Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010288.1 Corchorus capsularis cultivar CVL-1 contig10309, 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: 23169
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:198 original size:31 final size:29
Alignment explanation
Indices: 159--286 Score: 99
Period size: 31 Copynumber: 4.4 Consensus size: 29
149 TTCCGACGTG
*
159 GCACGCCACGTGTACCAAAAAGTGACATGT
1 GCACGCCACATGTACCAAAAAGTGACA-GT
*
189 GACACGCCACATGTATCAAAAAGT--C-GT
1 G-CACGCCACATGTACCAAAAAGTGACAGT
*
216 ----GCCACATGTACCAAAAAGTGACACAT
1 GCACGCCACATGTACCAAAAAGTGACA-GT
* *
242 GTCATGCCACGTGTACCAAAAAGTGACACGT
1 G-CACGCCACATGTACCAAAAAGTGACA-GT
*
273 GGCATGCCACATGT
1 -GCACGCCACATGT
287 TTAAAAAAGT
Statistics
Matches: 80, Mismatches: 7, Indels: 21
0.74 0.06 0.19
Matches are distributed among these distances:
22 18 0.22
24 1 0.01
26 1 0.01
27 2 0.03
29 1 0.01
30 1 0.01
31 55 0.69
32 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (29 bp):
GCACGCCACATGTACCAAAAAGTGACAGT
Found at i:251 original size:53 final size:53
Alignment explanation
Indices: 163--265 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
153 GACGTGGCAC
* ** *
163 GCCACGTGTACCAAAAAGTGACATGTGACACGCCACATGTATCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGACACGCCACATGTACCAAAAAGTCGT
* * *
216 GCCACATGTACCAAAAAGTGACACATGTCATGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGACACGCCACATGTACCAAAAAGT
266 GACACGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGACACGCCACATGTACCAAAAAGTCGT
Found at i:294 original size:31 final size:31
Alignment explanation
Indices: 215--323 Score: 128
Period size: 31 Copynumber: 3.5 Consensus size: 31
205 CAAAAAGTCG
* * *
215 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACAAAAAAGTGACACGTGGCA
* *
246 TGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACAAAAAAGTGACACGTGGCA
** *
277 TGCCACATGTTTAAAAAAGTGGCACGTGGCA
1 TGCCACATGTACAAAAAAGTGACACGTGGCA
* *
308 TGCCACGTGCACAAAA
1 TGCCACATGTACAAAA
324 GGATACGTGC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACAAAAAAGTGACACGTGGCA
Found at i:2909 original size:29 final size:29
Alignment explanation
Indices: 2867--2925 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2857 GCCTGCTTTC
2867 ATTCCATTTCCAGCAAAACATTAGAAAGG
1 ATTCCATTTCCAGCAAAACATTAGAAAGG
2896 ATTCCATTTCCAGCAAAACATTAGAAAGG
1 ATTCCATTTCCAGCAAAACATTAGAAAGG
2925 A
1 A
2926 AAGTGACGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (29 bp):
ATTCCATTTCCAGCAAAACATTAGAAAGG
Found at i:12632 original size:2 final size:2
Alignment explanation
Indices: 12625--12652 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12615 CTAAGATGAA
12625 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
12653 TGGTAAGTAG
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:22722 original size:328 final size:328
Alignment explanation
Indices: 21869--23166 Score: 1588
Period size: 328 Copynumber: 3.9 Consensus size: 328
21859 TAGCTTTAAG
* * * * * * *
21869 ATATATAATTCAAACTCCAAAAAGATTTAAGGGCTTTTCACGTTTTTAATATCGTTTTTCCTAGT
1 ATATATAATTC-AACGCCAAAAATATTAAAGGGCTTTTCACGCTTCTAAGATCGTTTTT-CTATT
* *
21934 TTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGGAAGAA-CAAATCCTTA
64 TTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCT-GTAA-AAGCAAATCCTTA
* *
21998 AA-TCATATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTGCCGCCAAAA
127 AATTCA-ATGTGACTTAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGCCGCCAAAA
