Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018162.1 Corchorus olitorius cultivar O-4 contig18195, 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: 1711
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:1277 original size:670 final size:668
Alignment explanation
Indices: 169--1711 Score: 1838
Period size: 670 Copynumber: 2.3 Consensus size: 668
159 CTTATGCAAA
* * ** *
169 AAAAATTTTTCTTAATTTTTTGCCACAATATTCTGAAAACTTGAATAATTCAACGCCAAAAATAT
1 AAAAATTTTTCTCAATTTTTTGCCACAATACTCTGAAAAAATGAATAATTCAACGCCAAAAACAT
*
234 TGAAGGGTTTTTCACGCTTCTAATTTCGTTTTTCCATTTTATTCCCAATTAATATCTAATAAAAT
66 TGAAGGATTTTTCACGCTTCTAATTTCGTTTTTCCATTTTATTCCCAATTAATATCTAATAAAAT
* ** * *
299 CGAAACAACATTCAGATACTCGAAAAAACAAATTGTTATATCGAATGTGGCTGGGATTTGGCTCG
131 CCAAACAACATTCAGATACTCGAAAAAACAAATTCATAAATCGAATGTGGCTGGGATTTGCCTCG
* * * * *
364 ATAAATGTAGATATTTCAAGAAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGCCTCGAA
196 ATAAATATAGATATTTCAAGAAGTCTTTACGCCAAAAATCATACAAAACTGAGCCGAGCCCCGAA
* *
429 ACGCGTTTTTAGCCAAAAGCCGTGATAGTTAATACACGATTTCGACTAAAATTTTGCAAAAACTG
261 ACGCGTTTTTAGCCAAAAACCGTGATAGTAAATACACGATTTCGACTAAAATTTTGCAAAAACTG
* *
494 ACCCGAAAAAATTTTTCCTCAAATTTTTTGTCACAATACTAAAAAAAATATATAATTCAATGCCG
326 ACCCGAAAAAATTGTTCCTCAAATTTTTTGTCACAATACTAAAAAAAATATATAATTCAATACCG
* *
559 AAAAAATTGAAGGATTTTTCACGTTTCTAATATCGTTTTTTTA-TTTTTTTCCTGAATTTATTTT
391 AAAAAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTGTATTTTTTTTCCTGAATTTATTTT
* * * * *
623 TGATTGAATCAAAACCAGATTCAAATGTTCGTAAAAACAAATCTTTAAATCGAATGTGGCTGTGA
456 TAATTAAATCAAAACAAGATTCAAATGTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGGA
688 TATGGCTCGAAGAATATAGATATTTCAGTGACTTTTTACGCCAAAAATCATACAGAACTGAGCTG
521 TATGGCTCGAAGAATATAGATATTTCAGTGACTTTTTACGCCAAAAATCATACAGAACTGAGCTG
753 GGGACCCGGAACGCGTTTTTAGCCAAAAAACCGTGATAGATAACACACGATTTCGTCTAAAATTT
586 GGGACCCGGAACGCGTTTTTAGCCAAAAAACCGTGATAGATAACACACGATTTCGTCTAAAATTT
818 TGCAAAAAAACTGACCCG
651 TGCAAAAAAACTGACCCG
* *
836 AAAAATTTTTCCTCAATTTTTTTGCCACAATACTCAT-AAAAAATGTATAATTCAATGCCAAAAA
1 AAAAATTTTT-CTCAA-TTTTTTGCCACAATACTC-TGAAAAAATGAATAATTCAACGCCAAAAA
** * * * *
900 CATTGAAGGATTTTTCACGCTTCTAATATT-GTTTTTGTATTTTTTTCCTGAATTTATTTCTAAT
63 CATTGAAGGATTTTTCACGCTTCTAAT-TTCGTTTTTCCATTTTATTCC-CAATTAATATCTAAT
* * * * *
964 TAAATCCAAACAAGATTCAGATGCTCGTAAAAACAAATTCATAAATCGAATGTGGCTGTGATTTG
126 AAAATCCAAACAACATTCAGATACTCGAAAAAACAAATTCATAAATCGAATGTGGCTGGGATTTG
