Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007592.1 Corchorus capsularis cultivar CVL-1 contig07613, 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: 66245
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:352 original size:16 final size:16
Alignment explanation
Indices: 331--367 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
321 TAACGCCTCT
331 TGTCTCTCCGTCTATC
1 TGTCTCTCCGTCTATC
* *
347 TGTCTCTCTGTCTATT
1 TGTCTCTCCGTCTATC
363 TGTCT
1 TGTCT
368 ATGCCAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.30, G:0.14, T:0.51
Consensus pattern (16 bp):
TGTCTCTCCGTCTATC
Found at i:2368 original size:2 final size:2
Alignment explanation
Indices: 2316--2349 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2306 ACTTTAAAGA
*
2316 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2350 GTTATTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10782 original size:26 final size:26
Alignment explanation
Indices: 10753--10806 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
10743 GTTAACTTGA
10753 TTGAACAAGCTTTTTTACATGTATGC
1 TTGAACAAGCTTTTTTACATGTATGC
***
10779 TTGAGTGAGCTTTTTTACATGTATGC
1 TTGAACAAGCTTTTTTACATGTATGC
10805 TT
1 TT
10807 ACTTAGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (26 bp):
TTGAACAAGCTTTTTTACATGTATGC
Found at i:11828 original size:86 final size:85
Alignment explanation
Indices: 11733--11896 Score: 233
Period size: 86 Copynumber: 1.9 Consensus size: 85
11723 TCTATTTTTA
* *
11733 TTAATTAAATATAATTTCTTTATAACTATTTTATCTTTAACA-TTTTACTATTTCAATTTTTA-A
1 TTAATTAAATATAATCTCCTTATAACTATTTTATCTTTAACATTTTTACTATTTCAA---TTACA
11796 AAACTTAGATATATTAAAAAATT
63 AAACTTAGATATATTAAAAAATT
* * * *
11819 TTAATTAAATCTAATCTCCTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACAAAA
1 TTAATTAAATATAATCTCCTTATAACTATTTTATCTTTAACATTTTTACTATTTCAATTACAAAA
11884 CTTAGATATATTA
66 CTTAGATATATTA
11897 TAATTTTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
84 3 0.04
85 17 0.24
86 37 0.53
87 13 0.19
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.50
Consensus pattern (85 bp):
TTAATTAAATATAATCTCCTTATAACTATTTTATCTTTAACATTTTTACTATTTCAATTACAAAA
CTTAGATATATTAAAAAATT
Found at i:11907 original size:86 final size:84
Alignment explanation
Indices: 11726--11910 Score: 228
Period size: 86 Copynumber: 2.1 Consensus size: 84
11716 TAAAAACTCT
* *
11726 ATTTTTATTAATTAAATATAATTTCTTTATAACTATTTTATCTTTAACATTTTACTATTTCAATT
1 ATTTTT-TTAATTAAATATAATCTCCTTATAACTATTTTATCTTTAACATTTTACTATTTCAA--
11791 TTTAAAAACTTAGATATATTAA
63 TTTAAAAACTTAGATATATTAA
*** * * * *
11813 AAAATTTTAATTAAATCTAATCTCCTTATAACTATTTTATTTTTACCATTTTTACTATTTTAA-T
1 ATTTTTTTAATTAAATATAATCTCCTTATAACTATTTTATCTTTAACA-TTTTACTATTTCAATT
11877 TACAAAACTTAGATATATTATA
65 TA-AAAACTTAGATATATTA-A
11899 ATTTTTTTAATT
1 ATTTTTTTAATT
11911 TATTTCTTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
84 3 0.04
85 17 0.20
86 47 0.57
87 16 0.19
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.52
Consensus pattern (84 bp):
ATTTTTTTAATTAAATATAATCTCCTTATAACTATTTTATCTTTAACATTTTACTATTTCAATTT
AAAAACTTAGATATATTAA
Found at i:13740 original size:18 final size:19
Alignment explanation
Indices: 13709--13746 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
