Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006740.1 Corchorus capsularis cultivar CVL-1 contig06761, 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: 25591
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:211 original size:25 final size:25
Alignment explanation
Indices: 183--241 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
173 ATAAAAAAGT
* *
183 TATCAAAATTTTATAGGGAGGTTTA
1 TATCAAAATTTTATAGGAAGATTTA
208 TATCAAAATTTTATAGGAAGATTTA
1 TATCAAAATTTTATAGGAAGATTTA
233 T-T-AAAATTT
1 TATCAAAATTT
242 CATAACGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 1 0.03
25 24 0.75
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (25 bp):
TATCAAAATTTTATAGGAAGATTTA
Found at i:277 original size:22 final size:22
Alignment explanation
Indices: 252--294 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
242 CATAACGAGG
* *
252 TTATCATAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
274 TTATCAAAATTTCAGAGTGTG
1 TTATCAAAATTTCAGAGTGTG
295 GTTACTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:427 original size:22 final size:22
Alignment explanation
Indices: 387--443 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
377 GTGTTGGTTA
**
387 TCAAAATTTCATATTGAGGTGT
1 TCAAAATTTCATAGGGAGGTGT
*
409 TCAAAATTTCTTAGGGAGGT-T
1 TCAAAATTTCATAGGGAGGTGT
*
430 AACAAAATTTCATA
1 -TCAAAATTTCATA
444 AGAAGGTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAGGGAGGTGT
Found at i:450 original size:22 final size:22
Alignment explanation
Indices: 410--473 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
400 TTGAGGTGTT
* * *
410 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAAGAAGGTTAA
432 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATAAGAAGGTTAA
* * *
454 AAAAATTTTATAAAAAGGTT
1 CAAAATTTCATAAGAAGGTT
474 CTCGAAATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (22 bp):
CAAAATTTCATAAGAAGGTTAA
Found at i:1084 original size:27 final size:27
Alignment explanation
Indices: 1052--1109 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
1042 ATACTTCCTC
*
1052 TGTTCCTTTTTAATTGTCCCTTTCCCT
1 TGTTCCTTTTTAATTGTCCATTTCCCT
1079 TGTTCCTTTTTAATTGTCCATTTCCCT
1 TGTTCCTTTTTAATTGTCCATTTCCCT
1106 TGTT
1 TGTT
1110 TTTCAGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.09, C:0.26, G:0.09, T:0.57
Consensus pattern (27 bp):
TGTTCCTTTTTAATTGTCCATTTCCCT
Found at i:5363 original size:2 final size:2
Alignment explanation
Indices: 5297--5349 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
5287 GTGGTGGTGG
* *
5297 AT AT AT AT -T AT AT AT A- AT AT AT AA AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5337 AT AT AT AT GT AT A
1 AT AT AT AT AT AT A
5350 ATAATAACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5669 original size:13 final size:13
Alignment explanation
Indices: 5651--5679 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5641 ATGTTTCGGC
5651 TTTAATTCTTTTA
1 TTTAATTCTTTTA
5664 TTTAATTCTTTTA
1 TTTAATTCTTTTA
5677 TTT
1 TTT
5680 TTTGTTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTAATTCTTTTA
Found at i:6945 original size:2 final size:2
Alignment explanation
Indices: 6936--6997 Score: 53
Period size: 2 Copynumber: 33.5 Consensus size: 2
6926 TTCTTTCTAA
* * *
