Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013235.1 Corchorus capsularis cultivar CVL-1 contig13256, 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: 25742
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1469 original size:41 final size:42
Alignment explanation
Indices: 1424--1575 Score: 288
Period size: 42 Copynumber: 3.6 Consensus size: 42
1414 ATTTTTATAC
*
1424 AATACACTGTCGGTGGAATTTAGCAGACTATAGACTATAAT-
1 AATACACTGTCGATGGAATTTAGCAGACTATAGACTATAATA
1465 AATACACTGTCGATGGAATTTAGCAGACTATAGACTATAATA
1 AATACACTGTCGATGGAATTTAGCAGACTATAGACTATAATA
1507 AATACACTGTCGATGGAATTTAGCAGACTATAGACTATAATA
1 AATACACTGTCGATGGAATTTAGCAGACTATAGACTATAATA
1549 AATACACTGTCGATGGAATTTAGCAGA
1 AATACACTGTCGATGGAATTTAGCAGA
1576 TTACGAGGTT
Statistics
Matches: 109, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 40 0.37
42 69 0.63
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (42 bp):
AATACACTGTCGATGGAATTTAGCAGACTATAGACTATAATA
Found at i:2934 original size:1 final size:1
Alignment explanation
Indices: 2928--2952 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2918 TCTCCCTATC
2928 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2953 ATCTTGGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4773 original size:4 final size:4
Alignment explanation
Indices: 4764--4791 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4754 GTTGTTTCGA
4764 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
4792 GTTGTACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:7566 original size:109 final size:109
Alignment explanation
Indices: 7408--7703 Score: 441
Period size: 109 Copynumber: 2.7 Consensus size: 109
7398 TAAATTAAAA
** * *
7408 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAG-ATTTTATTAAATGAAAATAGAGTTTTTAGT
7472 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
7519 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTTATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTTATTAAATGAAAATAGAGTTTTTAGTAGA
*
7584 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* * *
7628 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGA--T--TTT-ATTAAATGAAAATAGAGTTTTTA
7693 GTAGAATAAAA
61 GTAGAATAAAA
7704 CTATAATAGT
Statistics
Matches: 171, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
109 115 0.67
110 11 0.06
111 11 0.06
113 3 0.02
114 31 0.18
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTTATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:8156 original size:31 final size:28
Alignment explanation
Indices: 8118--8212 Score: 91
Period size: 31 Copynumber: 3.2 Consensus size: 28
8108 CGGGCATCCG
8118 ACGTGGCATGCCACGTGTACCCAAAAATGCC
1 ACGTGGCATGCCACGTGT---CAAAAATGCC
* * * *
8149 ACGTGGCATGCCATGTGTGTACAAAAGGAC
1 ACGTGGCATGCCACGTGT-CA-AAAATGCC
*
8179 ACATGGCCATGCCACGTGTCAAAAATGCC
1 ACGTGG-CATGCCACGTGTCAAAAATGCC
8208 ACGTG
1 ACGTG
8213 CCACATGCCA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 11 0.22
30 12 0.24
31 28 0.55
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.18
Consensus pattern (28 bp):
ACGTGGCATGCCACGTGTCAAAAATGCC
Found at i:10492 original size:63 final size:63
Alignment explanation
Indices: 10262--10519 Score: 277
Period size: 66 Copynumber: 4.0 Consensus size: 63
10252 GGCTGCTTTA
* * * * * *
10262 TTAATAGTTGCTGCAATTCCTCAACAAGTTCACTTCTCGGAATCACTTCCTGATTATGGGTGCTT
