Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015389.1 Corchorus olitorius cultivar O-4 contig15422, 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, 823
Length: 1373
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:369 original size:57 final size:57
Alignment explanation
Indices: 300--409 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
290 AAATAAGTAT
*
300 AATTCAACGCCAAAAATA-GTGAAGGATTTTTCACGCTTCTAATATCGATTTTCATAC
1 AATTCAACGCCAAAAAGATG-GAAGGATTTTTCACGCTTCTAATATCGATTTTCATAC
* * *
357 AATTCATCGCCAAAAAGATGGAAGGGTTTTTCATGCTTCTAATATCGATTTTC
1 AATTCAACGCCAAAAAGATGGAAGGATTTTTCACGCTTCTAATATCGATTTTC
410 CTATATGTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 47 0.98
58 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (57 bp):
AATTCAACGCCAAAAAGATGGAAGGATTTTTCACGCTTCTAATATCGATTTTCATAC
Found at i:1046 original size:101 final size:101
Alignment explanation
Indices: 871--1079 Score: 292
Period size: 101 Copynumber: 2.1 Consensus size: 101
861 GTCTCGGGGC
* * *** * * * *
871 CAAAAATCTTTGAAAACAGAGCCGGGGCCTTGGAACGCGTTTTTAGCCTAAAACCTTGATGGTTA
1 CAAAAAGCATTGAAAACAGAGCCGGGGCCCCAGAACGCGATTTTAGCCAAAAACCGTGATGATTA
*
936 GTACACGATTTCGGCTAAAATTTTGCAAAAGTTGAG
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGAG
* *
972 CAAAAAGCATTGAAAACTGAGCCGGGGCCCCATAACGCGATTTTAGCCAAAAACCGTGATGATTA
1 CAAAAAGCATTGAAAACAGAGCCGGGGCCCCAGAACGCGATTTTAGCCAAAAACCGTGATGATTA
*
1037 GTACACGATTTCGGTTAAAATTTTGCAAAAATTGAG
66 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGAG
*
1073 CCAAAAG
1 CAAAAAG
1080 TTTTTCCACA
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (101 bp):
CAAAAAGCATTGAAAACAGAGCCGGGGCCCCAGAACGCGATTTTAGCCAAAAACCGTGATGATTA
GTACACGATTTCGGCTAAAATTTTGCAAAAATTGAG
Found at i:1348 original size:433 final size:432
Alignment explanation
Indices: 539--1373 Score: 1316
Period size: 433 Copynumber: 1.9 Consensus size: 432
529 GTCTCGGGGC
* * *
539 CAAAAAGCATTGAAAACTGAGTCGGGACCCCAGAACGCGTTTTTAGCCAAAAACCGCGATTATTA
1 CAAAAAGCATTGAAAACTGAGCCGGGACCCCAGAACGCGATTTTAGCCAAAAACCGCGATGATTA
* * *
604 GTATACGATTTTGGTTAAAATTTTGCAAAAATTGACTCGAAAGTTTTTCCACAATCTTTGGCCAA
66 GTACACGATTTCGGTTAAAATTTTGCAAAAATTGACTCAAAAGTTTTTCCACAATCTTTGGCCAA
* * *
669 AATACTTATAGAATATGTATAATTCAACGCCAAAAAAATTGAAGCGGTTTTCACGCTTCTAATAT
131 AATACATATAGAATATGTATAATTCAACGCCAAAAAAATTGAAGAGATTTTCACGCTTCTAATAT
* *
734 CGATTTTCCTATATCTTTCCAAATTAATTTCTGATTAAATCGAAATATGATTCAGATGCTCCTAA
196 CGATTTTCCTATATCTTTCCAAATTAATTTCTGACTAAATCGAAACATGATTCAGATGCTCCTAA
* * * *
799 AATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAAATATGTCAAGGAGTC
261 AATCAAATCCTTAAATCCAATTTGCCCGAGATATGGTTAGAAGAATATAAATATGTCAAGGAGTC
* ** ** *
864 TCGGGGCCAAAAATCTTTGAAAACAGAGCCGGGGCCTTGGAACGCGTTTTTAGCCTAAAACCTTG
326 TCGGGGCCAAAAATCATTGAAAACAGAGCCGGGGCCCCGGAACAAGTTTTTAG-CTAAAACCGTG
929 ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAGTTGAG
390 ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAGTTGAG
* * *
972 CAAAAAGCATTGAAAACTGAGCCGGGGCCCCATAACGCGATTTTAGCCAAAAACCGTGATGATTA
1 CAAAAAGCATTGAAAACTGAGCCGGGACCCCAGAACGCGATTTTAGCCAAAAACCGCGATGATTA
1037 GTACACGATTTCGGTTAAAATTTTGCAAAAATTGAGC-CAAAAGTTTTTCCACAATCTTTGGCCA
66 GTACACGATTTCGGTTAAAATTTTGCAAAAATTGA-CTCAAAAGTTTTTCCACAATCTTTGGCCA
1101 AAATACATATAGAATATGTATAATTCAACGCCAAAAAAATTGAAGAGATTTTCACGCTTCTAATA
130 AAATACATATAGAATATGTATAATTCAACGCCAAAAAAATTGAAGAGATTTTCACGCTTCTAATA
* * * ** *
1166 TCGATTTTCCTATATCTTTCCGAATTATTTTCT-AGCTAAATCGAAACATTATTTTGATGCTCGT
195 TCGATTTTCCTATATCTTTCCAAATTAATTTCTGA-CTAAATCGAAACATGATTCAGATGCTCCT
* *
1230 AAAATTAAATCCTTAAATCCAATTTGCCCGAGATATGGTTAGAAGAATATAGATATGTCAAGGAG
259 AAAATCAAATCCTTAAATCCAATTTGCCCGAGATATGGTTAGAAGAATATAAATATGTCAAGGAG
1295 TCTCGGGGCCAAAAATCATTGAAAACTA-AGCCGGGGCCCCGGAACAAGTTTTTAGCTAAAACCG
324 TCTCGGGGCCAAAAATCATTGAAAAC-AGAGCCGGGGCCCCGGAACAAGTTTTTAGCTAAAACCG
*
1359 TGATGTTTAGTACAC
388 TGATGGTTAGTACAC
Statistics
Matches: 366, Mismatches: 33, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
432 23 0.06
433 341 0.93
434 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (432 bp):
CAAAAAGCATTGAAAACTGAGCCGGGACCCCAGAACGCGATTTTAGCCAAAAACCGCGATGATTA
GTACACGATTTCGGTTAAAATTTTGCAAAAATTGACTCAAAAGTTTTTCCACAATCTTTGGCCAA
AATACATATAGAATATGTATAATTCAACGCCAAAAAAATTGAAGAGATTTTCACGCTTCTAATAT
CGATTTTCCTATATCTTTCCAAATTAATTTCTGACTAAATCGAAACATGATTCAGATGCTCCTAA
AATCAAATCCTTAAATCCAATTTGCCCGAGATATGGTTAGAAGAATATAAATATGTCAAGGAGTC
TCGGGGCCAAAAATCATTGAAAACAGAGCCGGGGCCCCGGAACAAGTTTTTAGCTAAAACCGTGA
TGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAGTTGAG
Done.