Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010577.1 Corchorus olitorius cultivar O-4 contig10609, 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: 2296
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:581 original size:320 final size:319
Alignment explanation
Indices: 1--627 Score: 965
Period size: 320 Copynumber: 2.0 Consensus size: 319
* * *
1 CAGAAAAAATATATAATTTGTAACCAAAAAAATGATGGGTTTTCACGCTTCTAATATCGTTTTAC
1 CAGAAAAAATATATAATTTATAACCAAAAAAATGAAGGGTTTTCACGCTTCTAATATAGTTTTAC
* *
66 CATTTTTTTCTAATATATATCTAATTATGTCGAAACAAGATTCAGATGCTTATAAAAACAAATCC
66 CATTTTTTCCTAATATATATCTAATTATATCGAAACAAGATTCAGATGCTTATAAAAACAAATCC
* **
131 TTAAATCCATTGTGCCTGAGATTTGATTCGATAAATATAGATATTCCAGGGAGTGTTTTTGCCAA
131 TTAAATCCATTGTGCCTGAGATTTGATTCGATAAATATAGATATTCCAGGGAGTGTTTGTGAAAA
* ** *
196 AAATTATGCAAAACTCAGTCGGGGCCCCGAAACGCGTTTTTAGCCCAAAACCGTGATGGTAAGTA
196 AAATTATGCAAAACTCAGCCGGGGCCAAGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTA
*
261 CACAATTTCGGCTAAAAACTGACCCGAGAA-TTTTTTCTAAATTTTTTGCCACAATACT
261 CACAATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTAAATTTTTTGCCACAATACT
* *
319 CAGAAAAAATATATAATTTATAACCAAAAAATTGAAGGGTTTTTTACGCTTCTAATATAGTTTTA
1 CAGAAAAAATATATAATTTATAACCAAAAAAATGAAGGG-TTTTCACGCTTCTAATATAGTTTTA
* *
384 CCAATTTTTTCCTGAT-TAATATCTAATTATATCGAAACAAGATTCAGATGC-TAGTAAAAATAA
65 CC-ATTTTTTCCTAATAT-ATATCTAATTATATCGAAACAAGATTCAGATGCTTA-TAAAAACAA
** * *
447 ATCCTTAAATCCATTGTGGTTGAGATTTGGTTCGA-AGAATATAGATATTTCAGGGAGTGTTTGT
127 ATCCTTAAATCCATTGTGCCTGAGATTTGATTCGATA-AATATAGATATTCCAGGGAGTGTTTGT
*
511 GAAAAAAATTATGCAAAACTCAGCCGGGGCCAAGAAACGCGTTTTTAGCCAAAAATCGTGATGGT
191 GAAAAAAATTATGCAAAACTCAGCCGGGGCCAAGAAACGCGTTTTTAGCCAAAAACCGTGATGGT
* *
576 AAGTACACGATTTCGGCTAAAAATTGACCCGAAAATTTTTTTCTAAATTTTT
256 AAGTACACAATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTAAATTTTT
628 CACGTTTCTA
Statistics
Matches: 279, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
318 36 0.13
319 29 0.10
320 198 0.71
321 16 0.06
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (319 bp):
CAGAAAAAATATATAATTTATAACCAAAAAAATGAAGGGTTTTCACGCTTCTAATATAGTTTTAC
CATTTTTTCCTAATATATATCTAATTATATCGAAACAAGATTCAGATGCTTATAAAAACAAATCC
TTAAATCCATTGTGCCTGAGATTTGATTCGATAAATATAGATATTCCAGGGAGTGTTTGTGAAAA
AAATTATGCAAAACTCAGCCGGGGCCAAGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTA
CACAATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTAAATTTTTTGCCACAATACT
Found at i:1370 original size:318 final size:317
