Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006279.1 Corchorus capsularis cultivar CVL-1 contig06298, 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: 99559
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:448 original size:15 final size:16
Alignment explanation
Indices: 428--466 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
418 GTGAATGAAT
* *
428 ATAATTAAATTTGT-A
1 ATAATTAAACTTATAA
443 ATAATTAAACTTATAA
1 ATAATTAAACTTATAA
459 ATAATTAA
1 ATAATTAA
467 TTACAAAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (16 bp):
ATAATTAAACTTATAA
Found at i:693 original size:2 final size:2
Alignment explanation
Indices: 686--710 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
676 TGCTATAAAC
686 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
711 TGTTGCTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3996 original size:2 final size:2
Alignment explanation
Indices: 3989--4013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3979 CTATAATAAT
3989 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4014 TATCTAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11779 original size:20 final size:20
Alignment explanation
Indices: 11754--11793 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
11744 GTCCTAATAC
*
11754 GAGCTCTTAATTGAGTCTAT
1 GAGCTCTTAATTAAGTCTAT
11774 GAGCTCTTAATTAAGTCTAT
1 GAGCTCTTAATTAAGTCTAT
11794 AAAATTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (20 bp):
GAGCTCTTAATTAAGTCTAT
Found at i:12071 original size:24 final size:24
Alignment explanation
Indices: 12036--12081 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
12026 GGCCCAACCC
* *
12036 GTCAAGTTTTAAGTCAATTACCAG
1 GTCAAGTCTTAAGCCAATTACCAG
12060 GTCAAGTCTTAAGCCAATTACC
1 GTCAAGTCTTAAGCCAATTACC
12082 GGCTATCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (24 bp):
GTCAAGTCTTAAGCCAATTACCAG
Found at i:15114 original size:12 final size:12
Alignment explanation
Indices: 15097--15122 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15087 ACGACTCACT
15097 TTGGAGGTAAAG
1 TTGGAGGTAAAG
15109 TTGGAGGTAAAG
1 TTGGAGGTAAAG
15121 TT
1 TT
15123 CTCCCAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (12 bp):
TTGGAGGTAAAG
Found at i:15130 original size:42 final size:42
Alignment explanation
Indices: 15071--15218 Score: 111
Period size: 42 Copynumber: 3.4 Consensus size: 42
15061 GCCGGATTGA
15071 AGGTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGG
1 AGGTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGG
* * ** *** * * **
15113 AGGTAAAGTTCTCCCAAC-AAT-GGTCAAGAGCAGCAACTCAATCTCA
1 AGGTAAAGCTCTCCCAACGACTCACTTTGGAG--GTAA---AGT-TGG
*
15159 AAGTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGG
1 AGGTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGG
*
15201 AGGTAAAGTTCTCCCAAC
1 AGGTAAAGCTCTCCCAAC
15219 AATGGTCAAG
Statistics
Matches: 73, Mismatches: 25, Indels: 16
0.64 0.22 0.14
Matches are distributed among these distances:
40 4 0.05
41 2 0.03
42 37 0.51
43 2 0.03
45 2 0.03
46 20 0.27
47 2 0.03
48 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (42 bp):
AGGTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGG
Found at i:15202 original size:12 final size:12
Alignment explanation
Indices: 15185--15210 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15175 ACGACTCACT
15185 TTGGAGGTAAAG
1 TTGGAGGTAAAG
15197 TTGGAGGTAAAG
1 TTGGAGGTAAAG
15209 TT
1 TT
15211 CTCCCAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (12 bp):
TTGGAGGTAAAG
Found at i:15222 original size:88 final size:88
Alignment explanation
Indices: 15073--15248 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
15063 CGGATTGAAG
15073 GTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGGAGGTAAAGTTCTCCCAACAATGGTC
1 GTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGGAGGTAAAGTTCTCCCAACAATGGTC
15138 AAGAGCAGCAACTCAATCTCAAA
66 AAGAGCAGCAACTCAATCTCAAA
15161 GTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGGAGGTAAAGTTCTCCCAACAATGGTC
1 GTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGGAGGTAAAGTTCTCCCAACAATGGTC
