Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010953.1 Corchorus olitorius cultivar O-4 contig10985, 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, 894
Length: 1491
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Found at i:459 original size:21 final size:21
Alignment explanation
Indices: 435--610 Score: 259
Period size: 21 Copynumber: 8.4 Consensus size: 21
425 CTTAGGCAAT
*
435 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
456 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
477 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
498 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
519 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
*
540 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
561 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
582 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
603 TCCAATGA
1 TCCAATGA
611 ACTTCTAGCA
Statistics
Matches: 146, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.04
21 137 0.94
22 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:519 original size:63 final size:63
Alignment explanation
Indices: 435--614 Score: 301
Period size: 63 Copynumber: 2.9 Consensus size: 63
425 CTTAGGCAAT
* *
435 TCCAATGAGCTTGAAACCTTCTCCAATGATCTTGGAACCTT-CTCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAA-CTTGCTCCAATGAACTTGGAACCTTC
*
498 TCCAATGAACTTGGAACCTTCTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTTC
561 TCCAATGAGCTTGGAA-CTTGCTCCAATGAGCTTGGAACTTGCTCCAATGAACTT
1 TCCAATGAGCTTGGAACCTT-CTCCAATGAGCTTGGAACTTGCTCCAATGAACTT
615 CTAGCATCTT
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
62 6 0.05
63 105 0.95
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (63 bp):
TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACTTGCTCCAATGAACTTGGAACCTTC
Found at i:1002 original size:154 final size:154
Alignment explanation
Indices: 718--1491 Score: 1235
Period size: 154 Copynumber: 5.0 Consensus size: 154
708 GGCGCATCAC
*
718 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGAAAAGCATTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* *
783 TTTGCCAAATCGAAGATGATTCGAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
* *
848 TTCCAAATGAGCTAGAAACTTTAA
131 TTCCAAATGAGCTAAAAACTTCAA
*
872 AGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* * *
937 TTTGCCAAATCGAAGAAGATTCAATACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
* *
1002 TTACAAATGAGCTAAAAACTTCAC
131 TTCCAAATGAGCTAAAAACTTCAA
*
1026 GGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* * * *
1091 TTTGCCAAATCGAATACGATTCAAAACGTCACAAATGGACCCCGATAGGCCCAAAATAAAAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
*
1156 TTCCAAATGAGCTAGAAACTTCAA
131 TTCCAAATGAGCTAAAAACTTCAA
* *
1180 AGTTGACT-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATAGAAAGAAAAGCATTGAGG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* *
1244 TTTGCCAAATCGAAGAGGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
* *
1309 TTCCAAATTAGCTAAAAACTTCAC
131 TTCCAAATGAGCTAAAAACTTCAA
* *
1333 AGTGGACTAATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAACGAAAAAGCATTGAG
1 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAG
* ** * * *
1398 GGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGCACAAAATAAAAAGT
65 GTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGT
* *
1463 GTTCCAAATTAGCTAAAAACTTCAC
130 GTTCCAAATGAGCTAAAAACTTCAA
1488 AGTG
1 AGTG
Statistics
Matches: 572, Mismatches: 46, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
153 142 0.25
154 332 0.58
155 98 0.17
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
TTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
TTCCAAATGAGCTAAAAACTTCAA
Done.