13699 AGTAGTGAGC
13709 TACTCGAGCTCGAGCTCGA
1 TACTCGAGCTCGAGCTCGA
13728 TACTCGA-CTCGAGCTCGA
1 TACTCGAGCTCGAGCTCGA
13746 T
1 T
13747 CGAGTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.24
Consensus pattern (19 bp):
TACTCGAGCTCGAGCTCGA
Found at i:36671 original size:15 final size:16
Alignment explanation
Indices: 36651--36688 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
36641 GTATTTTTCA
*
36651 TTTTTTC-TTCTCTTT
1 TTTTTTCTTTCACTTT
36666 TTTTTTCTTTTCACTTT
1 TTTTTTC-TTTCACTTT
36683 TTTTTT
1 TTTTTT
36689 TTTAAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
17 13 0.65
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTCTTTCACTTT
Found at i:42394 original size:13 final size:12
Alignment explanation
Indices: 42376--42405 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
42366 TTTGAAATCC
42376 AAATAATATTTA
1 AAATAATATTTA
42388 TAAATAATATTTA
1 -AAATAATATTTA
42401 AAATA
1 AAATA
42406 TTGAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAATATTTA
Found at i:42828 original size:44 final size:46
Alignment explanation
Indices: 42771--42860 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 46
42761 CAAAAAGTCT
*
42771 CCAACTTTTTAAAATTAAAATGGT-AAA-AAAATATTTTTAAAAAA
1 CCAACTTTTTAAAATTAAAATGGTAAAATAAAATATTTATAAAAAA
42815 CCAA-TTTATTAAAATTAAAATGGTCAAAATAAAATATTTATAAAAA
1 CCAACTTT-TTAAAATTAAAATGGT-AAAATAAAATATTTATAAAAA
42861 TATTGCATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
43 3 0.07
44 20 0.49
46 3 0.07
47 15 0.37
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (46 bp):
CCAACTTTTTAAAATTAAAATGGTAAAATAAAATATTTATAAAAAA
Found at i:43040 original size:84 final size:84
Alignment explanation
Indices: 42952--43112 Score: 254
Period size: 85 Copynumber: 1.9 Consensus size: 84
42942 TTAAAAAATT
*
42952 ATATATCTAAG-TTATGTAATTAAAATAGTAAAAATGGT-AAAAATAAAATGGTTATAAAGAGAT
1 ATATATCTAAGTTTATGTAATTAAAATAGT-AAAATGGTAAAAAATAAAATAGTTATAAAGA-AT
*
43015 TATATTTAATTAAAAATTATA
64 TAGATTTAATTAAAAATTATA
* *
43036 ATATATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAAATAGTTATAAAGAATTA
1 ATATATCTAAGTTTATGTAATTAAAATAGTAAAATGGTAAAAAATAAAATAGTTATAAAGAATTA
43101 GATTTAATTAAA
66 GATTTAATTAAA
43113 TAAAAATAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
84 34 0.48
85 37 0.52
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.37
Consensus pattern (84 bp):
ATATATCTAAGTTTATGTAATTAAAATAGTAAAATGGTAAAAAATAAAATAGTTATAAAGAATTA
GATTTAATTAAAAATTATA
Found at i:43691 original size:16 final size:16
Alignment explanation
Indices: 43672--43705 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
43662 AAAATTGAGA
43672 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
43688 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
43704 AA
1 AA
43706 AAATCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:43920 original size:41 final size:41
Alignment explanation
Indices: 43857--44116 Score: 333
Period size: 41 Copynumber: 6.3 Consensus size: 41
43847 TTTTCATTTG
*
43857 TTCAAGATCAAGTTGTCAAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
** * *
43898 TTCAAGATTGAGTCGTCGAGACCCTTGAATTAAATTATTAA
1 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
* ** * *
