Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013224.1 Corchorus capsularis cultivar CVL-1 contig13245, 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: 38957
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:866 original size:18 final size:19
Alignment explanation
Indices: 845--884 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
835 TTCTTGAATT
*
845 AATTCTTC-AATTATCTTC
1 AATTCTTCAAAATATCTTC
863 AATTCTTCAAAATATCTTC
1 AATTCTTCAAAATATCTTC
882 AAT
1 AAT
885 CACGAACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAAATATCTTC
Found at i:1179 original size:43 final size:42
Alignment explanation
Indices: 1111--1575 Score: 549
Period size: 42 Copynumber: 10.9 Consensus size: 42
1101 AGCTCGATCA
*
1111 CTCCCCTTTTCGAAGGTTCTT-CGCCACCCCCGCAGGAACTAAC
1 CTCCCCTTTTCGAAGGTT-TTACGCCA-CCCTGCAGGAACTAAC
* * *
1154 CTCCCTTTTTTGAAGGTTTAACGCCA-CCTCGCAGGAACTAAC
1 CTCCCCTTTTCGAAGGTTTTACGCCACCCT-GCAGGAACTAAC
* * * *
1196 CTCCCATTTTCGAATGTTTTACACCACCCTGGAGGAACTAAC
1 CTCCCCTTTTCGAAGGTTTTACGCCACCCTGCAGGAACTAAC
* * * * * *
1238 CTCACCTTTTTGAAGAATTTT-CGCAACCCTGCAGAAACTGAC
1 CTCCCCTTTTCGAAG-GTTTTACGCCACCCTGCAGGAACTAAC
*
1280 CTCCCCTTTTCGAAGGTTTTACACCACCCTGCAGGAACTAAC
1 CTCCCCTTTTCGAAGGTTTTACGCCACCCTGCAGGAACTAAC
* *
1322 CTCCCCTTTTTCGAAGGTTCTACGCCACCCGGCAGGAACTAAC
1 CTCCCC-TTTTCGAAGGTTTTACGCCACCCTGCAGGAACTAAC
*
1365 CTCCCCTTTTCGAAGGTTTTTACGCTACCCTGCAGGAACTAAC
1 CTCCCCTTTTCGAAGG-TTTTACGCCACCCTGCAGGAACTAAC
* *
1408 CTCCCCTTTTCGAAGGTTCTACGCCACCCCCGCAGGAACTAAC
1 CTCCCCTTTTCGAAGGTTTTACGCCA-CCCTGCAGGAACTAAC
* * * * *
1451 CTTCCATTTTCGAAGGTTTCACACCACGCCACCCCGCAAGAACTAAC
1 CTCCCCTTTTCGAAGGTTT-----TACGCCACCCTGCAGGAACTAAC
* *
1498 CTCCCCTTTTCGAAGGTTTTACGCCACCTTGCAGGGACTAAC
1 CTCCCCTTTTCGAAGGTTTTACGCCACCCTGCAGGAACTAAC
*
1540 CTCCCCTTTTCGAAGGTTTTACGCCAACCTGCAGGA
1 CTCCCCTTTTCGAAGGTTTTACGCCACCCTGCAGGA
1576 TATCCAAGGA
Statistics
Matches: 358, Mismatches: 51, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
41 6 0.02
42 177 0.49
43 137 0.38
47 32 0.09
48 6 0.02
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (42 bp):
CTCCCCTTTTCGAAGGTTTTACGCCACCCTGCAGGAACTAAC
Found at i:1730 original size:42 final size:42
Alignment explanation
Indices: 1671--1913 Score: 266
Period size: 42 Copynumber: 5.7 Consensus size: 42
1661 TTGACTGCTA
1671 GGAACTAACCTCCCCTTTTCGAAGGTTTTAAGCCACCCTGCC
1 GGAACTAACCTCCCCTTTTCGAAGGTTTTAAGCCACCCTGCC
* *
1713 GGAACTAACCTCCCCTTTTCGAA-GTTTTAAGCCATCCAG-C
1 GGAACTAACCTCCCCTTTTCGAAGGTTTTAAGCCACCCTGCC
*
1753 GGAACTAACCTCCCC-TTTCGAAGGTTTTACGATTACGCCACACC-GCA
1 GGAACTAACCTCCCCTTTTCGAAGGTTTT---A--A-GCCAC-CCTGCC
* * * **
1800 GGAACGAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGTA
1 GGAACTAACCTCCCCTTTTCGAAGGTTTTAAGCCACCCTGCC
**
1842 GGAACTAACCTCCCCTTTTCGAAGG-TTTAACGCCA-AATGCAC
1 GGAACTAACCTCCCCTTTTCGAAGGTTTTAA-GCCACCCTGC-C
1884 GG-ACTAACCTCCCCTTTTCGAAGGTTTTAA
1 GGAACTAACCTCCCCTTTTCGAAGGTTTTAA
1914 CTCTCTGTCT
Statistics
Matches: 173, Mismatches: 14, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
39 7 0.04
40 21 0.12
41 43 0.25
42 65 0.38
43 1 0.01
45 2 0.01
46 5 0.03
47 16 0.09
48 13 0.08
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (42 bp):
GGAACTAACCTCCCCTTTTCGAAGGTTTTAAGCCACCCTGCC
Found at i:1813 original size:87 final size:84
Alignment explanation
Indices: 1669--1913 Score: 279
Period size: 83 Copynumber: 2.9 Consensus size: 84
1659 CATTGACTGC
* *
1669 TAGGAACTAACCTCCCCTTTTCGAAGGTTTTAAGCCACCCTGCCGGAACTAACCTCCCCTTTTCG
1 TAGGAACTAACCTCCCCTTTTCGAAGGTTTTAAGCCACCCTGCAGGAACGAACCTCCCCTTTTCG
*
1734 AA-GTTTTAAGCCATCCAG
66 AAGGTTTTAAGCCACCCAG
*
1752 -CGGAACTAACCTCCCC-TTTCGAAGGTTTTACGATTACGCCACACC-GCAGGAACGAACCTCCC
