Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010651.1 Corchorus capsularis cultivar CVL-1 contig10672, 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: 36018
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:7028 original size:31 final size:29
Alignment explanation
Indices: 6957--7028 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 29
6947 GTATATCATC
6957 TTTTAATTTGTTTAATTTAAGGTTTTAATT
1 TTTTAATTTGTTTAATTTAAGG-TTTAATT
* *
6987 TTAATGATTTGTTTAATTTAATGG-TTAATT
1 TT-TTAATTTGTTTAATTTAA-GGTTTAATT
7017 TGCTTTAATTTG
1 T--TTTAATTTG
7029 CAATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
30 9 0.26
31 22 0.65
32 3 0.09
ACGTcount: A:0.26, C:0.01, G:0.12, T:0.60
Consensus pattern (29 bp):
TTTTAATTTGTTTAATTTAAGGTTTAATT
Found at i:7301 original size:16 final size:16
Alignment explanation
Indices: 7280--7335 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
7270 AACCCGAGAT
7280 CGAACCCAAAAATACC
1 CGAACCCAAAAATACC
*
7296 CGAACCC-AACATAGCC
1 CGAACCCAAAAATA-CC
*
7312 CGAACCCGAAAATACC
1 CGAACCCAAAAATACC
7328 CGAACCCA
1 CGAACCCA
7336 TCCAATTGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.14
16 25 0.71
17 5 0.14
ACGTcount: A:0.43, C:0.41, G:0.11, T:0.05
Consensus pattern (16 bp):
CGAACCCAAAAATACC
Found at i:7611 original size:13 final size:13
Alignment explanation
Indices: 7579--7605 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7569 TGCAATTAAT
7579 AACTTATCAAAAC
1 AACTTATCAAAAC
7592 AACTTATCAAAAC
1 AACTTATCAAAAC
7605 A
1 A
7606 TGTTATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (13 bp):
AACTTATCAAAAC
Found at i:10271 original size:21 final size:20
Alignment explanation
Indices: 10232--10276 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10222 AGAAATTAAT
* *
10232 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
10252 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
10273 TAAA
1 TAAA
10277 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:16782 original size:74 final size:74
Alignment explanation
Indices: 16666--16813 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
16656 TTTATGATCG
*
16666 GTCGTCAGCAATCATAAAAATAATCCCCACAAAAACTAACTAGAGTAGTTAGGGCAAGTAGGGGT
1 GTCGTCAGCAATCATAAAAATAATCCCCAAAAAAACTAACTAGAGTAGTTAGGGCAAGTAGGGGT
16731 TGAATCCCA
66 TGAATCCCA
16740 GTCGTCAGCAATCATAAAAATAATCCCCAAAAAAACTAACTAGAGTAGTTAGGGCAAGTAGGGGT
1 GTCGTCAGCAATCATAAAAATAATCCCCAAAAAAACTAACTAGAGTAGTTAGGGCAAGTAGGGGT
16805 TGAATCCCA
66 TGAATCCCA
16814 CAGAGAAGGG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (74 bp):
GTCGTCAGCAATCATAAAAATAATCCCCAAAAAAACTAACTAGAGTAGTTAGGGCAAGTAGGGGT
TGAATCCCA
Found at i:16928 original size:20 final size:19
Alignment explanation
Indices: 16891--16936 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
16881 ACAGGGGATT
* *
16891 AAAGAAATTAAATAAAAAG
1 AAAGCAATTAAATAAAAAC
16910 AAAGCAATTAAACTAAAAAC
1 AAAGCAATTAAA-TAAAAAC
16930 AAAGCAA
1 AAAGCAA
16937 AGTAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.13
Consensus pattern (19 bp):
AAAGCAATTAAATAAAAAC
Found at i:21220 original size:22 final size:19
Alignment explanation
Indices: 21183--21222 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
21173 CAACCGCCTT
21183 TAAACGGACGGTTGAACCA
1 TAAACGGACGGTTGAACCA
21202 TAAACCGGACCGGATTGAACC
1 TAAA-CGGA-CGG-TTGAACC
21223 GGAAAAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 3 0.17
22 7 0.39
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (19 bp):
TAAACGGACGGTTGAACCA
Found at i:21550 original size:30 final size:28
Alignment explanation
Indices: 21454--21554 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 28
21444 TAATCTACCA
* *
21454 TTTTGCCCCCTGAACTTGTAACATTTAGACG
1 TTTTGCCCCCTGAAC-T-TCA-ATTTGGACG
* * *
21485 TTTTGCCCCCCGAACTTCAATCTCGGACA
1 TTTTGCCCCCTGAACTTCAAT-TTGGACG
21514 TTTTGCCCCCTGAACTTCAATTTTGGGACG
1 TTTTGCCCCCTGAACTTCAA-TTT-GGACG
21544 TTTTGCCCCCT
1 TTTTGCCCCCT
