Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013313.1 Corchorus capsularis cultivar CVL-1 contig13334, 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: 94598
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5286 original size:2 final size:2
Alignment explanation
Indices: 5279--5319 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5269 TGCTCTAAAA
5279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5320 ATAAAAGGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18560 original size:6 final size:6
Alignment explanation
Indices: 18549--18596 Score: 51
Period size: 6 Copynumber: 7.2 Consensus size: 6
18539 AGAGTATTAA
18549 TTAATT TTAATT TTAATT TATCAATACT GTTAATT TTAATT TTAATT T
1 TTAATT TTAATT TTAATT T-T-AAT--T -TTAATT TTAATT TTAATT T
18597 ATCAATACTG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 26 0.70
7 2 0.05
8 3 0.08
9 3 0.08
10 2 0.05
11 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (6 bp):
TTAATT
Found at i:18583 original size:17 final size:17
Alignment explanation
Indices: 18561--18607 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
18551 AATTTTAATT
18561 TTAATTTATCAATACTG
1 TTAATTTATCAATACTG
18578 TTAATTT-T-AAT--T-
1 TTAATTTATCAATACTG
18590 TTAATTTATCAATACTG
1 TTAATTTATCAATACTG
18607 T
1 T
18608 GCGTGAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
12 7 0.28
13 2 0.08
14 3 0.12
15 3 0.12
16 2 0.08
17 8 0.32
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (17 bp):
TTAATTTATCAATACTG
Found at i:18591 original size:29 final size:29
Alignment explanation
Indices: 18549--18607 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
18539 AGAGTATTAA
18549 TTAATTTTAATTTTAATTTATCAATACTG
1 TTAATTTTAATTTTAATTTATCAATACTG
18578 TTAATTTTAATTTTAATTTATCAATACTG
1 TTAATTTTAATTTTAATTTATCAATACTG
18607 T
1 T
18608 GCGTGAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (29 bp):
TTAATTTTAATTTTAATTTATCAATACTG
Found at i:29232 original size:22 final size:22
Alignment explanation
Indices: 29207--29271 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
29197 TCTGTTCTTG
29207 TTCTGATTGTTCTTGGCTTTAA
1 TTCTGATTGTTCTTGGCTTTAA
* ** *
29229 TTCTTACAGTTC-T--C-TT-G
1 TTCTGATTGTTCTTGGCTTTAA
29246 TTCTGATTGTTCTTGGCTTTAA
1 TTCTGATTGTTCTTGGCTTTAA
29268 TTCT
1 TTCT
29272 TGCAGTAGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 9 0.30
18 3 0.10
19 1 0.03
20 1 0.03
21 3 0.10
22 13 0.43
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.55
Consensus pattern (22 bp):
TTCTGATTGTTCTTGGCTTTAA
Found at i:29252 original size:39 final size:39
Alignment explanation
Indices: 29202--29277 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
29192 TTGCCTCTGT
29202 TCTTGTTCTGATTGTTCTTGGCTTTAATTCTTACAGTTC
1 TCTTGTTCTGATTGTTCTTGGCTTTAATTCTTACAGTTC
*
29241 TCTTGTTCTGATTGTTCTTGGCTTTAATTCTTGCAGT
1 TCTTGTTCTGATTGTTCTTGGCTTTAATTCTTACAGT
29278 AGAACTGTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (39 bp):
TCTTGTTCTGATTGTTCTTGGCTTTAATTCTTACAGTTC
Found at i:30782 original size:29 final size:30
Alignment explanation
Indices: 30718--30818 Score: 80
Period size: 31 Copynumber: 3.3 Consensus size: 30
30708 CCTGGTTTGT
* *
30718 CCTTATTTGATCC-CATTCGAAAAGGTTGGGC
1 CCTTATTTGA-CCTTATTCG-AAAGGTTAGGC
*
30749 TCTTATTTGACCTTATT-GAAAGGTTAGGC
1 CCTTATTTGACCTTATTCGAAAGGTTAGGC
** * * *
30778 CCTTAAATGAGCTTTTTCCTAAAGGTTAGGC
1 CCTTATTTGACCTTATT-CGAAAGGTTAGGC
*
30809 CCCTATTTGA
1 CCTTATTTGA
30819 ACTTTTAACA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
29 22 0.40
30 3 0.05
