT
TTTGCAAAAATTGACCCGAAAGATTTTCCCTCAATTTTTAGCCAAAATAATCATAAAAAATATAT
GATGCAACGCCAAAAAGATAGGAGGGATTTTCCCGCATCTAATATTATTTTTCATATTTTTTTAA
TTAATTTACAACTAAATCGAAACAAGATTCAGATACTCTTAAAAACAAATACTCAATTCAAATCT
TACCGAGATTTT
Found at i:3294 original size:331 final size:331
Alignment explanation
Indices: 1832--3462 Score: 1888
Period size: 332 Copynumber: 4.9 Consensus size: 331
1822 TTTTGAAATA
* ** * *
1832 GTTATATGAATATAGATATTTCAAGGAGTGTTGGCGCCAAAAATCATTCAAAACTGAA-TCAGGG
1 GTTAGATGAATATAGATATTTCAAGGAGTGTTGGCGCCAAAAATCATGAAAAACT-AAGCCGGGG
* * * ** * *
1896 CCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGT-TAGTACACGATTTCGGCTAAAATTTGGCA
65 CCAGGAACGCGTTTTTAACCAAAAATTGTGAGGGTAT-GTACACGATTTCGGCTAAAATTTTGCA
* * * *
1960 AAAATTGACCCGAAAGATTTTCCCTCCATTTTTAGCCAACAATA-A-CGTATAAAAATATATAAT
129 AAAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCC-ACAATACATCATA-AAAAATATAGAAT
* * *
2023 TCAATGCCAAAAAGATAGGAGGGCTTTTCTCGCTTTTAATATTGTTTTTCATATTTTTTTTCTGA
192 TCAACGCCAAAAAGATAGGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCATA-TTTTTTTCTGA
* * * * *
2088 GTTAATTTATAACTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATCTTGTTGAATTGTT
256 ATTAATTTACAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATCCTGTTGAAATGTT
* *
2153 TCTAAGATTTT
321 CCTGAGATTTT
* * **** *
2164 GTTAGATGAATATAGATATTTCAAGCAACGCGTTTTTAACCAAAAATCATGAAAAACTATGCCGG
1 GTTAGATGAATATAGATATTTCAAG-GA-GTG-TTGGCGCCAAAAATCATGAAAAACTAAGCCGG
*
2229 GGCCAAGGAACGCGTTTTTAACCAAAAATTGTGAGGGTATGTACATGATTTCGGCTAAAATTTTG
63 GGCC-AGGAACGCGTTTTTAACCAAAAATTGTGAGGGTATGTACACGATTTCGGCTAAAATTTTG
*
2294 CAAAAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCAAAATA-ATCATAAAAAATATATG-A
127 CAAAAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCACAATACATCATAAAAAATATA-GAA
* * * * * * *
2357 TTCAACTCCTAAAAGATTGGAGGGATTTTCCCGCATCTAATCTTGTTTTTCTTA-TTTTTT-T-A
191 TTCAACGCCAAAAAGATAGGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCATATTTTTTTCTGA
* ** * *
2419 ATTAATTTCCAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATACTCAATTCAAATC
256 ATTAATTTACAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAAT-C-CTGTTGAAATG
2484 TTACC-GAGATTTT
319 TT-CCTGAGATTTT
* * * * * * *
2497 GTTAGATGAACATAGATATTTCAAGGAGTTTTGCCACCAAAAATCATGAAAAAATGAGCTGGGGT
1 GTTAGATGAATATAGATATTTCAAGGAGTGTTGGCGCCAAAAATCATGAAAAACTAAGCCGGGG-
* * * * ** ** * *
2562 CCAGGAACGAGTTTTTAGCCAAAAACTGTGTGCTTACATACATGATTTCGGCTAAAATTTTGTAA
65 CCAGGAACGCGTTTTTAACCAAAAATTGTGAGGGTATGTACACGATTTCGGCTAAAATTTTGCAA
* * *
2627 AAATTGAACTGAAAGATTTTCCCTCAATTTTTAGCCACAATTC-TCATAAAAAATATATAATTCA