Alignment explanation
Indices: 624--2296 Score: 2051
Period size: 320 Copynumber: 5.2 Consensus size: 317
614 TTTTCTAAAT
* * *
624 TTTTCACGTTTCTAATATCATTTTTCCATTTTTTTTTCAAATTTATATCTAATTATTACGAAACA
1 TTTTCACGCTTCTAATATCGTTTTTCCA--TTTTTTTCAAATTTATATCTAATTATAACGAAACA
* * * * * * *
689 AGACTCAGATGCTCGTAAAAACAAATTCGTAAATCCATTGCGACTGAGATTGGGTTTGATTAATA
64 AGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATA
* * * * *
754 TAGATATTTCA-AGGAGTCTTTCTGCCAGAAATCATGGAAAACTCAGCCAGGGCCCCGAAACGCG
129 TAGATATTTCAGA-GAGTGTTTCTGCCAAAAATTATGCAAAACTCAGCCGGGGCCCCGAAACGCG
* * * *
818 TTCTTAG-CAAGAACCGTGATGGTAAGTACACGATTTCAGCTAAAAACTGACCCGAAAATTTTTT
193 TTTTTAGCCAAAAACCGTGAT-GT-AGTACACGATTTCGGCTAAAAACTGACACGAAAA-TTTTT
* * * * *
882 TCTAAATTTTCTGCCACAATACAT-AGAAAAAATATATAATTAGTA-ACCAAAAAAATTGAAGGA
255 TCTCAATTTTTTGGCACAATAC-TCAGAAAAAATATATAATT-TTATGCCAAAAAAATTGAAGG-
*
945 T
317 C
* * * * *
946 TTTTTACGCTTCTATTATCGTTTTACCATTTTTTTCCTAATTTATATCTAATTATATCGAAACAA
1 TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTT-CAAATTTATATCTAATTATAACGAAACAA
* * * *
1011 GATTCAGATGCTTGTAAAAACAAATCCTTAAATCCATTGTGGATGAGATTTGGATCGATGAATAT
65 GATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATAT
*
1076 AGATATTTCAGAGAGTGTTTCTGCCAAAAATTATGCAAAACTCAGTCGGGGCCCCGAAACGCGTT
130 AGATATTTCAGAGAGTGTTTCTGCCAAAAATTATGCAAAACTCAGCCGGGGCCCCGAAACGCGTT
* * *
1141 TTTAGCCCAAAACCGTGATG-AGTACACGATTTCGGCTAAAAACTGACACGAAATTTTTTTTTCA
195 TTTAGCCAAAAACCGTGATGTAGTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTCTCA
* *
1205 ATTTTTTGGCACAATACTCACAAAAAAATAAATAATTTTATGCCAAAAAAATTGAAGAGC
260 ATTTTTTGGCACAATACTCA-GAAAAAATATATAATTTTATGCCAAAAAAATTGAAG-GC
* * * * * * *
1265 TTTTCATGCTTGTAATAACATTTTTCCATTTTTTTCGAATTTATTTCTAATTATAACGTAACAAG
1 TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCAAATTTATATCTAATTATAACGAAACAAG
* *
1330 ATTCAGATGCTCGTAAATACAAATCCGTAAATTCATTGTGGCTGAGATTTGGTTCGATGAATATA
66 ATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATA
* * ***
1395 AATATTTCATG-GAGTGTTTCTGCCAAAAATTATGCAAAGCTCGAGCCGAAACCCCGAAACGCGT
131 GATATTTCA-GAGAGTGTTTCTGCCAAAAATTATGCAAAACTC-AGCCGGGGCCCCGAAACGCGT
* * * **
1459 TTTTAGCCGAAAACCGTGATG-GGTACACGATTTCGGCTAAAAACGGACTATAAAAAATTTTTTC
194 TTTTAGCCAAAAACCGTGATGTAGTACACGATTTCGGCTAAAAACTGAC-A-CGAAAATTTTTTC
* * * * *
1523 TCTATTTTTTGGCACAAAACTTAGAAAAAAAATATAA-TTTATTTCCAAAAAAATTGAAGCGC
257 TCAATTTTTTGGCACAATACTCAGAAAAAATATATAATTTTA-TGCCAAAAAAATTGAAG-GC
* * * *
1585 TTTTCACTCTTCTAATATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTATATCGAAACAAG
1 TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCAAATTTATATCTAATTATAACGAAACAAG
* *
1650 ATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGATATTCGGTTCGATGAATATA
66 ATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATA
* * * * * *
1715 GATATTTCA-AGGAATCTTTCTGCCAAAAATCATGCAAAACTCAGGC-GGGCCCTGAAACACGTT
131 GATATTTCAGA-GAGTGTTTCTGCCAAAAATTATGCAAAACTCAGCCGGGGCCCCGAAACGCGTT
* * * *
1778 TTTAGCCAAAAACTGTGATGTAGTACACGATTTCGGCTAAAAATTGACTCGAAAATTTTTTCTAA
195 TTTAGCCAAAAACCGTGATGTAGTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTCTCA
* * * * *
1843 ACTTTTTGGCCACAATACTCAGGAAAAATATATTATTTAATGCCAAAAAAGTTGAATGGC
260 ATTTTTTGG-CACAATACTCAGAAAAAATATATAATTTTATGCCAAAAAAATTGAA-GGC
* * * *
1903 TTTTCACGCTTCTAATATCGTTTTACCATTTTTTTTCCTAATTTATATCTCATTATATCGAAACA
1 TTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTT-CAAATTTATATCTAATTATAACGAAACA
** * * *
1968 AGATTCAGATGCTTATAAAAAAAAACCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATA
64 AGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATA
* * *
2033 TATATATTTCATG-GTGTGTTTCTGCCAAAAAAATATGCAAAACTCAGCCGGGGCCCCGAAACGC
129 TAGATATTTCA-GAGAGTGTTTCTGCC-AAAAATTATGCAAAACTCAGCCGGGGCCCCGAAACGC
* *
2097 GTTTTTAGGCAAAAACCGTGATGTAGTACACGATTTTCGGCTAAAAACTGACCCGAAAATTTTTT
192 GTTTTTAGCCAAAAACCGTGATGTAGTACACGA-TTTCGGCTAAAAACTGACACGAAAATTTTTT
* * *
2162 CTCAATTTTTTTGGCACAATACTCAGAAAAAATGTATAATTTGATGCC-AAAAAATTGAAGCGT
256 CTCAA-TTTTTTGGCACAATACTCAGAAAAAATATATAATTTTATGCCAAAAAAATTGAAG-GC
* *
2225 TTTTCACGTTTCTAATATCG-TTTTCCA-TTTTTTCAAATTTATATCTAATTATTACGAAACAAG
1 TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCAAATTTATATCTAATTATAACGAAACAAG
*
2288 ACTCAGATG
66 ATTCAGATG
Statistics
Matches: 1165, Mismatches: 159, Indels: 58
0.84 0.12 0.04
Matches are distributed among these distances:
317 21 0.02
318 275 0.24
319 199 0.17
320 295 0.25
321 197 0.17
322 108 0.09
323 63 0.05
324 7 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (317 bp):
TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCAAATTTATATCTAATTATAACGAAACAAG
ATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATA
GATATTTCAGAGAGTGTTTCTGCCAAAAATTATGCAAAACTCAGCCGGGGCCCCGAAACGCGTTT
TTAGCCAAAAACCGTGATGTAGTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTCTCAA
TTTTTTGGCACAATACTCAGAAAAAATATATAATTTTATGCCAAAAAAATTGAAGGC
Found at i:1872 original size:638 final size:634
Alignment explanation
Indices: 624--2296 Score: 2123
Period size: 638 Copynumber: 2.6 Consensus size: 634
