Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009810.1 Corchorus capsularis cultivar CVL-1 contig09831, 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: 16044
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Found at i:4532 original size:8 final size:8
Alignment explanation
Indices: 4504--4537 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4494 GAATCGGCTA
4504 TGAATTTT
1 TGAATTTT
*
4512 TGAAGTTTC
1 TGAA-TTTT
4521 TGAATTTT
1 TGAATTTT
4529 TGAATTTT
1 TGAATTTT
4537 T
1 T
4538 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:6440 original size:107 final size:107
Alignment explanation
Indices: 6287--6546 Score: 407
Period size: 107 Copynumber: 2.4 Consensus size: 107
6277 AGTTTAGCCT
* *
6287 TAATTTCACTAAGTTTAGTCCCAATTTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
6352 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
6394 TAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
6459 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAT
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * ** *
6501 TAA-TTCACTAAGTTAAGT-CTAAATTAAAATTAAAATTTTATTTTAA
1 TAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAA
6547 AGGTTAGAAA
Statistics
Matches: 142, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
105 24 0.17
106 14 0.10
107 104 0.73
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (107 bp):
TAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:8336 original size:43 final size:45
Alignment explanation
Indices: 8261--8344 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 45
8251 TTTTTCAAAT
*
8261 ATTTTTTCCCATATTTTTTGAAAAACAAAGCATAGT-ATAAAAAA
1 ATTTGTTCCCATATTTTTTGAAAAACAAAGCATAGTGATAAAAAA
**
8305 ATTTGTTCCCATATTTTTTG-AAAATGAAGCATAGTGATAA
1 ATTTGTTCCCATATTTTTTGAAAAACAAAGCATAGTGATAA
8345 CATAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 13 0.36
44 23 0.64
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (45 bp):
ATTTGTTCCCATATTTTTTGAAAAACAAAGCATAGTGATAAAAAA
Found at i:8819 original size:15 final size:14
Alignment explanation
Indices: 8799--8834 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
8789 AATATGAAAA
8799 TTTCAGTACTTAATT
1 TTTCAGTACTTAA-T
*
8814 TTTCAGCACTTAAT
1 TTTCAGTACTTAAT
8828 TTTCAGT
1 TTTCAGT
8835 TTATCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (14 bp):
TTTCAGTACTTAAT
Found at i:8833 original size:14 final size:15
Alignment explanation
Indices: 8799--8830 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
8789 AATATGAAAA
*
8799 TTTCAGTACTTAATT
1 TTTCAGCACTTAATT
8814 TTTCAGCACTTAATT
1 TTTCAGCACTTAATT
8829 TT
1 TT
8831 CAGTTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTCAGCACTTAATT
Found at i:9589 original size:72 final size:73
Alignment explanation
Indices: 9512--9661 Score: 230
Period size: 72 Copynumber: 2.0 Consensus size: 73
9502 ATTGATTCAA
* *
9512 TGTATTGATACTTATCTTTTTAAGTCTCCAGATTTATTCATGTATC-TTTTTTTTTTTTTGCATC
1 TGTATTAATACTTATCGTTTTAAGTCTCCAGATTTATTCATGTATCTTTTTTTTTTTTTTGCATC
9576 AATTCATG
66 AATTCATG
*