130 AAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCACAATACATCATAAAAAATATAGAATTCA
* * * *
2691 ACGCAAAAAATATTA-GCGGGCTTTTCCCGCTTCTAATATTGTTTTTC-TTTTTTTTTCTGAATT
195 ACGCCAAAAAGA-TAGGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCATATTTTTTTCTGAATT
* * *
2754 AAATT-CAAATTTAATCGAAACAAGATTCAGATACTCTTAAAAACAAATCCT-TAAATGAAATGT
259 AATTTAC-AATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATCCTGT---TGAAATGT
*
2817 TGCTGAGACTTTT
320 TCCTGAGA-TTTT
* * * *
2830 -TTAGATGAATATAGATATTTCAAGGAGTGTTAGCGCCAAAAATCATGCAAAACTGA-CCTGGAG
1 GTTAGATGAATATAGATATTTCAAGGAGTGTTGGCGCCAAAAATCATGAAAAACTAAGCC-GGGG
* * * * *
2893 CCTGAGAACGCGTTTTTATCCGAAAATCGTGATGGT-TAGTACACGATTTCGGCTAAAATTTTGC
65 CCAG-GAACGCGTTTTTAACCAAAAATTGTGAGGGTAT-GTACACGATTTCGGCTAAAATTTTGC
* * * *
2957 AAAAATTGACCCGAAATATTTTCCCTCAATTTTTAGCCACAATACGT-ATAAAAAATATAGAATG
128 AAAAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCACAATACATCATAAAAAATATAGAATT
* * *
3021 CAACGCCAAAAAGATAGGAGGGCTTTTCTCGCTTCTAATATTATTTTTCATATTTTTTTCTGAGT
193 CAACGCCAAAAAGATAGGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCATATTTTTTTCTGAAT
* * * *
3086 TAATTTATAACTAAATCGAAACAAGATTCAGATACTCTTAAAAACAAATCCTGTTGAATTGTTCC
258 TAATTTACAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATCCTGTTGAAATGTTCC
3151 TGAGATTTT
323 TGAGATTTT
* * * *
3160 GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCAGGAAAAACTAAGTCGGGGC
1 GTTAGATGAATATAGATATTTCAAGGAGTGTTGGCGCCAAAAATCATGAAAAACTAAGCCGGGGC
* *
3225 CAAGGAACGTGTTTTTAACCAAAAATTGTGAGGGTATGTACACGATTTCGGCTAAAATTTTGTAA
66 C-AGGAACGCGTTTTTAACCAAAAATTGTGAGGGTATGTACACGATTTCGGCTAAAATTTTGCAA
* *
3290 AAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCAAAATA-ATCATAAAAAATATATG-GTTC
130 AAATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCACAATACATCATAAAAAATATA-GAATTC
* * * *
3353 AACGCCTAAAAGATTGGAGGGATTTTCCCGCTTCTAATATTGTTTTTCTTA-TTTTTT-T-AATT
194 AACGCCAAAAAGATAGGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCATATTTTTTTCTGAATT
* *
3415 AATTTCCAATTAAATCCAAATAAGATTCAGATACTCTTAAAAACAAAT
259 AATTTACAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAAT
3463 ACTTAATTAA
Statistics
Matches: 1098, Mismatches: 163, Indels: 80
0.82 0.12 0.06
Matches are distributed among these distances:
328 46 0.04
329 3 0.00
330 193 0.18
331 282 0.26
332 283 0.26
333 110 0.10
334 5 0.00
335 85 0.08
336 90 0.08
337 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (331 bp):
GTTAGATGAATATAGATATTTCAAGGAGTGTTGGCGCCAAAAATCATGAAAAACTAAGCCGGGGC
CAGGAACGCGTTTTTAACCAAAAATTGTGAGGGTATGTACACGATTTCGGCTAAAATTTTGCAAA
AATTGACCTGAAAGATTTTCCCTCAATTTTTAGCCACAATACATCATAAAAAATATAGAATTCAA
