Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010161.1 Corchorus olitorius cultivar O-4 contig10193, 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: 10641
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:1442 original size:52 final size:52
Alignment explanation
Indices: 1364--1466 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
1354 TACATATTAA
*
1364 ATTTTTGTATTGATTTTGGTTGTAAATTTTTGGCAACTAGGGAATGTTGCCG
1 ATTTTTGTATTGATTTTGGTTGTAAATTTGTGGCAACTAGGGAATGTTGCCG
*
1416 ATTTTTGTATTGATTTTGGTTGTAAATTTGTGGCAACTAGGGTATGTTGCC
1 ATTTTTGTATTGATTTTGGTTGTAAATTTGTGGCAACTAGGGAATGTTGCC
1467 AAACATTTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.20, C:0.08, G:0.25, T:0.47
Consensus pattern (52 bp):
ATTTTTGTATTGATTTTGGTTGTAAATTTGTGGCAACTAGGGAATGTTGCCG
Found at i:3227 original size:52 final size:52
Alignment explanation
Indices: 3149--3252 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
3139 ACACATATTA
3149 GATTTTTGTATTGATTTTGGTTGTAAATTTCG-GGCAACTAGGGAATGTTGCC
1 GATTTTTGTATTGATTTTGGTTGTAAATTT-GTGGCAACTAGGGAATGTTGCC
*
3201 GATTTTTGTATTGATTTTGGTTGTAAATTTGTGGCAACTAGGGCATGTTGCC
1 GATTTTTGTATTGATTTTGGTTGTAAATTTGTGGCAACTAGGGAATGTTGCC
3253 AAACATTTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 1 0.02
52 49 0.98
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (52 bp):
GATTTTTGTATTGATTTTGGTTGTAAATTTGTGGCAACTAGGGAATGTTGCC
Found at i:3774 original size:2 final size:2
Alignment explanation
Indices: 3757--3800 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
3747 TAACTTGACC
3757 AT AT AT -T A- AT AGT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3797 AT AT
1 AT AT
3801 TCTAGCTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3777 original size:15 final size:16
Alignment explanation
Indices: 3757--3799 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
3747 TAACTTGACC
*
3757 ATATATTA-ATAGTAT
1 ATATATTATATAATAT
3772 ATATA-TATATAATAT
1 ATATATTATATAATAT
3787 ATATATATATATA
1 ATATAT-TATATA
3800 TTCTAGCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 2 0.08
15 16 0.67
17 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATATTATATAATAT
Found at i:4650 original size:24 final size:25
Alignment explanation
Indices: 4607--4653 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
4597 ATGAATACCC
**
4607 ATCAAAGGGTATACTGTAAACACCT
1 ATCAAAGGGTATACCATAAACACCT
4632 ATCAAA-GGTATACCATAAACAC
1 ATCAAAGGGTATACCATAAACAC
4654 ACCAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (25 bp):
ATCAAAGGGTATACCATAAACACCT
Found at i:6734 original size:36 final size:36
Alignment explanation
Indices: 6682--6813 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 36
6672 GGTTGTAATA
* *
6682 CCGCTGGCCTTGGTCGCCTAATACTTGGCTATAACG
1 CCGCTGGCCTTAGTCGCCCAATACTTGGCTATAACG
* *
6718 CCGCTGGCCTCAGTCGCCCAATGCTTGGCTATAACG
1 CCGCTGGCCTTAGTCGCCCAATACTTGGCTATAACG
**
6754 CCGCTGGCCTTAGTCGCCCAATGTTTGGCTATAACG
1 CCGCTGGCCTTAGTCGCCCAATACTTGGCTATAACG
* *
6790 CCGCTGGCCTAAGTCGCCTAATAC
1 CCGCTGGCCTTAGTCGCCCAATAC
6814 ATAATTGGCT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 86 1.00
ACGTcount: A:0.17, C:0.33, G:0.24, T:0.25
Consensus pattern (36 bp):
CCGCTGGCCTTAGTCGCCCAATACTTGGCTATAACG
Found at i:8133 original size:26 final size:26
Alignment explanation
Indices: 8070--8133 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
8060 ACTATGCGCT
* *
8070 AGGGAGGCGACCACCTGCTGTGAGTA
1 AGGGGGGCGACCCCCTGCTGTGAGTA
*
8096 A-GGGGGCGACCCCCTGGTGTGAGTA
1 AGGGGGGCGACCCCCTGCTGTGAGTA
8121 AGGGGGGCGACCC
1 AGGGGGGCGACCC
8134 TATTTTACGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 22 0.65
26 12 0.35
ACGTcount: A:0.19, C:0.25, G:0.44, T:0.12
Consensus pattern (26 bp):
AGGGGGGCGACCCCCTGCTGTGAGTA
Found at i:8613 original size:84 final size:85
Alignment explanation
Indices: 8475--8638 Score: 242
Period size: 84 Copynumber: 1.9 Consensus size: 85
8465 CCCTTCCAAA
* *
