Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012589.1 Corchorus capsularis cultivar CVL-1 contig12610, 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: 69437
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5115 original size:6 final size:6
Alignment explanation
Indices: 5104--5142 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
5094 ATAATATATC
5104 ATCTAT ATCTAT ATCTATCT ATCTAT ATCTAT A-CTAT AT
1 ATCTAT ATCTAT ATCTA--T ATCTAT ATCTAT ATCTAT AT
5143 TAAAAAGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
8 6 0.20
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (6 bp):
ATCTAT
Found at i:5126 original size:14 final size:15
Alignment explanation
Indices: 5109--5140 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5099 ATATCATCTA
5109 TATCTATATCTAT-C
1 TATCTATATCTATAC
5123 TATCTATATCTATAC
1 TATCTATATCTATAC
5138 TAT
1 TAT
5141 ATTAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (15 bp):
TATCTATATCTATAC
Found at i:5127 original size:20 final size:18
Alignment explanation
Indices: 5100--5140 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 18
5090 TCTTATAATA
5100 TATCATCTATATCTATATC
1 TATCATCTATATCTATA-C
5119 TATCTATCTATATCTATAC
1 TATC-ATCTATATCTATAC
5138 TAT
1 TAT
5141 ATTAAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.49
Consensus pattern (18 bp):
TATCATCTATATCTATAC
Found at i:5161 original size:16 final size:16
Alignment explanation
Indices: 5140--5171 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5130 ATCTATACTA
5140 TATTAAAAAGTACGTT
1 TATTAAAAAGTACGTT
5156 TATTAAAAAGTACGTT
1 TATTAAAAAGTACGTT
5172 CAGGTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
TATTAAAAAGTACGTT
Found at i:5406 original size:78 final size:70
Alignment explanation
Indices: 5246--5400 Score: 231
Period size: 70 Copynumber: 2.2 Consensus size: 70
5236 TTGTTTAGGT
* *
5246 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCTTTATAATT
5310 ATTTTA
65 ATTTTA
* * *
5316 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCTTTATAATTA
*
5381 TTATA
66 TTTTA
*
5386 TTTTACCATTTTACT
1 TTTTACTATTTTACT
5401 ATTTTAATTA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 75 0.97
71 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCTTTATAATTA
TTTTA
Found at i:13049 original size:117 final size:111
Alignment explanation
Indices: 12914--13224 Score: 317
Period size: 110 Copynumber: 2.8 Consensus size: 111
12904 GGAATTAAAT
* *
12914 TCATGTAAGAGTGTGGGTTCGAGTTGATCATTCCCCTTCACCTCCTTAATTCTAAACCAAAAGAA
1 TCATGTAAGGGTGTGGGTTCGAGTTGTTCA-TCCCCTT-ACCTCC----TTCTAAACCAAAAGAA
* * *
12979 AGTATTT-ATAGGTGTGGGATTTCCCTCTCTAGGCCC-GGG-GCTTAAATGAAAG
60 AGCATTTGATA-G-GCGGGATTTCCCTCTCTAGGCCCAGGGAG-TTAAAGGAAAG
* * * *
13031 TCATGTAAGGGTGTGGGTTCGAGTTGTTCATCCCC-TACCTCCTTGTAAACCGAATGAGAGCATT
1 TCATGTAAGGGTGTGGGTTCGAGTTGTTCATCCCCTTACCTCCTTCTAAACCAAAAGAAAGCATT
* **
13095 TGTTAGGCGGGATTTTTCTCTCTAGGCCCAGGGAGTTAAAGGAAAG
66 TGATAGGCGGGATTTCCCTCTCTAGGCCCAGGGAGTTAAAGGAAAG
* * * * **
13141 TCATGTAAGGGTGTGGATTCAAGTTGTTCATCCCC-TATCTCCTTGTAAACCAAACCAAAGCATT
1 TCATGTAAGGGTGTGGGTTCGAGTTGTTCATCCCCTTACCTCCTTCTAAACCAAAAGAAAGCATT
* * *
13205 TGTTAGGTGGGATTTACCTC
66 TGATAGGCGGGATTTCCCTC
13225 AGACATGTAA
Statistics
Matches: 169, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
109 20 0.12
110 106 0.63
111 3 0.02
114 6 0.04
115 1 0.01
116 5 0.03
117 28 0.17
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (111 bp):
TCATGTAAGGGTGTGGGTTCGAGTTGTTCATCCCCTTACCTCCTTCTAAACCAAAAGAAAGCATT
TGATAGGCGGGATTTCCCTCTCTAGGCCCAGGGAGTTAAAGGAAAG
Found at i:13121 original size:109 final size:110
Alignment explanation
Indices: 12994--13224 Score: 331
Period size: 110 Copynumber: 2.1 Consensus size: 110
12984 TTATAGGTGT
* * *
12994 GGGATTTCCCTCTCTAGGCCC-GGG-GCTTAAATGAAAGTCATGTAAGGGTGTGGGTTCGAGTTG
1 GGGATTTCCCTCTCTAGGCCCAGGGAG-TTAAAGGAAAGTCATGTAAGGGTGTGGATTCAAGTTG
* ** *
13057 TTCATCCCCTACCTCCTTGTAAACCGAATGAGAGCATTTGTTAGGC
65 TTCATCCCCTACCTCCTTGTAAACCAAACCAAAGCATTTGTTAGGC
