Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006499.1 Corchorus capsularis cultivar CVL-1 contig06520, 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: 23709
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:208 original size:12 final size:13
Alignment explanation
Indices: 193--237 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
183 AATCTAAATC
193 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
205 TAAAGCAAATTAA
1 TAAAGCAGATTAA
218 TAAAGCAGATTAA
1 TAAAGCAGATTAA
231 TAAAGCA
1 TAAAGCA
238 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:244 original size:25 final size:25
Alignment explanation
Indices: 193--245 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
183 AATCTAAATC
*
193 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
218 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
243 TAA
1 TAA
246 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:15870 original size:27 final size:27
Alignment explanation
Indices: 15840--15914 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
15830 AAGTGAACTT
*
15840 AAAATGACCAAAATACCCCTGAAAACA
1 AAAATGACCAAAATGCCCCTGAAAACA
* * ***
15867 AAAATGACTACAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAAAACA
15894 AAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
15915 GATGACCCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAAAACA
Found at i:16394 original size:67 final size:67
Alignment explanation
Indices: 16316--16445 Score: 206
Period size: 67 Copynumber: 1.9 Consensus size: 67
16306 CCCTTTGCCC
* *
16316 GGAGGACTTATCGGAATTAATACCCAAAGGTTTCTAAAATTGTGCCCGGAGGTCTTACCAATTAC
1 GGAGGACTTATCAGAATTAATAACCAAAGGTTTCTAAAATTGTGCCCGGAGGTCTTACCAATTAC
16381 CT
66 CT
* ** *
16383 GGAGGACTTATCATAATTAATAACCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACCAATT
1 GGAGGACTTATCAGAATTAATAACCAAAGGTTTCTAAAATTGTGCCCGGAGGTCTTACCAATT
16446 CAAACTCTGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (67 bp):
GGAGGACTTATCAGAATTAATAACCAAAGGTTTCTAAAATTGTGCCCGGAGGTCTTACCAATTAC
CT
Found at i:16870 original size:69 final size:69
Alignment explanation
Indices: 16578--16855 Score: 441
Period size: 69 Copynumber: 4.0 Consensus size: 69
16568 CTTATTTAAC
* * *
16578 TTGGCTTATGGAAAAGCCCTTTGTGGCTTGGATGGAACCAAGGCTTGAATTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAG-CCTATGTGGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAA
16643 CGAGT
65 CGAGT
* * * *
16648 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGTTGGAACCAAGGCTTGACTTGACCCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAAC
16713 GAGT
66 GAGT
* *
16717 TTGGCTTGTGGAAAAGTCTATGTGGCTTGGATGGAACCAAGGCTTAAATTAACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAAC
16782 GAGT
66 GAGT
*
16786 TTGGCTTGTGGAAAAGCCTATGTGCCTTGGAT-GACACCAAGGCTTAAATTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGA-ACCAAGGCTTAAATTGACTCGTATGGAAA
16850 CGAGT
65 CGAGT
16855 T
1 T
16856 GGACTTATAG
Statistics
Matches: 193, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
68 2 0.01
69 176 0.91
70 15 0.08
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.28
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAAC
GAGT
Found at i:17456 original size:50 final size:49
Alignment explanation
Indices: 17376--17473 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 49
17366 TTAAAAAGCA
* * *
17376 AATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTGAAAACTG
1 AATTTTGATATTGGACTCACAAATGAAATGCAATCTTATTAT-AAAACTG
17426 AATTTTGATATTGGACTCACAAATGAAATGCAATCTTATTATAAAACT
1 AATTTTGATATTGGACTCACAAATGAAATGCAATCTTATTATAAAACT
17474 TCTTGTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 6 0.13
50 39 0.87
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (49 bp):
AATTTTGATATTGGACTCACAAATGAAATGCAATCTTATTATAAAACTG
Found at i:17801 original size:6 final size:6
Alignment explanation
Indices: 17790--17847 Score: 75
Period size: 6 Copynumber: 9.8 Consensus size: 6
17780 TTCTTCATTC
*
17790 TCTTTT TCTTTT TCTTTT TC-TCT T-TTTT TCTTTT TCTTTT TCTTTCT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT-T
*
17837 TTTTTT TCTTT
1 TCTTTT TCTTT
17848 CATTTTCTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 6 0.13
6 34 0.76
7 5 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TCTTTT
