Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004876.1 Corchorus capsularis cultivar CVL-1 contig04894, 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: 10127
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:104 original size:2 final size:2
Alignment explanation
Indices: 99--139 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
89 TTCTATTTTT
99 TA TA TA -A TA -A TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
138 TA
1 TA
140 ATCCTTATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:224 original size:78 final size:83
Alignment explanation
Indices: 90--247 Score: 206
Period size: 78 Copynumber: 2.0 Consensus size: 83
80 AGAGCTATTT
*
90 TCTATTTTTTATATAATAATAATATATATATATATATATATATATATATAATCCTTATAGCG-AT
1 TCTATTTTTTATATAATAATAATATATATATATATATATATATATACATAATCCTTATAG-GTAT
154 AGGATTTGAAAAATCCTAA
65 AGGATTTGAAAAATCCTAA
*
173 TCTA-TTTTTA-ATAATAATAATA-ATATA-ATA-ATA-ATCATCAT-CATCATCCTTATAGGTA
1 TCTATTTTTTATATAATAATAATATATATATATATATATAT-AT-ATACATAATCCTTATAGGTA
*
231 TAGGATTTGTAAAATCC
64 TAGGATTTGAAAAATCC
248 GGTCTAATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
77 3 0.04
78 34 0.49
79 5 0.07
80 5 0.07
81 12 0.17
82 6 0.09
83 4 0.06
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (83 bp):
TCTATTTTTTATATAATAATAATATATATATATATATATATATATACATAATCCTTATAGGTATA
GGATTTGAAAAATCCTAA
Found at i:2020 original size:22 final size:22
Alignment explanation
Indices: 1995--2086 Score: 80
Period size: 22 Copynumber: 4.1 Consensus size: 22
1985 TATGAATTAG
*
1995 TAATTACACTCTGAAATTTTGA
1 TAATTACACTATGAAATTTTGA
* *
2017 TAATCACACTATGAAATTGTGA
1 TAATTACACTATGAAATTTTGA
* *
2039 TAACCT-CGCTATGAAATTTTGA
1 TAA-TTACACTATGAAATTTTGA
* *
2061 TAAATCTTC-CTATAAAATTTTGA
1 T-AAT-TACACTATGAAATTTTGA
2084 TAA
1 TAA
2087 ACCTCTGTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
22 39 0.68
23 17 0.30
24 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
TAATTACACTATGAAATTTTGA
Found at i:2101 original size:45 final size:45
Alignment explanation
Indices: 2006--2108 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
1996 AATTACACTC
*
2006 TGAAATTTTGAT-AATCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAAATCACACTATAAAATTGTGATAACCTCGCTA
* *
2050 TGAAATTTTGATAAATCTTC-CTATAAAATTTTGATAAACCTCTG-TA
1 TGAAATTTTGATAAATC-ACACTATAAAATTGTGAT-AACCTC-GCTA
2096 T-AAATTTTGATAA
1 TGAAATTTTGATAA
2109 CTTTCTTATG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
44 12 0.23
45 29 0.56
46 10 0.19
47 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (45 bp):
TGAAATTTTGATAAATCACACTATAAAATTGTGATAACCTCGCTA
Found at i:2103 original size:22 final size:23
Alignment explanation
Indices: 2030--2108 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
2020 TCACACTATG
* *
2030 AAATTGTGAT-AACCTC-GCTATG
1 AAATTTTGATAAACCTCTG-TATA
* *
2052 AAATTTTGATAAATCT-TCCTATA
1 AAATTTTGATAAACCTCT-GTATA
2075 AAATTTTGATAAACCTCTGTAT-
1 AAATTTTGATAAACCTCTGTATA
2097 AAATTTTGATAA
1 AAATTTTGATAA
2109 CTTTCTTATG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 21 0.45
23 25 0.53
24 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTCTGTATA
Found at i:2122 original size:22 final size:21
Alignment explanation
Indices: 2006--2314 Score: 145
Period size: 22 Copynumber: 14.6 Consensus size: 21
1996 AATTACACTC
*
2006 TGAAATTTTGATAA-TCACACTA
1 TGAAATTTTGATAACT-TC-CTA
* *
2028 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACTTC-CTA
2050 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AA-CTTCCTA
* * *
2073 TAAAATTTTGATAAACCTCTGTA
1 TGAAATTTTGAT-AACTTC-CTA
*
2096 T-AAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAAC-TTCCTA
* *
2117 TGAAATCTTGATGA----CTA
1 TGAAATTTTGATAACTTCCTA
* *
2134 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAA-CTTCCTA
* * * *
2155 TG-ATTTTTTATAACCTCATTA
1 TGAAATTTTGATAACTTC-CTA
* *
2176 TGAAATTTTGTTAATTTCACTA
1 TGAAATTTTGATAACTTC-CTA
* * *
2198 TGAAATTTTGATCTACATACTA
1 TGAAATTTTGAT-AACTTCCTA
* * *
2220 TGAAATTTTGATAACCCTCTTG
1 TGAAATTTTGATAA-CTTCCTA
*
2242 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAA-CTTCCTA
* * *
2264 TGAAATTTTGATATCCT-CTC
1 TGAAATTTTGATAACTTCCTA
* * *
2284 CG-AATTTTGATATCCTCCT-
1 TGAAATTTTGATAACTTCCTA
2303 TGAAATTTTGAT
1 TGAAATTTTGAT
2315 TACTCCATAA
Statistics
Matches: 221, Mismatches: 48, Indels: 38
0.72 0.16 0.12
Matches are distributed among these distances:
16 10 0.05
17 2 0.01
19 15 0.07
20 15 0.07
21 25 0.11
22 127 0.57
23 24 0.11
24 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (21 bp):
TGAAATTTTGATAACTTCCTA
Found at i:2177 original size:21 final size:21
Alignment explanation
Indices: 2138--2178 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2128 TGACTACAAA
