Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013435.1 Corchorus olitorius cultivar O-4 contig13468, 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: 53213
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:9625 original size:69 final size:70
Alignment explanation
Indices: 9539--9690 Score: 234
Period size: 69 Copynumber: 2.2 Consensus size: 70
9529 AACAACTCAT
* * *
9539 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTTTA-ATTTGCGCTCTTCAACAGCACAA
1 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCAACAGCACAA
9603 GTCCG
66 GTCCG
* * *
9608 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTTTGCATTCCTCAACAGCCCAA
1 GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCAACAGCACAA
*
9673 GTCCT
66 GTCCG
9678 GGACAGGACTTGG
1 GGACAGGACTTGG
9691 CCAAGATCTG
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
69 40 0.53
70 35 0.47
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (70 bp):
GGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCAACAGCACAA
GTCCG
Found at i:14158 original size:28 final size:28
Alignment explanation
Indices: 14133--14186 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
14123 TTAGCATTAA
14133 GGTC-ATT-CAGGGGCATTTTGGTCATT
1 GGTCAATTACAGGGGCATTTTGGTCATT
**
14159 TTTCAATTACAGGGGCATTTTGGTCATT
1 GGTCAATTACAGGGGCATTTTGGTCATT
14187 TTTACACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 3 0.12
28 19 0.79
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.41
Consensus pattern (28 bp):
GGTCAATTACAGGGGCATTTTGGTCATT
Found at i:14208 original size:26 final size:28
Alignment explanation
Indices: 14140--14214 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
14130 TAAGGTCATT
*
14140 CAGGGGCATTTTGGTCATTTTTCAATTA
1 CAGGGGCATTTTGGTCATTTTTCAACTA
14168 CAGGGGCATTTTGGTCATTTTT-ACACTA
1 CAGGGGCATTTTGGTCATTTTTCA-ACTA
*
14196 -A-GGGCATTCTGGTCATTTT
1 CAGGGGCATTTTGGTCATTTT
14215 AAGATCACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 17 0.39
27 2 0.05
28 25 0.57
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (28 bp):
CAGGGGCATTTTGGTCATTTTTCAACTA
Found at i:19605 original size:7 final size:7
Alignment explanation
Indices: 19595--19644 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
19585 CCGACCGACA
19595 TATATAT
1 TATATAT
19602 TATATAT
1 TATATAT
19609 TATATAT
1 TATATAT
*
19616 AAT-TAT
1 TATATAT
*
19622 T-TTTA-
1 TATATAT
19627 TATATAT
1 TATATAT
19634 TATAT-T
1 TATATAT
19640 TATAT
1 TATAT
19645 TATATTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
5 2 0.05
6 14 0.38
7 21 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATATAT
Found at i:19615 original size:16 final size:15
Alignment explanation
Indices: 19594--19650 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 15
19584 CCCGACCGAC
19594 ATATATATTATATATT
1 ATATATATTATAT-TT
*
19610 ATATATAATTATTTTT
1 ATATAT-ATTATATTT
19626 ATATATATTATATTT
1 ATATATATTATATTT
19641 ATATTATATT
1 ATA-TATATT
19651 TAATTAGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.30
16 20 0.54
17 6 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATATATTATATTT
Found at i:19668 original size:36 final size:37
Alignment explanation
Indices: 19596--19674 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 37
19586 CGACCGACAT
* * *
19596 ATATATTATATATTATATATAATTATTTTTATATATA
1 ATATATTATATATTATATATAATTAGTTATACATATA
* * *
19633 TTATATT-TATATTATATTTAATTAGTTATGCATATA
1 ATATATTATATATTATATATAATTAGTTATACATATA
19669 ATATAT
1 ATATAT
19675 CAGAAATCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
36 29 0.83
37 6 0.17
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (37 bp):
ATATATTATATATTATATATAATTAGTTATACATATA
Found at i:23954 original size:62 final size:62
Alignment explanation
Indices: 23857--23982 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
23847 TTTAGTTATT
23857 TAGCAAGCTAATGTTAGTTTAATAGTTAGTGTAGCAAATAGGCAATAGCAATTGCCAAACTG