1 TTAATAGCTGCTGCAGTTCCTCAACAAGTTTACTTCTCGGAATCACATCCTCA-T-T-GGTGGTT
10327 T
63 T
* **
10328 TTAA-ACGCTGCTGCAGTTCCTCAACAAGTTTACCTCTCGGAATC-TTTACCTCATTGGTGGTGC
1 TTAATA-GCTGCTGCAGTTCCTCAACAAGTTTACTTCTCGGAATCACAT-CCTCATTGGT-G-G-
10391 TTT
61 TTT
* * * * *
10394 TTAATCGCTGCTGCAGTTCCTCAACAAGTTTACTTCTCGGAATTAAATCCTCATTGCTGGTTC
1 TTAATAGCTGCTGCAGTTCCTCAACAAGTTTACTTCTCGGAATCACATCCTCATTGGTGGTTT
* * *
10457 CTAATAGCTGCTGCAGTTCCTCAACAAGTTTACTTCTCGAAATCACATCCTCCTTGGTGGTTT
1 TTAATAGCTGCTGCAGTTCCTCAACAAGTTTACTTCTCGGAATCACATCCTCATTGGTGGTTT
10520 CTACCTTCTT
Statistics
Matches: 163, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
63 60 0.37
64 3 0.02
65 5 0.03
66 94 0.58
67 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (63 bp):
TTAATAGCTGCTGCAGTTCCTCAACAAGTTTACTTCTCGGAATCACATCCTCATTGGTGGTTT
Found at i:13586 original size:74 final size:73
Alignment explanation
Indices: 13508--13663 Score: 260
Period size: 74 Copynumber: 2.1 Consensus size: 73
13498 TGGTCTTTTC
*
13508 ACACTTTTCAGG-TGACTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTT
1 ACACTTTTC-GGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
13572 TTTCGTAATT
65 TTT-GTAATT
*
13582 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTGCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
13647 TTGTAATT
66 TTGTAATT
*
13655 ACACATTTC
1 ACACTTTTC
13664 CTTCCTTAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
73 16 0.21
74 62 0.79
ACGTcount: A:0.21, C:0.29, G:0.10, T:0.40
Consensus pattern (73 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
TTGTAATT
Found at i:20777 original size:15 final size:15
Alignment explanation
Indices: 20752--20800 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
20742 GTTTGTTACT
20752 TTCCATGGGAGAGTGA
1 TTCC-TGGGAGAGTGA
20768 TTCCTGGGAGAGTGA
1 TTCCTGGGAGAGTGA
**
20783 TTCCCAGGAGAGTGA
1 TTCCTGGGAGAGTGA
20798 TTC
1 TTC
20801 TATATATGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 27 0.87
16 4 0.13
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (15 bp):
TTCCTGGGAGAGTGA
Found at i:22119 original size:22 final size:22
Alignment explanation
Indices: 22077--22120 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
22067 TATTCATATG
*
22077 AAATTATGATAATCTCTCTATT
1 AAATTATGATAATCTCACTATT
22099 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
22121 TTGTATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:22163 original size:22 final size:22
Alignment explanation
Indices: 22136--22681 Score: 137
Period size: 22 Copynumber: 24.6 Consensus size: 22
22126 TGATCCTATC
22136 ATGAAATTTTGATAACCTTCCT
1 ATGAAATTTTGATAACCTTCCT
* ** *
22158 ATGAAATTTTAATAACGATACT
1 ATGAAATTTTGATAACCTTCCT
* * **
22180 ATGAAATTTCGAGAACCTTTTT
1 ATGAAATTTTGATAACCTTCCT
* ** *
22202 AT-AACTTTTTTTTAACC-TCTT
1 ATGAA-ATTTTGATAACCTTCCT
* * *
22223 ATGAAATTTTGTTAACCTCCCA
1 ATGAAATTTTGATAACCTTCCT
* * *
22245 AAGGAATTTTGA-AGACC-TCAAT
1 ATGAAATTTTGATA-ACCTTC-CT
* *
22267 ATGAAATTTTGATAACTTCTCCA
1 ATGAAATTTTGATAACCT-TCCT
**
22290 ATGAAATTTTGATAACCAACACT
1 ATGAAATTTTGATAACCTTC-CT
* * *
22313 ATGAGATGTTGATAACCTTCAT
1 ATGAAATTTTGATAACCTTCCT
* * * *
22335 ATGATATATTGATAACC-ACGTT
1 ATGAAATTTTGATAACCTTC-CT
* * *
22357 ATGAAAATTTAAAAACC-TCCAT
1 ATGAAATTTTGATAACCTTCC-T
* *
22379 ATG-AATTGTT-AGTAATC-ACACT
1 ATGAAATT-TTGA-TAACCTTC-CT
* * *
22401 CTGAAATTTTGATAATC-ACACT