* * * * * * * *
1029 CCTTGATGAATATAGATATTTTAGGGATTCTTTACGCCAAATATCATACAGAACTGAGCCAGAGC
191 CCTCGATAAATATAGATATTTCAAGAAGTCTTTACGCCAAAAATCATACAAAACTGAGCC-GAGC
* *
1094 CCCGGAACTCGTTTTTAGCCAAAAACCGTGAT-GTAACATACACGATTTC-AGCTAAAATTTTGC
255 CCCGAAACGCGTTTTTAGCCAAAAACCGTGATAGTAA-ATACACGATTTCGA-CTAAAATTTTGC
* * * *
1157 AAAAACTGTCCTG-AAAAATTGTTCCTC-AATTTTATTGTCACAATACTCAAAAAATTATATAAT
318 AAAAACTGACCCGAAAAAATTGTTCCTCAAATTTT-TTGTCACAATACTAAAAAAAATATATAAT
*
1220 TCAATACCGAAAAAATTGAAGGATTTTTCATGCTTCTAATATCGTTTTTGTATTTTTTTTCCTGA
382 TCAATACCGAAAAAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTGTATTTTTTTTCCTGA
* * *
1285 ATTTATTTTTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATTGAATG
447 ATTTATTTTTAATTAAATCAAAACAAGATTCAAATGTTCGTAAAAACAAATCCTTAAATCGAATG
** * * ** *
1350 TGGCTGGGATATGGCTCGATTAATATAGATATTTCAGTGAGTTTTTATGCCAAAAATCATGTAAA
512 TGGCTGGGATATGGCTCGAAGAATATAGATATTTCAGTGACTTTTTACGCCAAAAATCATACAGA
* * * * * * * * * * ** *
1415 ACTGAGTCT-GTG-TCCGAAACGTGTTTTAAGAC-AAAAATCATGATTGTTAGTACATGATTTCA
577 ACTGAG-CTGGGGACCCGGAACGCGTTTTTAGCCAAAAAACCGTGATAGATAACACACGATTTC-
**
1477 G-CTAAAAACTT--------A-T-A--C-
640 GTCTAAAATTTTGCAAAAAAACTGACCCG
* ** * *
1492 ---AATTTTT-T---TTTTTTGCGACAATA-TCATGAAAACTTGAATAATTCAACACCAAAAAGA
1 AAAAATTTTTCTCAATTTTTTGCCACAATACTC-TGAAAAAATGAATAATTCAACGCCAAAAACA
* * * * *
1549 TAGAAGGATTTTTCACGCTTCTAATTTCATTTTTCCATTTTTTTTCCAAATTAATATCTGATAAA
65 TTGAAGGATTTTTCACGCTTCTAATTTCGTTTTTCCA-TTTTATTCCCAATTAATATCTAATAAA
* * ** * * *
1614 CTCGAAACAACATTCAGATACTCGAAAAAACAAATTGTTATATCGAATGTGGCAGGGATTTGGCT
129 ATCCAAACAACATTCAGATACTCGAAAAAACAAATTCATAAATCGAATGTGGCTGGGATTTGCCT
* *
1679 CGATAAATGTAGATGTTTCAA-ATAGTCTTTACG
194 CGATAAATATAGATATTTCAAGA-AGTCTTTACG
Statistics
Matches: 745, Mismatches: 115, Indels: 52
0.82 0.13 0.06
Matches are distributed among these distances:
646 6 0.01
647 158 0.21
648 9 0.01
651 1 0.00
653 7 0.01
657 1 0.00
659 1 0.00
660 1 0.00
661 1 0.00
667 10 0.01
668 4 0.01
669 116 0.16
670 227 0.30
671 201 0.27
672 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (668 bp):
AAAAATTTTTCTCAATTTTTTGCCACAATACTCTGAAAAAATGAATAATTCAACGCCAAAAACAT
TGAAGGATTTTTCACGCTTCTAATTTCGTTTTTCCATTTTATTCCCAATTAATATCTAATAAAAT
CCAAACAACATTCAGATACTCGAAAAAACAAATTCATAAATCGAATGTGGCTGGGATTTGCCTCG
ATAAATATAGATATTTCAAGAAGTCTTTACGCCAAAAATCATACAAAACTGAGCCGAGCCCCGAA
