Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010632.1 Corchorus olitorius cultivar O-4 contig10664, 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, 733
Length: 1222
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:50 original size:35 final size:34
Alignment explanation
Indices: 1--370 Score: 431
Period size: 35 Copynumber: 10.7 Consensus size: 34
*
1 TAGCATCTTTAAAATTGAA-TCCAGATGACTCGGTG
1 TAGCATCTTCAAAA-TGAACT-CAGATGACTCGGTG
36 TAGCATCTTCAAAATTGAACTCAGATGACTCGGTG
1 TAGCATCTTCAAAA-TGAACTCAGATGACTCGGTG
*
71 CAGCATCTTCAAAATTGAACTCAGATGACTCGGTG
1 TAGCATCTTCAAAA-TGAACTCAGATGACTCGGTG
* *
106 CAGCATCTTCAAAATTGAACACAGATGACTCGGTG
1 TAGCATCTTCAAAA-TGAACTCAGATGACTCGGTG
* * * *
141 TAGCATCCTCAAAGTTTAA-TCCAGATGACTCGATG
1 TAGCATCTTCAAA-ATGAACT-CAGATGACTCGGTG
* **
176 TAGCATCTTCAATATGAACTTGGATGACTCGGTG
1 TAGCATCTTCAAAATGAACTCAGATGACTCGGTG
* * *
210 TAGCATCTTCAAAGATGGATTCGGATGACTCGGTG
1 TAGCATCTTCAAA-ATGAACTCAGATGACTCGGTG
* *
245 TAGCATCTTCAATATGAACTCGGATGACTCGGTG
1 TAGCATCTTCAAAATGAACTCAGATGACTCGGTG
* *
279 TAGCATCTTCAAAGATGGATTCAGATGACTCGGTG
1 TAGCATCTTCAAA-ATGAACTCAGATGACTCGGTG
* *
314 CAGCATCTTCAATATGAACT-AGGATGACTCGGTG
1 TAGCATCTTCAAAATGAACTCA-GATGACTCGGTG
* *
348 TAGCATCTTCAATATGGACTCAG
1 TAGCATCTTCAAAATGAACTCAG
371 TGGGCTCAGT
Statistics
Matches: 294, Mismatches: 33, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
33 1 0.00
34 93 0.32
35 199 0.68
36 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (34 bp):
TAGCATCTTCAAAATGAACTCAGATGACTCGGTG
Found at i:222 original size:69 final size:69
Alignment explanation
Indices: 1--359 Score: 477
Period size: 69 Copynumber: 5.2 Consensus size: 69
* * * *
1 TAGCATCTTTAAAATTGAATCCAGATGACTCGGTGTAGCATCTTCAAAATTGAACTCAGATGACT
1 TAGCATCTTCAAAGTTGAATCCAGATGACTCGGTGTAGCATCTTCAATA-TGAACTCGGATGACT
66 CGGTG
65 CGGTG
* * * * * *
71 CAGCATCTTCAAAATTGAA-CTCAGATGACTCGGTGCAGCATCTTCAAAATTGAACACAGATGAC
1 TAGCATCTTCAAAGTTGAATC-CAGATGACTCGGTGTAGCATCTTCAATA-TGAACTCGGATGAC
135 TCGGTG
64 TCGGTG
* * * *
141 TAGCATCCTCAAAGTTTAATCCAGATGACTCGATGTAGCATCTTCAATATGAACTTGGATGACTC
1 TAGCATCTTCAAAGTTGAATCCAGATGACTCGGTGTAGCATCTTCAATATGAACTCGGATGACTC
206 GGTG
66 GGTG
* * * *
210 TAGCATCTTCAAAGATGGATTCGGATGACTCGGTGTAGCATCTTCAATATGAACTCGGATGACTC
1 TAGCATCTTCAAAGTTGAATCCAGATGACTCGGTGTAGCATCTTCAATATGAACTCGGATGACTC
275 GGTG
66 GGTG
* * * * *
279 TAGCATCTTCAAAGATGGATTCAGATGACTCGGTGCAGCATCTTCAATATGAACTAGGATGACTC
1 TAGCATCTTCAAAGTTGAATCCAGATGACTCGGTGTAGCATCTTCAATATGAACTCGGATGACTC
344 GGTG
66 GGTG
348 TAGCATCTTCAA
1 TAGCATCTTCAA
360 TATGGACTCA
Statistics
Matches: 262, Mismatches: 25, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
69 157 0.60
70 104 0.40
71 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (69 bp):
TAGCATCTTCAAAGTTGAATCCAGATGACTCGGTGTAGCATCTTCAATATGAACTCGGATGACTC
GGTG
Found at i:416 original size:103 final size:104
