Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023038.1 Corchorus olitorius cultivar O-4 contig23071, 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: 11323
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Found at i:7714 original size:22 final size:22
Alignment explanation
Indices: 7680--7739 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
7670 CATAAACCAA
*
7680 TTTAGGTTT-AGTTTTAGGTTT
1 TTTAGATTTAAGTTTTAGGTTT
* *
7701 TTTCGATTTAAGTTTCT-TGTTT
1 TTTAGATTTAAGTTT-TAGGTTT
*
7723 TTTAGATTTAAGATTTA
1 TTTAGATTTAAGTTTTA
7740 TTTTTAAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 8 0.26
22 22 0.71
23 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (22 bp):
TTTAGATTTAAGTTTTAGGTTT
Found at i:9365 original size:11 final size:10
Alignment explanation
Indices: 9349--9395 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
9339 AAACTCGTGT
9349 TTGAAGACTCA
1 TTGAAGA-TCA
*
9360 TTGAAGATAA
1 TTGAAGATCA
9370 TTTGAAGAT--
1 -TTGAAGATCA
9379 TTGAAGATCA
1 TTGAAGATCA
9389 TTGAAGA
1 TTGAAGA
9396 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:9384 original size:19 final size:18
Alignment explanation
Indices: 9360--9395 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9350 TGAAGACTCA
9360 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
9379 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
9396 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:10499 original size:13 final size:13
Alignment explanation
Indices: 10481--10513 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
10471 GATAAATAGG
10481 AAAATAAGTTAAA
1 AAAATAAGTTAAA
*
10494 AAAATAATTTAAA
1 AAAATAAGTTAAA
10507 AAAATAA
1 AAAATAA
10514 ATAGGTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AAAATAAGTTAAA
Found at i:10589 original size:15 final size:15
Alignment explanation
Indices: 10578--10764 Score: 116
Period size: 15 Copynumber: 12.5 Consensus size: 15
10568 AATAATAATA
*
10578 AATAAATAAATAGAT
1 AATAAATAAATAAAT
* *
10593 AATAACTAAATTAAT
1 AATAAATAAATAAAT
10608 AAATAAA-AAGATAAAT
1 -AATAAATAA-ATAAAT
* *
10624 AGTAAATAAATAGAT
1 AATAAATAAATAAAT
*
10639 AAT-AATTAA-AAAT
1 AATAAATAAATAAAT
*
10652 AAATAAAT-AGTAAAT
1 -AATAAATAAATAAAT
* *
10667 AGTAAATAAATAGAT
1 AATAAATAAATAAAT
* * *
10682 AAT-AGT-TACAAAT
1 AATAAATAAATAAAT
*
10695 AAATAAATAGATAAAT
1 -AATAAATAAATAAAT
** *
10711 GGTAAATAAATAGAT
1 AATAAATAAATAAAT
*
10726 AATAAAAAAATAAAT
1 AATAAATAAATAAAT
* *
10741 AGTAAATAAATAGAT
1 AATAAATAAATAAAT
10756 AAATAAATA
1 -AATAAATA
10765 GTGAATAAAT
Statistics
Matches: 127, Mismatches: 34, Indels: 21
0.70 0.19 0.12
Matches are distributed among these distances:
13 7 0.06
14 20 0.16
15 76 0.60
16 24 0.19
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (15 bp):
AATAAATAAATAAAT
Found at i:10596 original size:11 final size:11
Alignment explanation
Indices: 10526--10782 Score: 137
Period size: 11 Copynumber: 23.3 Consensus size: 11
10516 AGGTTTAGAG
10526 ATAAATAGATA
1 ATAAATAGATA
*
10537 CAGAGAATA-ATA
1 -ATA-AATAGATA
*
10549 GATAAATAGGTA
1 -ATAAATAGATA