1 TAGCAAGCTAATGTTAGTTTAATAGTTAGTGTAGCAAATAGGCAATAGCAATTGCCAAACTG
23919 TAGCAAGCTAATGTTAGTTTAATAGTTAGTGTAGCAAATAGGCAATAGCAATTGCCAAACTG
1 TAGCAAGCTAATGTTAGTTTAATAGTTAGTGTAGCAAATAGGCAATAGCAATTGCCAAACTG
23981 TA
1 TA
23983 TATATGGTAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (62 bp):
TAGCAAGCTAATGTTAGTTTAATAGTTAGTGTAGCAAATAGGCAATAGCAATTGCCAAACTG
Found at i:25077 original size:23 final size:23
Alignment explanation
Indices: 25039--25085 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
25029 AATAATTTAG
*
25039 TTATAGAAATAATAAATATAATAT
1 TTATAGAAATAATAAAAAT-ATAT
*
25063 TTATA-AAATATTAAAAATATAT
1 TTATAGAAATAATAAAAATATAT
25085 T
1 T
25086 ATTTACTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 11 0.52
24 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TTATAGAAATAATAAAAATATAT
Found at i:47517 original size:16 final size:16
Alignment explanation
Indices: 47492--47525 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47482 TTATTGCATC
47492 TTTCTATTTTCTGATT
1 TTTCTATTTTCTGATT
* *
47508 TTTCTCTTTTTTGATT
1 TTTCTATTTTCTGATT
47524 TT
1 TT
47526 GATCTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTCTATTTTCTGATT
Found at i:48111 original size:41 final size:41
Alignment explanation
Indices: 48066--48285 Score: 144
Period size: 41 Copynumber: 5.4 Consensus size: 41
48056 TTTCTAAAAC
*
48066 CAGGGACCAAATTGAATCAAATAGTAACTAAAATCCTAAAT
1 CAGGGACCAAATTGAATCAAATAGTAAATAAAATCCTAAAT
* * * * * *
48107 CAGGGACTAAATTGCATCAAACAATAAATAGCAA-CTTAAAT
1 CAGGGACCAAATTGAATCAAATAGTAAATA-AAATCCTAAAT
* * * ** *
48148 TAGGGACCAAGTTGAATGAAATCACACAAATAAAGA---AAAAT
1 CAGGGACCAAATTGAATCAAAT-A-GTAAATAAA-ATCCTAAAT
* * * *
48189 -AAGGACCAAATTGAATCAAATAGTAACTAGAATCCTAAAC
1 CAGGGACCAAATTGAATCAAATAGTAAATAAAATCCTAAAT
* ** * *
48229 CAGGGACTAAATTGTGTCAAATAGTAAATAGAATCTTAAAT
1 CAGGGACCAAATTGAATCAAATAGTAAATAAAATCCTAAAT
* * *
48270 TAGGTACCATATTGAA
1 CAGGGACCAAATTGAA
48286 CACTAGAGCC
Statistics
Matches: 133, Mismatches: 38, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
37 1 0.01
38 5 0.04
39 1 0.01
40 21 0.16
41 94 0.71
42 4 0.03
43 7 0.05
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.23
Consensus pattern (41 bp):
CAGGGACCAAATTGAATCAAATAGTAAATAAAATCCTAAAT
Found at i:49348 original size:28 final size:29
Alignment explanation
Indices: 49308--49372 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
49298 AAAAACCCAG
* *
49308 GGGGCTTTTTGGTCATTTTT-CACATTCA
1 GGGGCATTATGGTCATTTTTGCACATTCA
*
49336 GGGGCATTATGGTCATTTTTGCATATTCA
1 GGGGCATTATGGTCATTTTTGCACATTCA
*
49365 GGAGCATT
1 GGGGCATT
49373 TTGATCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.42
Consensus pattern (29 bp):
GGGGCATTATGGTCATTTTTGCACATTCA
Found at i:49380 original size:29 final size:28
Alignment explanation
Indices: 49314--49380 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 28
49304 CCAGGGGGCT
*
49314 TTTTGGTCATTTTTCACATTCAGGGGCA
1 TTTTGGTCATTTTTCACATTCAGGAGCA
* *
49342 TTATGGTCATTTTTGCATATTCAGGAGCA
1 TTTTGGTCATTTTT-CACATTCAGGAGCA
*
49371 TTTTGATCAT
1 TTTTGGTCAT
49381 ATTAAGTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (28 bp):
TTTTGGTCATTTTTCACATTCAGGAGCA
Found at i:49720 original size:60 final size:60
Alignment explanation
Indices: 49581--49722 Score: 275
Period size: 60 Copynumber: 2.4 Consensus size: 60
49571 TTTAGCAATT
*
49581 CTCCATCAATTTAACATTAATTTGTCATTTGCAAAATGTTTTCATTTGTTGCATTTAGAA
1 CTCCATCAATTTAACATTAGTTTGTCATTTGCAAAATGTTTTCATTTGTTGCATTTAGAA
49641 CTCCATCAATTTAACATTAGTTTGTCATTTGCAAAATGTTTTCATTTGTTGCATTTAGAA
1 CTCCATCAATTTAACATTAGTTTGTCATTTGCAAAATGTTTTCATTTGTTGCATTTAGAA
49701 CTCCATCAATTTAACATTAGTT
1 CTCCATCAATTTAACATTAGTT
49723 GTCGTTTAGC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 81 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (60 bp):
CTCCATCAATTTAACATTAGTTTGTCATTTGCAAAATGTTTTCATTTGTTGCATTTAGAA
Done.