Found at i:17801 original size:20 final size:20
Alignment explanation
Indices: 17778--17846 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 20
17768 CTAGAGCCTC
17778 TTTTCTTCATTCTCTTTTTCT
1 TTTTCTT-ATTCTCTTTTTCT
*
17799 TTTTCTTTTTCTCTTTTTTTCT
1 TTTTCTTATTCTC--TTTTTCT
*
17821 TTTTCTT-TT-TCTTTCTTTT
1 TTTTCTTATTCTCTTT-TTCT
17840 TTTTCTT
1 TTTTCTT
17847 TCATTTTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.07
19 10 0.23
20 7 0.16
21 9 0.21
22 14 0.33
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCTTATTCTCTTTTTCT
Found at i:17813 original size:34 final size:35
Alignment explanation
Indices: 17775--17845 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 35
17765 ACCCTAGAGC
17775 CTCTTTTCTTCATTCTCTTTTTCTTT-TTCTTTTT
1 CTCTTTTCTTCATTCTCTTTTTCTTTCTTCTTTTT
* * * *
17809 CTCTTTTTTTCTTTTTCTTTTTCTTTCTTTTTTTT
1 CTCTTTTCTTCATTCTCTTTTTCTTTCTTCTTTTT
17844 CT
1 CT
17846 TTCATTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 23 0.72
35 9 0.28
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (35 bp):
CTCTTTTCTTCATTCTCTTTTTCTTTCTTCTTTTT
Found at i:17820 original size:22 final size:22
Alignment explanation
Indices: 17792--17855 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
17782 CTTCATTCTC
17792 TTTTTCTTTTTCTTTTTCTCTT
1 TTTTTCTTTTTCTTTTTCTCTT
17814 TTTTTCTTTTTCTTTTTCTTTCTT
1 TTTTTCTTTTTCTTTTTC--TCTT
* *
17838 TTTTT-TCTTTCATTTTCT
1 TTTTTCTTTTTCTTTTTCT
17856 TTTCCTTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 1 0.03
22 18 0.47
23 10 0.26
24 9 0.24
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTTCTTTTTCTCTT
Found at i:17827 original size:28 final size:29
Alignment explanation
Indices: 17790--17864 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 29
17780 TTCTTCATTC
17790 TCTTTTTCTTTTTCTTT-TTCTCTTTT-TT
1 TCTTTTTCTTTTTCTTTCTT-TCTTTTCTT
*
17818 TCTTTTTCTTTTTCTTTCTTTTTTTTCTT
1 TCTTTTTCTTTTTCTTTCTTTCTTTTCTT
* *
17847 TCATTTTCTTTTCCTTTC
1 TCTTTTTCTTTTTCTTTC
17865 ATTTTACATG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 22 0.52
29 20 0.48
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (29 bp):
TCTTTTTCTTTTTCTTTCTTTCTTTTCTT
Found at i:17863 original size:16 final size:15
Alignment explanation
Indices: 17776--17869 Score: 77
Period size: 16 Copynumber: 6.1 Consensus size: 15
17766 CCCTAGAGCC
*
17776 TCTTTTC-TTCATTC
1 TCTTTTCTTTCATTT
*
17790 TCTTTTTCTTTTTCTTTT
1 TC-TTTTC--TTTCATTT
* *
17808 TCTCTTTTTTTCTTTT
1 TCT-TTTCTTTCATTT
17824 TCTTTTTCTTTC-TTT
1 TC-TTTTCTTTCATTT
17839 T-TTTTCTTTCATTT
1 TCTTTTCTTTCATTT
17853 TCTTTTCCTTTCATTT
1 TCTTTT-CTTTCATTT
17869 T
1 T
17870 ACATGCCCGA
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
13 9 0.13
14 6 0.09
15 13 0.19
16 27 0.40
17 2 0.03
18 10 0.15
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTTTTCTTTCATTT
Found at i:17864 original size:10 final size:11
Alignment explanation
Indices: 17793--17869 Score: 60
Period size: 10 Copynumber: 7.4 Consensus size: 11
17783 TTCATTCTCT
*
17793 TTTTCTTTTTC
1 TTTTCTCTTTC
17804 TTTTTCTCTTT-
1 -TTTTCTCTTTC
*
17815 TTTTCTTTTTC
1 TTTTCTCTTTC
17826 TTTT-TCTTTC
1 TTTTCTCTTTC
17836 TTTT-T-TTTC
1 TTTTCTCTTTC
17845 -TTTCAT-TTTC
1 TTTTC-TCTTTC
17855 TTTTC-CTTTC
1 TTTTCTCTTTC
17865 ATTTT
1 -TTTT
17870 ACATGCCCGA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
8 3 0.05
9 4 0.07
10 28 0.50
11 12 0.21
12 9 0.16
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTCTTTC
Found at i:18611 original size:45 final size:45
Alignment explanation
Indices: 18555--18695 Score: 232
Period size: 45 Copynumber: 3.2 Consensus size: 45
18545 CATAACTTTG
*
18555 GAAAA-CCATTTTATCAAAACCTTTCGAAAACCATGACTCTTTTT
1 GAAAACCCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
18599 GAAAACCCATTTTATCAAAACCTTTTGAAAACCATGA-TCCTTTTT
1 GAAAACCCATTTTATCAAAACCTTTTGAAAACCATGACT-CTTTTT
* *
18644 GAAAAACCATTTTATTAAAACCTTTTGAAAACCATGACTCTTTTT
1 GAAAACCCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
18689 GAAAACC
1 GAAAACC
18696 ACCGCTGCTT
Statistics
Matches: 90, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
44 6 0.07
45 83 0.92
46 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (45 bp):
GAAAACCCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
Done.