614 TTTTCTAAAT
* *
624 TTTTCACGTTTCTAATATCATTTTTCCATTTTTTTTTCAAATTTATATCTAATTATTACGAAACA
1 TTTTCACGCTTCTAATATCATTTTTCCA-TTTTTTTTCAAATTTATATCTAATTATAACGAAACA
* * * * * * *
689 AGACTCAGATGCTCGTAAAAACAAATTCGTAAATCCATTGCGACTGAGATTGGGTTTGATTAATA
65 AGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATA
* * * * * *
754 TAGATATTTCAAGGAGTCTTTCTGCCAGAAATCATGGAAAACTCAGCC-AGGGCCCCGAAACGCG
130 TAAATATTTCATGGAGTGTTTCTGCCAAAAATTATGCAAAACTCAGCCGA-GGCCCCGAAACGCG
* * * *
818 TTCTTAGCAAGAACCGTGATGGTAAGTACACGATTTCAGCTAAAAACTGACCCGAAAATTTTTTT
194 TTTTTAGCAA-AACCGTGATGG---GTACACGATTTCGGCTAAAAACTGA-CCAAAAAATTTTTT
* * * * *
883 CTAAATTTTCTGCCACAATACATAGAAAAAATATATAA-TTAGTAACCAAAAAAATTGAAG-GAT
254 CTCAATTTTTTGGCACAATACTTAGAAAAAATATATAATTTA-TTACCAAAAAAATTGAAGCG-T
* * * * *
946 TTTTTACGCTTCTATTATCGTTTTACCATTTTTTTCCTAATTTATATCTAATTATATCGAAACAA
317 TTTTCACTCTTCTAATATCGTTTTTCCATTTTTTT-CAAATTTATATCTAATTATATCGAAACAA
* * *
1011 GATTCAGATGCTTGTAAAAACAAATCCTTAAATCCATTGTGGATGAGATTTGGATCGATGAATAT
381 GATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGATGAGATTCGGATCGATGAATAT
* * * * *
1076 AGATATTTCAGAGAGTGTTTCTGCCAAAAATTATGCAAAACTCAGTCGGGGCCCCGAAACGCGTT
446 AGATATTTCAGAGAATCTTTCTGCCAAAAATCATGCAAAACTCAGGCGGGGCCCCGAAACACGTT
* * * *
1141 TTTAGCCCAAAACCGTGATGAGTACACGATTTCGGCTAAAAACTGACACGAAATTTTTTTTTCAA
511 TTTAGCCAAAAACCGTGATGAGTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTCTAAA
* *
1206 TTTTTTGGCACAATACTCACAAAAAAATAAATAATTTTATGCCAAAAAAATTGAA-GAGC
576 CTTTTTGGCACAATACTCACAAAAAAATAAATAATTTAATGCCAAAAAAATTGAATG-GC
* * * * * *
1265 TTTTCATGCTTGTAATAACATTTTTCCA-TTTTTTTCGAATTTATTTCTAATTATAACGTAACAA
1 TTTTCACGCTTCTAATATCATTTTTCCATTTTTTTTCAAATTTATATCTAATTATAACGAAACAA
* *
1329 GATTCAGATGCTCGTAAATACAAATCCGTAAATTCATTGTGGCTGAGATTTGGTTCGATGAATAT
66 GATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATAT
* **
1394 AAATATTTCATGGAGTGTTTCTGCCAAAAATTATGCAAAGCTCGAGCCGAAACCCCGAAACGCGT
131 AAATATTTCATGGAGTGTTTCTGCCAAAAATTATGCAAAACTC-AGCCGAGGCCCCGAAACGCGT
* *
1459 TTTTAGCCGAAAACCGTGATGGGTACACGATTTCGGCTAAAAACGGACTATAAAAAATTTTTTCT
195 TTTTAG-C-AAAACCGTGATGGGTACACGATTTCGGCTAAAAACTGAC--CAAAAAATTTTTTCT
* * * * *
1524 CTATTTTTTGGCACAAAACTTAGAAAAAAAATATAATTTATTTCCAAAAAAATTGAAGCGCTTTT
256 CAATTTTTTGGCACAATACTTAGAAAAAATATATAATTTATTACCAAAAAAATTGAAGCGTTTTT
* *
1589 CACTCTTCTAATATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTATATCGAAACAAGATTC
321 CACTCTTCTAATATCGTTTTTCCATTTTTTTCAAATTTATATCTAATTATATCGAAACAAGATTC
* * *
