Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011544.1 Corchorus olitorius cultivar O-4 contig11577, 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: 2058
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Found at i:362 original size:154 final size:154
Alignment explanation
Indices: 1--1803 Score: 2519
Period size: 154 Copynumber: 11.7 Consensus size: 154
* * * * *
1 CCCAAAGTAACAAGTGTTCCAAATGAGTTAAAAACTTCAAAGTGGACTAATCTCACGATAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* *
66 TACAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGAG-TTG-CAAAGTCGAAGACGATTCA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-GTTTGCCAAA-TCGAAGACGATTCA
* * *
129 AAACGGAAATAGTGGG-CCCGATAGG
129 AAACGGAACTAATGGGCCCCGAAAGG
* * *
154 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTCGACTAATCTCACCAAAATTAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
** * ** * *
219 TATAGTTAGGCCATAATGAATGGAAAGAAAAGCATCGAGGGATGCCAAAACGAAGACTATT-AAT
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA-
* *
283 AACGAAACTAAAGGGCCCCGAAAGG
130 AACGGAACTAATGGGCCCCGAAAGG
* * *
308 CCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAACTAATCTCACCAAAATTAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* ** * * *
373 TATAGTTAGGCCATAAACAATGGAAAG-AAAGCATCGAGGGATGCCAAAACGAAGCCTATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
*
437 AC-GAACTAAAGGGCCCCGAAAGG
131 ACGGAACTAATGGGCCCCGAAAGG
*
460 CCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-CACAAATGA
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA-AAATGA
* * * ** *
524 TTAGAGTTAGGCCATAAACAATGGAAAGACAACCAACGAGGTTTCCCAAATCGAAGGACGATTCA
65 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA-GACGATTCA
* *
589 AAACAGAACTAATGGGCCTCGAAAGG
129 AAACGGAACTAATGGGCCCCGAAAGG
* * * *
615 GCCAAAATAACAAGTGTTCCAAATGTGTTAAAAACTTCACAGTGGACTAATCTCACAAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* * * ** *
680 TAGAGTTAGGCCATAAACAATGGAAAGACAATCAACGAGGTTTCCCAAATCGAAGACGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
* * *
745 ACAGAACTAATGGGGCTCGAAAGG
131 ACGGAACTAATGGGCCCCGAAAGG
* *
769 CCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCATAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* *
834 TATAGTTAGGCCATAAACAATTGGGAAAAAAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTC
66 TATAGTTAGGCCATAAACAA-T-GG-AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC
899 AAAACGGAACTAATGGGCCCCGAAAGG
128 AAAACGGAACTAATGGGCCCCGAAAGG
* *
926 CCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCACACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
991 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
*
1056 ACGGAACTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGAAAGG
* * *
1080 CCCAAAGTAACAAGTGTTCCAACTGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* * * *
1145 TATAGTTTGGTCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACCATTTAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
*
1210 ACGGAACTAATGGGCCCCGATAGG
131 ACGGAACTAATGGGCCCCGAAAGG
* * * * *
1234 CCCAAAGTAATAAGTTTTCCAACTGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* * * *
1299 TATAGTTAGGTCATGAACAATGGAAA-AAAAGCATTGAGGTTTGCCAAATCTAAGACCATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
* * * *
1363 ACGGAATTAATGAGCCCCGATAGA
131 ACGGAACTAATGGGCCCCGAAAGG
* * * *
1387 CCCAAAATAACAAGT-TCTCCGAATTAGCTAAAAACATCACAGTGGACTAATCTCACAAAAATGA
1 CCCAAAATAACAAGTGT-TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* *
1451 ATGTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
65 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
*
1516 AACGGAACTAATGGGCCCCGATAGG
130 AACGGAACTAATGGGCCCCGAAAGG
* * * * *
1541 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGAACTAATCTAAACAAAATGAG
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* * * *
1606 TATAGTTAGGCCATAAACAATTGAAAGAAAAGTATTGAGGTTTGCCAAATCGTAGACGATTCAAT
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
**
1671 ACGTCACTAATGGG-CCCGAAATAGG
131 ACGGAACTAATGGGCCCCG-AA-AGG
*
1696 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
*
1761 TATAGTTAGGCCATAAACGATGGAAAGAAAAGCATTGAGGTTT
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT
1804 ACAAGAGTTA
Statistics
Matches: 1502, Mismatches: 130, Indels: 34
0.90 0.08 0.02
Matches are distributed among these distances:
151 2 0.00
152 110 0.07
153 307 0.20
154 704 0.47
155 236 0.16
156 4 0.00
157 139 0.09
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
ACGGAACTAATGGGCCCCGAAAGG
Found at i:1522 original size:461 final size:461
Alignment explanation
Indices: 1--1803 Score: 2542
Period size: 461 Copynumber: 3.9 Consensus size: 461
* * * * *