ACGCGTTTTTAGCCAAAAACCGTGATAGTAAATACACGATTTCGACTAAAATTTTGCAAAAACTG
ACCCGAAAAAATTGTTCCTCAAATTTTTTGTCACAATACTAAAAAAAATATATAATTCAATACCG
AAAAAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTGTATTTTTTTTCCTGAATTTATTTT
TAATTAAATCAAAACAAGATTCAAATGTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGGA
TATGGCTCGAAGAATATAGATATTTCAGTGACTTTTTACGCCAAAAATCATACAGAACTGAGCTG
GGGACCCGGAACGCGTTTTTAGCCAAAAAACCGTGATAGATAACACACGATTTCGTCTAAAATTT
TGCAAAAAAACTGACCCG
Found at i:1420 original size:334 final size:331
Alignment explanation
Indices: 1--1420 Score: 1552
Period size: 337 Copynumber: 4.3 Consensus size: 331
* * *
1 AAAAGAAATCATTAAATCGAATATGGCTGGGATATGGCTCGATGAATATAGATATTTCAGTGAGT
1 AAAACAAATCCTTAAATCGAATGTGGCTGGGATATGGCTCGATGAATATAGATATTTCAGTGAGT
* * * ** * * * * * * *
66 TTTTATGCCAAAAATCAAGTAAAACTGAGTTTGTG-TCTGAAACGTGTTTTAAGACAAAAACCAT
66 TTTTACGCCAAAAATCATGCAAAACTGAG-CCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGT
* * * * *
130 GATTGTTAGTACACGATTTCAGA-TAAAAACTTATGC---AA---A----AAAAATTTTT-CTTA
130 GATAGTAAATACACGATTTC-GACT-AAAA-TTTTGCAAAAACTGACCCGAAAAATTTTTCCTCA
* ** * * * *
183 ATTTTTTGCCACAATATTCTGAAAACT-TGAATAATTCAACGCCAAAAATATTGAAGGGTTTTTC
192 ATTTTTTGCCACAATACTCAAAAAAATAT--ATAATTCAATGCCAAAAACATTGAAGGATTTTTC
* ** * * * * * *
247 ACGCTTCTAATTTCGTTTTTCCATTTTATTCC-CAATTAATATCTAATAAAATCGAAACAACATT
255 ACGCTTCTAATATCGTTTTTGTATTTTTTTCCTGAATTTATTTCTAATTAAATCGAAACAAGATT
* *
311 CAGATACTCGAA
320 CAGATGCTCGTA
** * * * * *
323 AAAACAAATTGTTATATCGAATGTGGCTGGGATTTGGCTCGATAAATGTAGATATTTCAAG-AAG
1 AAAACAAATCCTTAAATCGAATGTGGCTGGGATATGGCTCGATGAATATAGATATTTC-AGTGAG
* * * *
387 TCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGCCTCGAAACGCGTTTTTAGCCAAAAGCCGT
65 TTTTTACGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGT
*
452 GATAGTTAATACACGATTTCGACTAAAATTTTGCAAAAACTGACCCGAAAAAATTTTTCCTCAAA
130 GATAGTAAATACACGATTTCGACTAAAATTTTGCAAAAACTGACCCG-AAAAATTTTTCCTC-AA
* *
517 TTTTTTGTCACAATACTAAAAAAAATATATAATTCAATGCCGAAAAA-ATTGAAGGATTTTTCAC
193 TTTTTTGCCACAATACTCAAAAAAATATATAATTCAATGCC-AAAAACATTGAAGGATTTTTCAC
* * * * * * *
581 GTTTCTAATATCGTTTTTTTATTTTTTTCCTGAATTTATTTTTGATTGAATCAAAACCAGATTCA
257 GCTTCTAATATCGTTTTTGTATTTTTTTCCTGAATTTATTTCTAATTAAATCGAAACAAGATTCA
* *
646 AATGTTCGTA
322 GATGCTCGTA
* * * *
656 AAAACAAATCTTTAAATCGAATGTGGCTGTGATATGGCTCGAAGAATATAGATATTTCAGTGACT
1 AAAACAAATCCTTAAATCGAATGTGGCTGGGATATGGCTCGATGAATATAGATATTTCAGTGAGT
* * * * *
