Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010583.1 Corchorus capsularis cultivar CVL-1 contig10604, 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: 57943
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:2486 original size:16 final size:16
Alignment explanation
Indices: 2465--2497 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2455 TAATTAGCCA
2465 TTAAAACGAAGAATAC
1 TTAAAACGAAGAATAC
2481 TTAAAACGAAGAATAC
1 TTAAAACGAAGAATAC
2497 T
1 T
2498 CTAACAGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (16 bp):
TTAAAACGAAGAATAC
Found at i:9786 original size:19 final size:19
Alignment explanation
Indices: 9758--9799 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
9748 GTTTTGGTAA
*
9758 AAAATTAAAAA-ACTAAAAT
1 AAAA-TAAAAATAATAAAAT
*
9777 AAAATAAAAATTATAAAAT
1 AAAATAAAAATAATAAAAT
9796 AAAA
1 AAAA
9800 ATGTGGGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAATAAAAATAATAAAAT
Found at i:9792 original size:14 final size:14
Alignment explanation
Indices: 9775--9801 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9765 AAAAACTAAA
9775 ATAAAATAAAAATT
1 ATAAAATAAAAATT
9789 ATAAAATAAAAAT
1 ATAAAATAAAAAT
9802 GTGGGGAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAATAAAAATT
Found at i:25874 original size:3 final size:3
Alignment explanation
Indices: 25868--25904 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
25858 AAAAAAACTC
25868 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
25905 GCACAGCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:26959 original size:6 final size:6
Alignment explanation
Indices: 26948--26981 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
26938 ATTCCATGCA
* *
26948 AATTGC AATTGC AATTGC AATTCC AATTCC AATT
1 AATTGC AATTGC AATTGC AATTGC AATTGC AATT
26982 TGCATGCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (6 bp):
AATTGC
Found at i:28407 original size:11 final size:11
Alignment explanation
Indices: 28383--28417 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28373 TTGACAGCGC
28383 AACAAAAACAA
1 AACAAAAACAA
* *
28394 AACGAAAACGA
1 AACAAAAACAA
28405 AACAAAAACAA
1 AACAAAAACAA
28416 AA
1 AA
28418 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:43604 original size:69 final size:67
Alignment explanation
Indices: 43494--43631 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 67
43484 AGGAACAGAT
*
43494 TAGGAACATTTTAACGAGTACAACAATGAACTATAAAGGTTTAAGCAACAGACCTTCAAGGTTCT
1 TAGGAACATTTTAACGAGTACAACAATAAACTATAAAGGTTTAAGCAACAGACCTTCAAGGTTCT
43559 CA
66 CA
43561 TAGGAACATTTTAACGAGTACACAACAATAAACTATAAAGGTTTAAGCAACAGACCTTCAAGGTT
1 TAGGAACATTTTAACGAGT--ACAACAATAAACTATAAAGGTTTAAGCAACAGACCTTCAAGGTT
43626 CTCA
64 CTCA
43630 TA
1 TA
43632 TAATGTCCAA
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 19 0.28
69 49 0.72
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.25
Consensus pattern (67 bp):
TAGGAACATTTTAACGAGTACAACAATAAACTATAAAGGTTTAAGCAACAGACCTTCAAGGTTCT
CA
Found at i:45531 original size:43 final size:43
Alignment explanation
Indices: 45470--45555 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
45460 TAGATTGGAT
* * *
