Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006515.1 Corchorus capsularis cultivar CVL-1 contig06536, 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: 34767
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4721 original size:17 final size:17
Alignment explanation
Indices: 4687--4725 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4677 GACATTTCAG
4687 TTTTA-TTATTATTGTT
1 TTTTATTTATTATTGTT
* *
4703 TTTTATTTATTTTTTTT
1 TTTTATTTATTATTGTT
4720 TTTTAT
1 TTTTAT
4726 AAATGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTATTTATTATTGTT
Found at i:4999 original size:16 final size:16
Alignment explanation
Indices: 4981--5055 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
4971 ATTTTTGGGT
* *
4981 ACCCGAATCCGAAATT
1 ACCCGAACCCGAAATG
* *
4997 ACCCGAATCC-AAA-C
1 ACCCGAACCCGAAATG
5011 AGCCCGAACCCGAAATG
1 A-CCCGAACCCGAAATG
* *
5028 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
5044 ACCCGAACCCGA
1 ACCCGAACCCGA
5056 TCAACCCGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
14 1 0.02
15 11 0.22
16 36 0.73
17 1 0.02
ACGTcount: A:0.40, C:0.39, G:0.13, T:0.08
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:5024 original size:31 final size:32
Alignment explanation
Indices: 4981--5055 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
4971 ATTTTTGGGT
* * * *
4981 ACCCGAATCCGAAATTACCCGAATCCAAACA-G
1 ACCCGAACCCGAAATGACCCAAACCCAAA-ATG
5013 -CCCGAACCCGAAATGACCCAAACCCAAAATG
1 ACCCGAACCCGAAATGACCCAAACCCAAAATG
5044 ACCCGAACCCGA
1 ACCCGAACCCGA
5056 TCAACCCGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 25 0.68
32 11 0.30
ACGTcount: A:0.40, C:0.39, G:0.13, T:0.08
Consensus pattern (32 bp):
ACCCGAACCCGAAATGACCCAAACCCAAAATG
Found at i:6065 original size:2 final size:2
Alignment explanation
Indices: 6058--6090 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
6048 CATGGCCTAA
6058 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
6091 TTGTACTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6429 original size:15 final size:17
Alignment explanation
Indices: 6394--6431 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
6384 AACCGAAAAC
6394 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
6410 GACCCGAACCCA-AA-T
1 GACCCGAACCCAGAATT
6425 GACCCGA
1 GACCCGA
6432 CATTTGATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:9248 original size:2 final size:2
Alignment explanation
Indices: 9241--9273 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
9231 AGTTGAAACT
9241 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
9274 AAATGAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12800 original size:32 final size:32
Alignment explanation
Indices: 12764--12825 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
12754 GGGGCATTCC
* *
12764 TTTATCTCACTTAGGTTTTATATATCATGTAT
1 TTTATCTCACTTAGGGTTTAGATATCATGTAT
*
12796 TTTATCTCACTTAGGGTTTAGATTTCATGT
1 TTTATCTCACTTAGGGTTTAGATATCATGT
12826 CATGTCATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.52
Consensus pattern (32 bp):
TTTATCTCACTTAGGGTTTAGATATCATGTAT
Found at i:13005 original size:32 final size:32
Alignment explanation
Indices: 12964--13025 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
12954 GGGACATTTC
*
12964 TTTATCTCACTTAGGATTTATATATCATGTAT
1 TTTATCTCACTTAGGATTTAGATATCATGTAT
* *
12996 TTTATCTCACTTAGGGTTTAGATTTCATGT
1 TTTATCTCACTTAGGATTTAGATATCATGT
13026 CATGTCATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (32 bp):
TTTATCTCACTTAGGATTTAGATATCATGTAT
Found at i:13017 original size:200 final size:200
Alignment explanation
Indices: 12669--13052 Score: 698
Period size: 200 Copynumber: 1.9 Consensus size: 200
12659 ATGTCACAAC
12669 TTTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATGTTGAAATTTAGACTATCTCAC
1 TTTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATGTTGAAATTTAGACTATCTCAC
* *
12734 TTAGGGTTTAATATAGTTTTGGGGCATTCCTTTATCTCACTTAGGTTTTATATATCATGTATTTT