6936 AT AT -T AT AT AT AT A- AT AT AT AT AG AA AT A- AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6975 GT AT A- AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6998 CTAGTTTTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
1 5 0.10
2 43 0.90
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:6956 original size:11 final size:11
Alignment explanation
Indices: 6940--6997 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
6930 TTCTAAATAT
6940 TATATATATAA
1 TATATATATAA
*
6951 TATATATAGAA
1 TATATATATAA
6962 -ATA-ATAT-A
1 TATATATATAA
* *
6970 GATATGTATAA
1 TATATATATAA
6981 TATA-ATAT-A
1 TATATATATAA
6990 TATATATA
1 TATATATA
6998 CTAGTTTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
8 1 0.03
9 11 0.29
10 12 0.32
11 14 0.37
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (11 bp):
TATATATATAA
Found at i:7358 original size:21 final size:22
Alignment explanation
Indices: 7290--7428 Score: 78
Period size: 21 Copynumber: 6.5 Consensus size: 22
7280 TGTTATACTC
* *
7290 TGAAATTTTTATAAT-TACACTA
1 TGAAATTTTGATAATCTTC-CTA
* *
7312 TGAAATTGTGAT-A-CCT-CTA
1 TGAAATTTTGATAATCTTCCTA
7331 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAATCTTCCTA
*
7353 T-AAATTTTGATAATCTGATCTGTA
1 TGAAATTTTGATAATCT--TC-CTA
* * *
7377 TAAAATTTCGATAATC-ACTCTA
1 TGAAATTTTGATAATCTTC-CTA
* *
7399 TGAGA-TTTGATAACCTT-CTA
1 TGAAATTTTGATAATCTTCCTA
*
7419 TCAAATTTTG
1 TGAAATTTTG
7429 GTACTCCTTA
Statistics
Matches: 90, Mismatches: 17, Indels: 21
0.70 0.13 0.16
Matches are distributed among these distances:
19 14 0.16
20 7 0.08
21 30 0.33
22 21 0.23
23 2 0.02
24 3 0.03
25 13 0.14
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAATCTTCCTA
Found at i:7557 original size:22 final size:22
Alignment explanation
Indices: 7465--7560 Score: 72
Period size: 22 Copynumber: 4.4 Consensus size: 22
7455 ATAACCTTCA
* *
7465 TATGAAATTTTGATAACCACAT
1 TATGAAATTTTGTTAACCACAC
* * *
7487 TATAAAATTTT-TATAACCTCCC
1 TATGAAATTTTGT-TAACCACAC
* * *
7509 CATGAAATATTAG-TAACCTC-C
1 TATGAAAT-TTTGTTAACCACAC
7530 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGTTAACCACAC
7553 TATGAAAT
1 TATGAAAT
7561 CCTTATAACA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
21 4 0.07
22 49 0.86
23 4 0.07
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGTTAACCACAC
Found at i:7708 original size:22 final size:22
Alignment explanation
Indices: 7680--7811 Score: 151
Period size: 22 Copynumber: 6.0 Consensus size: 22
7670 TATCCTGATC
7680 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
7702 CTATGAAATTTTGGTGACCACA
1 CTATGAAATTTTGGTAACCACA
7724 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* * *
7746 CTATGGAATTTTGCTAACCTC-
1 CTATGAAATTTTGGTAACCACA
* **
7767 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGGTAACCA-CA
* *
7790 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGGTAACCACA
7812 TAGAGACAAG
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
21 3 0.03
22 89 0.95
23 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:8272 original size:32 final size:31
Alignment explanation
Indices: 8235--8308 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
8225 TTTAGTAATG
*
8235 ACAATTTAGAAATATGTTTCAAAAAAAAGGAT
1 ACAA-TTAGAAATATATTTCAAAAAAAAGGAT
* * * *
8267 ACAATTGGAAATATATTTTAAAAATAAGGGT