45470 TTCAATTGTCTGCATTTTCTAAGAAGGAAACTGCTGCAAATGG
1 TTCAATTATCCGCATTTTCCAAGAAGGAAACTGCTGCAAATGG
45513 TTCAATTATCCGCATTTTCCAAGAAGGAAACTGCTGCAAATGG
1 TTCAATTATCCGCATTTTCCAAGAAGGAAACTGCTGCAAATGG
45556 CATGGCTGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (43 bp):
TTCAATTATCCGCATTTTCCAAGAAGGAAACTGCTGCAAATGG
Found at i:51865 original size:42 final size:42
Alignment explanation
Indices: 51786--52001 Score: 272
Period size: 42 Copynumber: 5.1 Consensus size: 42
51776 CATGCGGGAT
* * * * * *
51786 GTTCCTGCGGGGTGGCATAAAACTTTCAAAAAAGGGAGATTA
1 GTTCCTGCGGAGTGGCGTAAAACCTTCGAAAAGGGGAGGTTA
* * *
51828 GTTCTTACGGAATGGCGTAAAACCTTCGAAAAGGGGAGGTTA
1 GTTCCTGCGGAGTGGCGTAAAACCTTCGAAAAGGGGAGGTTA
* * *
51870 GTTCATGCAGG-GTGTCGTAAAACCTTCGAAAATGGGAGGTTA
1 GTTCCTGC-GGAGTGGCGTAAAACCTTCGAAAAGGGGAGGTTA
51912 GTTCCTGCGGAGTGGCGTAAAACCTTCGAAAAGGGGAGGTTA
1 GTTCCTGCGGAGTGGCGTAAAACCTTCGAAAAGGGGAGGTTA
* * *
51954 GTTCCTGCGGGGTGGCATAAAATCTTCGAAAAGGGGAGGTTA
1 GTTCCTGCGGAGTGGCGTAAAACCTTCGAAAAGGGGAGGTTA
*
51996 GCTCCT
1 GTTCCT
52002 AGCACTCAAT
Statistics
Matches: 151, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 2 0.01
42 147 0.97
43 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (42 bp):
GTTCCTGCGGAGTGGCGTAAAACCTTCGAAAAGGGGAGGTTA
Found at i:52399 original size:79 final size:79
Alignment explanation
Indices: 52265--52423 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 79
52255 CTTGGTTAAG
* * *
52265 GATCGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTGCGAGTCTTCACGCTCCAACTTGAGGAGG
1 GATCGGTTTGAATCATTAGTGTTCAAATTGGGCGTTGCGAATCTTCACGCGCCAACTTGAGGAGG
52330 GAGTGATGAAATCA
66 GAGTGATGAAATCA
52344 GATCGGTTTGAATCATTAGTGTTCAAATTGGGCGTTGCGAATCTTCACGCGCCAACTTGAGGAGG
1 GATCGGTTTGAATCATTAGTGTTCAAATTGGGCGTTGCGAATCTTCACGCGCCAACTTGAGGAGG
52409 GAGTGATGAAATCA
66 GAGTGATGAAATCA
52423 G
1 G
52424 TCAATAGTGA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.28
Consensus pattern (79 bp):
GATCGGTTTGAATCATTAGTGTTCAAATTGGGCGTTGCGAATCTTCACGCGCCAACTTGAGGAGG
GAGTGATGAAATCA
Found at i:52514 original size:30 final size:30
Alignment explanation
Indices: 52480--52536 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
52470 TGATGGAATC
*
52480 AAGTCAACGGTGCATTTACAGCAGGATTCA
1 AAGTCAACAGTGCATTTACAGCAGGATTCA
** *
52510 AAGTCAACAGTGTGTTTACAGCGGGAT
1 AAGTCAACAGTGCATTTACAGCAGGAT
52537 CCTAGATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (30 bp):
AAGTCAACAGTGCATTTACAGCAGGATTCA
Found at i:52763 original size:6 final size:6
Alignment explanation
Indices: 52752--52780 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52742 TTTCTTCCTT
52752 CTTCTC CTTCTC CTTCTC CTTCTC CTTCT
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCT
52781 TCCCAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTCTC
Found at i:55501 original size:30 final size:29
Alignment explanation
Indices: 55439--55508 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
55429 ACTGAACCGT
****
55439 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
55468 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
55498 CAAATAAGCCC
1 CAAATAAGCCC
55509 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Done.