Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010266.1 Corchorus capsularis cultivar CVL-1 contig10287, 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: 9064
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:1768 original size:22 final size:22
Alignment explanation
Indices: 1743--1959 Score: 66
Period size: 22 Copynumber: 9.8 Consensus size: 22
1733 ATGATCCCAT
1743 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * ** *
1765 TATGAAATGTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* ** * * **
1787 TATGGAATTTCAAGAATCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** * *
1809 TAT-AATTTTTTTTTAACTTTCT
1 TATGAA-ATTTTGATAACCTTCC
* * *
1831 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
1853 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
*
1875 TATGAAATTTTGATAA-TTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
1897 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
1920 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
1941 ATATGATATATTGATAACC
1 -TATGAAATTTTGATAACC
1960 ACTTTATAAA
Statistics
Matches: 136, Mismatches: 49, Indels: 20
0.66 0.24 0.10
Matches are distributed among these distances:
21 4 0.03
22 112 0.82
23 20 0.15
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:2082 original size:23 final size:24
Alignment explanation
Indices: 2004--2113 Score: 77
Period size: 23 Copynumber: 4.8 Consensus size: 24
1994 TTAGTAATTA
* * *
2004 CACTTTAAAATTTTGATATATC-A
1 CACTATAAAATTTTGATAAATCTT
* * *
2027 CACTATGAAATTGTGAT-AA-CCT
1 CACTATAAAATTTTGATAAATCTT
* *
2049 CGCTATGAAATTTTGATAAATCTT
1 CACTATAAAATTTTGATAAATCTT
* *
2073 C-CTATAAAATTTTAATAAA-CCT
1 CACTATAAAATTTTGATAAATCTT
* *
2095 CCCTATAAAATTTGGATAA
1 CACTATAAAATTTTGATAA
2114 CTTTTTTATG
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.01
22 19 0.27
23 47 0.67
24 3 0.04
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (24 bp):
CACTATAAAATTTTGATAAATCTT
Found at i:2083 original size:45 final size:46
Alignment explanation
Indices: 2009--2113 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 46
1999 AATTACACTT
* * * *
2009 TAAAATTTTGATATATCACACTATGAAATTGTGAT-AACCTCGCTA
1 TAAAATTTTGATAAATCACACTATAAAATTGTAATAAACCTCCCTA
* * *
2054 TGAAATTTTGATAAATCTTC-CTATAAAATTTTAATAAACCTCCCTA
1 TAAAATTTTGATAAATC-ACACTATAAAATTGTAATAAACCTCCCTA
*
2100 TAAAATTTGGATAA
1 TAAAATTTTGATAA
2114 CTTTTTTATG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
45 27 0.55
46 22 0.45
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (46 bp):
TAAAATTTTGATAAATCACACTATAAAATTGTAATAAACCTCCCTA
Found at i:2190 original size:22 final size:22
Alignment explanation
Indices: 2165--2305 Score: 67
Period size: 22 Copynumber: 6.3 Consensus size: 22
2155 CCCTATGATT
2165 TTTTGATTACCTCATTATGAAA
1 TTTTGATTACCTCATTATGAAA
* **
2187 TTTTG-TTCATCTCGCTATGAAA
1 TTTTGATT-ACCTCATTATGAAA
* **
2209 CTTTGATCTAGAT-ATACTATGAAA
1 TTTTGAT-TACCTCAT--TATGAAA
*
2233 TTTTGATAACCCTC-TTATGAAA
1 TTTTGATTA-CCTCATTATGAAA
* * * *
2255 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATTACCT-CATTATGAAA
* *
2277 ATTTGATCACCTTCA-TATGAAA
1 TTTTGATTACC-TCATTATGAAA
2299 TTTTGAT
1 TTTTGAT
2306 ATCCTCACTG
Statistics
Matches: 88, Mismatches: 20, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
20 2 0.02
21 4 0.05
22 58 0.66
23 7 0.08
24 17 0.19
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (22 bp):
TTTTGATTACCTCATTATGAAA
Found at i:2369 original size:19 final size:19
Alignment explanation
Indices: 2297--2363 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
2287 CTTCATATGA
*
2297 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTCCCTG
*
2316 AATTTCGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
*
2335 AATTTTGGTATCCTCCCTG
1 AATTTTGATATCCTCCCTG
2354 AAATTTTGAT
1 -AATTTTGAT
2364 TACTCCATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 34 0.81
20 8 0.19
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:2560 original size:66 final size:66
Alignment explanation
Indices: 2471--2663 Score: 203
Period size: 66 Copynumber: 2.9 Consensus size: 66
2461 AATCACATTT
* * * * * * * *
2471 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCACTCT
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATCTTTATGAAATTTTGATAACAACACT
2536 A
66 A
* * * *
2537 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACAC
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATC-TTTATGAAATTTTGATAACAACAC
2601 TA
65 TA
2603 TGAAATTTTGATAATCTTCA-TAT-AAATTTTGATAATCCTATCTTTATGAAATTTTTGATAA
1 TGAAATTTTGATAATC-TCATTATGAAATTTTGATAA--C-ATCTTTATGAAA-TTTTGATAA
2664 TCAGTTTATG
Statistics
Matches: 104, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
65 11 0.11
66 70 0.67
67 7 0.07
68 7 0.07
69 9 0.09
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (66 bp):
TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATCTTTATGAAATTTTGATAACAACACT
A
Found at i:2609 original size:88 final size:88
Alignment explanation
Indices: 2446--2612 Score: 230
Period size: 88 Copynumber: 1.9 Consensus size: 88
2436 AGAAATACCA
* * *
2446 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC
1 CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
2511 TTTATAAAATTTTGTTGACCACT
66 ACTATAAAATTTTGTTGACCACT
* *
2534 CTATGAAA-TTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTTTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
2597 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
2613 ATAATCTTCA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
87 5 0.07
88 62 0.90
89 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCACT
Found at i:2830 original size:22 final size:22
Alignment explanation
Indices: 2446--2833 Score: 183
Period size: 22 Copynumber: 17.5 Consensus size: 22
2436 AGAAATACCA
*
2446 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAACCAC-T
* * *
2469 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAACCACT
*
2490 TTATGAAATTTTGATAA-CATCT
1 CTATGAAATTTTGATAACCA-CT
* * * *
2512 TTATAAAATTTTGTTGACCACT
1 CTATGAAATTTTGATAACCACT
*
2534 CTATGAAATTTTGATAATCACAT
1 CTATGAAATTTTGATAACCAC-T
* * *
2557 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAACCACT
* * *
2578 CTTTGAAATTTTGATAACAACA
1 CTATGAAATTTTGATAACCACT
* *
2600 CTATGAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAACCACT
2621 CATAT-AAATTTTGATAATCCTATCT
1 C-TATGAAATTTTGATAA-CC-A-CT
* * *
2646 TTATGAAATTTTTGATAATCAGT
1 CTATGAAA-TTTTGATAACCACT
* * *
2669 TTATGAGA-TTTGATAACC-TT
1 CTATGAAATTTTGATAACCACT
* * *
2689 CTATCAAATTTTGGTAATC-CT
1 CTATGAAATTTTGATAACCACT
* *
2710 -TATGAAATTGAGACTTTTATAACC-TT
1 CTATGAAA-T-----TTTGATAACCACT
*
2736 CATATGAAATTTTGATAACCACA
1 C-TATGAAATTTTGATAACCACT
* * *
2759 CTATAAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCACT
* * *
2781 CGATGAAGTATT-AGTAA-C-CT
1 CTATGAAATTTTGA-TAACCACT
*
2801 CTAATGAAATTTTGTTAACCACT
1 CT-ATGAAATTTTGATAACCACT
2824 CTATGAAATT
1 CTATGAAATT
2834 CGTATAGCCT
Statistics
Matches: 274, Mismatches: 63, Indels: 57
0.70 0.16 0.14
Matches are distributed among these distances:
20 14 0.05
21 51 0.19
22 159 0.58
23 16 0.06
24 4 0.01
25 5 0.02
26 17 0.06
27 1 0.00
28 7 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACT
Found at i:2958 original size:24 final size:22
Alignment explanation
Indices: 2897--3036 Score: 77