CGCCAAAAAGATAGGAGGGCTTTTCCCGCTTCTAATATTGTTTTTCATATTTTTTTCTGAATTAA
TTTACAATTAAATCGAAATAAGATTCAGATACTCTTAAAAACAAATCCTGTTGAAATGTTCCTGA
GATTTT
Found at i:4142 original size:330 final size:331
Alignment explanation
Indices: 3562--4280 Score: 1126
Period size: 330 Copynumber: 2.2 Consensus size: 331
3552 TGAGCTAACA
3562 TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCAC
1 TACACGATTTCGGCTAAAATTTTGTAAAAATTGA-CCGAAAGATTTTTCCTCAATTTTTAGCCAC
* * *
3627 AATTCTCATAAAAAAATATATAATTCAACGCAAAAAATATTAGCGGGCATTTCCCGCTTCTAATA
65 AATTCTCAT-AAAAAATATATAATTCAACACAAAAAACATTAGCGGGCATTTCCCGCTTCAAATA
* *
3692 TTGTTTTTCTTTTTTTTTCTGAATTAAATTCAAATTTAATCGAAACAAGATTCAGATACTCTTAA
129 TTGTTTTTCTTATTTTTTCTGAATTAAATTCAAATTAAATCGAAACAAGATTCAGATACTCTTAA
* *
3757 AAACAAATCCTTAAATGAAATGTTGCTGAGACTTTTTTAGATAAATATGGATATTTCAAGGAGTG
194 AAACAAATCCTTAAATGAAATGTTGCTGAGACTTTTTTAGATAAATATAGATATTTCAAGGAGTC
3822 TTAGC-GCAAAAAATCATGCAAAACTGAGTC-GGGCCC-GAGAAAACGTTTTTAGCCAAAAACCG
259 TT-GCTGCAAAAAATCATGCAAAACTGAGTCAGGGCCCAG-GAAAACGTTTTTAGCCAAAAACCG
3884 TAATGATTAG
322 TAATGATTAG
* *
3894 TACACGATTTTCGGCTAAAATTTTGTAAAAATTGAGCCGAAAGATTTTTGCTGAATTTTTAGCCA
1 TACACGA-TTTCGGCTAAAATTTTGTAAAAATTGA-CCGAAAGATTTTTCCTCAATTTTTAGCCA
* *
3959 CAATTC-CAT-AAAAATATATAATTCAACACCAAAAACATTAGCGGGCTTTTCCCGCTTCAAATA
64 CAATTCTCATAAAAAATATATAATTCAACACAAAAAACATTAGCGGGCATTTCCCGCTTCAAATA
* * * *
4022 TTTTTTTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAATATTCAGATACTCTTAA
129 TTGTTTTTCTTATTTTTTCTGAATTAAATTCAAATTAAATCGAAACAAGATTCAGATACTCTTAA
*
4087 AAACAAATCCTTAAATGAAATGTTGCTGAGA-TTTTGTTAGATGAATATAGATATTTCAAGGAGT
194 AAACAAATCCTTAAATGAAATGTTGCTGAGACTTTT-TTAGATAAATATAGATATTTCAAGGAGT
* **
4151 CTTGCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCAGGAACGCGTTTTTAGCCAAAAACCGT
258 CTTGCTGCAAAAAATCATGCAAAACTGAGTCAGGGCCCAGGAAAACGTTTTTAGCCAAAAACCGT
*
4216 GATGATTAG
323 AATGATTAG
* *
4225 TACACGATATCGGCTAAAATTTTGCAAAAATTGACCGAAAAGATTTTTCCTCAATT
1 TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCG-AAAGATTTTTCCTCAATT
4281 ATTTCCAAAA
Statistics
Matches: 356, Mismatches: 25, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
329 9 0.03
330 232 0.65
331 44 0.12
332 11 0.03
333 60 0.17
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (331 bp):
TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCGAAAGATTTTTCCTCAATTTTTAGCCACA
ATTCTCATAAAAAATATATAATTCAACACAAAAAACATTAGCGGGCATTTCCCGCTTCAAATATT
GTTTTTCTTATTTTTTCTGAATTAAATTCAAATTAAATCGAAACAAGATTCAGATACTCTTAAAA
ACAAATCCTTAAATGAAATGTTGCTGAGACTTTTTTAGATAAATATAGATATTTCAAGGAGTCTT
GCTGCAAAAAATCATGCAAAACTGAGTCAGGGCCCAGGAAAACGTTTTTAGCCAAAAACCGTAAT
GATTAG
Done.