Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016363.1 Corchorus olitorius cultivar O-4 contig16396, 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: 2456
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:2357 original size:654 final size:654
Alignment explanation
Indices: 459--2456 Score: 3450
Period size: 654 Copynumber: 3.1 Consensus size: 654
449 AAAAACCAAG
* *
459 ATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAACTGTCCCGAAAATTTTTTACCTCAATT
1 ATGGTTAGTACACGATTTTGGCAAAAATTTTGCAAAAACTGACCCGAAAATTTTTTACCTCAATT
**
524 TCTTGCCACAATACTCTTAAAAAATATATAATTCAACGCGAAAAAGATTGAAGGGTTTTTTCACT
66 TCTTGCCACAATACTCAGAAAAAATATATAATTCAACGCGAAAAAGATTGAAGGGTTTTTTCACT
* * * *
589 CTTCTAATACCGTTTTCCCATTCTTTTCCAAATTTTTTCCTAACTAAATCGAAACTAAATTCAGA
131 CTTCTAATACCGTTTTCCCATTCTTTTCCGAATTTTTTTCTAATTAAATCGAAACAAAATTCAGA
654 TACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATACAGATATTT
196 TACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATACAGATATTT
*
719 CAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCTCTGGAACGCGTTTTTAGCTA
261 CAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCTA
* * *
784 AAAATCATGATGGTTAGTACACTATTTCGGCTAAAAACTGACCCGAAATGTTTTTTCTCAATTTT
326 AAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGTTTTTTCTCAATTTT
* *
849 TTGCCATATTACTCAGAAAAAATATATAATTCAACGCCAAAAATCTTGACCGGATTTTTACGTTT
391 TTGCCGTAATACTCAGAAAAAA-ATATAATTCAACGCCAAAAATCTTGACCGGATTTTTACGTTT
*
914 CTTATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATAGAAACAAAATTCAGATGC
455 CTTATATC-TTTTTCCATTTTTTTCTGAATTAATTTCTAATTTAATAGAAACAAAATTCAGATGC
* *
979 TCTTAAAAACAAATCCTTATATCCAATGTGGCTAAGATTTGGTCCGATGAATTTAGATATTTCAA
519 TCTTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTCCGATGAATATAGATATTTCAA
* *
1044 AGAGTCTTGGTGCCAAAACTCAAGCAAAGTTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAA
584 AGAGTCTTTGTGCCAAAACTCATGCAAAGTTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAA
1109 ACCGTA
649 ACCGTA
* * *
1115 ATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTACCACAATT
1 ATGGTTAGTACACGATTTTGGCAAAAATTTTGCAAAAACTGACCCGAAAATTTTTTACCTCAATT
* *
1180 TTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTTACAC
66 TCTTGCCACAATACTCAGAAAAAATATATAATTCAACGCGAAAAAGATTGAAGGGTTTTTT-CAC
* * *
1245 TCTTATAATACCGTTTTCCCATTCTTTTCCGAATTGTTTTCTAATTAAATCGAAACAAGATTCAG
130 TCTTCTAATACCGTTTTCCCATTCTTTTCCGAATTTTTTTCTAATTAAATCGAAACAAAATTCAG
* * *
1310 ATTCTCCTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATATAGATATT
195 ATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATACAGATATT
*
1375 TCAAGG-GTCTTTCTGCCAAAAATCATGCAAAACTGAGTAGGGGCTCCGGAACGCGTTTTTAGCT
260 TCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCT
1439 AAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGTTTTTTCTCAATTT
325 AAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGTTTTTTCTCAATTT
* * *
1504 TTTGCCGTAATATTCA-AAAAAAATATTATTCAACGCCAAAAATCTTGACCAGATTTTTAC-TTT
390 TTTGCCGTAATACTCAGAAAAAAATATAATTCAACGCCAAAAATCTTGACCGGATTTTTACGTTT
*
1567 CCTTATATCTTTTTCCATTTTTTTCTGAATTAATTTCTAATTTAATAGAAACAAAATTTAGATGC
