Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020470.1 Corchorus olitorius cultivar O-4 contig20503, 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: 49710
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8113 original size:20 final size:21
Alignment explanation
Indices: 8080--8118 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
8070 AAAGAAAAAG
* *
8080 AAAAAATTAGAAATTTTCAAC
1 AAAAAAATAGAAATCTTCAAC
8101 AAAAAAATA-AAATCTTCA
1 AAAAAAATAGAAATCTTCA
8119 CAAGAAAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.26
Consensus pattern (21 bp):
AAAAAAATAGAAATCTTCAAC
Found at i:9644 original size:12 final size:12
Alignment explanation
Indices: 9627--9661 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
9617 AAGGAGTCAT
9627 TTTCAAAAAGAG
1 TTTCAAAAAGAG
9639 TTTCAAAAAGAG
1 TTTCAAAAAGAG
9651 TTTCAAAAAGA
1 TTTCAAAAAGA
9662 AGGAATTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (12 bp):
TTTCAAAAAGAG
Found at i:19740 original size:21 final size:22
Alignment explanation
Indices: 19716--19759 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
19706 ATAAGATAAT
*
19716 TCCAAAGGAAGATTTT-GGAAA
1 TCCAAAAGAAGATTTTGGGAAA
19737 TCCAAAAGAAGATTTTGGGAAA
1 TCCAAAAGAAGATTTTGGGAAA
19759 T
1 T
19760 TAATAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (22 bp):
TCCAAAAGAAGATTTTGGGAAA
Found at i:21728 original size:16 final size:16
Alignment explanation
Indices: 21704--21743 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
21694 ACCCGAACCT
* *
21704 GAACCCGAAATTACTC
1 GAACCCGAAAATACCC
*
21720 GAGCCCGAAAATACCC
1 GAACCCGAAAATACCC
21736 GAACCCGA
1 GAACCCGA
21744 GGCAGCCCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.35, G:0.17, T:0.10
Consensus pattern (16 bp):
GAACCCGAAAATACCC
Found at i:21769 original size:17 final size:17
Alignment explanation
Indices: 21733--21790 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 17
21723 CCCGAAAATA
**
21733 CCCGAACCCGAGGC-AG
1 CCCGAACCCGACCCGAG
21749 CCCGAACCCGACCCGAG
1 CCCGAACCCGACCCGAG
*
21766 CCCGATCCCGACCCGAG
1 CCCGAACCCGACCCGAG
*
21783 CCTGAACC
1 CCCGAACC
21791 TGAAATAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
16 12 0.33
17 24 0.67
ACGTcount: A:0.22, C:0.50, G:0.24, T:0.03
Consensus pattern (17 bp):
CCCGAACCCGACCCGAG
Found at i:22000 original size:9 final size:9
Alignment explanation
Indices: 21986--22010 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21976 TGTGTGTATA
21986 TATATAACT
1 TATATAACT
21995 TATATAACT
1 TATATAACT
22004 TATATAA
1 TATATAA
22011 GTTAAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (9 bp):
TATATAACT
Found at i:22597 original size:13 final size:12
Alignment explanation
Indices: 22561--22607 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
22551 TCAATCTTTA
*
22561 TATATATTGATAA
1 TATATATT-ATAT
*
22574 TA-ATGTTATAT
1 TATATATTATAT
22585 TATATTATTATAT
1 TATA-TATTATAT
22598 TATATATTAT
1 TATATATTAT
22608 TAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:22837 original size:6 final size:6
Alignment explanation
Indices: 22826--22869 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
22816 GTCCGAAAAT
*
22826 ACCCGA ACCCGAA GTACCCGA ACCTGA ACCCGA ACCCGA ACCCG
1 ACCCGA ACCCG-A --ACCCGA ACCCGA ACCCGA ACCCGA ACCCG
22870 CCCGAGCCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 26 0.79
7 1 0.03