Period size: 22 Copynumber: 6.3 Consensus size: 22
2887 TTGTGATAAT
* * *
2897 TAACCACCCAATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
2919 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
2941 TAACCTTATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
* **
2965 TAA-CTACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* * *
2987 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * * *
3009 TAATCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
3031 TAACCA
1 TAACCA
3037 CATAGAGACA
Statistics
Matches: 91, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
21 3 0.03
22 67 0.74
23 5 0.05
24 16 0.18
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:3348 original size:30 final size:31
Alignment explanation
Indices: 3314--3378 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
3304 TGGCAATTTA
*
3314 GAAATATGTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
3344 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
3375 GAAA
1 GAAA
3379 ACATAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.28
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:5557 original size:158 final size:155
Alignment explanation
Indices: 5340--5622 Score: 399
Period size: 154 Copynumber: 1.8 Consensus size: 155
5330 TTCAATTGTT
* * *
5340 GAGGTATGCTAATTAAAGTTTTCGATATATTGCATATCATTGCTTTTGGAATATTTCTTTCTGAT
1 GAGGTATGCTAATTAAAGTTTTCCATATATTGCA-ATCACTGCTTTTGGAATATTTCTTTCTAAT
* *
5405 TCTTGTGTTTCTTAATTTAGGGAATACAATTTTTACTTAGCCACAAGAAGATTGAGGTCGATAAG
65 TCTTGTGTTTC----TTTAGGGAATACAATCTTTACTTAGCCACAAGAAAATTGAGGTCGATAAG
5470 CTTTCAAAACCTTACGATTTGACCCTTTTG
126 CTTTCAAAACCTTACGATTTGACCCTTTTG
*
5500 GAGGTATGCTAATTAAAGTTTTCCATATTTTGC-ATCACTGCTTTTGGAAGT-TTTCTTTCTAAT
1 GAGGTATGCTAATTAAAGTTTTCCATATATTGCAATCACTGCTTTTGGAA-TATTTCTTTCTAAT
** * * *
5563 TCTTGTGTTTCTTTAGGGTTTACAATCTTTGCTTAGCCTCAAGAAAATTGAGGTGGATAA
65 TCTTGTGTTTCTTTAGGGAATACAATCTTTACTTAGCCACAAGAAAATTGAGGTCGATAA
5623 ACTTCCAATA
Statistics
Matches: 111, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
154 42 0.38
158 37 0.33
159 1 0.01
160 31 0.28
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (155 bp):
GAGGTATGCTAATTAAAGTTTTCCATATATTGCAATCACTGCTTTTGGAATATTTCTTTCTAATT
CTTGTGTTTCTTTAGGGAATACAATCTTTACTTAGCCACAAGAAAATTGAGGTCGATAAGCTTTC
AAAACCTTACGATTTGACCCTTTTG
Found at i:5644 original size:154 final size:156
Alignment explanation
Indices: 5340--5655 Score: 397
Period size: 154 Copynumber: 2.0 Consensus size: 156
5330 TTCAATTGTT
* * *
5340 GAGGTATGCTAATTAAAGTTTTCGATATATTGCATATCATTGCTTTTGGAATATTTCTTTCTGAT
1 GAGGTATGCTAATTAAAGTTTTCCATATATTGCA-ATCACTGCTTTTGGAATATTTCTTTCTAAT
* * *
5405 TCTTGTGTTTCTTAATTTAGGGAATACAATTTTTACTTAGCCACAAGAAGATTGAGGTCGATAAG
65 TCTTGTGTTTC---ATTTAGGGAATACAATCTTTACTTAGCCACAAGAAAATTGAGGTCGATAAA
* * *
5470 CTTTCAAAACCTTACGATTTGACCCTTTTG
127 CTTCCAAAACCTTACAATTTGACCCATTTG
*
5500 GAGGTATGCTAATTAAAGTTTTCCATATTTTGC-ATCACTGCTTTTGGAAGT-TTTCTTTCTAAT
1 GAGGTATGCTAATTAAAGTTTTCCATATATTGCAATCACTGCTTTTGGAA-TATTTCTTTCTAAT
** * * *
5563 TCTTGTGTTTC-TTTAGGGTTTACAATCTTTGCTTAGCCTCAAGAAAATTGAGGTGGATAAACTT
65 TCTTGTGTTTCATTTAGGGAATACAATCTTTACTTAGCCACAAGAAAATTGAGGTCGATAAACTT
* *
5627 CCAATA-TTCTACAATTTGACCCATTTG
130 CCAAAACCT-TACAATTTGACCCATTTG
5654 GA
1 GA
5656 ATTGGGAATA
Statistics
Matches: 137, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
153 1 0.01
154 67 0.49
158 37 0.27
159 1 0.01
160 31 0.23
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (156 bp):
GAGGTATGCTAATTAAAGTTTTCCATATATTGCAATCACTGCTTTTGGAATATTTCTTTCTAATT
CTTGTGTTTCATTTAGGGAATACAATCTTTACTTAGCCACAAGAAAATTGAGGTCGATAAACTTC
CAAAACCTTACAATTTGACCCATTTG
Done.