Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011695.1 Corchorus olitorius cultivar O-4 contig11728, 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: 1945
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:336 original size:154 final size:154
Alignment explanation
Indices: 6--1945 Score: 2985
Period size: 154 Copynumber: 12.7 Consensus size: 154
1 ACGCC
* ** *
6 TTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACT-ATGGGCCTCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* *
70 CAAGTGATCCAAATGA-CTAAAAACCTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG-
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
*
133 CCATAAAAAATGGAAAGAAAAG-A
131 CCATAAACAATGGAAAGAAAAGCA
* *
156 CTTGAGGTTTGCCAAATAGAAGACGATTCAAAACGGAACTAATAGGCCCCGATAGGCCCAAAATA
1 -TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
221 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
65 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
286 TCCATAAACAATGGAAAGAAAAGCA
130 TCCATAAACAATGGAAAGAAAAGCA
* ** *
311 TTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGCCCCAAAAT-A
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* * * * *
375 CAAGTGATCCAAATGAGCTAAGAACTTCACAGTGTACTAATCTCACCAAATTGATTATAGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
*
440 CCATAAACAACGGAAAGAAAAGCA
131 CCATAAACAATGGAAAGAAAAGCA
**
464 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* *
529 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCAAAATGATTATAGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
*** * *
594 CCATAAACAACATAAAGAATAGCT
131 CCATAAACAATGGAAAGAAAAGCA
* * * * * * *
618 TTGAGGTTTGGCAAATTGAAGACTATTCAAAACGGAACAAATGGGCACAGATAGGCCAAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* * *
683 CAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAAAGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
748 CCATAAACAATGGAAAGAAAAGCA
131 CCATAAACAATGGAAAGAAAAGCA
* **
772 TTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACT-A---------ATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
827 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
* * *
892 CCATAAATATTGGAAAG-AAAGCT
131 CCATAAACAATGGAAAGAAAAGCA
* *
915 TTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCTAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* * *
980 CAAGTGTTCCAAATGAGCTAAAAACTTAACAATGGACTAATCTCATCAAAATGATTATAGTTAGT
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
*
1045 CCATAACCAATGGAAAGAAAAGCA
131 CCATAAACAATGGAAAGAAAAGCA
*
1069 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGGCCCCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
*
1134 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
*
1199 CCATAAACAATGGAAAGAAAAGCC
131 CCATAAACAATGGAAAGAAAAGCA
* * * ** * *
1223 TTGAGGCTTGCCAAATCGAAGAAGATTCAAAATGTCAGTAATGGGCCCCGATAGGACCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* * *
1288 CAAGTGATCCAAATGAGTTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
1353 CCATAAACAATGGAAAGAAAAGCA
131 CCATAAACAATGGAAAGAAAAGCA
* **
1377 TTGAGATTTGCCAAATCGAAGACGATTCAAAACGGAACTCTTGGGCCCCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* * *
1442 CAAGTGTTTCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAACTGATTATAGTTAGT
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
1507 CCATAAACAATGGAAAGAAAAGCA
131 CCATAAACAATGGAAAGAAAAGCA
* *
1531 TTGACGTTTGCCAAATTGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* *
1596 CAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCGCCAAAATGATTATAGTTAGT
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
* *
1661 CCATAAAAAATGGAAAGAAAAGCT
131 CCATAAACAATGGAAAGAAAAGCA
* * *
1685 TTGAGGTTTGCCAAATCGAAGAGGATTCAAAACGGTACTAATGGGCCCCGATTGGCCCAAAATAA
1 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
* * * *
1750 CAAGTGTTTCAAATGAGCTAAGAACTTCACAGTGCACTAATCTCATCAAAATGATTATAGTTAGT
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
*
1815 CCATAACCAATGGAAAGAAAAGCA
131 CCATAAACAATGGAAAGAAAAGCA
* *
1839 TTGAGGTTTAGCCAAATCGAAGACGATTCAAAACAGAACTAATAGGCCCCGATAGGCCCAAAATA
1 TTGAGGTTT-GCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
1904 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
65 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
Statistics
Matches: 1625, Mismatches: 147, Indels: 30
0.90 0.08 0.02
Matches are distributed among these distances:
143 40 0.02
144 92 0.06
151 35 0.02
152 38 0.02
153 282 0.17
154 1048 0.64
155 90 0.06
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGT
CCATAAACAATGGAAAGAAAAGCA
Found at i:1359 original size:605 final size:606
Alignment explanation
Indices: 3--1945 Score: 2912
Period size: 605 Copynumber: 3.2 Consensus size: 606
1 AC
* *
3 GCCTTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACT-ATGGGCCTCGATAGGCCCAAAA
1 GCCTTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTAACTAATGGGCCCCGATAGGCCCAAAA
*