* ** * * * * *
22062 ATCATGCAAAAATGAGCTAGGACCCCGGAACGCGTTTTTTGCCAAAAACCGTGATTGTTAGTACA
191 ATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAATACA
* * * * *
22127 TGATTTCGGCTAAAATTTT-CAAAAATTGATCCGAAAGATTTTGCCTTTATTTTTGGCCACAATA
256 AGATTTCAGCTAAATTTTTGCAAAAATTGA-CCGAAAGATTTTTCCTTAATTTTTGGCCACAATA
*
22191 CTAAAATATA
320 CTAAAA-ACA
* * *
22201 TATATATAATTCAATGCCAAAAATATTAAAGGACTTTTCACGCTTCTAAAATCGTTTTTCCTATT
1 -ATATATAATTCAACGCCAAAAATATTAAAGGGCTTTTCACGCTTCTAAGATCGTTTTT-CTATT
* * *
22266 TTTTCTAAATTAATTTCTAATTAAATTGAAACATGATTCAGATGCTGTAAAAGAAAATCCTTAAA
64 TTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTGTAAAAGCAAATCCTTAAA
* * * * *
22331 TTTAATGCGATTTAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTGCCACCAAAAATC
129 TTCAATGTGACTTAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGCCGCCAAAAATC
* * * * *
22396 ATGCAAAACTCAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCGTGACGGTTAACACAAGA
194 ATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAATACAAGA
* * *
22461 TTTCGGCTAAATTTTTGCAAAAATTGACCAAAAATATTTTTCCTTAATTTTTGGCCACAATACTA
259 TTTCAGCTAAATTTTTGCAAAAATTGACC-GAAAGATTTTTCCTTAATTTTTGGCCACAATACTA
*
22526 AGAA-A
323 AAAACA
* * *
22531 ATATATCATTCAACGCCAAAAATATTAAAGGGCTTTTCACGCTTCTAAGATTGTTTTAT-TGTTT
1 ATATATAATTCAACGCCAAAAATATTAAAGGGCTTTTCACGCTTCTAAGATCGTTTT-TCTATTT
* * * *
22595 TATTCCAAATTACTTTCTAATTAAATCGAAACACGATTTAGATGCTGTAAATGCAAAT-CTTAAA
65 T-TTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTGTAAAAGCAAATCCTTAAA
* *
22659 TTCAATGTGGCTTAGATTTGGTTAGATGAATATAGATACTTCAAGGAGTCTTGCCGCCAAAAATC
129 TTCAATGTGACTTAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGCCGCCAAAAATC
* * * * * *
22724 ATGTAAAAGTGAGCCGGGGTCCCGGAATGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGA
194 ATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAATACAAGA
* * * * *
22789 GTTCAGCTAGAA-TTTTGCAAAATTTAACCCGAAAGAATTTTCCTTAATTTTTGGCAACAATACT
259 TTTCAGCTA-AATTTTTGCAAAAATTGA-CCGAAAGATTTTTCCTTAATTTTTGGCCACAATACT
22853 AAAAACA
322 AAAAACA
* * * * * *
22860 ATATATAACTCAACGCCAAAAATATTAAAGGGCTTTTCACTCTTGTAAGA-CGGTTTCCTACTTT
1 ATATATAATTCAACGCCAAAAATATTAAAGGGCTTTTCACGCTTCTAAGATCGTTTTTCTATTTT
** *
22924 TTCTGAATTATTTTCTAATTAAATCGAAACATGATTCAGATGCTGTAAAAGCAAATCCTTAAATT
66 TTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTGTAAAAGCAAATCCTTAAATT
** * ** * * * * *
22989 CAATGTGGTTTGGATTCAGCTAGATGAAAATAGATATCTCAAGGAGTCTTGCTGCCGAAAATCAT
131 CAATGTGACTTAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGCCGCCAAAAATCAT
* * * *
23054 GCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATAGTTAATACAAGATT
196 GCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAATACAAGATT
* * *
23119 TCAGCAAAATTTTTACAATAATTGACCGAAAGA-TTTTCCTTAATTTTT
261 TCAGCTAAATTTTTGCAAAAATTGACCGAAAGATTTTTCCTTAATTTTT
23167 TGG
Statistics
Matches: 833, Mismatches: 120, Indels: 31
0.85 0.12 0.03
Matches are distributed among these distances:
326 15 0.02
327 60 0.07
328 319 0.38
329 152 0.18
330 4 0.00
331 140 0.17
332 132 0.16
333 11 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (328 bp):
ATATATAATTCAACGCCAAAAATATTAAAGGGCTTTTCACGCTTCTAAGATCGTTTTTCTATTTT
TTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTGTAAAAGCAAATCCTTAAATT
CAATGTGACTTAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGCCGCCAAAAATCAT
GCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAATACAAGATT
TCAGCTAAATTTTTGCAAAAATTGACCGAAAGATTTTTCCTTAATTTTTGGCCACAATACTAAAA
ACA
Done.