Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011565.1 Corchorus olitorius cultivar O-4 contig11598, 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: 1696
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Found at i:388 original size:38 final size:40
Alignment explanation
Indices: 346--422 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
336 CTTTAGTTTG
*
346 TATGCTTGGGTCTTA-TCCTTT-TATGATGGTTTTTAATT
1 TATGCTTGGGCCTTACTCCTTTATATGATGGTTTTTAATT
*
384 TATGCTTGGGCCTTACTTCTTTTATATGATGGTTTTTAA
1 TATGCTTGGGCCTTAC-TCCTTTATATGATGGTTTTTAA
423 ATACATTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 14 0.41
40 5 0.15
41 15 0.44
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.53
Consensus pattern (40 bp):
TATGCTTGGGCCTTACTCCTTTATATGATGGTTTTTAATT
Found at i:1389 original size:154 final size:154
Alignment explanation
Indices: 613--1696 Score: 1474
Period size: 154 Copynumber: 7.1 Consensus size: 154
603 ATGCATTCCT
*
613 TAAACAATGTAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT-AGAAACGGAACTAATG
1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA-AAACGGAACTAATG
* * *
677 GGCCCCGATAGGCCC-AAATAACAAGTGTTCCAAATGAGCTAAGAACTTCATAGTAGACTAATCT
65 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* **
741 CATCAAAATGATTATAACTAGGCCA
130 CACCAAAATGATTATAGTTAGGCCA
* ***
766 TAAAAAATCTTTAAGAAAA-CACTTTGAGGTTT-CCAAATCGAAGACGATTCAAAACGGAACTAA
1 TAAACAAT-GGAAAGAAAAGCA--TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
* * * * * *
829 TGGGACCCGATAGGCCCAAAATAATAAGTGTTCCAAATGAGCTAAGAACTTAATAGTAGACTAAT
63 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* **
894 CTCATCAAAATGATTATAACTAGGCCA
128 CTCACCAAAATGATTATAGTTAGGCCA
* * *
921 TAAACAACT-TAAAGAAAAAC-TCTGAGGTAT-CCAAATCGAAGACGATTCAAAACGGAACTAAT
1 TAAACAA-TGGAAAGAAAAGCAT-TGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* *
983 GGGCCCCGATAGGCCCAAAATAACAAGTGTACCAAATTAGCTAAAAACTTCACAGTGGACTAATC
64 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
*
1048 TCACCAAAATGATTATAGTTAGTCCA
129 TCACCAAAATGATTATAGTTAGGCCA
* * *
1074 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACGATT-TAAACGGTACTAATGG
1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
* * * *
1138 GCCTCGAAAGGCCTAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTC
66 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
*
1203 ACCAAAATGATTATAGTTAGTCCA
131 ACCAAAATGATTATAGTTAGGCCA
* * *
1227 TAAACAATGGAAAGATAAGCATTGAGGTTTGCCAAATCAAAGACGTTTCAAAACGGAACTAATGG
1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
* * *
1292 GCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAATGGACTAATCTC
66 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
* * *
1357 ACCAAAATAAATATAGTTAGGGCA
131 ACCAAAATGATTATAGTTAGGCCA
* *
1381 TAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
** * * *
1446 TTCCCGAAAGGCACAAAACAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
66 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
*
1511 ACTAAAATGATTATAGTTAGGCCA
131 ACCAAAATGATTATAGTTAGGCCA
**
1535 TAAACAATGGAAAGAAAAGC-TT----TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGG
1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
* * * * *
1595 GCCCTGATAGGCCCAAAATAAGAAATGTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATCTA
66 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
* *
1660 AGCAAAATGATTATAAGATAGGCCA
131 ACCAAAATGATTAT-AGTTAGGCCA
1685 TAAACAATGGAA
1 TAAACAATGGAA
Statistics
Matches: 844, Mismatches: 74, Indels: 29
0.89 0.08 0.03
Matches are distributed among these distances:
149 102 0.12
150 21 0.02
152 2 0.00
153 296 0.35
154 333 0.39
155 89 0.11
156 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (154 bp):
TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