8 1 0.03
9 5 0.15
ACGTcount: A:0.32, C:0.45, G:0.18, T:0.05
Consensus pattern (6 bp):
ACCCGA
Found at i:22837 original size:16 final size:15
Alignment explanation
Indices: 22764--22865 Score: 59
Period size: 16 Copynumber: 6.7 Consensus size: 15
22754 ATACCTGAGA
22764 CCGAACCCGAAAATAC
1 CCGAACCCG-AAATAC
* *
22780 CCGATCCCGACATAAC
1 CCGAACCCGAAAT-AC
* **
22796 CCGAGCCCGACTTAAC
1 CCGAACCCGAAAT-AC
*
22812 CC-AAGTCCGAAAATAC
1 CCGAA-CCCG-AAATAC
*
22828 CCGAACCCGAAGTAC
1 CCGAACCCGAAATAC
*
22843 CCGAACCTG--A-AC
1 CCGAACCCGAAATAC
22855 CCGAACCCGAA
1 CCGAACCCGAA
22866 CCCGCCCGAG
Statistics
Matches: 67, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
12 10 0.15
15 17 0.25
16 36 0.54
17 4 0.06
ACGTcount: A:0.35, C:0.40, G:0.16, T:0.09
Consensus pattern (15 bp):
CCGAACCCGAAATAC
Found at i:22845 original size:15 final size:14
Alignment explanation
Indices: 22823--22865 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
22813 CAAGTCCGAA
22823 AATACCCGAACCCG
1 AATACCCGAACCCG
*
22837 AAGTACCCGAACCTG
1 AA-TACCCGAACCCG
22852 -A-ACCCGAACCCG
1 AATACCCGAACCCG
22864 AA
1 AA
22866 CCCGCCCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 10 0.40
13 1 0.04
14 3 0.12
15 11 0.44
ACGTcount: A:0.37, C:0.40, G:0.16, T:0.07
Consensus pattern (14 bp):
AATACCCGAACCCG
Found at i:43992 original size:32 final size:32
Alignment explanation
Indices: 43945--44122 Score: 259
Period size: 32 Copynumber: 5.5 Consensus size: 32
43935 AAAAAGCAGT
*
43945 TAAATATAGCGGCGTTTTGTTTTGAAGACGCCGC
1 TAAATA-AG-GGCGTTTTGTTCTGAAGACGCCGC
*
43979 TAAATAAGGGCGTTTTGTTCTTAAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTGAAGACGCCGC
* *
44011 TAAATAAGGGCGTTTTGTACTGTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTGAAGACGCCGC
* *
44043 TAAATAAAGGCGTTTTGTTCTGTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTGAAGACGCCGC
*
44075 TAAATAAGGGCGTTTTGTTCT-ATAGACGCTGC
1 TAAATAAGGGCGTTTTGTTCTGA-AGACGCCGC
44107 TAAATAAGGGCGTTTT
1 TAAATAAGGGCGTTTT
44123 CTATTCACAC
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
32 125 0.94
33 2 0.02
34 6 0.05
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTCTGAAGACGCCGC
Found at i:45671 original size:17 final size:17
Alignment explanation
Indices: 45646--45680 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
45636 TGCATAATGT
45646 TAATATACCAACAAGAA
1 TAATATACCAACAAGAA
*
45663 TAATGTACCAACAAGAA
1 TAATATACCAACAAGAA
45680 T
1 T
45681 GCACTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (17 bp):
TAATATACCAACAAGAA
Found at i:46321 original size:13 final size:13
Alignment explanation
Indices: 46303--46328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46293 ATGAGTTAGT
46303 AAATTATAAAAAA
1 AAATTATAAAAAA
46316 AAATTATAAAAAA
1 AAATTATAAAAAA
46329 TTGGAAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATTATAAAAAA
Found at i:46533 original size:27 final size:27
Alignment explanation
Indices: 46495--46569 Score: 150
Period size: 27 Copynumber: 2.8 Consensus size: 27
46485 CGACCCGAGG
46495 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
46522 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
46549 CGAAGTGGGAGGATCCACTGC
1 CGAAGTGGGAGGATCCACTGC
46570 GGCAACAGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.20, C:0.20, G:0.43, T:0.17
Consensus pattern (27 bp):
CGAAGTGGGAGGATCCACTGCTGGGGT
Done.