Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010109.1 Corchorus capsularis cultivar CVL-1 contig10130, 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: 31180
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1544 original size:129 final size:129
Alignment explanation
Indices: 1402--1662 Score: 513
Period size: 129 Copynumber: 2.0 Consensus size: 129
1392 AAATTAAATT
1402 TTACATATTTTTTTTTATAAATAATTATCAAAGTTTAGTGTTAGTTGACCAAGAGTTGACATCTA
1 TTACATATTTTTTTTTATAAATAATTATCAAAGTTTAGTGTTAGTTGACCAAGAGTTGACATCTA
*
1467 ATTAGGAACTGAGGGAGTAACCATTTTCGTGAATTTCTCTTATTTAATCGAGATAGTTAAGAGA
66 ATTAGAAACTGAGGGAGTAACCATTTTCGTGAATTTCTCTTATTTAATCGAGATAGTTAAGAGA
1531 TTACATATTTTTTTTTATAAATAATTATCAAAGTTTAGTGTTAGTTGACCAAGAGTTGACATCTA
1 TTACATATTTTTTTTTATAAATAATTATCAAAGTTTAGTGTTAGTTGACCAAGAGTTGACATCTA
1596 ATTAGAAACTGAGGGAGTAACCATTTTCGTGAATTTCTCTTATTTAATCGAGATAGTTAAGAGA
66 ATTAGAAACTGAGGGAGTAACCATTTTCGTGAATTTCTCTTATTTAATCGAGATAGTTAAGAGA
1660 TTA
1 TTA
1663 ATCTTTCTCG
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 131 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (129 bp):
TTACATATTTTTTTTTATAAATAATTATCAAAGTTTAGTGTTAGTTGACCAAGAGTTGACATCTA
ATTAGAAACTGAGGGAGTAACCATTTTCGTGAATTTCTCTTATTTAATCGAGATAGTTAAGAGA
Found at i:3121 original size:2 final size:2
Alignment explanation
Indices: 3114--3140 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3104 CTCCTACTCC
3114 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3141 GTGCACACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27396 original size:45 final size:47
Alignment explanation
Indices: 27338--27425 Score: 110
Period size: 45 Copynumber: 1.9 Consensus size: 47
27328 AAGACCTCAA
* *
27338 TATGAAATTTTGATAACTTCCCA-ATGAGAT-T-TTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAGATATATTGATAACCAACAC
* *
27383 TATGAGATGTTGATAACCTCCATATGATATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAGATATATTGATAACCA
27426 CGTTATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 3 0.08
45 22 0.61
46 1 0.03
47 10 0.28
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (47 bp):
TATGAAATGTTGATAACCTCCATATGAGATATATTGATAACCAACAC
Found at i:27489 original size:22 final size:21
Alignment explanation
Indices: 27338--27593 Score: 98
Period size: 22 Copynumber: 11.7 Consensus size: 21
27328 AAGACCTCAA
27338 TATGAAATTTTGATAACTTCC-C
1 TATGAAATTTTGATAA--TCCAC
* * *
27360 AATGAGATTTTGATAACCAACAC
1 TATGAAATTTTGATAATC--CAC
* *
27383 TATGAGATGTTGATAACCTCCA-
1 TATGAAATTTTGATAA--TCCAC
*
27405 TATGATATATATTGATAA-CCAC
1 TATGA-A-ATTTTGATAATCCAC
** *
27427 GTTATGAAAATTTAAAAAGATCCA-
1 --TATG-AAATTTTGATA-ATCCAC
27451 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAATC-CAC
*
27473 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAATC-CAC
* * *
27495 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAATC-CAC
27517 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AATC--CAC
* *
27540 TATAAAATTTTGAT-ATCCTC
1 TATGAAATTTTGATAATCCAC
** *
27560 CCTGAAATTTTGAT-ATCCTC
1 TATGAAATTTTGATAATCCAC
*
27580 TCTGAAATTTTGAT
1 TATGAAATTTTGAT
27594 TACTCCATAA
Statistics
Matches: 185, Mismatches: 27, Indels: 46
0.72 0.10 0.18
Matches are distributed among these distances:
19 1 0.01
20 40 0.22
21 10 0.05
22 68 0.37
23 44 0.24
24 17 0.09
25 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAATCCAC
Found at i:27569 original size:20 final size:20
Alignment explanation
Indices: 27544--27593 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
27534 TCTTCCTATA
27544 AAATTTTGATATCCTCCCTG
1 AAATTTTGATATCCTCCCTG
*
27564 AAATTTTGATATCCTCTCTG
1 AAATTTTGATATCCTCCCTG
27584 AAATTTTGAT
1 AAATTTTGAT
27594 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (20 bp):
AAATTTTGATATCCTCCCTG
Found at i:27766 original size:22 final size:22
Alignment explanation
Indices: 27675--27824 Score: 94
Period size: 22 Copynumber: 6.8 Consensus size: 22
27665 GAAATACCAC
27675 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAATCACAT
* * * * *
27697 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACAT
* * * * *
27719 TATAAAATTTTGTTGA-CCCCT
1 TATGAAATTTTGATAATCACAT
*
27740 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* *
