Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020799.1 Corchorus olitorius cultivar O-4 contig20832, 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: 3523
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:405 original size:14 final size:14
Alignment explanation
Indices: 381--415 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
371 TTGATTTCTT
381 TTGACATGGACGAAA
1 TTGA-ATGGACGAAA
396 TTGAATGGACGAAA
1 TTGAATGGACGAAA
410 TTGAAT
1 TTGAAT
416 TTTTTGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (14 bp):
TTGAATGGACGAAA
Found at i:1222 original size:2 final size:2
Alignment explanation
Indices: 1215--1252 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1205 AACATTTTAT
*
1215 TA TA TA TA TA TA TA TA TA TA TA TA TA CA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1253 GACATTCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3110 original size:330 final size:331
Alignment explanation
Indices: 2068--3523 Score: 2379
Period size: 330 Copynumber: 4.4 Consensus size: 331
2058 CGGGGCATCA
* * **
2068 GAAAAATATATAATTCAACGCCAAAAAGACTGAAGCATTTTTCAAACTTCTAATATCGTTTTTCC
1 GAAAAACATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCC
*
2133 ATTCTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCAG
66 ATTCTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCAG
2198 AAATCCAATGTGGCTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAA
131 AAATCCAATGTGGCTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAA
* * * * *
2263 ATCATGCAAAATTGAGTCGGGGCCTCGGAATGCTTTTTTAGGCATAAACCGTGATGATTAATACA
196 ATCATGCAAAACTGAGTCGGGGCCTCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACA
* * *
2328 CGATTTCGGCTAAAATTTTGCGAAAGTTATCCCGAAAATTTTTTTCCTCAATTTTCTGCAAGAAT
261 CGATTTCGGCTAAAATTTTGCGAAAATTACCCCGAAAATTTTTTTCCTCAATTTTCTGCAACAAT
2393 ATTCAG
326 ATTCAG
* *
2399 GAAAAACATATAATTCAACGACAAAAAGACTAAAGCGTTTTTCACGCTTCTAATATCGTTTTTCC
1 GAAAAACATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCC
*
2464 ATTCTTTCGAATTAATTTCTAATTAAATCGAAA-TAGATTCAGATGCTCGTAAAAACAAATCCAG
66 ATTCTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCAG
* * *
2528 AAATCCAATGTGGCTGGGATTCCGATCTGTGAATATACGTATTTCGAGGAGTCTTTACACCAAAA
131 AAATCCAATGTGGCTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAA
* * * *
2593 ATCATGCAAAACTGAGTCGGGGCC-CAGAACGCGTTTTTAGGCAAAAATCGTGATTGTTATTACA
196 ATCATGCAAAACTGAGTCGGGGCCTCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACA
* * *
2657 CGATTTCGACTAAAATTTTACG-AAATTACCCCGAAAA-TTTTTTCCTCAATTTTTCTGCTACAA
261 CGATTTCGGCTAAAATTTTGCGAAAATTACCCCGAAAATTTTTTTCCTCAA-TTTTCTGCAACAA
2720 T-TCTCAG
325 TAT-TCAG
*
2727 GAAAAACATATAATTCAACGCCAAAAAGACTGAAGCGTTTTCCACGCTTCTAATATCGTTTTTCC
1 GAAAAACATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCC
* * *
2792 ATTCTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTG
66 ATTCTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCAG
* *
2857 AAATCCATTGTGGTTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAA
131 AAATCCAATGTGGCTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAA
* *
2922 TTCATGCAAAACTGAGTCGGGGCCTCGGAACGCGTTTTTAGGCAAAAATCGTGATGGTTAATACA
196 ATCATGCAAAACTGAGTCGGGGCCTCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACA
2987 CGATTTCGGCTAAAATTTTGCGAAAATTACCCCGAAAA-TTTTTTCGC-CAACTTTT-TGCAACA
261 CGATTTCGGCTAAAATTTTGCGAAAATTACCCCGAAAATTTTTTTC-CTCAA-TTTTCTGCAACA
3049 ATATTCAG
324 ATATTCAG
* * *
3057 GAAAAACACATGATTCAATGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCC
1 GAAAAACATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCC
* * * *
3122 ATTCTTTCAAATTAATTTCTAATTAAATCGGAACAAGATTAAAATGCTCGTAAAAACAAATCCAG
66 ATTCTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCAG
* **
3187 AAATCCAATGTGGCTGGGATTCCGATCGGTGAATATACGTGCTTCGAGGAGTCTTTACGCCAAAA
131 AAATCCAATGTGGCTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAA
*
3252 ATCATGCAAAACAGAGTCGGGGCCTCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACA
196 ATCATGCAAAACTGAGTCGGGGCCTCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACA
3317 CGATTTCGGCTAAAATTTTGCGAAAATTACCCCGAAAATTTTTTTCCTCAATTTTCTGCAACAAT
261 CGATTTCGGCTAAAATTTTGCGAAAATTACCCCGAAAATTTTTTTCCTCAATTTTCTGCAACAAT
3382 ATTCAG
326 ATTCAG
* * *
3388 GAAAAACATATAATTCAATGACAAAAAGACTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC
1 GAAAAACATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCC
*
3453 ATTCTTTCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCAG
66 ATTCTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCAG
3518 AAATCC
131 AAATCC
Statistics
Matches: 1041, Mismatches: 74, Indels: 20
0.92 0.07 0.02
Matches are distributed among these distances:
327 13 0.01
328 123 0.12
329 163 0.16
330 467 0.45
331 274 0.26
332 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (331 bp):
GAAAAACATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCC
ATTCTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCAG
AAATCCAATGTGGCTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAA
ATCATGCAAAACTGAGTCGGGGCCTCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACA
CGATTTCGGCTAAAATTTTGCGAAAATTACCCCGAAAATTTTTTTCCTCAATTTTCTGCAACAAT
ATTCAG
Done.