Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013263.1 Corchorus olitorius cultivar O-4 contig13296, 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: 25906
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:831 original size:15 final size:16
Alignment explanation
Indices: 798--837 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
788 TTATTTTGCT
798 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
814 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
829 TTGCTTTCT
1 TTGTTTTCT
838 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:6439 original size:19 final size:17
Alignment explanation
Indices: 6389--6430 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
6379 ATTTTCGTTA
6389 TTTTTCTTTTTATTTTT
1 TTTTTCTTTTTATTTTT
* *
6406 GTTTT-TGTTTATTTTT
1 TTTTTCTTTTTATTTTT
6422 TTTTTCTTT
1 TTTTTCTTT
6431 GTTACTTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.86
Consensus pattern (17 bp):
TTTTTCTTTTTATTTTT
Found at i:6439 original size:28 final size:29
Alignment explanation
Indices: 6386--6444 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
6376 TTCATTTTCG
* *
6386 TTATTTTTCTTTTTATTTTT-GTTTTTGT
1 TTATTTTTCTTTTTATTTTTACTTTTAGT
*
6414 TTATTTTT-TTTTTCTTTGTTACTTTTAGT
1 TTATTTTTCTTTTTATTT-TTACTTTTAGT
6443 TT
1 TT
6445 TTGAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 8 0.31
28 10 0.38
29 8 0.31
ACGTcount: A:0.08, C:0.05, G:0.07, T:0.80
Consensus pattern (29 bp):
TTATTTTTCTTTTTATTTTTACTTTTAGT
Found at i:6453 original size:33 final size:32
Alignment explanation
Indices: 6389--6454 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
6379 ATTTTCGTTA
* *
6389 TTTTTCTTTTTATTTTTGTTTTTGTTTATTTTT
1 TTTTTCTTTTTATTTTAGTTTTTG-TAATTTTT
6422 TTTTTCTTTGTTACTTTTAGTTTTTG-AATTTTT
1 TTTTTCTTT-TTA-TTTTAGTTTTTGTAATTTTT
6455 CGTTTAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 15 0.52
34 3 0.10
35 11 0.38
ACGTcount: A:0.09, C:0.05, G:0.08, T:0.79
Consensus pattern (32 bp):
TTTTTCTTTTTATTTTAGTTTTTGTAATTTTT
Found at i:11284 original size:28 final size:27
Alignment explanation
Indices: 11209--11280 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
11199 TGTGAACTTA
* * *
11209 AAATGACCAAAATTCCCCT-GAATGTGC
1 AAATGACAAAAATGCCCCTAG-ACGTGC
11236 AAATGACAAAAATGCCCCTAGACGTGC
1 AAATGACAAAAATGCCCCTAGACGTGC
*
11263 AAATGACTAAAATGCCCC
1 AAATGACAAAAATGCCCC
11281 CTAGGTGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.18
Consensus pattern (27 bp):
AAATGACAAAAATGCCCCTAGACGTGC
Found at i:18575 original size:22 final size:22
Alignment explanation
Indices: 18550--18600 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
18540 AAGAGGAAAT
18550 CACGGAGATTCCTGAGA-AA-AAG
1 CACGGAGATT--TGAGAGAATAAG
*
18572 CACGGAGCTTTGAGAGAATAAG
1 CACGGAGATTTGAGAGAATAAG
18594 CACGGAG
1 CACGGAG
18601 CTTGATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
21 2 0.08
22 19 0.73
ACGTcount: A:0.37, C:0.18, G:0.31, T:0.14
Consensus pattern (22 bp):
CACGGAGATTTGAGAGAATAAG
Found at i:20727 original size:15 final size:16
Alignment explanation
Indices: 20703--20736 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
20693 AGAAATTATA
20703 TTATATATATTTCTAT
1 TTATATATATTTCTAT
20719 TTATA-ATATTTCTAT
1 TTATATATATTTCTAT
20734 TTA
1 TTA
20737 GAAATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATATATTTCTAT
Found at i:20804 original size:21 final size:21
Alignment explanation
Indices: 20778--20843 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
20768 ATTAAGTTAC
20778 TAAATTATTATTATAATAATA
1 TAAATTATTATTATAATAATA
* *
20799 TAAATTTTTATTATAATATTAGA
1 TAAATTATTATTATAATA--ATA
*
20822 TATAATTA-TAATATAATAATA
1 TA-AATTATTATTATAATAATA
20843 T
1 T
20844 CTAATATAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 20 0.54
23 13 0.35
24 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAATTATTATTATAATAATA
Found at i:20828 original size:24 final size:24
Alignment explanation
Indices: 20782--20842 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
20772 AGTTACTAAA
*
20782 TTATTATTATAATAATATAAATTT
1 TTATTATAATAATAATATAAATTT
*
20806 TTATTATAATATTAGATAT-AA-TT
1 TTATTATAATAATA-ATATAAATTT
* *
20829 ATAATATAATAATA
1 TTATTATAATAATA
20843 TCTAATATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 13 0.42
24 14 0.45
25 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TTATTATAATAATAATATAAATTT
Found at i:20925 original size:22 final size:24
Alignment explanation
Indices: 20874--20927 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
20864 GAAATATATT
20874 AATATATTATATTAATAATATAGA
1 AATATATTATATTAATAATATAGA
*
20898 ATTATATTAATATT-AT-A-ATAGA
1 AATATATT-ATATTAATAATATAGA
20920 AATATATT
1 AATATATT
20928 CTAATAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 12 0.44
23 1 0.04
24 9 0.33
25 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
AATATATTATATTAATAATATAGA
Found at i:20926 original size:16 final size:16
Alignment explanation
Indices: 20907--20939 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20897 AATTATATTA
20907 ATATTATAATAGAAAT
1 ATATTATAATAGAAAT
*
20923 ATATTCTAATAGAAAT
1 ATATTATAATAGAAAT
20939 A
1 A
20940 GAAGTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (16 bp):
ATATTATAATAGAAAT
Found at i:21057 original size:18 final size:18
Alignment explanation
Indices: 21034--21069 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21024 ATAATAATTG
21034 ATAGTAAGAATTGATAAT
1 ATAGTAAGAATTGATAAT
21052 ATAGTAAGAATTGATAAT
1 ATAGTAAGAATTGATAAT
21070 CATTTGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
ATAGTAAGAATTGATAAT
Done.