1 ACAATTAGAAATATATTTCAAAAAAAAGGAT
*
8298 ATAATTAGAAA
1 ACAATTAGAAA
8309 ACATAAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.30
Consensus pattern (31 bp):
ACAATTAGAAATATATTTCAAAAAAAAGGAT
Found at i:8472 original size:11 final size:11
Alignment explanation
Indices: 8426--8472 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
8416 TACCTTTGTC
8426 AAAAAA-AATA
1 AAAAAATAATA
*
8436 AATAAATAATA
1 AAAAAATAATA
*
8447 AATAAATAA-A
1 AAAAAATAATA
*
8457 GAAAAATAATA
1 AAAAAATAATA
8468 AAAAA
1 AAAAA
8473 GAACCAAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 13 0.42
11 18 0.58
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:9538 original size:15 final size:16
Alignment explanation
Indices: 9520--9554 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
9510 TTTCATAGAT
*
9520 TTAATTAAA-TAAAAA
1 TTAATAAAATTAAAAA
9535 TTAATAAAATTAAAAA
1 TTAATAAAATTAAAAA
9551 TTAA
1 TTAA
9555 AATTGTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAATAAAATTAAAAA
Found at i:9572 original size:129 final size:129
Alignment explanation
Indices: 9424--9683 Score: 520
Period size: 129 Copynumber: 2.0 Consensus size: 129
9414 ATTTTAACAG
9424 AAAATTGTGTTGTTAATAGTGGATTAATTGAGACGTGTTGGGTAACTTCTGCTATAGTTTGGATT
1 AAAATTGTGTTGTTAATAGTGGATTAATTGAGACGTGTTGGGTAACTTCTGCTATAGTTTGGATT
9489 GATGTAAAATTGAGATATATATTTCATAGATTTAATTAAATAAAAATTAATAAAATTAAAAATT
66 GATGTAAAATTGAGATATATATTTCATAGATTTAATTAAATAAAAATTAATAAAATTAAAAATT
9553 AAAATTGTGTTGTTAATAGTGGATTAATTGAGACGTGTTGGGTAACTTCTGCTATAGTTTGGATT
1 AAAATTGTGTTGTTAATAGTGGATTAATTGAGACGTGTTGGGTAACTTCTGCTATAGTTTGGATT
9618 GATGTAAAATTGAGATATATATTTCATAGATTTAATTAAATAAAAATTAATAAAATTAAAAATT
66 GATGTAAAATTGAGATATATATTTCATAGATTTAATTAAATAAAAATTAATAAAATTAAAAATT
9682 AA
1 AA
9684 TTGTATTATG
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 131 1.00
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (129 bp):
AAAATTGTGTTGTTAATAGTGGATTAATTGAGACGTGTTGGGTAACTTCTGCTATAGTTTGGATT
GATGTAAAATTGAGATATATATTTCATAGATTTAATTAAATAAAAATTAATAAAATTAAAAATT
Found at i:9667 original size:15 final size:16
Alignment explanation
Indices: 9649--9685 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
9639 TTTCATAGAT
9649 TTAATTAAA-TAAAAA
1 TTAATTAAATTAAAAA
*
9664 TTAATAAAATTAAAAA
1 TTAATTAAATTAAAAA
9680 TTAATT
1 TTAATT
9686 GTATTATGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAATTAAATTAAAAA
Found at i:9756 original size:31 final size:31
Alignment explanation
Indices: 9718--9779 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
9708 TATATTAGAC
* *
9718 AAATAAGGATATAATAGTCGTTTCAAAAGTT
1 AAATAAGGATACAATAGGCGTTTCAAAAGTT
*
9749 AAATAAGGGTACAATAGGCGTTTCAAAAGTT
1 AAATAAGGATACAATAGGCGTTTCAAAAGTT
9780 TTACAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (31 bp):
AAATAAGGATACAATAGGCGTTTCAAAAGTT
Found at i:13589 original size:55 final size:56
Alignment explanation
Indices: 13497--13605 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 56
13487 GTCACGCACC
* * ** * *
13497 TTGGTTTGGTGGATGAGTTTACCAACGAGGGGGCTGCGTACGCAATGACTCGAACT
1 TTGGTTTGGTGGATGAGTTTACAAACAAGGGAACTGCGCACGCAAGGACTCGAACT
** *
13553 TTGGTTTGGTGG-TGAGTTTACAAACAAGTTAACTGCGCACGCAAGGTCTCGAA
1 TTGGTTTGGTGGATGAGTTTACAAACAAGGGAACTGCGCACGCAAGGACTCGAA
13606 TCTGATGCCT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