*
2138 TTTTGATAACCTCCCTATGAT
1 TTTTGATAACCTCACTATGAT
* *
2159 TTTTTATAACCTCATTATGA
1 TTTTGATAACCTCACTATGA
2179 AATTTTGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (21 bp):
TTTTGATAACCTCACTATGAT
Found at i:2445 original size:22 final size:22
Alignment explanation
Indices: 2420--2525 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
2410 AATCACATTT
2420 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
2442 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
2464 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
2486 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* *
2508 TGTAATTTTGATAACCTC
1 TGAAAATTTGATAACCTC
2526 GCTTTAAAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
21 5 0.08
22 56 0.86
23 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:2515 original size:44 final size:44
Alignment explanation
Indices: 2396--2587 Score: 163
Period size: 44 Copynumber: 4.4 Consensus size: 44
2386 GAAATACCAT
* * * *
2396 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCCCTC
* * * * * *
2440 TATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCTC
* * * *
2484 TATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCTC
* * * * * * **
2528 TTTAAAATTTTGATAATAACACTATGGAATTTTGATAATCTTTC
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCTC
2572 TAT-AAATTTTGATAAT
1 TATGAAATTTTGATAAT
2588 TCGATCTCTA
Statistics
Matches: 117, Mismatches: 30, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
43 18 0.15
44 99 0.85
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCTC
Found at i:2553 original size:66 final size:66
Alignment explanation
Indices: 2439--2567 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 66
2429 GATAACCTCT
* * * ** *
2439 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
2504 A
66 A
* * * *
2505 TTATGTAATTTTGATAACCTCGCTT-TAAAATTTTGATAATAACACTATGGAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATC
2568 TTTCTATAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:2701 original size:22 final size:21
Alignment explanation
Indices: 2672--2723 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
2662 AAATTGAGAG
2672 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
** *
2693 TTTTGATAACCACACTATAAAA
1 TTTTGATAACC-TTCTATGAAA
2715 TTTTGATAA
1 TTTTGATAA
2724 TTTCCCCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 21 0.81
23 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:2925 original size:22 final size:22
Alignment explanation
Indices: 2897--2951 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2887 ACCTGATCCT
2897 ATGAAATTTTGGTAACCACACA
1 ATGAAATTTTGGTAACCACACA
* *
2919 ATGAAATTTTGGTAACTACACT
1 ATGAAATTTTGGTAACCACACA
2941 ATGAAATTTTG
1 ATGAAATTTTG
2952 ATAAACTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGGTAACCACACA
Found at i:2966 original size:22 final size:21
Alignment explanation
Indices: 2893--2999 Score: 81
Period size: 22 Copynumber: 4.9 Consensus size: 21
2883 AATAACCTGA
* *
2893 TCCTATGAAATTTTGGTAACC
1 TCCTATGAAATTTTGATAAAC
* * *
2914 ACACAATGAAATTTTGGT-AAC
1 TC-CTATGAAATTTTGATAAAC
2935 TACACTATGAAATTTTGATAAAC
1 T-C-CTATGAAATTTTGATAAAC
* * *
2958 TCCTCATGAAATTATAATAATC
1 TCCT-ATGAAATTTTGATAAAC
*
2980 ATCTTATGAAATTTTGATAA
1 -TCCTATGAAATTTTGATAA
3000 CCACATAGAG
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
21 5 0.07
22 57 0.83
23 7 0.10
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (21 bp):
TCCTATGAAATTTTGATAAAC
Found at i:3199 original size:19 final size:20
Alignment explanation
Indices: 3168--3205 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3158 TATTGACATT
3168 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
3187 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
3206 AAATAATAGT
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:3548 original size:31 final size:32
Alignment explanation
Indices: 3513--3578 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
3503 TTAGTAATGG
3513 CAATTTAAAAAT-TATTTTAAAGAA-AAGGGTA
1 CAATTTAAAAATATATTTTAAA-AATAAGGGTA
**
3544 CAA-TTGGAAATATATTTTAAAAATAAGGGTA
1 CAATTTAAAAATATATTTTAAAAATAAGGGTA
3575 CAAT
1 CAAT
3579 CGGAAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32
Consensus pattern (32 bp):
CAATTTAAAAATATATTTTAAAAATAAGGGTA
Found at i:3584 original size:31 final size:30
Alignment explanation
Indices: 3521--3584 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
3511 GGCAATTTAA
*
3521 AAATTATTTTAAAGAAAAGGGTACAATTGG
1 AAATTATTTTAAAGAAAAGGGTACAATCGG
3551 AAATATATTTTAAA-AATAAGGGTACAATCGG
1 AAAT-TATTTTAAAGAA-AAGGGTACAATCGG
3582 AAA
1 AAA
3585 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (30 bp):
AAATTATTTTAAAGAAAAGGGTACAATCGG
Done.