Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024424.1 Corchorus olitorius cultivar O-4 contig24457, 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: 1948
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Found at i:611 original size:4 final size:4
Alignment explanation
Indices: 583--784 Score: 66
Period size: 4 Copynumber: 50.8 Consensus size: 4
573 GACCAAAACG
* * * * *
583 ATTT TTTT A-TT ATTT ATTC A-CT ATTT ATTTT TTTT ATTT ATTT -TTA
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT
* * **
629 ACTATT ATCT ATTT ATTT A-CT ATTT ATCTT -TTT ATTT ATTT -TCA ACTATT
1 A-T-TT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT A-T-TT
* * * * *
679 ATCT ATTT ATTT A-CT ATTT ATCT ATTT ATTT ATTT -TTA ACTATT ATCT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-T-TT ATTT
* ** **
727 ATTT -TTT AATTT ATCTT -TTT ATTT ATTA ATTT AACT A-TT ACCT ATTT
1 ATTT ATTT -ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
774 ATTT ATTT ATT
1 ATTT ATTT ATT
785 ATTATCCTTT
Statistics
Matches: 141, Mismatches: 36, Indels: 42
0.64 0.16 0.19
Matches are distributed among these distances:
3 22 0.16
4 98 0.70
5 16 0.11
6 5 0.04
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (4 bp):
ATTT
Found at i:620 original size:9 final size:10
Alignment explanation
Indices: 606--716 Score: 62
Period size: 11 Copynumber: 10.4 Consensus size: 10
596 TTATTCACTA
606 TTTATTT-TT
1 TTTATTTATT
615 TTTATTTATT
1 TTTATTTATT
**
625 TTTAACTATT
1 TTTATTTATT
*
635 ATCTATTTATT
1 -TTTATTTATT
*
646 TACTATTTATCTT
1 T-TTATTTA--TT
659 TTTATTTATT
1 TTTATTTATT
* **
669 TTCAACTATT
1 TTTATTTATT
*
679 ATCTATTTATT
1 -TTTATTTATT
*
690 TACTATTTATCT
1 T-TTATTTAT-T
702 ATTTATTTATT
1 -TTTATTTATT
713 TTTA
1 TTTA
717 ACTATTATCT
Statistics
Matches: 79, Mismatches: 14, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
9 7 0.09
10 25 0.32
11 29 0.37
12 14 0.18
13 4 0.05
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATTTATT
Found at i:647 original size:19 final size:20
Alignment explanation
Indices: 625--710 Score: 90
Period size: 19 Copynumber: 4.2 Consensus size: 20
615 TTTATTTATT
625 TTTAACTA-TTATCTATTTA
1 TTTAACTATTTATCTATTTA
644 TTT-ACTATTTATCTTTTTATTTA
1 TTTAACTATTTATC----TATTTA
667 TTTTCAACTA-TTATCTATTTA
1 -TTT-AACTATTTATCTATTTA
688 TTT-ACTATTTATCTATTTA
1 TTTAACTATTTATCTATTTA
707 TTTA
1 TTTA
711 TTTTTAACTA
Statistics
Matches: 57, Mismatches: 0, Indels: 19
0.75 0.00 0.25
Matches are distributed among these distances:
18 8 0.14
19 22 0.39
20 3 0.05
21 6 0.11
23 6 0.11
24 3 0.05
25 5 0.09
26 4 0.07
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAACTATTTATCTATTTA
Found at i:676 original size:44 final size:44
Alignment explanation
Indices: 589--778 Score: 280
Period size: 44 Copynumber: 4.3 Consensus size: 44
579 AACGATTTTT
* *
589 TTAT-TATTTATTCACTATTTATTTTTTTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTA-TCTTTTTATTTATTTTTAACTA
*
633 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTCAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
*
677 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
721 TTATCTATTT-TTTA--ATTTATCTTTTTATTTATTAATTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATT--TTTAACTA
*
764 TTACCTATTTATTTA
1 TTATCTATTTATTTA
779 TTTATTATTA
Statistics
Matches: 135, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
41 18 0.13
43 21 0.16
44 80 0.59
45 16 0.12
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
Found at i:703 original size:8 final size:8
Alignment explanation
Indices: 617--843 Score: 72
Period size: 8 Copynumber: 28.1 Consensus size: 8
607 TTATTTTTTT
617 TATTTAT-
1 TATTTATC
*
624 T-TTTAAC
1 TATTTATC
631 TA-TTATC
1 TATTTATC
638 TATTTATTTAC
1 TATTTA--T-C
649 TATTTATC
1 TATTTATC
* *
657 TTTTTATT
1 TATTTATC
665 TATTT-TC
1 TATTTATC
*
672 AACTATTATC
1 TA-T-TTATC
682 TATTTATTTAC
1 TATTTA--T-C
693 TATTTATC
1 TATTTATC
*
701 TATTTATT
1 TATTTATC
*
709 TATTTTTAAC
1 TA--TTTATC
719 TA-TTATC
1 TATTTATC
*
726 TATTT-TT
1 TATTTATC
733 TAATTTATC
1 T-ATTTATC
742 --TTT-T-
1 TATTTATC
746 TATTTAT-
1 TATTTATC
*
753 TAATTTAAC
1 T-ATTTATC
*
762 TA-TTACC
1 TATTTATC
*
769 TATTTATT
1 TATTTATC
777 TATTTAT-
1 TATTTATC
784 TA-TTATCC
1 TATTTAT-C
792 T-TTTAGTTACC
1 TATTTA--T--C
803 TATTTATC
1 TATTTATC
811 TA-TTATTC
1 TATTTA-TC
* *
819 TCTGTATC
1 TATTTATC
827 TATTTATC
1 TATTTATC
835 TATTTATC
1 TATTTATC
843 T
1 T
844 CTATACCTAT
Statistics
Matches: 166, Mismatches: 22, Indels: 63
0.66 0.09 0.25
Matches are distributed among these distances:
5 1 0.01
6 14 0.08
7 31 0.19
8 77 0.46
9 9 0.05
10 13 0.08
11 17 0.10
12 4 0.02
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.63
Consensus pattern (8 bp):
TATTTATC
Found at i:832 original size:24 final size:24
Alignment explanation
Indices: 799--855 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
789 TCCTTTTAGT
*
799 TACCTATTTATCTA-TTATTCTCTG
1 TACCTATTTATCTATTTA-TCTCTA
*
823 TATCTATTTATCTATTTATCTCTA
1 TACCTATTTATCTATTTATCTCTA
847 TACCTATTT
1 TACCTATTT
856 TTTTTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.23, C:0.19, G:0.02, T:0.56
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCTCTA
Found at i:883 original size:16 final size:17
Alignment explanation
Indices: 851--885 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
841 TCTCTATACC
*
851 TATTTTTTTTATTATTT
1 TATTTATTTTATTATTT
868 TATTTATTTT-TTATTT
1 TATTTATTTTATTATTT
884 TA
1 TA
886 AACTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TATTTATTTTATTATTT
Done.