1 ATGAAATTTTGATAACCTTC-CT
*
22423 ATGAAATTGTGATAACC-TCGCT
1 ATGAAATTTTGATAACCTTC-CT
* * *
22445 ACGAAATTTTGATAAATCTCCCT
1 ATGAAATTTTGAT-AACCTTCCT
22468 A-GAAAATTTTGATAAACCTCCCTCTTTCTT
1 ATG-AAATTTTGAT-AACCT---TC---C-T
*
22498 ATGAAATCTTGATAA-----CT
1 ATGAAATTTTGATAACCTTCCT
* *
22515 A-CAAATTTTGATAACCTCCCT
1 ATGAAATTTTGATAACCTTCCT
** * *
22536 ATGATTTTTTGATAA-CATCATT
1 ATGAAATTTTGATAACCTTC-CT
* * **
22558 ATGAATTTTTGTTAATTTTCCT
1 ATGAAATTTTGATAACCTTCCT
* * *
22580 ATGAAATTTTGATCTA-CATACT
1 ATGAAATTTTGAT-AACCTTCCT
*
22602 ATGAAATTTTGATAATCC-TCTT
1 ATGAAATTTTGATAA-CCTTCCT
* * **
22624 ATGAAATTTTAAGAA-CTAAACT
1 ATGAAATTTTGATAACCT-TCCT
* * *
22646 ATGGAATTCTGATAACCTTCAT
1 ATGAAATTTTGATAACCTTCCT
22668 ATGAAATTTTGATA
1 ATGAAATTTTGATA
22682 TCCTCCCTGC
Statistics
Matches: 377, Mismatches: 106, Indels: 82
0.67 0.19 0.15
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 1 0.00
21 30 0.08
22 246 0.65
23 67 0.18
24 3 0.01
26 1 0.00
29 3 0.01
30 11 0.03
31 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTTCCT
Found at i:22836 original size:22 final size:22
Alignment explanation
Indices: 22811--23027 Score: 126
Period size: 22 Copynumber: 10.0 Consensus size: 22
22801 ATTTTGAAAA
*
22811 TTGATAACCTCTTTATGAAGTT
1 TTGATAACCTCTTTATGAAATT
*
22833 TTGATAACCTCTTTATAAAATT
1 TTGATAACCTCTTTATGAAATT
* * *
22855 TTGTTGACC-CTCTATGAAATT
1 TTGATAACCTCTTTATGAAATT
* * * * * *
22876 CTGATAATCACATTACGTAATT
1 TTGATAACCTCTTTATGAAATT
*
22898 TTGATAACCTCGCTT-TGAAATT
1 TTGATAACCTC-TTTATGAAATT
* *
22920 TCGATAATCT-TTCTAT-AAATT
1 TTGATAACCTCTT-TATGAAATT
*
22941 TTGATAATCCGATCTCTATGAAATT
1 TTGATAA-CC--TCTTTATGAAATT
* * * *
22966 TTGATAATCACTCTATGAGA-T
1 TTGATAACCTCTTTATGAAATT
* *
22987 TTGATAACC-CTCTATCAAATT
1 TTGATAACCTCTTTATGAAATT
* *
23008 TTGGT-A-CTCCTTATGAAATT
1 TTGATAACCTCTTTATGAAATT
23028 GAGACTTTTA
Statistics
Matches: 148, Mismatches: 36, Indels: 24
0.71 0.17 0.12
Matches are distributed among these distances:
19 1 0.01
20 19 0.13
21 41 0.28
22 67 0.45
23 2 0.01
24 5 0.03
25 13 0.09
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (22 bp):
TTGATAACCTCTTTATGAAATT
Found at i:22981 original size:46 final size:42
Alignment explanation
Indices: 22811--23010 Score: 147
Period size: 43 Copynumber: 4.6 Consensus size: 42
22801 ATTTTGAAAA
* * * * *
22811 TTGATAACCTCTTTATGAAGTTTTGATAACCTCTTTATAAAATT
1 TTGATAACCTCTCTATGAAATTTTGATAATCACTCTAT--AATT
* * *
22855 TTGTTGACC-CTCTATGAAATTCTGATAATCACAT-TACGTAATT
1 TTGATAACCTCTCTATGAAATTTTGATAATCAC-TCTA--TAATT
* * * **
22898 TTGATAACCTCGCTTTGAAATTTCGATAATCTTTCTATAAATT
1 TTGATAACCTCTCTATGAAATTTTGATAATCACTCTAT-AATT
22941 TTGATAATCCGATCTCTATGAAATTTTGATAATCACTCTATGAGA-T
1 TTGATAA-CC--TCTCTATGAAATTTTGATAATCACTCTAT-A-ATT
*
22987 TTGATAACC-CTCTATCAAATTTTG
1 TTGATAACCTCTCTATGAAATTTTG
23011 GTACTCCTTA
Statistics
Matches: 124, Mismatches: 22, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
42 15 0.12
43 43 0.35
44 29 0.23
45 3 0.02
46 33 0.27
47 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (42 bp):
TTGATAACCTCTCTATGAAATTTTGATAATCACTCTATAATT
Found at i:23001 original size:20 final size:22
Alignment explanation
Indices: 22780--23027 Score: 120
Period size: 22 Copynumber: 11.5 Consensus size: 22
22770 ATAAATACCA
22780 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