**
13103 GGGATTTTTCTCTCTAGGCCCAGGGAGTTAAAGGAAAGTCATGTAAGGGTGTGGATTCAAGTTGT
1 GGGATTTCCCTCTCTAGGCCCAGGGAGTTAAAGGAAAGTCATGTAAGGGTGTGGATTCAAGTTGT
* *
13168 TCATCCCCTATCTCCTTGTAAACCAAACCAAAGCATTTGTTAGGT
66 TCATCCCCTACCTCCTTGTAAACCAAACCAAAGCATTTGTTAGGC
*
13213 GGGATTTACCTC
1 GGGATTTCCCTC
13225 AGACATGTAA
Statistics
Matches: 107, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
109 19 0.18
110 87 0.81
111 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (110 bp):
GGGATTTCCCTCTCTAGGCCCAGGGAGTTAAAGGAAAGTCATGTAAGGGTGTGGATTCAAGTTGT
TCATCCCCTACCTCCTTGTAAACCAAACCAAAGCATTTGTTAGGC
Found at i:15316 original size:12 final size:12
Alignment explanation
Indices: 15281--15318 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
15271 CATTTGGATC
* *
15281 AGAAGTAAGTGA
1 AGAAGTAAATGG
15293 AGAAGTAAATGG
1 AGAAGTAAATGG
15305 AGAAGTAAATGG
1 AGAAGTAAATGG
15317 AG
1 AG
15319 GCCCATGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (12 bp):
AGAAGTAAATGG
Found at i:31677 original size:29 final size:30
Alignment explanation
Indices: 31618--31694 Score: 138
Period size: 31 Copynumber: 2.6 Consensus size: 30
31608 GTTGCATTGC
31618 AAAATCAGAAAATGGGGGTTCACCATAAAAA
1 AAAATCAGAAAATGGGGGTTCACCA-AAAAA
31649 AAAATCAGAAAATGGGGGTTCACC-AAAAA
1 AAAATCAGAAAATGGGGGTTCACCAAAAAA
31678 AAAATCAGAAAATGGGG
1 AAAATCAGAAAATGGGG
31695 ATCAAGTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 22 0.48
31 24 0.52
ACGTcount: A:0.52, C:0.12, G:0.22, T:0.14
Consensus pattern (30 bp):
AAAATCAGAAAATGGGGGTTCACCAAAAAA
Found at i:34906 original size:29 final size:29
Alignment explanation
Indices: 34873--34930 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
34863 TTTTTCTTTG
34873 AACCTCTCTCTCATTATGATATATCAAGT
1 AACCTCTCTCTCATTATGATATATCAAGT
34902 AACCTCTCTCTCATTATGATATATCAAGT
1 AACCTCTCTCTCATTATGATATATCAAGT
34931 TCTTATCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (29 bp):
AACCTCTCTCTCATTATGATATATCAAGT
Found at i:45982 original size:7 final size:7
Alignment explanation
Indices: 45970--45996 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
45960 TTAAAAATAA
45970 TATATAG
1 TATATAG
45977 TATATAG
1 TATATAG
45984 TATATAG
1 TATATAG
45991 TATATA
1 TATATA
45997 TTAGATATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (7 bp):
TATATAG
Found at i:47846 original size:14 final size:14
Alignment explanation
Indices: 47829--47868 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
47819 TCTTTGATCA
*
47829 ATGATCATGGATTC
1 ATGATCATGAATTC
*
47843 ATGATCGTGAATTC
1 ATGATCATGAATTC
*
47857 GTGATCATGAAT
1 ATGATCATGAAT
47869 ATGATCCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (14 bp):
ATGATCATGAATTC
Found at i:48128 original size:15 final size:16
Alignment explanation
Indices: 48108--48137 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48098 ATTAGTAATT
48108 TTAATTAA-TTAATAA
1 TTAATTAATTTAATAA
48123 TTAATTAATTTAATA
1 TTAATTAATTTAATA
48138 CTATTCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATTAATTTAATAA
Found at i:48604 original size:2 final size:2
Alignment explanation
Indices: 48597--48632 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
48587 ATGAATATGC
48597 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48633 CACACACTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49772 original size:21 final size:20
Alignment explanation
Indices: 49734--49772 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49724 GTTTTTATTA
**
49734 AAATGCACTTTTTTTTAGAT
1 AAATGCACTTTTAATTAGAT
49754 AAATGCACTTTTAAATTAG
1 AAATGCACTTTT-AATTAG
49773 TGGAAATGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (20 bp):
AAATGCACTTTTAATTAGAT
Found at i:65005 original size:21 final size:20
Alignment explanation
Indices: 64975--65015 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
64965 AACAAAAGTC
* *
64975 AAAAAGTAAAGAAAGAAAGA
1 AAAAAGTAAAAAAAAAAAGA
64995 AAAAAGTTAAAAAAAAAAAGA
1 AAAAAG-TAAAAAAAAAAAGA
65016 GAGAGAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAAAGTAAAAAAAAAAAGA
Done.