1 TAGGAACTAACCTCCCCTTTTCGAAGGTTTT---A--A-GCCAC-CCTGCAGGAACGAACCTCCC
* *
1814 CTTTTCGAAGGTTTTACGCCACCCCG
59 CTTTTCGAAGGTTTTAAGCCACCCAG
** *
1840 TAGGAACTAACCTCCCCTTTTCGAAGG-TTTAACGCCA-AATGCACGG-ACTAACCTCCCCTTTT
1 TAGGAACTAACCTCCCCTTTTCGAAGGTTTTAA-GCCACCCTGCA-GGAACGAACCTCCCCTTTT
1902 CGAAGGTTTTAA
64 CGAAGGTTTTAA
1914 CTCTCTGTCT
Statistics
Matches: 139, Mismatches: 11, Indels: 24
0.80 0.06 0.14
Matches are distributed among these distances:
81 13 0.09
82 15 0.11
83 29 0.21
84 9 0.06
86 2 0.01
87 29 0.21
88 15 0.11
89 18 0.13
90 9 0.06
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (84 bp):
TAGGAACTAACCTCCCCTTTTCGAAGGTTTTAAGCCACCCTGCAGGAACGAACCTCCCCTTTTCG
AAGGTTTTAAGCCACCCAG
Found at i:2015 original size:60 final size:60
Alignment explanation
Indices: 1916--2035 Score: 186
Period size: 60 Copynumber: 2.0 Consensus size: 60
1906 GGTTTTAACT
* * * * *
1916 CTCTGTCTGATCTACTAGAAGATGCAGATTTGCTGCTCTCTCTGTTAGATCTGGCCATGG
1 CTCTATCTGATCTACCAGAAGATGCAGATTCGCTACTCTCTCTGTTAGATCTGACCATGG
*
1976 CTCTATCTGATCTACCAGAGGATGCAGATTCGCTACTCTCTCTGTTAGATCTGACCATGG
1 CTCTATCTGATCTACCAGAAGATGCAGATTCGCTACTCTCTCTGTTAGATCTGACCATGG
2036 TTTTACCAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (60 bp):
CTCTATCTGATCTACCAGAAGATGCAGATTCGCTACTCTCTCTGTTAGATCTGACCATGG
Found at i:2111 original size:3 final size:3
Alignment explanation
Indices: 2096--2132 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2086 TTGTGTTTTG
*
2096 AGA AGA GGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2133 AAATGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2182 original size:17 final size:17
Alignment explanation
Indices: 2160--2197 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2150 AACGGATTAC
*
2160 ATTTTTCTTTCACTTGT
1 ATTTTTCATTCACTTGT
2177 ATTTTTCATTCACTTGT
1 ATTTTTCATTCACTTGT
2194 -TTTT
1 ATTTT
2198 ATTGACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.13, C:0.16, G:0.05, T:0.66
Consensus pattern (17 bp):
ATTTTTCATTCACTTGT
Found at i:2205 original size:14 final size:15
Alignment explanation
Indices: 2161--2210 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 15
2151 ACGGATTACA
*
2161 TTTTTCTTTCACTTG
1 TTTTTCATTCACTTG
2176 TATTTTTCATTCACTTG
1 --TTTTTCATTCACTTG
*
2193 TTTTT-ATTGACTTG
1 TTTTTCATTCACTTG
2207 TTTT
1 TTTT
2211 AGGTTACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 12 0.39
15 5 0.16
17 14 0.45
ACGTcount: A:0.12, C:0.14, G:0.08, T:0.66
Consensus pattern (15 bp):
TTTTTCATTCACTTG
Found at i:2491 original size:59 final size:59
Alignment explanation
Indices: 2399--2514 Score: 214
Period size: 59 Copynumber: 2.0 Consensus size: 59
2389 TCAATCTTGG
*
2399 ATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTACTTGATTGATTTGA
1 ATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACATACTTGATTGATTTGA
*
2458 ATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACATGCTTGATTGATTT
1 ATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACATACTTGATTGATTT
2515 CATCACTCCC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (59 bp):
ATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACATACTTGATTGATTTGA
Found at i:2503 original size:28 final size:28
Alignment explanation
Indices: 2385--2505 Score: 84
Period size: 28 Copynumber: 4.2 Consensus size: 28
2375 TTGACTTTGT
* *
2385 TGCTTCAATCTTGGATCCCGCTGTAATCA
1 TGCTTCAATCAT-GATCCCGCGGTAATCA
* *
2414 TGCTTCAATCATGATCCTGCGGTAGA-CC
1 TGCTTCAATCATGATCCCGCGGTA-ATCA
* * * * *
2442 TACTTGATTGATTTGAATCCCGCTGTAATCA
1 TGCTTCAATCA--TG-ATCCCGCGGTAATCA
*
2473 TGCTTCAATCATGATCCTGCGGTAGA-CA
1 TGCTTCAATCATGATCCCGCGGTA-ATCA
2501 TGCTT
1 TGCTT
2506 GATTGATTTC
Statistics