27763 TATGTAATTTTGATAACCTCGC-T
1 TATGAAATTTTGATAA--TCACAT
*
27786 T-TGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAATC-ACAT
27807 TATGAAATTTTGATAATC
1 TATGAAATTTTGATAATC
27825 TGATCTCTAT
Statistics
Matches: 95, Mismatches: 24, Indels: 17
0.70 0.18 0.12
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 8 0.08
22 76 0.80
23 6 0.06
24 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:27793 original size:66 final size:66
Alignment explanation
Indices: 27672--27824 Score: 175
Period size: 66 Copynumber: 2.3 Consensus size: 66
27662 TCAGAAATAC
* * * *
27672 CACTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTATAAAATTTTGTTGAC
1 CACTATGAAA-TTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGATAAC
**
27736 CC
65 AA
* * * * *
27738 CTCTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAAC
1 CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATAAAATTTTGATAAC
27802 AA
65 AA
27804 CACTATGAAATTTTGATAATC
1 CACTATGAAATTTTGATAATC
27825 TGATCTCTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
65 4 0.06
66 66 0.92
67 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (66 bp):
CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGATAACA
A
Found at i:28044 original size:22 final size:21
Alignment explanation
Indices: 27699--28218 Score: 120
Period size: 22 Copynumber: 23.8 Consensus size: 21
27689 AATCACATTT
* *
27699 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
* * * *
27721 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTC-CTA
* * * *
27743 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTC-CTA
* *
27765 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTC-CTA
**
27787 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTC-CTA
*
27809 TGAAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTC-CTA
* *
27834 TGAAATTTCGATAA-TTACTCTA
1 TGAAATTTTGATAACCT-C-CTA
* * *
27856 GGAGA-TTTGATAACCTTCTA
1 TGAAATTTTGATAACCTCCTA
* **
27876 TCAAATTTTG-GCA-CTCCTTA
1 TGAAATTTTGATAACCTCC-TA
* * *
27896 TGAAATTGAGACTTTATAGCCTTCATA
1 TGAAATT-----TTGATAACC-TCCTA
*
27923 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
* *
27945 T-AAA-ATTGATAACCTCCCCA
1 TGAAATTTTGATAACCT-CCTA
*
27965 TGAAATATT-AGTAACCTCCTAA
1 TGAAATTTTGA-TAACCTCCT-A
* *
27987 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
28009 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTC-CTA
* * *
28031 TGACATTTTGATAATCT-CTT
1 TGAAATTTTGATAACCTCCTA
** *
28051 TGATAACCTTTCT-ATAAAAT--TG
1 TGA-AA--TTT-TGATAACCTCCTA
*
28073 TGATAA---T--TAACCACCCTA
1 TGA-AATTTTGATAACC-TCCTA
** *
28091 TGAAATTTCAATAACCAACCTA
1 TGAAATTTTGATAACC-TCCTA
* * *
28113 AGAAATTTTAATAACTTGACACTA
1 TGAAATTTTGATAACCT--C-CTA
* *
28137 TGAAATTTTGGTAACCACGCTA
1 TGAAATTTTGATAACCTC-CTA
*
28159 TGGAATTTTGATAACCTCCTCA
1 TGAAATTTTGATAACCTCCT-A
* * *
28181 TGAAATTATAATAACCATCTTA
1 TGAAATTTTGATAACC-TCCTA
28203 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
28219 AGATAGAGAC
Statistics
Matches: 363, Mismatches: 93, Indels: 84
0.67 0.17 0.16
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 2 0.01
18 4 0.01
19 3 0.01
20 31 0.09
21 28 0.08
22 226 0.62
23 17 0.05
24 16 0.04
25 20 0.06
27 10 0.03
28 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:28416 original size:19 final size:20
Alignment explanation
Indices: 28385--28422 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28375 TATTGACATT
28385 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
28404 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
28423 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:29620 original size:37 final size:37
Alignment explanation
Indices: 29528--29623 Score: 111
Period size: 38 Copynumber: 2.6 Consensus size: 37
29518 ATTTAAGCCC
* *
29528 AAATAGGATGTTGGAGACAAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
*** * * *
29565 AAATTCAACGATTCGAAACAATGACAAAAGGCAAAATT
1 AAATAGGACG-TTGGAAACAAAGACAAAAAGCAAAATT
29603 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
29624 AAGGCAAATT
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
37 15 0.33
38 30 0.67
ACGTcount: A:0.53, C:0.11, G:0.19, T:0.17
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Done.