66 TTAGGGTTTAATATAGTTTTGGGACATTCCTTTATCTCACTTAGGATTTATATATCATGTATTTT
12799 ATCTCACTTAGGGTTTAGATTTCATGTCATGTCATGTCATTTTTTGTCTCTCATAGTCAACTTTT
131 ATCTCACTTAGGGTTTAGATTTCATGTCATGTCAT-TCATTTTTTGTCTCTCATAGTCAACTTTT
12864 TTTTTA
195 TTTTTA
* *
12870 TTTT-AAATTTTGACTCTTCCACCACTTTTTATGACATAGAATGTTGAAATTTATACTATCTCAC
1 TTTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATGTTGAAATTTAGACTATCTCAC
*
12934 TTAGGGTTTAATATAGTTTTGGGACATTTCTTTATCTCACTTAGGATTTATATATCATGTATTTT
66 TTAGGGTTTAATATAGTTTTGGGACATTCCTTTATCTCACTTAGGATTTATATATCATGTATTTT
*
12999 ATCTCACTTAGGGTTTAGATTTCATGTCATGTCATTCTTTTTTTGTCTCTCATA
131 ATCTCACTTAGGGTTTAGATTTCATGTCATGTCATTCATTTTTTGTCTCTCATA
13053 ACCTTTTTTA
Statistics
Matches: 177, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
199 18 0.10
200 155 0.88
201 4 0.02
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (200 bp):
TTTTGAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATGTTGAAATTTAGACTATCTCAC
TTAGGGTTTAATATAGTTTTGGGACATTCCTTTATCTCACTTAGGATTTATATATCATGTATTTT
ATCTCACTTAGGGTTTAGATTTCATGTCATGTCATTCATTTTTTGTCTCTCATAGTCAACTTTTT
TTTTA
Found at i:13765 original size:2 final size:2
Alignment explanation
Indices: 13758--13790 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
13748 ATTTTCTTTT
*
13758 TA TA TA TA AA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13791 AGATGGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16793 original size:30 final size:30
Alignment explanation
Indices: 16753--16815 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
16743 TGTCTTCAAG
*
16753 TCCATAATAAGTCCTTGG-CGCATCATTCCC
1 TCCATAATAAG-CCTCGGCCGCATCATTCCC
*
16783 TCCATGATAAGCCTCGGCCGCATCATTCCC
1 TCCATAATAAGCCTCGGCCGCATCATTCCC
16813 TCC
1 TCC
16816 CCCTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.21, C:0.38, G:0.14, T:0.27
Consensus pattern (30 bp):
TCCATAATAAGCCTCGGCCGCATCATTCCC
Found at i:17300 original size:33 final size:33
Alignment explanation
Indices: 17156--17302 Score: 192
Period size: 33 Copynumber: 4.5 Consensus size: 33
17146 CTCGTCACCA
* *
17156 AAAACAGATTTATTTTCAATGCCA---TCAACC
1 AAAACAGAATTATTTTCAATGCTATGTTCAACC
* * *
17186 AAAACAGAATTATTTGCAATGTTATGATCAACC
1 AAAACAGAATTATTTTCAATGCTATGTTCAACC
* *
17219 AAAACAGGATTATTTGCAATGCTATGTTCAACC
1 AAAACAGAATTATTTTCAATGCTATGTTCAACC
* *
17252 AAAACAAAATTATTTTTAATGCTATGTTCAACC
1 AAAACAGAATTATTTTCAATGCTATGTTCAACC
17285 AAAACAGAATTATTTTCA
1 AAAACAGAATTATTTTCA
17303 TCACAATTAG
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
30 20 0.20
33 81 0.80
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (33 bp):
AAAACAGAATTATTTTCAATGCTATGTTCAACC
Found at i:20848 original size:2 final size:2
Alignment explanation
Indices: 20841--20867 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20831 TCATAGACTA
20841 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 A
20868 AAGTTTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22148 original size:69 final size:69
Alignment explanation
Indices: 22069--22210 Score: 284
Period size: 69 Copynumber: 2.1 Consensus size: 69
22059 TACAATGTCT
22069 CATATCTTACTTTCTATAATTGTTTATAAAACAGATGCATCAAATAAACAAAAATATCTCACATA
1 CATATCTTACTTTCTATAATTGTTTATAAAACAGATGCATCAAATAAACAAAAATATCTCACATA
22134 AAAA
66 AAAA
22138 CATATCTTACTTTCTATAATTGTTTATAAAACAGATGCATCAAATAAACAAAAATATCTCACATA
1 CATATCTTACTTTCTATAATTGTTTATAAAACAGATGCATCAAATAAACAAAAATATCTCACATA
22203 AAAA
66 AAAA
22207 CATA
1 CATA
22211 GCTGTCATGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (69 bp):
CATATCTTACTTTCTATAATTGTTTATAAAACAGATGCATCAAATAAACAAAAATATCTCACATA
AAAA
Found at i:22394 original size:12 final size:12
Alignment explanation
Indices: 22379--22403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22369 CTCTTTTTGG
22379 TTTTTTTTTTCA
1 TTTTTTTTTTCA
22391 TTTTTTTTTTCA
1 TTTTTTTTTTCA
22403 T
1 T