1654 AGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGATATTCGGTTCGATGAATATAGATA
386 AGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGATGAGATTCGGATCGATGAATATAGATA
*
1719 TTTCA-AGGAATCTTTCTGCCAAAAATCATGCAAAACTCAGGC-GGGCCCTGAAACACGTTTTTA
451 TTTCAGA-GAATCTTTCTGCCAAAAATCATGCAAAACTCAGGCGGGGCCCCGAAACACGTTTTTA
* * *
1782 GCCAAAAACTGTGATGTAGTACACGATTTCGGCTAAAAATTGACTCGAAAATTTTTTCTAAACTT
515 GCCAAAAACCGTGATG-AGTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTCTAAACTT
** * * *
1847 TTTGGCCACAATACTCA-GGAAAAATATATTATTTAATGCCAAAAAAGTTGAATGGC
579 TTTGG-CACAATACTCACAAAAAAATAAATAATTTAATGCCAAAAAAATTGAATGGC
* * * * *
1903 TTTTCACGCTTCTAATATCGTTTTACCATTTTTTTTCCTAATTTATATCTCATTATATCGAAACA
1 TTTTCACGCTTCTAATATCATTTTTCCATTTTTTTT-CAAATTTATATCTAATTATAACGAAACA
** * * *
1968 AGATTCAGATGCTTATAAAAAAAAACCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATA
65 AGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATA
* * * *
2033 TATATATTTCATGGTGTGTTTCTGCCAAAAAAATATGCAAAACTCAGCCGGGGCCCCGAAACGCG
130 TAAATATTTCATGGAGTGTTTCTGCC-AAAAATTATGCAAAACTCAGCCGAGGCCCCGAAACGCG
* **
2098 TTTTTAGGCAAAAACCGTGATGTAGTACACGATTTTCGGCTAAAAACTGACCCGAAAATTTTTTC
194 TTTTTA-GC-AAAACCGTGATG-GGTACACGA-TTTCGGCTAAAAACTGACCAAAAAATTTTTTC
* * *
2163 TCAATTTTTTTGGCACAATACTCAGAAAAAATGTATAATTTGA-TGCC-AAAAAATTGAAGCGTT
255 TCAA-TTTTTTGGCACAATACTTAGAAAAAATATATAATTT-ATTACCAAAAAAATTGAAGCGTT
2226 TTTCACGT-TTCTAATATCG-TTTTCCA-TTTTTTCAAATTTATATCTAATTAT-TACGAAACAA
318 TTTCAC-TCTTCTAATATCGTTTTTCCATTTTTTTCAAATTTATATCTAATTATAT-CGAAACAA
*
2287 GACTCAGATG
381 GATTCAGATG
Statistics
Matches: 896, Mismatches: 114, Indels: 47
0.85 0.11 0.04
Matches are distributed among these distances:
637 36 0.04
638 291 0.32
639 238 0.27
640 213 0.24
641 98 0.11
642 20 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (634 bp):
TTTTCACGCTTCTAATATCATTTTTCCATTTTTTTTCAAATTTATATCTAATTATAACGAAACAA
GATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATAT
AAATATTTCATGGAGTGTTTCTGCCAAAAATTATGCAAAACTCAGCCGAGGCCCCGAAACGCGTT
TTTAGCAAAACCGTGATGGGTACACGATTTCGGCTAAAAACTGACCAAAAAATTTTTTCTCAATT
TTTTGGCACAATACTTAGAAAAAATATATAATTTATTACCAAAAAAATTGAAGCGTTTTTCACTC
TTCTAATATCGTTTTTCCATTTTTTTCAAATTTATATCTAATTATATCGAAACAAGATTCAGATG
CTCGTAAAAACAAATCCGTAAATCCATTGTGGATGAGATTCGGATCGATGAATATAGATATTTCA
GAGAATCTTTCTGCCAAAAATCATGCAAAACTCAGGCGGGGCCCCGAAACACGTTTTTAGCCAAA
AACCGTGATGAGTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTCTAAACTTTTTGGCA
CAATACTCACAAAAAAATAAATAATTTAATGCCAAAAAAATTGAATGGC
Done.