455 -CTTATATCTTTTTCCATTTTTTTCTGAATTAATTTCTAATTTAATAGAAACAAAATTCAGATGC
* *
1632 TCTTAAAAACAAATCCTTATCTCCAATGTGGCTGAAATTTGGTCCGATGAATATAGATATTTCAA
519 TCTTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTCCGATGAATATAGATATTTCAA
1697 AGAGTCTTTGTGCCAAAACTCATGCAAAGTTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAA
584 AGAGTCTTTGTGCCAAAACTCATGCAAAGTTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAA
1762 ACCGTA
649 ACCGTA
*
1768 ATGGTTGGTACACGATTTT-GCAAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTACCTCAAT
1 ATGGTTAGTACACGATTTTGGCAAAAATTTTGCAAAAACTGACCCGAAAA-TTTTTTACCTCAAT
* *
1832 TTCTTGCCACAATACTCCGAAAAAATATATAATCCAACGCGAAAAAGATTGAAGGGTTTTTTCAC
65 TTCTTGCCACAATACTCAGAAAAAATATATAATTCAACGCGAAAAAGATTGAAGGGTTTTTTCAC
*
1897 TCTTCTAATACCGTTTTCCCATTCTTTTCCGATTTTTTTTTCTAATTAAATCGAAACAAAATTCA
130 TCTTCTAATACCGTTTTCCCATTCTTTTCCGA-ATTTTTTTCTAATTAAATCGAAACAAAATTCA
*
1962 GATACTCGTAAAAACAAATCCTTAAATGCAATATGTCTGAGATTTTGTTTGATGAATACAGATAT
194 GATACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATACAGATAT
* *
2027 TTCGAGGAGTCTTTTTGCCAAAAATCATGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGC
259 TTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGC
* *
2092 TAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAAGTGACCCGAAATGATTTTTCTCAATT
324 TAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGTTTTTTCTCAATT
2157 TTTTGCCGTAATACTCAGAAAAAAATATAATTCAACGCCAAAAATCTTGACCGGATTTTTACGTT
389 TTTTGCCGTAATACTCAGAAAAAAATATAATTCAACGCCAAAAATCTTGACCGGATTTTTACGTT
2222 TCTTATATCTTTTTCCA-TTTTTTCTGAATTAATTTCTAATTTAATAGAAACAAAATTCAGATGC
454 TCTTATATCTTTTTCCATTTTTTTCTGAATTAATTTCTAATTTAATAGAAACAAAATTCAGATGC
* *
2286 TCTTAAAAACAAATCCTTATATCCAATGCGGCTGAGATCTGGTCCGATGAATATAGATATTTCAA
519 TCTTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTCCGATGAATATAGATATTTCAA
*
2351 AGAGTCTTTGTGACAAAACTCATGCAAAGTTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAA
584 AGAGTCTTTGTGCCAAAACTCATGCAAAGTTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAA
2416 ACCGTA
649 ACCGTA
*
2422 ATGGTTGGTACACGATTTT-GCAAAAATTTTGCAAA
1 ATGGTTAGTACACGATTTTGGCAAAAATTTTGCAAA
Statistics
Matches: 1270, Mismatches: 65, Indels: 16
0.94 0.05 0.01
Matches are distributed among these distances:
652 63 0.05
653 371 0.29
654 390 0.31
655 64 0.05
656 253 0.20
657 129 0.10
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (654 bp):
ATGGTTAGTACACGATTTTGGCAAAAATTTTGCAAAAACTGACCCGAAAATTTTTTACCTCAATT
TCTTGCCACAATACTCAGAAAAAATATATAATTCAACGCGAAAAAGATTGAAGGGTTTTTTCACT
CTTCTAATACCGTTTTCCCATTCTTTTCCGAATTTTTTTCTAATTAAATCGAAACAAAATTCAGA
TACTCGTAAAAACAAATCCTTAAATCCAATATGTCTGAGATTTTGTTTGATGAATACAGATATTT
CAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCTA
AAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATGTTTTTTCTCAATTTT
TTGCCGTAATACTCAGAAAAAAATATAATTCAACGCCAAAAATCTTGACCGGATTTTTACGTTTC
TTATATCTTTTTCCATTTTTTTCTGAATTAATTTCTAATTTAATAGAAACAAAATTCAGATGCTC
TTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTCCGATGAATATAGATATTTCAAAG
AGTCTTTGTGCCAAAACTCATGCAAAGTTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAAC
CGTA
Done.