Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010801.1 Corchorus olitorius cultivar O-4 contig10833, 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: 1752
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Found at i:771 original size:154 final size:154
Alignment explanation
Indices: 348--1745 Score: 2227
Period size: 154 Copynumber: 9.1 Consensus size: 154
338 TTGGCGCATC
* *
348 AGTTAGGTCATAAACAATAGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
*
413 GAACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
66 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
478 GACTAATCTCACCAAAATGATTAT
131 GACTAATCTCACCAAAATGATTAT
* * *
502 AGTTAGGCCATAAACAATGG-AAGGAAAGCATTGAGGGTTGCCAAATCGAAGACGAATCAAAACA
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
*
566 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGTG
66 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
*
631 GACTAATCTCACCAAATTGATTAT
131 GACTAATCTCACCAAAATGATTAT
* *
655 AGTTAGGCCATAAACAATGGAAGGAAAAGCATTGAGGGTTGTCAAATCGAAGACGATTCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
** * * *
720 TCACTAATGGGCCCCGATAGGCTCAAAATATCAAGTGTTCCAAATGAGCTAAAAACTTCATAGTG
66 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
785 GACTAATCTCACCAAAATGATTAT
131 GACTAATCTCACCAAAATGATTAT
*
809 AGTTAGGCCATAAACAATGGAAA-AAAGAGCATAT-AGGGTTGCCAAATCGAAGACGAATCAAAA
1 AGTTAGGCCATAAACAATGGAAAGAAA-AGCAT-TGAGGGTTGCCAAATCGAAGACGATTCAAAA
* * * *
872 CGGAACTAATGGGCCCCAAAAGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAACACTTCACAG
64 CGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* *
937 TGAACTAATCTCAACAAAATGATTAT
129 TGGACTAATCTCACCAAAATGATTAT
* *
963 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGGCGATTCAAAA-G
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
* * *
1027 GTCACTAATGGGCCTCGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
66 G-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
*
1092 GGACTAATCTCACCAAAACGATTAT
130 GGACTAATCTCACCAAAATGATTAT
*
1117 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGAATCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
*
1182 GAACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
66 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
*
1247 GACTAATCTACAACAAAATGATTAT
131 GACTAATCT-CACCAAAATGATTAT
*
1272 AGTTAGGCCATAAACAATAGAAAGAAAAGCATTGAGGGTTGCCAAATCGAA-ATCGATTCAAAA-
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGA-CGATTCAAAAC
* * * *
1335 GGTCACTAATGGGCCACGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAG
65 GG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
1400 TGGACTAATCTCACCAAAATGATTAT
129 TGGACTAATCTCACCAAAATGATTAT
* * * *
1426 AGTTAGGCCACAAACAATGGAAAGAGAAGCATTGAGGGATGCCAAATC-AAGGACGATTCAAAAT
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAA-GACGATTCAAAAC
** * * *
1490 GTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCATAGT
65 GGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
1555 GGACTAATCTCACCAAAATGATTAT
130 GGACTAATCTCACCAAAATGATTAT
* **
1580 AGTTAGGCCATAAACAATGGAAAGAAAACCATTGAGGGTTGCCAAATCGAAGACGATTCTTAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
*
1645 GAACTAATAGGG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGT
66 GAACTAAT-GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
1709 GGACTAATCTCACCAAAATGATTAT
130 GGACTAATCTCACCAAAATGATTAT
1734 AGTTAGGCCATA
1 AGTTAGGCCATA
1746 TAGAATG
Statistics
Matches: 1143, Mismatches: 86, Indels: 30
0.91 0.07 0.02
Matches are distributed among these distances:
153 155 0.14
154 835 0.73
155 153 0.13
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (154 bp):
AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
GACTAATCTCACCAAAATGATTAT
Found at i:1520 original size:617 final size:613
Alignment explanation
Indices: 348--1745 Score: 2282
Period size: 617 Copynumber: 2.3 Consensus size: 613
338 TTGGCGCATC
* *
348 AGTTAGGTCATAAACAATAGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA-G
413 GAACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