15226 AAGAGCAGCAACTCAATCTCAAA
66 AAGAGCAGCAACTCAATCTCAAA
15249 ATCCATAAAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (88 bp):
GTAAAGCTCTCCCAACGACTCACTTTGGAGGTAAAGTTGGAGGTAAAGTTCTCCCAACAATGGTC
AAGAGCAGCAACTCAATCTCAAA
Found at i:25533 original size:9 final size:9
Alignment explanation
Indices: 25519--25543 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
25509 CAAAGACATT
25519 TCCTTCTTC
1 TCCTTCTTC
25528 TCCTTCTTC
1 TCCTTCTTC
25537 TCCTTCT
1 TCCTTCT
25544 CCTCTTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
TCCTTCTTC
Found at i:31611 original size:19 final size:19
Alignment explanation
Indices: 31587--31624 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31577 CCTTAATTAG
31587 TAGTAATAGATCAGTTCAA
1 TAGTAATAGATCAGTTCAA
31606 TAGTAATAGATCAGTTCAA
1 TAGTAATAGATCAGTTCAA
31625 ATGATTCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
TAGTAATAGATCAGTTCAA
Found at i:31764 original size:26 final size:25
Alignment explanation
Indices: 31717--31770 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
31707 CACCCAACTT
*
31717 AAAAAAAAATTAGTTGTTTCTTTCA
1 AAAAAAAAATTAGTTGTATCTTTCA
*
31742 AAAAAAAAATTAGTTGTAATCTTTTA
1 AAAAAAAAATTAGTTGT-ATCTTTCA
31768 AAA
1 AAA
31771 TGAATACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (25 bp):
AAAAAAAAATTAGTTGTATCTTTCA
Found at i:35635 original size:48 final size:48
Alignment explanation
Indices: 35564--35661 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
35554 AAGTTTGGTT
*
35564 TGGGAGAAGTGCTTTTGAAAAGTGCTTTTTTAAATTACAGCTTAAACA
1 TGGGAGAAGTGCTTTTGAAAAGTGCTTTTTGAAATTACAGCTTAAACA
*
35612 TGGGAGAAGTGCTTTTGAAAAGTGCTTTTTGAAATTGCAGCTTAAACA
1 TGGGAGAAGTGCTTTTGAAAAGTGCTTTTTGAAATTACAGCTTAAACA
35660 TG
1 TG
35662 TAAATAATGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (48 bp):
TGGGAGAAGTGCTTTTGAAAAGTGCTTTTTGAAATTACAGCTTAAACA
Found at i:39037 original size:60 final size:59
Alignment explanation
Indices: 38901--39037 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
38891 CTCATTTAAG
* * *
38901 CATTTTTGCATACGTCAGGGTCTTTTTAACAAAATTCAAAGCATGTGCCCTAATTTGAA
1 CATTTTTGCATACGTTAGAGTCTTTTTAACAAAATTAAAAGCATGTGCCCTAATTTGAA
* * * *
38960 CATTTTCGCGTACGTTAGAGTCTTATTTAACTAAATTAAAAGTATG-GACCCTAGA-TTGAA
1 CATTTTTGCATACGTTAGAGTCTT-TTTAACAAAATTAAAAGCATGTG-CCCTA-ATTTGAA
* *
39020 CATTTTTACATATGTTAG
1 CATTTTTGCATACGTTAG
39038 GGGCTATTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
59 21 0.33
60 42 0.66
61 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (59 bp):
CATTTTTGCATACGTTAGAGTCTTTTTAACAAAATTAAAAGCATGTGCCCTAATTTGAA
Found at i:45202 original size:23 final size:23
Alignment explanation
Indices: 45192--45249 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
45182 TGTCACAAGG
45192 GAGTCCCAAAAACTCTCACAAAA
1 GAGTCCCAAAAACTCTCACAAAA
*
45215 GAGTCCCAAAAACTTTCACTAAAA
1 GAGTCCCAAAAACTCTCAC-AAAA
*
45239 -TGTCCCAAAAA
1 GAGTCCCAAAAA
45250 AAATAGAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 28 0.88
24 4 0.12
ACGTcount: A:0.47, C:0.28, G:0.09, T:0.17
Consensus pattern (23 bp):
GAGTCCCAAAAACTCTCACAAAA
Found at i:47785 original size:76 final size:76
Alignment explanation
Indices: 47679--47826 Score: 206
Period size: 76 Copynumber: 1.9 Consensus size: 76
47669 AAACCTCTAT
* * * * *
47679 AAATTATTAATGTTGGGACCATGAAAAATTATTAACTTAAAGAGATTATTAATTTATTGAGTGTT
1 AAATTAATAATGTTGGAACCATGAAAAATTATTAACTTAAAGAGATTATTAATATATCGAGTATT
47744 AATTTATATGG
66 AATTTATATGG
* * * * *
47755 AAATTAATAATGTTGGAACTATGAACAATTATTAATTTAGAGAGGTTATTAATATATCGAGTATT
1 AAATTAATAATGTTGGAACCATGAAAAATTATTAACTTAAAGAGATTATTAATATATCGAGTATT
47820 AATTTAT
66 AATTTAT
47827 GAAGGTTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.41
Consensus pattern (76 bp):
AAATTAATAATGTTGGAACCATGAAAAATTATTAACTTAAAGAGATTATTAATATATCGAGTATT
AATTTATATGG
Found at i:54375 original size:30 final size:31
Alignment explanation
Indices: 54310--54375 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
54300 AAAAAGTTTG
*
54310 AGGGCTTATTTGGTTATTTTGAATAAGGTAA
1 AGGGCTTATTTGGTCATTTTGAATAAGGTAA