721 TTTTACGCCAAAAATCATACAGAACTGAGCTGGGGACCCGGAACGCGTTTTTAGCCAAAAAACCG
66 TTTTACGCCAAAAATCATGCAAAACTGAGC-CGGGCCCCGAAACGCGTTTTTAGCC-AAAAACCG
* *
786 TGATAG-ATAACACACGATTTCGTCTAAAATTTTGCAAAAAAACTGACCCGAAAAATTTTTCCTC
129 TGATAGTA-AATACACGATTTCGACTAAAATTTTGC--AAAAACTGACCCGAAAAATTTTTCCTC
*
850 AATTTTTTTGCCACAATACTCATAAAAAATGTATAATTCAATGCCAAAAACATTGAAGGATTTTT
191 AA-TTTTTTGCCACAATACTCA-AAAAAATATATAATTCAATGCCAAAAACATTGAAGGATTTTT
* *
915 CACGCTTCTAATATTGTTTTTGTATTTTTTTCCTGAATTTATTTCTAATTAAATCCAAACAAGAT
254 CACGCTTCTAATATCGTTTTTGTATTTTTTTCCTGAATTTATTTCTAATTAAATCGAAACAAGAT
980 TCAGATGCTCGTA
319 TCAGATGCTCGTA
* * * * * * * *
993 AAAACAAATTCATAAATCGAATGTGGCTGTGATTTGCCTTGATGAATATAGATATTTTAGGGA-T
1 AAAACAAATCCTTAAATCGAATGTGGCTGGGATATGGCTCGATGAATATAGATATTTCAGTGAGT
* * * * * *
1057 TCTTTACGCCAAATATCATACAGAACTGAGCCAGAGCCCCGGAACTCGTTTTTAGCCAAAAACCG
66 T-TTTACGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGAAACGCGTTTTTAGCCAAAAACCG
* * *
1122 TGAT-GTAACATACACGATTTC-AGCTAAAATTTTGCAAAAACTGTCCTGAAAAATTGTTCCTCA
129 TGATAGTAA-ATACACGATTTCGA-CTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCA
* * *
1185 ATTTTATTGTCACAATACTCAAAAAATTATATAATTCAATACCGAAAAA-ATTGAAGGATTTTTC
192 ATTTT-TTGCCACAATACTCAAAAAAATATATAATTCAATGCC-AAAAACATTGAAGGATTTTTC
* *
1249 ATGCTTCTAATATCGTTTTTGTATTTTTTTTCCTGAATTTATTTTTAATTAAATCGAAACAAGAT
255 ACGCTTCTAATATCGTTTTTGTA-TTTTTTTCCTGAATTTATTTCTAATTAAATCGAAACAAGAT
*
1314 TCAGATGTTCGTA
319 TCAGATGCTCGTA
* *
1327 AAAACAAATCCTTAAATTGAATGTGGCTGGGATATGGCTCGATTAATATAGATATTTCAGTGAGT
1 AAAACAAATCCTTAAATCGAATGTGGCTGGGATATGGCTCGATGAATATAGATATTTCAGTGAGT
* *
1392 TTTTATGCCAAAAATCATGTAAAACTGAG
66 TTTTACGCCAAAAATCATGCAAAACTGAG
1421 TCTGTGTCCG
Statistics
Matches: 929, Mismatches: 132, Indels: 62
0.83 0.12 0.06
Matches are distributed among these distances:
320 5 0.01
321 9 0.01
322 118 0.13
323 4 0.00
326 1 0.00
331 10 0.01
332 57 0.06
333 194 0.21
334 194 0.21
335 44 0.05
336 74 0.08
337 219 0.24
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (331 bp):
AAAACAAATCCTTAAATCGAATGTGGCTGGGATATGGCTCGATGAATATAGATATTTCAGTGAGT
TTTTACGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTG
ATAGTAAATACACGATTTCGACTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAATTT
TTTGCCACAATACTCAAAAAAATATATAATTCAATGCCAAAAACATTGAAGGATTTTTCACGCTT
CTAATATCGTTTTTGTATTTTTTTCCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATG
CTCGTA
Done.