65 GAACTAATGGG-CCCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
*
478 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGGAAAGCATTGAGGGTTGC
129 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGAAAAGCATTGAGGGTTGC
*
543 CAAATCGAAGACGAATCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
194 CAAATCGAAGACGAATCAAAACAGAACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* * *
608 AATGAGCTAAATACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAACAAT
259 AATGAGCTAAAAACTTCACAGTGGACTAATCTCAACAAAATGATTATAGTTAGGCCATAAACAAT
* * * *
673 GGAAGGAAAAGCATTGAGGGTTGTCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGAT
324 AGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACGAT
* *
738 AGGCTCAAAATATCAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATCTCACCAAAAT
389 AGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* *
803 GATTATAGTTAGGCCATAAACAATGGAAAAAAGAGCATATAGGGTTGCCAAATCGAAGACGAATC
454 GATTATAGTTAGGCCACAAACAATGGAAAAAAGAGCATATAGGGATGCCAAATCGAAGACGAATC
* * *
868 AAAACGGAACTAATGGGCCCCAAAAGGCCCAAAATAACAAGTTTTCCAAATGAGCTAAACACTTC
519 AAAACGGAACTAATGGGCCCCAAAAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTC
933 ACAGTGAACTAATCTCAACAAAATGATTAT
584 ACAGTGAACTAATCTCAACAAAATGATTAT
* *
963 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGGCGATTCAAAAGG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAGG
* *
1028 TCACTAATGGGCCTCGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
66 -AACTAATGGGCC-CGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
*
1093 GACTAATCTCACCAAAACGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG
129 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG-AAGAAAAGCATTGAGGGTTG
*
1158 CCAAATCGAAGACGAATCAAAACGGAACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
193 CCAAATCGAAGACGAATCAAAACAGAACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
1223 AAATGAGCTAAAAACTTCACAGTGGACTAATCTACAACAAAATGATTATAGTTAGGCCATAAACA
258 AAATGAGCTAAAAACTTCACAGTGGACTAATCT-CAACAAAATGATTATAGTTAGGCCATAAACA
*
1288 ATAGAAAGAAAAGCATTGAGGGTTGCCAAATCGAA-ATCGATTCAAAAGGTCACTAATGGGCCAC
322 ATAGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGA-CGATTCAAAACGTCACTAATGGGCCAC
*
1352 GATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGTGGACTAATCTCACCAA
386 GATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
1417 AATGATTATAGTTAGGCCACAAACAATGG-AAAGAGAAGCAT-TGAGGGATGCCAAATC-AAGGA
451 AATGATTATAGTTAGGCCACAAACAATGGAAAAAAG-AGCATAT-AGGGATGCCAAATCGAA-GA
* * ** * * *
1479 CGATTCAAAATGTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAACGAGCTAAA
513 CGAATCAAAACGGAACTAATGGGCCCCAAAAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAA
* * *
1544 AACTTCATAGTGGACTAATCTCACCAAAATGATTAT
578 AACTTCACAGTGAACTAATCTCAACAAAATGATTAT
* * *
1580 AGTTAGGCCATAAACAATGGAAAGAAAACCATTGAGGGTTGCCAAATCGAAGACGATTCTTAACG
1 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC-AAAAG
* *
1645 GAACTAATAGGGCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGTG
65 GAACTAAT-GGGCCCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
1710 GACTAATCTCACCAAAATGATTATAGTTAGGCCATA
129 GACTAATCTCACCAAAATGATTATAGTTAGGCCATA
1746 TAGAATG
Statistics
Matches: 727, Mismatches: 46, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
614 4 0.01
615 161 0.22
616 123 0.17
617 430 0.59
618 9 0.01
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (613 bp):
AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAGG
AACTAATGGGCCCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGAAAAGCATTGAGGGTTGCCA
AATCGAAGACGAATCAAAACAGAACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
TGAGCTAAAAACTTCACAGTGGACTAATCTCAACAAAATGATTATAGTTAGGCCATAAACAATAG
AAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACGATAG
GCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
TTATAGTTAGGCCACAAACAATGGAAAAAAGAGCATATAGGGATGCCAAATCGAAGACGAATCAA
AACGGAACTAATGGGCCCCAAAAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCAC
AGTGAACTAATCTCAACAAAATGATTAT
Done.