22803 -TTTGAAA-ATTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * *
22823 TTATGAAGTTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * *
22845 TTATAAAATTTTGTTGA-CCCT
1 CTATGAAATTTTGATAATCACT
*
22866 CTATGAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * * *
22889 -TACGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* * **
22910 CTTTGAAATTTCGATAATCTTT
1 CTATGAAATTTTGATAATCACT
22932 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAAT-C-A-CT
22956 CTATGAAATTTTGATAATCACT
1 CTATGAAATTTTGATAATCACT
* *
22978 CTATGAGA-TTTGATAA-CCCT
1 CTATGAAATTTTGATAATCACT
* * *
22998 CTATCAAATTTTGGTACTC-CT
1 CTATGAAATTTTGATAATCACT
23019 -TATGAAATT
1 CTATGAAATT
23028 GAGACTTTTA
Statistics
Matches: 171, Mismatches: 42, Indels: 27
0.71 0.17 0.11
Matches are distributed among these distances:
20 21 0.12
21 53 0.31
22 76 0.44
23 2 0.01
24 6 0.04
25 13 0.08
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:23062 original size:22 final size:20
Alignment explanation
Indices: 23033--23177 Score: 62
Period size: 22 Copynumber: 6.7 Consensus size: 20
23023 AAATTGAGAC
23033 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TC-TATGAAA
* *
23054 TTTTGATAACCACACTATAAAA
1 TTTTGATAA-C-CTCTATGAAA
*
23076 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT--CTATGAAA
*
23098 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCT-CT-ATGAAA
* *
23120 TTTTGTTAACCACATTATGAAA
1 TTTTGATAACCTC--TATGAAA
* *
23142 TTCTT-AAAACCTCGCTATGATA
1 TT-TTGATAACCT--CTATGAAA
*
23164 TTTTGATAATCTCT
1 TTTTGATAACCTCT
23178 TTGATAACCT
Statistics
Matches: 94, Mismatches: 16, Indels: 29
0.68 0.12 0.21
Matches are distributed among these distances:
20 3 0.03
21 11 0.12
22 73 0.78
23 5 0.05
24 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.38
Consensus pattern (20 bp):
TTTTGATAACCTCTATGAAA
Found at i:23272 original size:24 final size:22
Alignment explanation
Indices: 23208--23273 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
23198 TTGTGATAAT
* *
23208 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
23230 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
*
23252 TAACCTGATCCTATGAAATTTT
1 TAACC--AACCTATGAAATTTT
23274 GGTAACCACA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 23 0.66
24 12 0.34
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:23480 original size:15 final size:15
Alignment explanation
Indices: 23460--23508 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
23450 ATTAAGTATT
23460 ATAATTAATAATGGA
1 ATAATTAATAATGGA
* *
23475 ATAATTAATGAT-TA
1 ATAATTAATAATGGA
23489 A-AA--AATAATGGA
1 ATAATTAATAATGGA
23501 ATAATTAA
1 ATAATTAA
23509 AATATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 5 0.19
12 2 0.08
13 4 0.15
14 2 0.08
15 13 0.50
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
ATAATTAATAATGGA
Found at i:23596 original size:31 final size:28
Alignment explanation
Indices: 23534--23596 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 28
23524 TGGCAATTTA
* *
23534 GAAATATGTTTTAAAAAGGGTATAATTG
1 GAAATATGTTTTAAAAAGGGTACAATCG
23562 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTT--AAA-AAGGGTACAATCG
23593 GAAA
1 GAAA
23597 ACATAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 12 0.40
30 3 0.10
31 15 0.50
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.30
Consensus pattern (28 bp):
GAAATATGTTTTAAAAAGGGTACAATCG
Done.