31 30 0.55
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (30 bp):
CCTTATTTGACCTTATTCGAAAGGTTAGGC
Found at i:39126 original size:27 final size:26
Alignment explanation
Indices: 39100--39164 Score: 96
Period size: 25 Copynumber: 2.5 Consensus size: 26
39090 AAATTATTTA
*
39100 AAATATATAAATTAATTATATTTTTT
1 AAATATATAAATTAATTATAGTTTTT
*
39126 AAATCT-TAAATTAATTATAGTTTTT
1 AAATATATAAATTAATTATAGTTTTT
39151 AAATATATTAAATT
1 AAATATA-TAAATT
39165 CCACGTCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 23 0.68
26 5 0.15
27 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
AAATATATAAATTAATTATAGTTTTT
Found at i:40999 original size:23 final size:22
Alignment explanation
Indices: 40969--41030 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
40959 CTTTTTCTAC
*
40969 TTTTATTTTATTTATTTAT-AT
1 TTTTATTTTATTTATTAATGAT
*
40990 TTGTATATTTATATTATTAATGGAT
1 TTTTAT-TTTAT-TTATTAAT-GAT
41015 TTTTATTTTATTTATT
1 TTTTATTTTATTTATT
41031 CATTTTCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 5 0.15
22 5 0.15
23 12 0.35
24 5 0.15
25 7 0.21
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTTATTTTATTTATTAATGAT
Found at i:44220 original size:3 final size:3
Alignment explanation
Indices: 44116--44205 Score: 144
Period size: 3 Copynumber: 30.0 Consensus size: 3
44106 AGAATGAAAA
* * * *
44116 TTG TTA TTG TTG TTA TTG TTA TTA TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
44164 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
44206 AATGAATATT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.04, C:0.00, G:0.29, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:45929 original size:18 final size:18
Alignment explanation
Indices: 45906--45948 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
45896 TCTTGTGTGG
*
45906 AAACAATATTAGATTTGA
1 AAACAATATTAGATTTAA
*
45924 AAACAATATTTGATTTAA
1 AAACAATATTAGATTTAA
45942 AAACAAT
1 AAACAAT
45949 CTCAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (18 bp):
AAACAATATTAGATTTAA
Found at i:47259 original size:4 final size:4
Alignment explanation
Indices: 47250--47285 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
47240 ACTATTTCTG
*
47250 CATA CATA CAAA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
47286 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (4 bp):
CATA
Found at i:58856 original size:6 final size:6
Alignment explanation
Indices: 58847--58873 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58837 TTTGCCATTG
58847 CCAATC CCAATC CCAATC CCAATC CCA
1 CCAATC CCAATC CCAATC CCAATC CCA
58874 GGCTCACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
CCAATC
Found at i:64175 original size:3 final size:3
Alignment explanation
Indices: 64167--64253 Score: 129
Period size: 3 Copynumber: 28.7 Consensus size: 3
64157 CCATAACACA
* * *
64167 AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT AAT AAT CAT CAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
64215 AAT AAT AAA AAT AAT AAT AAT AAAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
64254 AAATCAGTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
3 74 0.96
4 3 0.04
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:66467 original size:22 final size:22
Alignment explanation
Indices: 66439--66541 Score: 84
Period size: 22 Copynumber: 4.7 Consensus size: 22
66429 GTAAACCTCG
* *
66439 TGAAATTTTGATATCCACGCTA
1 TGAAATTTTGATAACCACGATA
*
66461 TGAAATTTTGATAACCTCGATA
1 TGAAATTTTGATAACCACGATA
* * * *
66483 CGAAATTTTGATAGCCTC-ATTG
1 TGAAATTTTGATAACCACGA-TA