21555 CAACCTAACG
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.03
29 26 0.44
30 17 0.29
31 14 0.24
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.35
Consensus pattern (28 bp):
TTTTGCCCCCTGAACTTCAATTTGGACG
Found at i:21785 original size:30 final size:30
Alignment explanation
Indices: 21745--21824 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
21735 CATAGCCGTT
*
21745 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
** *
21775 AAGTTCAGGGGGCAAAATAT-CCAAGATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
*
21804 AAGTTCGGGGGGCAAAACGTC
1 AAGTTCAGGGGGCAAAACGTC
21825 TAAACGCTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.17
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCCCAAAATTG
Found at i:23343 original size:2 final size:2
Alignment explanation
Indices: 23336--23363 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23326 AAAAGTTGAC
23336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23364 CTTTTCCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30627 original size:34 final size:34
Alignment explanation
Indices: 30584--30660 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
30574 TTTAGCTTCA
30584 TTTAATAATTTAATATTGTTGCATTTTAAGCCCT
1 TTTAATAATTTAATATTGTTGCATTTTAAGCCCT
*
30618 TTTAATAATTTAGTATTGTTGCATTTTAAGCCCT
1 TTTAATAATTTAATATTGTTGCATTTTAAGCCCT
*
30652 TTTAGTAAT
1 TTTAATAAT
30661 AGGTCTAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (34 bp):
TTTAATAATTTAATATTGTTGCATTTTAAGCCCT
Found at i:30749 original size:33 final size:33
Alignment explanation
Indices: 30712--30778 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
30702 CTTCTTCATG
30712 TTCCCATTAGTTATATTGATTATAGTCATATTT
1 TTCCCATTAGTTATATTGATTATAGTCATATTT
30745 TTCCCATTAGTTATATTGATTATAGTCATATTT
1 TTCCCATTAGTTATATTGATTATAGTCATATTT
30778 T
1 T
30779 CACATTACTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (33 bp):
TTCCCATTAGTTATATTGATTATAGTCATATTT
Found at i:30842 original size:3 final size:3
Alignment explanation
Indices: 30834--30876 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
30824 ATATCCATTT
30834 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30877 CATATCATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:32629 original size:30 final size:30
Alignment explanation
Indices: 32593--32706 Score: 120
Period size: 33 Copynumber: 3.6 Consensus size: 30
32583 CTCGTCACCA
*
32593 AAAACAGATTTATTTTCAATGCTATCAACC
1 AAAACAGAATTATTTTCAATGCTATCAACC
* *
32623 AAAACAGGATTATTTGCAATGCTATAATCAACC
1 AAAACAGAATTATTTTCAATGC--T-ATCAACC
* *
32656 AAAACAGAATTGTTTTTAATGCTATGTTCAACC
1 AAAACAGAATTATTTTCAATGCTA---TCAACC
*
32689 AAAACAGAATTGTTTTCA
1 AAAACAGAATTATTTTCA
32707 TCACAATTAG
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
30 20 0.29
31 1 0.01
32 1 0.01
33 48 0.69
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (30 bp):
AAAACAGAATTATTTTCAATGCTATCAACC
Found at i:34428 original size:8 final size:8
Alignment explanation
Indices: 34400--34433 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
34390 GAATCGGCTA
34400 TGAATTTT
1 TGAATTTT
*
34408 TGAAGTTTC
1 TGAA-TTTT
34417 TGAATTTT
1 TGAATTTT
34425 TGAATTTT
1 TGAATTTT
34433 T
1 T
34434 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:35903 original size:30 final size:30
Alignment explanation
Indices: 35867--35980 Score: 120
Period size: 33 Copynumber: 3.6 Consensus size: 30
35857 CTCGTCACCA
*
35867 AAAACAGATTTATTTTCAATGCTATCAACC
1 AAAACAGAATTATTTTCAATGCTATCAACC
* *
35897 AAAACAGGATTATTTGCAATGCTATAATCAACC
1 AAAACAGAATTATTTTCAATGC--T-ATCAACC
* *
35930 AAAACAGAATTGTTTTTAATGCTATGTTCAACC
1 AAAACAGAATTATTTTCAATGCTA---TCAACC
*
35963 AAAACAGAATTGTTTTCA
1 AAAACAGAATTATTTTCA
35981 TCACAATTAG
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
30 20 0.29
31 1 0.01
32 1 0.01
33 48 0.69
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (30 bp):
AAAACAGAATTATTTTCAATGCTATCAACC
Done.