43939 CTCAAGATTGAGTCATCAAGACCCTTGAATTAAATTGTCAA
1 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
*
43980 TTCAAGATCAAGTCGTCAAGACCCTTAAATTAAATTATCAA
1 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
** * *
44021 TTCAAGATTGAGTCATCAA-AGGCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCGTCAAGA-CCCTTGAATTAAATTATCAA
* *
44062 TTCAAGATCAAGTCGTCAAAACCCTTGAATTAAATTGTCAA
1 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
* *
44103 CTCAAGACCAAGTC
1 TTCAAGATCAAGTC
44117 ATTCAACCCT
Statistics
Matches: 189, Mismatches: 28, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
40 1 0.01
41 187 0.99
42 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (41 bp):
TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
Found at i:44086 original size:123 final size:123
Alignment explanation
Indices: 43857--44116 Score: 387
Period size: 123 Copynumber: 2.1 Consensus size: 123
43847 TTTTCATTTG
* * * *
43857 TTCAAGATCAAGTTGTCAAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCGTCGAGACCC
1 TTCAAGATCAAGTCGTCAAGACCCTTAAATTAAATTATCAATTCAAGATTGAGTCATCAAGACCC
* ** *
43922 TTGAATTAAATTATTAACTCAAGATTGAGTCATCAAGACCCTTGAATTAAATTGTCAA
66 TTGAATTAAATTATCAACTCAAGATCAAGTCATCAAAACCCTTGAATTAAATTGTCAA
*
43980 TTCAAGATCAAGTCGTCAAGACCCTTAAATTAAATTATCAATTCAAGATTGAGTCATCAA-AGGC
1 TTCAAGATCAAGTCGTCAAGACCCTTAAATTAAATTATCAATTCAAGATTGAGTCATCAAGA-CC
* *
44044 CTTGAATTAAATTATCAATTCAAGATCAAGTCGTCAAAACCCTTGAATTAAATTGTCAA
65 CTTGAATTAAATTATCAACTCAAGATCAAGTCATCAAAACCCTTGAATTAAATTGTCAA
* *
44103 CTCAAGACCAAGTC
1 TTCAAGATCAAGTC
44117 ATTCAACCCT
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
122 1 0.01
123 122 0.99
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (123 bp):
TTCAAGATCAAGTCGTCAAGACCCTTAAATTAAATTATCAATTCAAGATTGAGTCATCAAGACCC
TTGAATTAAATTATCAACTCAAGATCAAGTCATCAAAACCCTTGAATTAAATTGTCAA
Found at i:44118 original size:82 final size:82
Alignment explanation
Indices: 43872--44109 Score: 370
Period size: 82 Copynumber: 2.9 Consensus size: 82
43862 GATCAAGTTG
** * *
43872 TCAAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCGTCGAGACCCTTGAATTAAATTATT
1 TCAAGACCCTTGAATTAAATTATCAATTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATC
43937 AACTCAAGATTGAGTCA
66 AACTCAAGATTGAGTCA
* *
43954 TCAAGACCCTTGAATTAAATTGTCAATTCAAGATCAAGTCGTCAAGACCCTTAAATTAAATTATC
1 TCAAGACCCTTGAATTAAATTATCAATTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATC
*
44019 AATTCAAGATTGAGTCA
66 AACTCAAGATTGAGTCA
* * *
44036 TCAA-AGGCCTTGAATTAAATTATCAATTCAAGATCAAGTCGTCAAAACCCTTGAATTAAATTGT
1 TCAAGA-CCCTTGAATTAAATTATCAATTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTAT
44100 CAACTCAAGA
65 CAACTCAAGA
44110 CCAAGTCATT
Statistics
Matches: 142, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
81 1 0.01
82 141 0.99
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (82 bp):
TCAAGACCCTTGAATTAAATTATCAATTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATC
AACTCAAGATTGAGTCA
Found at i:44524 original size:109 final size:110
Alignment explanation
Indices: 44376--44595 Score: 388
Period size: 109 Copynumber: 2.0 Consensus size: 110
44366 ATACAAGTTG
* *
44376 ATCGGCTCACGCTGGCGCGTCGAGAATTCTTGATTTGTGGCTAGCAAATCATTTTAGTTATAGAG