*
66505 TGAAATTTCGATAACCAC-ACTA
1 TGAAATTTTGATAACCACGA-TA
* *
66527 TGAGATTTTAATAAC
1 TGAAATTTTGATAAC
66542 ATTCTTGTAA
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
21 1 0.02
22 64 0.98
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (22 bp):
TGAAATTTTGATAACCACGATA
Found at i:66585 original size:24 final size:24
Alignment explanation
Indices: 66555--66605 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
66545 CTTGTAAAAT
66555 TTTAATAACCTAATCCCTATGAAA
1 TTTAATAACCTAATCCCTATGAAA
66579 TTTAATAACCTAATCCCTATGAAA
1 TTTAATAACCTAATCCCTATGAAA
66603 TTT
1 TTT
66606 TATTGCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (24 bp):
TTTAATAACCTAATCCCTATGAAA
Found at i:66722 original size:35 final size:36
Alignment explanation
Indices: 66659--66729 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
66649 TTGATACTTT
66659 AAATTTTGATAACCACACACAAAACAGAATTAGGAGA
1 AAATTTTGATAACCACACAC-AAACAGAATTAGGAGA
*
66696 AAATTTTGATAACCACACAC-AGCAGAATTAGGAG
1 AAATTTTGATAACCACACACAAACAGAATTAGGAG
66730 CATAGGATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 13 0.39
37 20 0.61
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (36 bp):
AAATTTTGATAACCACACACAAACAGAATTAGGAGA
Found at i:85954 original size:137 final size:139
Alignment explanation
Indices: 85788--86041 Score: 476
Period size: 139 Copynumber: 1.8 Consensus size: 139
85778 TATATCACTT
85788 AATCTACAATTTATTTTAATTAAATTATAGTTGAGTTAAATTAT-TTT-TATATTTAGTTAAATT
1 AATCTACAATTTATTTTAATTAAATTATAGTTGAGTTAAATTATATTTATATATTTAGTTAAATT
*
85851 GTATCACTTAATCTATAATTAGAGTGATGGCCAAAAAAAGAATCTACAATTAATCTACATTTTTT
66 GTATCACTTAATCTATAATTAGAGTGATGGCAAAAAAAAGAATCTACAATTAATCTACATTTTTT
85916 TTTGAGATA
131 TTTGAGATA
*
85925 AATCTACAATTTATTTTAATTAAATTATAGTTGAGTTAAATTATATTTATATATTTAGTTAATTT
1 AATCTACAATTTATTTTAATTAAATTATAGTTGAGTTAAATTATATTTATATATTTAGTTAAATT
85990 GTATCACTTAATCTATAATTAGAGTGATGGCAAAAAAAAGAATCTACAATTA
66 GTATCACTTAATCTATAATTAGAGTGATGGCAAAAAAAAGAATCTACAATTA
86042 GAGTTATATA
Statistics
Matches: 113, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
137 44 0.39
138 3 0.03
139 66 0.58
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.43
Consensus pattern (139 bp):
AATCTACAATTTATTTTAATTAAATTATAGTTGAGTTAAATTATATTTATATATTTAGTTAAATT
GTATCACTTAATCTATAATTAGAGTGATGGCAAAAAAAAGAATCTACAATTAATCTACATTTTTT
TTTGAGATA
Found at i:93829 original size:22 final size:23
Alignment explanation
Indices: 93775--93856 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 23
93765 ATATTAGGAA
93775 GTTATCAAAATTTCATAAAAATG
1 GTTATCAAAATTTCATAAAAATG
* * ***
93798 TTTATTAAAATTTCATAGTTA-G
1 GTTATCAAAATTTCATAAAAATG
* *
93820 GTTATCAAAATTTCAT-AAAGTA
1 GTTATCAAAATTTCATAAAAATG
*
93842 ATTATCAAAATTTCA
1 GTTATCAAAATTTCA
93857 CAAGAATATT
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
22 29 0.64
23 16 0.36
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (23 bp):
GTTATCAAAATTTCATAAAAATG
Found at i:94464 original size:22 final size:23
Alignment explanation
Indices: 94410--94491 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 23
94400 ATATTAGGAA
94410 GTTATCAAAATTTCATAAAAATG
1 GTTATCAAAATTTCATAAAAATG
* * ***
94433 TTTATTAAAATTTCATAGTTA-G
1 GTTATCAAAATTTCATAAAAATG
* *
94455 GTTATCAAAATTTCAT-AAAGTA
1 GTTATCAAAATTTCATAAAAATG
*
94477 ATTATCAAAATTTCA
1 GTTATCAAAATTTCA
94492 CAAGAATATT
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
22 29 0.64
23 16 0.36
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (23 bp):
GTTATCAAAATTTCATAAAAATG
Done.