* *
54341 AGGGCTTGTTTGGTCATTTTGAA-AAGGTAC
1 AGGGCTTATTTGGTCATTTTGAATAAGGTAA
54371 AGGGC
1 AGGGC
54376 CAAAAGAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.26, C:0.08, G:0.30, T:0.36
Consensus pattern (31 bp):
AGGGCTTATTTGGTCATTTTGAATAAGGTAA
Found at i:70560 original size:12 final size:13
Alignment explanation
Indices: 70543--70582 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
70533 ATTTAGTACT
70543 AATAAT-ATAATA
1 AATAATCATAATA
*
70555 AATAATGATAAT-
1 AATAATCATAATA
70567 AATAATCATAATA
1 AATAATCATAATA
70580 AAT
1 AAT
70583 TAAGCTACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (13 bp):
AATAATCATAATA
Found at i:71632 original size:40 final size:40
Alignment explanation
Indices: 71574--71654 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
71564 TTTATAAGCA
** *
71574 GGGGCTAAACCTGGATTTAATTTCTTACCTTAATTATTAG
1 GGGGCTAAACCTAAATTTAATTTATTACCTTAATTATTAG
* *
71614 GGGGCTAAATCTAAATTTAATTTATTTCCTTAATTATTAG
1 GGGGCTAAACCTAAATTTAATTTATTACCTTAATTATTAG
71654 G
1 G
71655 AGGGTCAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (40 bp):
GGGGCTAAACCTAAATTTAATTTATTACCTTAATTATTAG
Found at i:71855 original size:13 final size:13
Alignment explanation
Indices: 71830--71862 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
71820 TTTGTAACAA
71830 ATATTTTTATTTT
1 ATATTTTTATTTT
71843 AT-TTTTATATTTT
1 ATATTTT-TATTTT
71856 ATATTTT
1 ATATTTT
71863 GATTGAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 10 0.56
14 4 0.22
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATATTTTTATTTT
Found at i:71857 original size:7 final size:7
Alignment explanation
Indices: 71830--71862 Score: 52
Period size: 6 Copynumber: 5.0 Consensus size: 7
71820 TTTGTAACAA
71830 ATATTTT
1 ATATTTT
71837 -TATTTT
1 ATATTTT
71843 AT-TTTT
1 ATATTTT
71849 ATATTTT
1 ATATTTT
71856 ATATTTT
1 ATATTTT
71863 GATTGAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
ATATTTT
Found at i:76848 original size:12 final size:12
Alignment explanation
Indices: 76809--76934 Score: 117
Period size: 12 Copynumber: 10.5 Consensus size: 12
76799 CAGTAGAAGA
*
76809 CCTGGAGGCATG
1 CCTGGAGGTATG
* * *
76821 CCTGGCGGTTTT
1 CCTGGAGGTATG
76833 CCTGGAGGTATG
1 CCTGGAGGTATG
*
76845 CCTGGAGGAATG
1 CCTGGAGGTATG
* * *
76857 CCTGGTGGTTTC
1 CCTGGAGGTATG
*
76869 CCTGGAGGAATG
1 CCTGGAGGTATG
*
76881 CCTGGAGGAATG
1 CCTGGAGGTATG
* *
76893 CCTGGAGGTTTC
1 CCTGGAGGTATG
*
76905 CCTGGTGGTATG
1 CCTGGAGGTATG
* *
76917 CCTGGTGGGATG
1 CCTGGAGGTATG
76929 CCTGGA
1 CCTGGA
76935 AATGTTGATT
Statistics
Matches: 90, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 90 1.00
ACGTcount: A:0.13, C:0.21, G:0.40, T:0.26
Consensus pattern (12 bp):
CCTGGAGGTATG
Found at i:76849 original size:36 final size:36
Alignment explanation
Indices: 76809--76934 Score: 180
Period size: 36 Copynumber: 3.5 Consensus size: 36
76799 CAGTAGAAGA
* * *
76809 CCTGGAGGCATGCCTGGCGGTTTTCCTGGAGGTATG
1 CCTGGAGGAATGCCTGGAGGTTTCCCTGGAGGTATG
* *
76845 CCTGGAGGAATGCCTGGTGGTTTCCCTGGAGGAATG
1 CCTGGAGGAATGCCTGGAGGTTTCCCTGGAGGTATG
*
76881 CCTGGAGGAATGCCTGGAGGTTTCCCTGGTGGTATG
1 CCTGGAGGAATGCCTGGAGGTTTCCCTGGAGGTATG
* *
76917 CCTGGTGGGATGCCTGGA
1 CCTGGAGGAATGCCTGGA
76935 AATGTTGATT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 81 1.00
ACGTcount: A:0.13, C:0.21, G:0.40, T:0.26
Consensus pattern (36 bp):
CCTGGAGGAATGCCTGGAGGTTTCCCTGGAGGTATG
Found at i:82066 original size:2 final size:2
Alignment explanation
Indices: 82055--82092 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
82045 TACATCTAGT
82055 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
82093 TTGACGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96364 original size:14 final size:14
Alignment explanation
Indices: 96345--96373 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
96335 ACAATACCAC
96345 CAGCAGCTGCCATA
1 CAGCAGCTGCCATA
96359 CAGCAGCTGCCATA
1 CAGCAGCTGCCATA
96373 C
1 C
96374 CAGGATTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.38, G:0.21, T:0.14
Consensus pattern (14 bp):
CAGCAGCTGCCATA
Done.