9584 TGTATTAATACTTATCGTTTTAAGTCTCCATATTTATTCATGTATCTGTTTTTTTTTTTTTTTTG
1 TGTATTAATACTTATCGTTTTAAGTCTCCAGATTTATTCATGTATC----TTTTTTTTTTTTTTG
9649 CATCAATTCATG
62 CATCAATTCATG
9661 T
1 T
9662 CTCTGTTCAA
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
72 43 0.61
77 27 0.39
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.57
Consensus pattern (73 bp):
TGTATTAATACTTATCGTTTTAAGTCTCCAGATTTATTCATGTATCTTTTTTTTTTTTTTGCATC
AATTCATG
Found at i:10898 original size:39 final size:39
Alignment explanation
Indices: 10835--10918 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 39
10825 AACTGATTAA
* *
10835 ATTGAGAAGGTAGCTCACTAAATTTGCTCTACTTTCCATC
1 ATTG-GAAAGTAGCTCACAAAATTTGCTCTACTTTCCATC
*
10875 ATTGGAAAGTAGCTCTCAAAATTTGCTCTACTTTCCATC
1 ATTGGAAAGTAGCTCACAAAATTTGCTCTACTTTCCATC
10914 ATTGG
1 ATTGG
10919 TTGTTGTGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 37 0.90
40 4 0.10
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (39 bp):
ATTGGAAAGTAGCTCACAAAATTTGCTCTACTTTCCATC
Found at i:14478 original size:13 final size:13
Alignment explanation
Indices: 14462--14488 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14452 AAGTTTATTG
14462 ATAATATAATATA
1 ATAATATAATATA
14475 ATAATATAATATA
1 ATAATATAATATA
14488 A
1 A
14489 CATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATATAATATA
Found at i:14780 original size:21 final size:21
Alignment explanation
Indices: 14738--14784 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
14728 ATTTAAAATT
* **
14738 AATTAATGCAAATTGATCCAA
1 AATTAATGCAAATTAAAACAA
*
14759 AATTACTGCAAATTAAAAC-A
1 AATTAATGCAAATTAAAACAA
14779 AATTAA
1 AATTAA
14785 GCATTAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (21 bp):
AATTAATGCAAATTAAAACAA
Found at i:15190 original size:21 final size:23
Alignment explanation
Indices: 15157--15212 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 23
15147 GATACTACGG
**
15157 AATTTTGAGAACCCTT-TTAT-A
1 AATTTTGTTAACCCTTCTTATGA
* *
15178 ATTTTTTTTAA-CCTTCTTATGA
1 AATTTTGTTAACCCTTCTTATGA
15200 AATTTTGTTAACC
1 AATTTTGTTAACC
15213 TCCCTAAGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 4 0.15
21 11 0.42
22 10 0.38
23 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (23 bp):
AATTTTGTTAACCCTTCTTATGA
Found at i:15388 original size:22 final size:22
Alignment explanation
Indices: 15363--15646 Score: 96
Period size: 22 Copynumber: 13.1 Consensus size: 22
15353 GAATTGTTAG
*
15363 TAATCATACTCTGAAATTTTGA
1 TAATCATACTATGAAATTTTGA
*
15385 TAATCACACTATGAAATTTTGA
1 TAATCATACTATGAAATTTTGA
* *
15407 TAA-CCTCGCTATGAAATTTTGA
1 TAATCAT-ACTATGAAATTTTGA
* * *
15429 TAAATCTTCCTATAAAATTTTGA
1 T-AATCATACTATGAAATTTTGA
* * * * *
15452 TAAACCTCCCTATAAAATGTTGA
1 TAATCAT-ACTATGAAATTTTGA
* * * *
15475 TAA-CTTTCTTGTGAAATCTTGA
1 TAATCATAC-TATGAAATTTTGA
15497 TAA-C-TAC----AAATTTTGA
1 TAATCATACTATGAAATTTTGA
* * *
15513 TAA-CCTCCCTAT-AATTTTTTGA
1 TAATCAT-ACTATGAA-ATTTTGA
*
15535 TAACGTCAT--TATGAAATTTTGT
1 TAA--TCATACTATGAAATTTTGA
*
15557 TAATC-TCCCTATGAAATTTTGA
1 TAATCAT-ACTATGAAATTTTGA
*