8475 TTTTGTTGGGTAGGAGGCGTTACGCCCCCCCTTCCAAATTTTTTTGGCTAGGAGGCATTACGCCT
1 TTTTGTTGGGTAGGAGGCGTTACGCCCCCCCTTCCAAAATTTTTTGGATAGGAGGCATTACGCC-
*
8540 CCCCTTC-CAAATTTTAAAAT
65 CCCCTTCTAAAATTTTAAAAT
* ** *
8560 TTTTTTTGGGTA-GAGGCGTTACGCTTCCCCTTCCAAAATTTTTTGGATAGGAGGCGTTACGCCC
1 TTTTGTTGGGTAGGAGGCGTTACGCCCCCCCTTCCAAAATTTTTTGGATAGGAGGCATTACGCCC
8624 CCCTTCTAAAATTTT
66 CCCTTCTAAAATTTT
8639 TTGGGTTGGA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
83 7 0.10
84 53 0.75
85 11 0.15
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (85 bp):
TTTTGTTGGGTAGGAGGCGTTACGCCCCCCCTTCCAAAATTTTTTGGATAGGAGGCATTACGCCC
CCCTTCTAAAATTTTAAAAT
Found at i:8627 original size:37 final size:37
Alignment explanation
Indices: 8451--8664 Score: 200
Period size: 38 Copynumber: 5.5 Consensus size: 37
8441 TAATATGGGG
*
8451 GGAGGCCTTACG-CCCCCTTCC-AAATTTTGTTGGGTA
1 GGAGGCGTTACGCCCCCCTTCCAAAATTTT-TTGGGTA
* *
8487 GGAGGCGTTACGCCCCCCCTTCCAAATTTTTTTGGCTA
1 GGAGGCGTTACG-CCCCCCTTCCAAAATTTTTTGGGTA
*
8525 GGAGGCATTACGCCTCCCCTTCCAAATTTTAAAATTTTTTTTGGGTA
1 GGAGGCGTTACGCC-CCCCTTCC-------AAAA--TTTTTTGGGTA
* *
8572 -GAGGCGTTACGCTTCCCCTTCCAAAATTTTTTGGATA
1 GGAGGCGTTACGC-CCCCCTTCCAAAATTTTTTGGGTA
* *
8609 GGAGGCGTTACGCCCCCCTTCTAAAATTTTTTGGGTT
1 GGAGGCGTTACGCCCCCCTTCCAAAATTTTTTGGGTA
*
8646 GGAGGCGTTAACCCCCCCC
1 GGAGGCGTT-ACGCCCCCC
8665 CCCCCCCCTC
Statistics
Matches: 148, Mismatches: 14, Indels: 30
0.77 0.07 0.16
Matches are distributed among these distances:
36 11 0.07
37 41 0.28
38 54 0.36
39 10 0.07
45 3 0.02
46 19 0.13
47 10 0.07
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (37 bp):
GGAGGCGTTACGCCCCCCTTCCAAAATTTTTTGGGTA
Found at i:9026 original size:23 final size:23
Alignment explanation
Indices: 8981--9026 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
8971 ACAATCCCTT
*
8981 GCTCTTATGCGGAGGCTCACCCA
1 GCTCTTACGCGGAGGCTCACCCA
*
9004 GCTCTTACGCTGAGCGCTC-CCCA
1 GCTCTTACGCGGAG-GCTCACCCA
9027 AGAAGCAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.22
Consensus pattern (23 bp):
GCTCTTACGCGGAGGCTCACCCA
Found at i:9426 original size:24 final size:25
Alignment explanation
Indices: 9388--9434 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
9378 ATGAATACCC
*
9388 ATCAAAGGGTATACCGTAAACACCT
1 ATCAAAGGGTATACCATAAACACCT
9413 ATCAAA-GGTATACCATAAACAC
1 ATCAAAGGGTATACCATAAACAC
9435 ACCAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (25 bp):
ATCAAAGGGTATACCATAAACACCT
Found at i:9444 original size:26 final size:25
Alignment explanation
Indices: 9390--9444 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
9380 GAATACCCAT
* * *
9390 CAAAGGGTATACCGTAAACACCTAT
1 CAAAGGGTATACCATAAACACCAAC
9415 CAAA-GGTATACCATAAACACACCAAC
1 CAAAGGGTATACCAT-AA-ACACCAAC
9441 CAAA
1 CAAA
9445 TATTATACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 9 0.36
25 6 0.24
26 10 0.40
ACGTcount: A:0.47, C:0.27, G:0.11, T:0.15
Consensus pattern (25 bp):
CAAAGGGTATACCATAAACACCAAC
Found at i:10202 original size:29 final size:29
Alignment explanation
Indices: 10167--10246 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
10157 GCTAAATACC
* *
10167 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT--TTTCGGGA
*
10198 CAAAATAATCCTTTATGTTTTTTTCGGGA
1 CAAAATAATCCCTTATGTTTTTTTCGGGA
* *
10227 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
10247 CAAAAATGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 24 0.56
31 19 0.44
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (29 bp):
CAAAATAATCCCTTATGTTTTTTTCGGGA
Found at i:10405 original size:31 final size:32
Alignment explanation
Indices: 10370--10435 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
10360 AAGGGACTGA
10370 TTTGTCCCAAAAGAAAAACATAAGAG-ATTTT
1 TTTGTCCCAAAAGAAAAACATAAGAGAATTTT
*
10401 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
1 TTTGTCCCAAAAGAAAAACATAAGAGAATTTT
10433 TTT
1 TTT
10436 TAGTATTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (32 bp):
TTTGTCCCAAAAGAAAAACATAAGAGAATTTT
Done.