67 TAACAAGTGATCCAAATGA-CTAAAAACCTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * *
131 AGCCATAAAAAATGGAAAGAAAAG-ACTTGAGGTTTGCCAAATAGAAGACGATTCAAAACGGAAC
131 AGCCATAAACAATGGAAAGAAAAGCA-TTGAGGTTTGCCAAATCGAAGACGATTCAAAACTG-AC
*
195 TAATAGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
194 -ACTA-------ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
260 AATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
251 AATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* ** * *
325 ATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGCCCCAAAAT-ACAAGTGATCCAAAT
316 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
* * * * *
389 GAGCTAAGAACTTCACAGTGTACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAACGGA
381 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGA
**
454 AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGG
446 AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGG
519 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCAAAATGAT
511 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCAAAATGAT
*** *
584 TATAGTTAGGCCATAAACAACATAAAGAATA
576 TATAGTTAGGCCATAAACAATGGAAAGAAAA
* * * * * * * * * *
615 GCTTTGAGGTTTGGCAAATTGAAGACTATTCAAAACGGAACAAATGGGCACAGATAGGCCAAAAA
1 GCCTTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTAACTAATGGGCCCCGATAGGCCCAAAA
*
680 TAACAAGTG-TCCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAAAGT
66 TAACAAGTGAT-CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
*
744 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA-TGTC
130 TA-GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACTGAC
808 ACTAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
194 ACTAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
* * * *
873 CAAAATGATTATAGTTAGTCCATAAATATTGGAAAG-AAAGCTTTGAGGTTTTCCAAATCGAAGA
259 CAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA
*
937 CGATTCAAAACGGAACTAATGGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAA
324 CGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* * * *
1002 AACTTAACAATGGACTAATCTCATCAAAATGATTATAGTTAGTCCATAACCAATGGAAAGAAAAG
389 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAG
*
1067 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGGCCCCGATAGGCCCAAAAT
454 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT
*
1132 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
519 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCAAAATGATTATAGTTA
1197 GGCCATAAACAATGGAAAGAAAA
584 GGCCATAAACAATGGAAAGAAAA
* * * * *
1220 GCCTTGAGGCTTGCCAAATCGAAGAAGATTCAAAATGTCAGTAATGGGCCCCGATAGGACCAAAA
1 GCCTTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTAACTAATGGGCCCCGATAGGCCCAAAA
* *
1285 TAACAAGTGATCCAAATGAGTTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
1350 AGTCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAAGACGATTCAAAACGGAAC
131 AG-CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACTG-AC
* * * *
1415 TCTTGGGCCCCGATAGGCCCAAAATAACAAGTGTTTCAAACGAGCTAAAAACTTCACAGTGGACT
194 AC-T-------AATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* *
1480 AATCTCACCAAACTGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGACGTTTGCCAA
251 AATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* *
1545 ATTGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCTAAAT
316 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
* *
1610 GAGCTAAAAACTTCACAGTGGACTAATCTCGCCAAAATGATTATAGTTAGTCCATAAAAAATGGA
381 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGA
* * * *
1675 AAGAAAAGCTTTGAGGTTTGCCAAATCGAAGAGGATTCAAAACGGTACTAATGGGCCCCGATTGG
446 AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGG
* * *
1740 CCCAAAATAACAAGTGTTTCAAATGAGCTAAGAACTTCACAGTGCACTAATCTCATCAAAATGAT
511 CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCAAAATGAT
* *
1805 TATAGTTAGTCCATAACCAATGGAAAGAAAA
576 TATAGTTAGGCCATAAACAATGGAAAGAAAA
* * *
1836 GCATTGAGGTTTAGCCAAATCGAAGACGATTCAAAACAG-AACTAATAGGCCCCGATAGGCCCAA
1 GCCTTGAGGTTT-GCCAAATCGAAGACGATTCAAAA-TGTAACTAATGGGCCCCGATAGGCCCAA
*
1900 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
64 AATAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
Statistics
Matches: 1202, Mismatches: 108, Indels: 37
0.89 0.08 0.03
Matches are distributed among these distances:
604 63 0.05
605 484 0.40
606 2 0.00
607 2 0.00
608 1 0.00
612 38 0.03
613 36 0.03
614 45 0.04
615 145 0.12
616 299 0.25
617 86 0.07
618 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (606 bp):
GCCTTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTAACTAATGGGCCCCGATAGGCCCAAAA
TAACAAGTGATCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
AGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACTGACAC
TAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
AAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCA
TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCAAAATGATTATAGTTAGG
CCATAAACAATGGAAAGAAAA
Done.