22404 GTACACACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:23320 original size:18 final size:18
Alignment explanation
Indices: 23283--23334 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
23273 CCGTTTAGAT
*
23283 TATATAATAATATAAA-A
1 TATATAATTATATAAATA
*
23300 TATAATCATTATCATAAATA
1 TAT-ATAATTAT-ATAAATA
23320 TATATAATTATATAA
1 TATATAATTATATAA
23335 TTAAATCGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.10
18 10 0.34
19 12 0.41
20 4 0.14
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
TATATAATTATATAAATA
Found at i:27337 original size:81 final size:81
Alignment explanation
Indices: 27202--27357 Score: 267
Period size: 81 Copynumber: 1.9 Consensus size: 81
27192 TATCTAGTTT
* *
27202 GGAGGACATGCCATTTTTCGATCAGTCAACACCCGGTGTTGACTGGTTTAAAACCGGACTGATTT
1 GGAGGACATGCCATTTTCCGATCAGTCAACACCCGGTGTTGACTGGTTTAAAACCGGACCGATTT
27267 TGGACATGTTGAGTCC
66 TGGACATGTTGAGTCC
* * *
27283 GGAGGACATGCCATTTTCCGGTTAGTCAACACCTGGTGTTGACTGGTTTAAAACCGGACCGATTT
1 GGAGGACATGCCATTTTCCGATCAGTCAACACCCGGTGTTGACTGGTTTAAAACCGGACCGATTT
27348 TGGACATGTT
66 TGGACATGTT
27358 AGCTAAATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (81 bp):
GGAGGACATGCCATTTTCCGATCAGTCAACACCCGGTGTTGACTGGTTTAAAACCGGACCGATTT
TGGACATGTTGAGTCC
Found at i:29918 original size:31 final size:31
Alignment explanation
Indices: 29883--29948 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
29873 AACTTTATGT
* * *
29883 TTTCCGATTATACCCTTATTTT-TAAAACATA
1 TTTCCAATTATACCATT-TTTTAAAAAACATA
*
29914 TTTCCAATTGTACCATTTTTTAAAAAACATA
1 TTTCCAATTATACCATTTTTTAAAAAACATA
29945 TTTC
1 TTTC
29949 TAAATTACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.45
Consensus pattern (31 bp):
TTTCCAATTATACCATTTTTTAAAAAACATA
Found at i:30245 original size:96 final size:97
Alignment explanation
Indices: 30128--30321 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 97
30118 TCGTTGTATT
30128 TAATTTTTCTTTTTGTCTTTATCTCCAACGTCCTCTTTAGGTTTAGATAATTTAAAGCAAATGAG
1 TAATTTTTCTTTTTGTCTTTATCTCCAACGTCCTCTTTAGGTTTAGATAATTTAAAGCAAATGAG
30193 CAATGGGTCTTTGCTTTGAATGGTCCAATTTC
66 CAATGGGTCTTTGCTTTGAATGGTCCAATTTC
30225 TAATTTTT-TTTTTGTCTTTATCTCCAACGTCCTCTTTAGGTTTAGATAATTTAAAGCAAATGAG
1 TAATTTTTCTTTTTGTCTTTATCTCCAACGTCCTCTTTAGGTTTAGATAATTTAAAGCAAATGAG
30289 CAATGGGTCTTTGCTTTGAATGGTCCAATTTC
66 CAATGGGTCTTTGCTTTGAATGGTCCAATTTC
30321 T
1 T
30322 CATTCCTATA
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 89 0.92
97 8 0.08
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (97 bp):
TAATTTTTCTTTTTGTCTTTATCTCCAACGTCCTCTTTAGGTTTAGATAATTTAAAGCAAATGAG
CAATGGGTCTTTGCTTTGAATGGTCCAATTTC
Found at i:31941 original size:106 final size:106
Alignment explanation
Indices: 31756--31969 Score: 383
Period size: 106 Copynumber: 2.0 Consensus size: 106
31746 GCAAGAAACA
* *
31756 AACAATCTCTAAGGAACCAGGCTGAGTCGCCTTACCCAAAACATTCTCAAAAATCATCCCTTCCA
1 AACAATCTCCAAGGAACCAAGCTGAGTCGCCTTACCCAAAACATTCTCAAAAATCATCCCTTCCA
* *
31821 TACCAAACTGTATATCATCAATTAGCTGAATGATTCAATTC
66 TACCAAACCGTATATCACCAATTAGCTGAATGATTCAATTC
31862 AACAATCTCCAAGGAACCAAGCTGAGTCGCCTTACCCAAAACATTCTCAAAAATCATCCCTTCCA
1 AACAATCTCCAAGGAACCAAGCTGAGTCGCCTTACCCAAAACATTCTCAAAAATCATCCCTTCCA
*
31927 TACCAAACCGTATATCACCAATTAGCTGAATGGTTCAATTC
66 TACCAAACCGTATATCACCAATTAGCTGAATGATTCAATTC
31968 AA
1 AA
31970 AATATCTCTC
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.36, C:0.29, G:0.10, T:0.25
Consensus pattern (106 bp):
AACAATCTCCAAGGAACCAAGCTGAGTCGCCTTACCCAAAACATTCTCAAAAATCATCCCTTCCA
TACCAAACCGTATATCACCAATTAGCTGAATGATTCAATTC
Found at i:34443 original size:17 final size:17
Alignment explanation
Indices: 34406--34444 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
34396 TCATAGTACC
*
34406 TAGGTAGTATGAGATGC
1 TAGGTAGTATGAGATGA
*
34423 TAGGTAGTATGAGGTGA
1 TAGGTAGTATGAGATGA
34440 TAGGT
1 TAGGT
34445 TGCATCTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.31
Consensus pattern (17 bp):
TAGGTAGTATGAGATGA
Done.