1 CCCAAAGTAACAAGTGTTCCAAATGAGTTAAAAACTTCAAAGTGGACTAATCTCACGATAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGAT
* *
66 TACAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGAG-TTG-CAAAGTCGAAGACGATTCA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-GTTTGCCAAA-TCGAAGACGATTCA
* *
129 AAACGGAAATAGTGGG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
129 AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
* * * **
193 TAGTCGACTAATCTCACCAAAATTATTATAGTTAGGCCATAATGAATGGAAAGAAAAGCATCGAG
194 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAG
** * * * * *
258 GGATGCCAAAACGAAGACTATT-AATAACGAAACTAAAGGGCCCCGAAAGGCCAAAAATAACAAG
259 GTTTGCCAAATCGAAGACGATTCAA-AACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAG
* *
322 TGTTCCAAATGAGCTAAAAACTTCACAGTGAACTAATCTCACCAAAATTATTATAGTTAGGCCAT
323 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * ** * *
387 AAACAATGGAAAGAAAGCATCGAGGGATGCCAAAACGAAG-CCTATTCAAAAC-GAACTAAAGGG
388 AAACAATGGAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACC-ATTCAAAACGGAACTAATGGG
450 CCCCGAAAGG
452 CCCCGAAAGG
* *
460 CCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACACAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGAT
* * * ** *
525 TAGAGTTAGGCCATAAACAATGGAAAGACAACCAACGAGGTTTCCCAAATCGAAGGACGATTCAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA-GACGATTCAA
* * * * * *
590 AACAGAACTAATGGGCCTCGAAAGGGCCAAAATAACAAGTGTTCCAAATGTGTTAAAAACTTCAC
130 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* * * * *
655 AGTGGACTAATCTCACAAAAATGATTAGAGTTAGGCCATAAACAATGGAAAGACAATCAACGAGG
195 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGG
* * * *
720 TTTCCCAAATCGAAGACGATTCAAAACAGAACTAATGGGGCTCGAAAGGCCCAAAATAACAAGTG
260 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
* *
785 TTCCAAATGAGTTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
325 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
* *
850 ACAATTGGGAAAAAAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGGAACTAATGG
390 ACAA-T-GG--AAAAAAAGCATTGAGGTTTGCCAAATCGAAGACCATTCAAAACGGAACTAATGG
915 GCCCCGAAAGG
451 GCCCCGAAAGG
* * *
926 CCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCACACCAAAATGAT
1 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGAT
991 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
66 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
* * *
1056 ACGGAACTAATGGGCCCCGATAGGCCCAAAGTAACAAGTGTTCCAACTGAGCTAAAAAGTTCACA
131 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
* * *
1121 GTGGACTAATCTCACCAAAATGATTATAGTTTGGTCATAAACAATGGAAAGAAAAGCATTGAGGT
196 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGT
* * * * * *
1186 TTGCCAAATCGAAGACCATTTAAAACGGAACTAATGGGCCCCGATAGGCCCAAAGTAATAAGTTT
261 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGT
* * * *
1251 TCCAACTGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGTCATGAA
326 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * *
1316 CAATGGAAAAAAAGCATTGAGGTTTGCCAAATCTAAGACCATTCAAAACGGAATTAATGAGCCCC
391 CAATGGAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACCATTCAAAACGGAACTAATGGGCCCC
* *
1381 GATAGA
456 GAAAGG
* * *
1387 CCCAAAATAACAAGT-TCTCCGAATTAGCTAAAAACATCACAGTGGACTAATCTCACAAAAATGA
1 CCCAAAATAACAAGTGT-TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGA
* *
1451 ATGTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
65 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
*
1516 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAT
130 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* * * * * * *
1581 AGTGAACTAATCTAAACAAAATGAGTATAGTTAGGCCATAAACAATTGAAAGAAAAGTATTGAGG
195 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGG
* * **
1646 TTTGCCAAATCGTAGACGATTCAATACGTCACTAATGGG-CCCGAAATAGGCCCAAAATAACAAG
260 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG-AA-AGGCCCAAAATAACAAG
*
1710 TGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
323 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
*
1775 AAACGATGGAAAGAAAAGCATTGAGGTTT
388 AAACAATGGAAA-AAAAGCATTGAGGTTT
1804 ACAAGAGTTA
Statistics
Matches: 1190, Mismatches: 139, Indels: 26
0.88 0.10 0.02
Matches are distributed among these distances:
458 1 0.00
459 98 0.08
460 31 0.03
461 545 0.46
462 90 0.08
463 20 0.02
464 1 0.00
465 275 0.23
466 129 0.11
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (461 bp):
CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGAT
TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGT
TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGT
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
CAATGGAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACCATTCAAAACGGAACTAATGGGCCCC
GAAAGG
Done.