1 ATCGGCTCACGCTAGCGCGTCGAGAATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAG
44441 TTTTTTTTT-CTCTCGATTCTTATCATATATGTGAGTAGGTGGTT
66 TTTTTTTTTCCTCTCGATTCTTATCATATATGTGAGTAGGTGGTT
* *
44485 ATCGGCTCGCGCTAGCGCGTCGAGCATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAG
1 ATCGGCTCACGCTAGCGCGTCGAGAATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAG
*
44550 TTTTTTTTTCCTCTCGGTTCTTATCATATATGTGAGTAGGTGGTT
66 TTTTTTTTTCCTCTCGATTCTTATCATATATGTGAGTAGGTGGTT
44595 A
1 A
44596 GTAAATTCGA
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
109 70 0.67
110 35 0.33
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (110 bp):
ATCGGCTCACGCTAGCGCGTCGAGAATTCTTGATGTGTGGCTAGCAAATCATTTTAGTTATAGAG
TTTTTTTTTCCTCTCGATTCTTATCATATATGTGAGTAGGTGGTT
Found at i:48385 original size:116 final size:116
Alignment explanation
Indices: 48175--48400 Score: 337
Period size: 116 Copynumber: 1.9 Consensus size: 116
48165 CAGAGCTTAA
* * **
48175 TTAGACTCGATCGGTGTGGCCCATGAGCATGGTGAACCTGGTGTCTCCAATCCGCCAGGGGCGTG
1 TTAGACTCGATCAGTGTGGCCCATAAGCACAGTGAACCTGGTGTCTCCAATCCGCCAGGGGCGTG
* * * * *
48240 CAATTTTTGTGTGTTGGGTCCTTGGACTCCATGGGTTAATTCTTGCCTTGG
66 CAATTGTGGAGTGTTGGGTCCTTGCACTCCATGGGTTAAGTCTTGCCTTGG
*
48291 TTAGACTCGATCAGTGTGGCCCATAAGCACAGTGAACCTGGTGTCTCCAATCCGCCAAGGGTC-T
1 TTAGACTCGATCAGTGTGGCCCATAAGCACAGTGAACCTGGTGTCTCCAATCCGCC-AGGGGCGT
*
48355 GCAATTGTGGAGTGTTGGGTCTTTGCACTCCATGGGTTAAGTCTTG
65 GCAATTGTGGAGTGTTGGGTCCTTGCACTCCATGGGTTAAGTCTTG
48401 ATGGCAGGTA
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
116 93 0.95
117 5 0.05
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.31
Consensus pattern (116 bp):
TTAGACTCGATCAGTGTGGCCCATAAGCACAGTGAACCTGGTGTCTCCAATCCGCCAGGGGCGTG
CAATTGTGGAGTGTTGGGTCCTTGCACTCCATGGGTTAAGTCTTGCCTTGG
Found at i:49652 original size:32 final size:32
Alignment explanation
Indices: 49616--49684 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
49606 AAGGGTAAAC
49616 ATGTAGTTTTATTTAATTTAGATTAATTAATT
1 ATGTAGTTTTATTTAATTTAGATTAATTAATT
* *
49648 ATGTATTTTTATTTCATTTAGATTAATTAATT
1 ATGTAGTTTTATTTAATTTAGATTAATTAATT
49680 ATGTA
1 ATGTA
49685 ATTATGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.33, C:0.01, G:0.09, T:0.57
Consensus pattern (32 bp):
ATGTAGTTTTATTTAATTTAGATTAATTAATT
Found at i:50533 original size:2 final size:2
Alignment explanation
Indices: 50528--50555 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50518 ATATCCAATC
50528 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
50556 CTGTGTGTGT
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:51987 original size:3 final size:3
Alignment explanation
Indices: 51979--52009 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
51969 TGTCAGGGGA
51979 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
52010 GGAGGAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:52090 original size:21 final size:22
Alignment explanation
Indices: 52059--52101 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
52049 TAGGTTATAT
52059 ATATATATATATAAATTAAAAA
1 ATATATATATATAAATTAAAAA
**
52081 ATATA-ATATATATTTTAAAAA
1 ATATATATATATAAATTAAAAA
52102 TATTGGTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATATATATATAAATTAAAAA
Done.