15579 T-CTGCATACTATGAAATTTTGA
1 TAAT-CATACTATGAAATTTTGA
* * *
15601 TAACCCT-CTTATGAAAATTTGA
1 TAATCATAC-TATGAAATTTTGA
* * *
15623 -AAACTAAACTATAAAATTTTGA
1 TAATC-ATACTATGAAATTTTGA
15645 TA
1 TA
15647 TCCTCCCTGA
Statistics
Matches: 202, Mismatches: 35, Indels: 49
0.71 0.12 0.17
Matches are distributed among these distances:
16 12 0.06
17 1 0.00
18 1 0.00
19 1 0.00
20 2 0.01
21 11 0.05
22 132 0.65
23 38 0.19
24 2 0.01
25 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TAATCATACTATGAAATTTTGA
Found at i:15446 original size:23 final size:24
Alignment explanation
Indices: 15376--15477 Score: 90
Period size: 23 Copynumber: 4.5 Consensus size: 24
15366 TCATACTCTG
* *
15376 AAATTTTGAT-AATC-ACACTATG
1 AAATTTTGATAAATCTTCACTATA
* * *
15398 AAATTTTGAT-AA-CCTCGCTATG
1 AAATTTTGATAAATCTTCACTATA
15420 AAATTTTGATAAATCTTC-CTATA
1 AAATTTTGATAAATCTTCACTATA
* *
15443 AAATTTTGATAAA-CCTCCCTATA
1 AAATTTTGATAAATCTTCACTATA
*
15466 AAATGTTGATAA
1 AAATTTTGATAA
15478 CTTTCTTGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
21 1 0.01
22 31 0.44
23 35 0.50
24 3 0.04
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (24 bp):
AAATTTTGATAAATCTTCACTATA
Found at i:15497 original size:45 final size:46
Alignment explanation
Indices: 15393--15499 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 46
15383 GATAATCACA
* * *
15393 CTATGAAATTTTGAT-AACCTCGCTATGAAATTTTGATAAATCTTC
1 CTATGAAATTTTGATAAACCTCCCTATAAAATGTTGATAAATCTTC
* *
15438 CTATAAAATTTTGATAAACCTCCCTATAAAATGTTGATAACT-TTC
1 CTATGAAATTTTGATAAACCTCCCTATAAAATGTTGATAAATCTTC
* * *
15483 TTGTGAAATCTTGATAA
1 CTATGAAATTTTGATAA
15500 CTACAAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 30 0.58
46 22 0.42
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (46 bp):
CTATGAAATTTTGATAAACCTCCCTATAAAATGTTGATAAATCTTC
Found at i:15577 original size:44 final size:44
Alignment explanation
Indices: 15186--15666 Score: 239
Period size: 44 Copynumber: 11.0 Consensus size: 44
15176 TAATTTTTTT
* * *
15186 TAACCTTC-TTATGAAATTTTGTTAACCTCCCTAAGGAATTTTGA
1 TAACC-TCATTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * *
15230 -AGACCTCAGTATGAAATTTTGATAACTTCCCAATGAAATTTTGA
1 TA-ACCTCATTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * * * * *
15274 TAA-CTAACACTATGAGATGTTGATAACCTCCATATGATATATTGA
1 TAACCT--CATTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* * * * * *
15319 TAACCACGTTATGAAAATTTAAAAACCTCCATATG-AATTGTT-A
1 TAACCTCATTATGAAATTTTGATAACCTCCCTATGAAATT-TTGA
* * * *
15362 GTAA--TCATACTCTGAAATTTTGATAATCACACTATGAAATTTTGA
1 -TAACCTCAT--TATGAAATTTTGATAACCTCCCTATGAAATTTTGA
** * * *
15407 TAACCTCGCTATGAAATTTTGATAAATCTTCCTATAAAATTTTGA
1 TAACCTCATTATGAAATTTTGAT-AACCTCCCTATGAAATTTTGA
** * * * * * * *
15452 TAAACCTCCCTATAAAATGTTGATAACTTTCTTGTGAAATCTTGA
1 T-AACCTCATTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* *
15497 TAA---C--TA-CAAATTTTGATAACCTCCCTAT-AATTTTTTGA
1 TAACCTCATTATGAAATTTTGATAACCTCCCTATGAA-ATTTTGA
* * *
15535 TAACGTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGA
1 TAACCTCATTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
* *
15579 T---CTGCATACTATGAAATTTTGATAACC-CTCTTATGAAAATTTGA
1 TAACCT-CAT--TATGAAATTTTGATAACCTC-CCTATGAAATTTTGA
* * * * *
15623 -AAACTAAACTATAAAATTTTGATATCCTCCC--TGAAATTTTGA
1 TAACCT-CATTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
15665 TA
1 TA
15667 TCTTCCATAA
Statistics
Matches: 330, Mismatches: 74, Indels: 67
0.70 0.16 0.14
Matches are distributed among these distances:
37 2 0.01
38 24 0.07
39 2 0.01
41 3 0.01
42 15 0.05
43 12 0.04
44 171 0.52
45 76 0.23
46 25 0.08
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TAACCTCATTATGAAATTTTGATAACCTCCCTATGAAATTTTGA
Found at i:15824 original size:22 final size:22
Alignment explanation
Indices: 15772--15938 Score: 119
Period size: 22 Copynumber: 7.6 Consensus size: 22
15762 AATCACATTC
* *
15772 TGAAAATTTGATAACCTCTTTC
1 TGAAATTTTGATAACCTCTTTA
15794 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * *
15816 TAAAATTTTGTTGATCC-CTTTA
1 TGAAATTTTGAT-AACCTCTTTA
* * * * *
15838 TAAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
15860 TGTAATTTTGATAACCTCACTT-
1 TGAAATTTTGATAACCTC-TTTA
* ** *
15882 TGGAATTTTGATAACAACATTA
1 TGAAATTTTGATAACCTCTTTA
15904 TGAAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
15926 T-AAATTTTGATAA
1 TGAAATTTTGATAA
15939 TCTGATCTCT
Statistics
Matches: 116, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.02
21 16 0.14
22 93 0.80
23 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:15928 original size:88 final size:86
Alignment explanation
Indices: 15761--15940 Score: 193
Period size: 88 Copynumber: 2.1 Consensus size: 86
15751 GAAATTTTTG
* * ** *
15761 TAATCACATTCTGAAAATTTGATAACCTCTTTCTGAAATTTTGATAACCTCTTTATAAAATTTTG
1 TAATCACATTATGAAAATTTGATAACCTCCTTCTGAAATTTTGATAACAACATTATAAAATTTTG
* *
15826 TTGATCCCTTTATAAAATTCTGA
66 ATAATCCC-TTAT-AAATTCTGA
* * * *
15849 TAATCACATTATGTAATTTTGATAACCTCACTT-TGGAATTTTGATAACAACATTATGAAATTTT
1 TAATCACATTATGAAAATTTGATAACCTC-CTTCTGAAATTTTGATAACAACATTATAAAATTTT
*
15913 GATAATCTTCC-TATAAATTTTGA
65 GATAATC--CCTTATAAATTCTGA
15936 TAATC
1 TAATC
15941 TGATCTCTAT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
87 13 0.17
88 60 0.78
89 2 0.03
90 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.43
Consensus pattern (86 bp):
TAATCACATTATGAAAATTTGATAACCTCCTTCTGAAATTTTGATAACAACATTATAAAATTTTG
ATAATCCCTTATAAATTCTGA
Found at i:15956 original size:25 final size:22
Alignment explanation
Indices: 15902--16001 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 22
15892 ATAACAACAT
15902 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATCTTCC
15924 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATCT--TC-C
* * *
15948 TATGGAATTTCGATAATC-ACTC
1 TATGAAATTTTGATAATCTTC-C
* *
15970 TATGAGA-TTTGATAACCTT-C
1 TATGAAATTTTGATAATCTTCC
*
15990 TATTAAATTTTG
1 TATGAAATTTTG
16002 GTACTCCTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
20 6 0.10
21 27 0.44
22 11 0.18
23 2 0.03
24 4 0.06
25 12 0.19
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCC
Done.