10561 ACTAAGA-A-ATA
1 A-TAA-ATAGATA
*
10572 AT-AATAAATAA
1 ATAAATAGAT-A
10583 ATAAATAGATA
1 ATAAATAGATA
* *
10594 ATAACTAAATTA
1 ATAAATAGA-TA
* *
10606 ATAAATAAAAA
1 ATAAATAGATA
10617 GATAAATAG-TAA
1 -ATAAATAGAT-A
10629 ATAAATAGATA
1 ATAAATAGATA
* *
10640 ATAATTA-AAA
1 ATAAATAGATA
*
10650 ATAAATAAATA
1 ATAAATAGATA
*
10661 GTAAATAG-TAA
1 ATAAATAGAT-A
10672 ATAAATAGATA
1 ATAAATAGATA
** *
10683 ATAGTTACA-A
1 ATAAATAGATA
*
10693 ATAAATAAATA
1 ATAAATAGATA
*
10704 GATAAAT-GGTAA
1 -ATAAATAGAT-A
10716 ATAAATAGATA
1 ATAAATAGATA
10727 ATAAA-A-A-A
1 ATAAATAGATA
10735 ATAAATAG-TAA
1 ATAAATAGAT-A
10746 ATAAATAGATAA
1 ATAAATAGAT-A
10758 ATAAATAG-TGA
1 ATAAATAGAT-A
10769 ATAAATAGATA
1 ATAAATAGATA
10780 ATA
1 ATA
10783 GTTAAAAATG
Statistics
Matches: 191, Mismatches: 29, Indels: 51
0.70 0.11 0.19
Matches are distributed among these distances:
8 7 0.04
9 4 0.02
10 20 0.10
11 95 0.50
12 60 0.31
13 5 0.03
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (11 bp):
ATAAATAGATA
Found at i:10596 original size:19 final size:19
Alignment explanation
Indices: 10567--10775 Score: 127
Period size: 19 Copynumber: 11.1 Consensus size: 19
10557 GGTAACTAAG
10567 AAATA-ATAATAAATAAAT
1 AAATAGATAATAAATAAAT
*
10585 AAATAGATAATAACTAAAT
1 AAATAGATAATAAATAAAT
*
10604 TAAT--A-AATAAA-AAGAT
1 AAATAGATAATAAATAA-AT
*
10620 AAATAG-TAAATAAATAGAT
1 AAATAGAT-AATAAATAAAT
10639 -AATA-ATTAA-AAATAAAT
1 AAATAGA-TAATAAATAAAT
*
10656 AAATAG-TAA-ATAGTAAAT
1 AAATAGATAATA-AATAAAT
* *
10674 AAATAGATAATAGTTACAAAT
1 AAATAGATAATA--AATAAAT
*
10695 AAATAAATAGATAAATGGTAAAT
1 AAATAGATA-ATAAA---TAAAT
*
10718 AAATAGATAATAAAAAAAT
1 AAATAGATAATAAATAAAT
*
10737 AAATAG-TAAATAAATAGAT
1 AAATAGAT-AATAAATAAAT
* * *
10756 AAATAAATAGTGAATAAAT
1 AAATAGATAATAAATAAAT
10775 A
1 A
10776 GATAATAGTT
Statistics
Matches: 149, Mismatches: 21, Indels: 41
0.71 0.10 0.19
Matches are distributed among these distances:
15 2 0.01
16 10 0.07
17 12 0.08
18 28 0.19
19 60 0.40
20 4 0.03
21 13 0.09
22 8 0.05
23 12 0.08
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (19 bp):
AAATAGATAATAAATAAAT
Found at i:10731 original size:30 final size:31
Alignment explanation
Indices: 10524--10765 Score: 158
Period size: 31 Copynumber: 8.1 Consensus size: 31
10514 ATAGGTTTAG
* * *
10524 AGATAAATAGATACAGAGAATA-ATAGATAAAT
1 AGATAAATAG-TAAATA-AATAGATAAATAAAT
* *
10556 AGGTAACTAAG-AAAT-AATA-ATAAATAAAT
1 AGATAAAT-AGTAAATAAATAGATAAATAAAT
* * * * *
10585 AAATAGATAATAACTAAATTA-ATAAATAAAA
1 AGATAAATAGTAAATAAA-TAGATAAATAAAT
10616 AGATAAATAGTAAATAAATAGATAATAATTAAA-
1 AGATAAATAGTAAATAAATAGAT-A-AA-TAAAT
10649 A-ATAAATA--AATAGTAAATAG-TAAATAAAT
1 AGATAAATAGTAA-A-TAAATAGATAAATAAAT
*
10678 AGAT-AATAGT---TACA-A-ATAAATAAAT
1 AGATAAATAGTAAATAAATAGATAAATAAAT
* *
10703 AGATAAATGGTAAATAAATAGAT-AATAAAA
1 AGATAAATAGTAAATAAATAGATAAATAAAT
*
10733 AAATAAATAGTAAATAAATAGATAAATAAAT
1 AGATAAATAGTAAATAAATAGATAAATAAAT
10764 AG
1 AG
10766 TGAATAAATA
Statistics
Matches: 164, Mismatches: 24, Indels: 45
0.70 0.10 0.19
Matches are distributed among these distances:
25 14 0.09
