Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008853.1 Corchorus capsularis cultivar CVL-1 contig08874, 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: 22713
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Found at i:2476 original size:17 final size:17
Alignment explanation
Indices: 2438--2481 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
2428 CTCATGGTAT
*
2438 CAGGTAGCATGAGGTAC
1 CAGGTAGCATGAGGCAC
*
2455 TAGGTAGCATGAGGCAC
1 CAGGTAGCATGAGGCAC
*
2472 CAGGTGGCAT
1 CAGGTAGCAT
2482 CTGGTGTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (17 bp):
CAGGTAGCATGAGGCAC
Found at i:3208 original size:156 final size:156
Alignment explanation
Indices: 2820--3208 Score: 409
Period size: 158 Copynumber: 2.5 Consensus size: 156
2810 CTGGACTTCT
* * *
2820 CACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGA
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGATGA
* *
2885 AACTTTGCCA--AGATACTTAGATTCTCTCCACAAGACTATGGAAAAAAATTCTAAGTAAAACCG
66 AA-TTT-CCACCAGATACTTAGATTATCTCCAAAAGACTATGGAAAAAAATTCTAAGTAAAACCG
* ** * * *
2948 AGCTCCTCTTGATGGTGAACTAGGTTTT
129 AACTCCTCTACATAGAGAACTAGGTTTA
* *
2976 CTCCCCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAATGA-AG
1 C-ACCCC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGA-
* * * * *
3039 TTAATTTTCCACCAG-TAGGCTTAGATTATCTTCATAAAG-TTATGGGAAAAAA-TCTAAGTAAA
63 TGAAATTTCCACCAGATA--CTTAGATTATCTCCA-AAAGACTATGGAAAAAAATTCTAAGTAAA
* *
3101 ACCGAACT-CTCTAACATAGAGAAGTTGGTTTGA
125 ACCGAACTCCTCT-ACATAGAGAACTAGGTTT-A
* * **
3134 CACCCCAAACTGTCCTTAATTGAAAAACTAGCATAAGTTTTTCATCCTAAGTCTGTTTGAGATGA
1 CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGATGA
3199 AATTT-CACCA
66 AATTTCCACCA
3209 AGATGACCTA
Statistics
Matches: 193, Mismatches: 28, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
155 3 0.02
156 60 0.31
157 55 0.28
158 72 0.37
159 3 0.02
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (156 bp):
CACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGATGA
AATTTCCACCAGATACTTAGATTATCTCCAAAAGACTATGGAAAAAAATTCTAAGTAAAACCGAA
CTCCTCTACATAGAGAACTAGGTTTA
Found at i:5916 original size:156 final size:154
Alignment explanation
Indices: 5612--5973 Score: 376
Period size: 156 Copynumber: 2.3 Consensus size: 154
5602 CTTCTTACCT
* *
5612 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAATCT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCT-AAAGAGCTG-AATCT
* * *
5677 TTCCAAGGGTCTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCCTC
64 TTCCAAGGATCTTAGAATATCCACATAAGACTATGGAAAAAATTCCAAGTAAAACCGAACTCCTC
* * *
5742 TTGATGGTGAACTAGGTTT-CCACCC
129 TAGATAGAGAACTAGGTTTGCCACCC
****
5767 CTGGGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTAAAGAAGCTG-AT-T
1 C-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTAAAG-AGCTGAATCT
* * ** *
5830 TTCCACCAGTATACTTAGATTAT-CACCATAAGGTTATGGGAAAAAA-TCCAAGTGAAACCGAAC
64 TTCCA--AGGAT-CTTAGAATATCCA-CATAAGACTAT-GGAAAAAATTCCAAGTAAAACCGAAC
* * * *
5893 T-CTCTAGCATAGAGAAGTTGGTTTGTCTCCC
124 TCCTCTAG-ATAGAGAACTAGGTTTGCCACCC
* * *
5924 CAAACTGTCCTTAACTGAAAAACTGGCATAAGTTTTTCATGCTAAGTCTA
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTA
5974 TTTGAGATGA
Statistics
Matches: 170, Mismatches: 28, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
153 6 0.04
154 2 0.01
155 14 0.08
156 135 0.79
157 13 0.08
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (154 bp):
CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTAAAGAGCTGAATCTTT
CCAAGGATCTTAGAATATCCACATAAGACTATGGAAAAAATTCCAAGTAAAACCGAACTCCTCTA
GATAGAGAACTAGGTTTGCCACCC
Found at i:7892 original size:184 final size:185
Alignment explanation
Indices: 7672--8077 Score: 475
Period size: 185 Copynumber: 2.2 Consensus size: 185
7662 ATTCCTTATA
* *
7672 ATTTTCGGCCTAATTGATTAAATT-AGCCAAAAATCAGTAGG-TAAACCCTCCAAAATTAGG-TC
1 ATTTT-GGCCAAATTGATT-AATTAAGCCAAAAATCAGTAGGTTAAACCCT-CAAAACTAGGCT-
* * * * * *
7734 ATATCACATGACCATAAACCTAATTTGATGAAATCAAGCAAACCCTAAT-AGGGCGAACCC-TTT
62 ATATCACATAAACATAAACCCAATTTAATG-AACCAAGCAAACCCTAATGA-GCCGAACCCTTTT
7797 TTTGC-AAAAATTACAACATAGGCGGCAAATTAGCTAGCTTGATAAATTAGGGTTCTTGTG
125 TTTGCGAAAAATTACAACATAGGCGGCAAATTAGCTAGCTTGATAAATTAGGGTTCTTGTG
* * **
7857 ATTTTGGCCAAATTGATTAATTAAGCCTAAAATCAGTAGGTTAAGCCCTTTAAACTAGGCTATAT
1 ATTTTGGCCAAATTGATTAATTAAGCCAAAAATCAGTAGGTTAAACCCTCAAAACTAGGCTATAT
* *** *
7922 CACATAAATATAAACCCAATTTAATGAACCAAGCTTCCCCTAATGAGCCGAGCCCTTTTTTTGCG
66 CACATAAACATAAACCCAATTTAATGAACCAAGCAAACCCTAATGAGCCGAACCCTTTTTTTGCG
* * * * *
7987 AAAAATTGCAACATAGGCGGCAAATTAGCTTGCTTGGTGAATTAGGGTTTTTGTG
131 AAAAATTACAACATAGGCGGCAAATTAGCTAGCTTGATAAATTAGGGTTCTTGTG
* * *
8042 ATCTAGGCAAAATT-ATTTAATTAAGCCAAAAATCAG
1 ATTTTGGCCAAATTGA-TTAATTAAGCCAAAAATCAG
8078 GGGGTTTAGT
Statistics
Matches: 188, Mismatches: 26, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
183 25 0.13
184 70 0.37
185 93 0.49
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (185 bp):
ATTTTGGCCAAATTGATTAATTAAGCCAAAAATCAGTAGGTTAAACCCTCAAAACTAGGCTATAT
CACATAAACATAAACCCAATTTAATGAACCAAGCAAACCCTAATGAGCCGAACCCTTTTTTTGCG
AAAAATTACAACATAGGCGGCAAATTAGCTAGCTTGATAAATTAGGGTTCTTGTG
Found at i:20452 original size:17 final size:17
Alignment explanation
Indices: 20415--20452 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20405 TCATAGTACC
*
20415 TAGGTAGTATGAGATGC
1 TAGGTAGTATGAGATGA
*
20432 TAGGTAGTATGAGGTGA
1 TAGGTAGTATGAGATGA
20449 TAGG
1 TAGG
20453 CTGCATCTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.39, T:0.29
Consensus pattern (17 bp):
TAGGTAGTATGAGATGA
Found at i:21105 original size:156 final size:155
Alignment explanation
Indices: 20805--21162 Score: 357
Period size: 156 Copynumber: 2.3 Consensus size: 155
20795 TTACCTCAAA
* *
20805 TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAATCTTGCC
1 TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTGAAAGAGCTG-AATCTTGCC
* * * * * *
20870 AAGGGTCTTAGAATATCAACATAAGACTATGTGAAAAATTCTAAGTAAAACCGAGCTCCCCTTGA
65 AAGGATCTTAGAATATCAACATAAGACTATGGGAAAAAATCCAAGTAAAACCGAACTCCCCTAGA
* * **
20935 TGGTGAACTAGGTTT-CCACCCCTGGG
130 TAGAGAACTAGGTTTGCCACCCC-AAG
*
20961 TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCT-AAAGAAGCTG-AT-TTTCC
1 TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTGAAAG-AGCTGAATCTTGCC
* * * * ** * *
21023 ACCAGTATACTTATATTATCACCATAAGGTTATGGGAAAAAATCCAAGTGAAACCGAACT-CTCT
65 A--AGGAT-CTTAGAATATCAACATAAGACTATGGGAAAAAATCCAAGTAAAACCGAACTCCCCT
* * * *
21087 AGCATAGAGAAGTTGGTTTGTCTCCCCAAG
127 AG-ATAGAGAACTAGGTTTGCCACCCCAAG
* * * *
21117 CTGTCCTTAATTGAAAAACTGGCATAAGTTTTTCATGCTAAGTCTG
1 TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTG
21163 TTTGAGATGA
Statistics
Matches: 166, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
153 5 0.03
154 2 0.01
155 10 0.06
156 144 0.87
157 5 0.03
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (155 bp):
TTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTGAAAGAGCTGAATCTTGCCA
AGGATCTTAGAATATCAACATAAGACTATGGGAAAAAATCCAAGTAAAACCGAACTCCCCTAGAT
AGAGAACTAGGTTTGCCACCCCAAG
Done.