Alignment explanation
Indices: 24--396 Score: 336
Period size: 103 Copynumber: 3.6 Consensus size: 104
14 ATTGAATCCA
* * *
24 GATGACTCGGTGTAGCATCTTCAAAATTGAACTCAGATGACTCGGTGCAGCATCTTCAAA-ATTG
1 GATGACTCGGTGTAGCATCTTCAATA-TGAACTCAGATGACTCAGTGCAGCATCTTCAAAGATAG
* * *
88 AACTCAGATGACTCGGTGCAGCATCTTCAAA-ATTGAAC-ACA
65 -ATTCAGATAACTCGGTGCAGCATCTTCAAAGA-TGAACTA-G
* * *
129 GATGACTCGGTGTAGCATCCTCAA-AGTTTAA-TCCAGATGACTC-GATGTAGCATCTTCAATAT
1 GATGACTCGGTGTAGCATCTTCAATA--TGAACT-CAGATGACTCAG-TGCAGCATCTTCAA-A-
* * * * * * *
191 GA-A-CTT-GGATGACTCGGTGTAGCATCTTCAAAGATGGATTCG
60 GATAGATTCAGATAACTCGGTGCAGCATCTTCAAAGATGAACTAG
* * * *
233 GATGACTCGGTGTAGCATCTTCAATATGAACTCGGATGACTCGGTGTAGCATCTTCAAAGATGGA
1 GATGACTCGGTGTAGCATCTTCAATATGAACTCAGATGACTCAGTGCAGCATCTTCAAAGATAGA
* *
298 TTCAGATGACTCGGTGCAGCATCTTC-AATATGAACTAG
66 TTCAGATAACTCGGTGCAGCATCTTCAAAGATGAACTAG
* *
336 GATGACTCGGTGTAGCATCTTCAATATGGACTCAG-TGGGCTCAGTGCAGCAAATCTTCAAA
1 GATGACTCGGTGTAGCATCTTCAATATGAACTCAGAT-GACTCAGTGCAGC--ATCTTCAAA
397 TAGATTAGGT
Statistics
Matches: 223, Mismatches: 28, Indels: 34
0.78 0.10 0.12
Matches are distributed among these distances:
101 2 0.01
102 2 0.01
103 79 0.35
104 76 0.34
105 62 0.28
106 1 0.00
108 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (104 bp):
GATGACTCGGTGTAGCATCTTCAATATGAACTCAGATGACTCAGTGCAGCATCTTCAAAGATAGA
TTCAGATAACTCGGTGCAGCATCTTCAAAGATGAACTAG
Found at i:416 original size:138 final size:136
Alignment explanation
Indices: 16--405 Score: 462
Period size: 138 Copynumber: 2.8 Consensus size: 136
6 TCTTTAAAAT
* *
16 TGAATCCAGATGACTCGGTGTAGCATCTTCAAAATTGAACTCA-GATGACTCGGTGCAGCATCTT
1 TGAATCCAGATGACTCGGTGTAGCATCTTCAATA-TGAACT-AGGATGACTCGGTGTAGCATCTT
* * * *
80 CAAAATTGAACTCAGATGACTCGGTGCAGCATCTTCAAAATTGAACACAGATGACTCGGTGTAGC
64 CAAAA-TGGACTCAGATGACTCGGTGCAGCATCTTC-AAATAGAATA-GGATGACTCGGTGTAGC
*
145 ATCCTCAAAGT
126 ATCCTCAAAGA
* * *
156 TTAATCCAGATGACTCGATGTAGCATCTTCAATATGAACTTGGATGACTCGGTGTAGCATCTTCA
1 TGAATCCAGATGACTCGGTGTAGCATCTTCAATATGAACTAGGATGACTCGGTGTAGCATCTTCA
* * * *
221 AAGATGGATTCGGATGACTCGGTGTAGCATCTTC-AATATGAACTCGGATGACTCGGTGTAGCAT
66 AA-ATGGACTCAGATGACTCGGTGCAGCATCTTCAAATA-GAA-TAGGATGACTCGGTGTAGCAT
*
285 CTTCAAAGA
128 CCTCAAAGA
* * *
294 TGGATTCAGATGACTCGGTGCAGCATCTTCAATATGAACTAGGATGACTCGGTGTAGCATCTTCA
1 TGAATCCAGATGACTCGGTGTAGCATCTTCAATATGAACTAGGATGACTCGGTGTAGCATCTTCA
* * * *
359 ATATGGACTCAG-TGGGCTCAGTGCAGCAAATCTTCAAATAGATTAGG
66 AAATGGACTCAGAT-GACTCGGTGCAGC--ATCTTCAAATAGAATAGG
406 TTAATTCGGT
Statistics
Matches: 213, Mismatches: 29, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
136 1 0.00
137 21 0.10
138 91 0.43
139 64 0.30
140 36 0.17
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (136 bp):
TGAATCCAGATGACTCGGTGTAGCATCTTCAATATGAACTAGGATGACTCGGTGTAGCATCTTCA
AAATGGACTCAGATGACTCGGTGCAGCATCTTCAAATAGAATAGGATGACTCGGTGTAGCATCCT
CAAAGA
Done.