26 8 0.05
28 5 0.03
29 30 0.18
30 37 0.23
31 40 0.24
32 21 0.13
33 5 0.03
34 4 0.02
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.25
Consensus pattern (31 bp):
AGATAAATAGTAAATAAATAGATAAATAAAT
Found at i:10775 original size:4 final size:4
Alignment explanation
Indices: 10574--10764 Score: 109
Period size: 4 Copynumber: 50.0 Consensus size: 4
10564 AAGAAATAAT
* * *
10574 AATA AATA AATA AATA GAT- AATA ACTA AATT AATA AATA AA-A AGATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA
* * * *
10621 AAT- AGTA AATA AATA GAT- AAT- AATT AA-A AATA AATA AAT- AGTA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * * *
10664 AAT- AGTA AATA AATA GAT- AATA GTTACA AATA AATA AATA GATA AAT-
1 AATA AATA AATA AATA AATA AATA --AATA AATA AATA AATA AATA AATA
** * * * *
10711 GGTA AATA AATA GAT- AATA AAAA AATA AAT- AGTA AATA AATA GATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
10757 AATA AATA
1 AATA AATA
10765 GTGAATAAAT
Statistics
Matches: 138, Mismatches: 35, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
3 24 0.17
4 110 0.80
5 2 0.01
6 2 0.01
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:10780 original size:19 final size:19
Alignment explanation
Indices: 10607--10784 Score: 116
Period size: 18 Copynumber: 10.1 Consensus size: 19
10597 ACTAAATTAA
*
10607 TAAATAAAAAGATAAATAG
1 TAAATAAATAGATAAATAG
*
10626 TAAATAAATAGAT-AATAA
1 TAAATAAATAGATAAATAG
* *
10644 TTAA-AAATAAATAAATAG
1 TAAATAAATAGATAAATAG
* *
10662 TAAAT-AGTAAATAAATAG
1 TAAATAAATAGATAAATAG
*
10680 ---AT-AATAGTTACAA-A-
1 TAAATAAATAGATA-AATAG
*
10694 TAAATAAATAGATAAATGG
1 TAAATAAATAGATAAATAG
*
10713 TAAATAAATAGAT-AATAAA
1 TAAATAAATAGATAAAT-AG
*
10732 AAAATAAATAG-T-AA-A-
1 TAAATAAATAGATAAATAG
* *
10747 TAAATAGATAAATAAATAG
1 TAAATAAATAGATAAATAG
*
10766 TGAATAAATAGAT-AATAG
1 TAAATAAATAGATAAATAG
10784 T
1 T
10785 TAAAAATGTA
Statistics
Matches: 124, Mismatches: 21, Indels: 29
0.71 0.12 0.17
Matches are distributed among these distances:
15 16 0.13
16 4 0.03
17 13 0.10
18 46 0.37
19 45 0.36
ACGTcount: A:0.63, C:0.01, G:0.10, T:0.26
Consensus pattern (19 bp):
TAAATAAATAGATAAATAG
Found at i:10852 original size:30 final size:30
Alignment explanation
Indices: 10695--10852 Score: 101
Period size: 30 Copynumber: 5.1 Consensus size: 30
10685 AGTTACAAAT
*
10695 AAATAAATAGATAAATGGTAAATAAATAGATAA
1 AAATAAA-A-ATAAATAGTAAATAAATA-ATAA
*
10728 TAA-AAAAATAAATAGTAAATAAATAGATAAA
1 AAATAAAAATAAATAGTAAATAAATA-AT-AA
** **
10759 TAAATAGTGAATAAATAG-ATAATAGTTAA-AA
1 -AAATA-AAAATAAATAGTA-AATAAATAATAA
** * *
10790 ATGTAAAAA-AAA-AGTAAAATAAAAAAGGAA
1 AAATAAAAATAAATAGT-AAATAAATAA-TAA
10820 AAATAAAAATAAATAGTAAATAAATAATAA
1 AAATAAAAATAAATAGTAAATAAATAATAA
10850 AAA
1 AAA
10853 AATCTTTTTG
Statistics
Matches: 96, Mismatches: 18, Indels: 25
0.69 0.13 0.18
Matches are distributed among these distances:
27 2 0.02
28 9 0.09
29 3 0.03
30 37 0.39
31 17 0.18
32 8 0.08
33 5 0.05
34 15 0.16
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.22
Consensus pattern (30 bp):
AAATAAAAATAAATAGTAAATAAATAATAA
Done.