55 32 0.73
56 12 0.27
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (56 bp):
TTGGTTTGGTGGATGAGTTTACAAACAAGGGAACTGCGCACGCAAGGACTCGAACT
Found at i:14163 original size:26 final size:26
Alignment explanation
Indices: 14130--14181 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
14120 ATTGCCATCC
14130 AATTGTTAATAAAATTTAATCAATTT
1 AATTGTTAATAAAATTTAATCAATTT
14156 AATTGTTAATAAAATTTAATCAATTT
1 AATTGTTAATAAAATTTAATCAATTT
14182 CTTTTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (26 bp):
AATTGTTAATAAAATTTAATCAATTT
Found at i:16122 original size:22 final size:21
Alignment explanation
Indices: 16091--16131 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16081 AGTTGGGTGG
*
16091 GAAAATAGAAATAAAAAAAAAA
1 GAAAAAAGAAA-AAAAAAAAAA
*
16113 GAAAAAAGAAAAAGAAAAA
1 GAAAAAAGAAAAAAAAAAA
16132 TTTAAAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (21 bp):
GAAAAAAGAAAAAAAAAAAAA
Found at i:16667 original size:18 final size:17
Alignment explanation
Indices: 16644--16687 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
16634 AAAAAAAAAA
*
16644 AAAAAAACAACCACAATC
1 AAAAAAACAACCA-AAGC
*
16662 AAAAAAATCAAGCAAAGC
1 AAAAAAA-CAACCAAAGC
16680 AAAAAAAC
1 AAAAAAAC
16688 CCAATCCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 5 0.22
ACGTcount: A:0.70, C:0.20, G:0.05, T:0.05
Consensus pattern (17 bp):
AAAAAAACAACCAAAGC
Found at i:16667 original size:19 final size:18
Alignment explanation
Indices: 16643--16686 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
16633 AAAAAAAAAA
*
16643 AAAAAAAACAACCACAATC
1 AAAAAAAACAACCA-AAGC
* *
16662 AAAAAAATCAAGCAAAGC
1 AAAAAAAACAACCAAAGC
16680 AAAAAAA
1 AAAAAAA
16687 CCCAATCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.73, C:0.18, G:0.05, T:0.05
Consensus pattern (18 bp):
AAAAAAAACAACCAAAGC
Found at i:16835 original size:28 final size:25
Alignment explanation
Indices: 16776--16842 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
16766 TCCATAAATT
* *
16776 AAAGAAGATGAGAGAAGAAGAAGGC
1 AAAGAAGAAGAGAGAAGAAGAACGC
16801 AAAGAAGAAGAGAGAAGAAGAACGC
1 AAAGAAGAAGAGAGAAGAAGAACGC
*
16826 -AAGCATGAAGAGAGAAG
1 AAAG-AAGAAGAGAGAAG
16843 CGGGAGCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 3 0.08
25 35 0.92
ACGTcount: A:0.57, C:0.06, G:0.34, T:0.03
Consensus pattern (25 bp):
AAAGAAGAAGAGAGAAGAAGAACGC
Found at i:21089 original size:13 final size:13
Alignment explanation
Indices: 21071--21097 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21061 TTCTCTAACC
21071 TCATAAATCATAT
1 TCATAAATCATAT
21084 TCATAAATCATAT
1 TCATAAATCATAT
21097 T
1 T
21098 TATTATATTT
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:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:23598 original size:35 final size:35
Alignment explanation
Indices: 23558--23627 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
23548 CAAAATCACC
* *
23558 CTTCAACACACACACA-CATAGATGGAGACAAAATA
1 CTTCAACA-ACACACATCACACATGGAGACAAAATA
*
23593 CTTCAACAACACACATCACACATGGAGACGAAATA
1 CTTCAACAACACACATCACACATGGAGACAAAATA
23628 AAGCTCTCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 7 0.23
35 24 0.77
ACGTcount: A:0.47, C:0.27, G:0.11, T:0.14
Consensus pattern (35 bp):
CTTCAACAACACACATCACACATGGAGACAAAATA
Done.