Matches: 69, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
28 34 0.49
29 15 0.22
30 3 0.04
31 17 0.25
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (28 bp):
TGCTTCAATCATGATCCCGCGGTAATCA
Found at i:8223 original size:7 final size:7
Alignment explanation
Indices: 8211--8243 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
8201 CCAAAGTGTG
8211 CCACTCT
1 CCACTCT
8218 CCACTCT
1 CCACTCT
8225 CCACTCT
1 CCACTCT
8232 CCACTCT
1 CCACTCT
8239 CCACT
1 CCACT
8244 TCATATGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.58, G:0.00, T:0.27
Consensus pattern (7 bp):
CCACTCT
Found at i:8860 original size:25 final size:25
Alignment explanation
Indices: 8832--8887 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
8822 CTGGAAAGTG
8832 TGTCAAGTTTCCGGTCAGTCAACAA
1 TGTCAAGTTTCCGGTCAGTCAACAA
*
8857 TGTCAAGTTTTCGGTCAGTCAACAA
1 TGTCAAGTTTCCGGTCAGTCAACAA
*
8882 AGTCAA
1 TGTCAA
8888 CATTCGGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (25 bp):
TGTCAAGTTTCCGGTCAGTCAACAA
Found at i:10246 original size:3 final size:3
Alignment explanation
Indices: 10238--10263 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10228 ACCAGAACTT
10238 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
10264 GAGACCGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12741 original size:13 final size:14
Alignment explanation
Indices: 12710--12741 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12700 CCTGAAAAAC
12710 GAAGTCATCTCCTT
1 GAAGTCATCTCCTT
12724 GAAGTCATCTCC-T
1 GAAGTCATCTCCTT
12737 GAAGT
1 GAAGT
12742 GATTGAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (14 bp):
GAAGTCATCTCCTT
Found at i:17877 original size:2 final size:2
Alignment explanation
Indices: 17870--17902 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17860 AGGTCAAGCT
17870 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
17903 TACTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28647 original size:17 final size:17
Alignment explanation
Indices: 28625--28660 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28615 TCTTCCACCG
28625 CAAATCCAAACCTTTAC
1 CAAATCCAAACCTTTAC
28642 CAAATCCAAACCTTTAC
1 CAAATCCAAACCTTTAC
28659 CA
1 CA
28661 CTGTGAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (17 bp):
CAAATCCAAACCTTTAC
Found at i:30308 original size:6 final size:6
Alignment explanation
Indices: 30290--30320 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
30280 AGGACCCACC
*
30290 GGCGGA GGAGGA GGCGGA GGCGGA GGCGGA G
1 GGCGGA GGCGGA GGCGGA GGCGGA GGCGGA G
30321 ACGGTGGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.13, G:0.68, T:0.00
Consensus pattern (6 bp):
GGCGGA
Found at i:34236 original size:2 final size:2
Alignment explanation
Indices: 34229--34263 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
34219 TATGCCACAA
34229 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
34264 TCTTTTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36172 original size:15 final size:15
Alignment explanation
Indices: 36152--36185 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
36142 AAAACAACTT
36152 ATAAAACAAGTTA-TA
1 ATAAAACAA-TTAGTA
36167 ATAAAACAATTAGTA
1 ATAAAACAATTAGTA
36182 ATAA
1 ATAA
36186 TAAATCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
ATAAAACAATTAGTA
Found at i:37944 original size:8 final size:8
Alignment explanation
Indices: 37931--37961 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
37921 GAAGAGGTGT
37931 GGGAGAGG
1 GGGAGAGG
37939 GGGAGAGG
1 GGGAGAGG
37947 GGGAGAGG
1 GGGAGAGG
37955 GGGAGAG
1 GGGAGAG
37962 TTCGGTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (8 bp):
GGGAGAGG
Done.