ACCAAAATGATTATAGTTAGGCCA
Found at i:1488 original size:461 final size:458
Alignment explanation
Indices: 613--1696 Score: 1463
Period size: 461 Copynumber: 2.4 Consensus size: 458
603 ATGCATTCCT
* * *
613 TAAACAATGTAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTAGAAACGGAACTAATGG
1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTAAAAACGGTACTAATGG
* * * *
678 GCCCCGATAGGCCCAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCATAGTAGACTAATCTCA
66 G-CCCGATAGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
* * *** *
743 TCAAAATGATTATA-ACTAGGCCATAAAAAATCTTTAAGAAAACACTTTGAGGTTTCCAAATCGA
130 CCAAAATGATTATAGA-TAGGCCATAAACAAT-GGAAAGAAAACAC-TTGAGGTTTCCAAATCAA
* *
807 AGACGATTCAAAACGGAACTAATGGGACCCGATAGGCCCAAAATAATAAGTGTTCCAAATGAGCT
192 AGACGATTCAAAACGGAACTAATGGGACCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* * * * * * *
872 AAGAACTTAATAGTAGACTAATCTCATCAAAATGATTATAACTAGGCCATAAACAACTTAAAGAA
257 AAAAACTTAACAATAGACTAATCTCACCAAAATAAATATAACTAGGCCATAAACAACTGAAAGAA
* *
937 AAACTCTGAGGTATCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAA
322 AAACTCTGAGGTATCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAA
* *
1002 ATAACAAGTGTACCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
387 ACAACAAGTGTACCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
*
1067 TAGTCCA
452 TAGGCCA
* *
1074 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACGATT-TAAACGGTACTAATGG
1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTAAAAACGGTACTAATGG
* *
1138 GCCTCGAAAGGCCTAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTC
66 GCC-CGATAGGCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
* * *
1203 ACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGATAAGCA-TTGAGGTTTGCCAAATCAA
129 ACCAAAATGATTATAGATAGGCCATAAACAATGGAAAGA-AAACACTTGAGGTTT-CCAAATCAA
* * *
1267 AGACGTTTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATTAGCT
192 AGACGATTCAAAACGGAACTAATGGGACCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* * ** *
1332 AAAAACTTCACAATGGACTAATCTCACCAAAATAAATATAGTTAGGGCATAAACAA-TGGAAAGA
257 AAAAACTTAACAATAGACTAATCTCACCAAAATAAATATAACTAGGCCATAAACAACT-GAAAGA
* **
1396 AAAGCATC-GAGGGT-TGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTTCCCGAAAGGCA
321 AAAAC-TCTGA-GGTAT-CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCA
* *
1459 CAAAACAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTA
383 CAAAACAACAAGTGTACCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
1524 TAGTTAGGCCA
448 TAGTTAGGCCA
*
1535 TAAACAATGGAAAGAAAAGC-TT----TTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATG
1 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTAAAAACGGT-ACTAATG
* * *
1594 GGCCCTGATAGGCCCAAAATAAGAAATGTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATCT
65 GGCCC-GATAGG-CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* *
1659 AAGCAAAATGATTATAAGATAGGCCATAAACAATGGAA
128 CACCAAAATGATTAT-AGATAGGCCATAAACAATGGAA
Statistics
Matches: 552, Mismatches: 57, Indels: 31
0.86 0.09 0.05
Matches are distributed among these distances:
456 23 0.04
457 79 0.14
458 22 0.04
459 12 0.02
460 154 0.28
461 262 0.47
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (458 bp):
TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTAAAAACGGTACTAATGG
GCCCGATAGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
CAAAATGATTATAGATAGGCCATAAACAATGGAAAGAAAACACTTGAGGTTTCCAAATCAAAGAC
GATTCAAAACGGAACTAATGGGACCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTAACAATAGACTAATCTCACCAAAATAAATATAACTAGGCCATAAACAACTGAAAGAAAAAC
TCTGAGGTATCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAACAA
CAAGTGTACCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
CCA
Done.