Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013361.1 Corchorus capsularis cultivar CVL-1 contig13382, 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: 51480
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:96 original size:14 final size:14
Alignment explanation
Indices: 77--107 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
67 TTCTTCTTCT
77 TTTTTTTTTTCATC
1 TTTTTTTTTTCATC
*
91 TTTTTTTTTTCTTC
1 TTTTTTTTTTCATC
105 TTT
1 TTT
108 AAAGGCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTTCATC
Found at i:7032 original size:6 final size:6
Alignment explanation
Indices: 7021--7083 Score: 101
Period size: 6 Copynumber: 10.3 Consensus size: 6
7011 AGTGGTGCAA
7021 TTTGTT TTTGTTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTTT
1 TTTGTT TTTG-TT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTG-TT
7071 TTTGTT TTT-TT TT
1 TTTGTT TTTGTT TT
7084 GGGGTAATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
5 4 0.07
6 39 0.71
7 12 0.22
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTGTT
Found at i:7053 original size:18 final size:19
Alignment explanation
Indices: 7021--7083 Score: 112
Period size: 18 Copynumber: 3.4 Consensus size: 19
7011 AGTGGTGCAA
7021 TTTGTTTTTGTTTTTTGTT
1 TTTGTTTTTGTTTTTTGTT
7040 TTTGTTTTTG-TTTTTGTT
1 TTTGTTTTTGTTTTTTGTT
7058 TTTGTTTTTGTTTTTTGTT
1 TTTGTTTTTGTTTTTTGTT
7077 TTT-TTTT
1 TTTGTTTT
7084 GGGGTAATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 22 0.51
19 21 0.49
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (19 bp):
TTTGTTTTTGTTTTTTGTT
Found at i:14761 original size:2 final size:2
Alignment explanation
Indices: 14754--14790 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
14744 GGCTAAAGGG
14754 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14791 GCTGCATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24456 original size:31 final size:30
Alignment explanation
Indices: 24378--24456 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
24368 AAATGGTTCC
* *
24378 AAATTGCAAGTTTAGGGGGAAAAACGTCCA
1 AAATTACAAGTTTAGGGGGAAAAACATCCA
*
24408 AAATTA-AAGTTTAGGGGGTAAAACAT-CA
1 AAATTACAAGTTTAGGGGGAAAAACATCCA
*
24436 AAATCATACAAGTTTGGGGGG
1 AAAT--TACAAGTTTAGGGGG
24457 GGGGGGAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.14
29 18 0.43
30 7 0.17
31 11 0.26
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.23
Consensus pattern (30 bp):
AAATTACAAGTTTAGGGGGAAAAACATCCA
Found at i:28138 original size:7 final size:7
Alignment explanation
Indices: 28126--28156 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
28116 AAAAATAATG
28126 TCAAGCC
1 TCAAGCC
28133 TCAAGCC
1 TCAAGCC
28140 TCAAGCC
1 TCAAGCC
28147 TCAAGCC
1 TCAAGCC
28154 TCA
1 TCA
28157 GATATGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.42, G:0.13, T:0.16
Consensus pattern (7 bp):
TCAAGCC
Found at i:32465 original size:12 final size:11
Alignment explanation
Indices: 32438--32482 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
32428 TTGAGTGAAT
32438 TATAATTAGTA
1 TATAATTAGTA
32449 T-TAATTAGTA
1 TATAATTAGTA
32459 TAATAATTAGTA
1 T-ATAATTAGTA
*
32471 T-TAATCAGTA
1 TATAATTAGTA
32481 TA
1 TA
32483 GATTATCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 19 0.63
11 1 0.03
12 10 0.33
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (11 bp):
TATAATTAGTA
Found at i:32466 original size:22 final size:22
Alignment explanation
Indices: 32439--32482 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
32429 TGAGTGAATT
*
32439 ATAATTAGTATTAATTAGTATA
1 ATAATTAGTATTAATCAGTATA
32461 ATAATTAGTATTAATCAGTATA
1 ATAATTAGTATTAATCAGTATA
32483 GATTATCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (22 bp):
ATAATTAGTATTAATCAGTATA
Found at i:38226 original size:75 final size:75
Alignment explanation
Indices: 38103--38251 Score: 298
Period size: 75 Copynumber: 2.0 Consensus size: 75
38093 CTATACTTTT
38103 AATTTTAATAAATTAATCCAGATAAATTCCATTTTCATCCAACAAAAACTTGATTTCTTTCATTT
1 AATTTTAATAAATTAATCCAGATAAATTCCATTTTCATCCAACAAAAACTTGATTTCTTTCATTT
38168 AAAAGATTTG
66 AAAAGATTTG
38178 AATTTTAATAAATTAATCCAGATAAATTCCATTTTCATCCAACAAAAACTTGATTTCTTTCATTT
1 AATTTTAATAAATTAATCCAGATAAATTCCATTTTCATCCAACAAAAACTTGATTTCTTTCATTT
38243 AAAAGATTT
66 AAAAGATTT
38252 TTAAATCAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (75 bp):
AATTTTAATAAATTAATCCAGATAAATTCCATTTTCATCCAACAAAAACTTGATTTCTTTCATTT
AAAAGATTTG
Found at i:38517 original size:12 final size:12
Alignment explanation
Indices: 38500--38524 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38490 GATCTGAAAG
38500 AAAAAAGAAAAA
1 AAAAAAGAAAAA
38512 AAAAAAGAAAAA
1 AAAAAAGAAAAA
38524 A
1 A
38525 GAGAGAGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:39377 original size:6 final size:6
Alignment explanation
Indices: 39368--39395 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39358 GCAAACCGGA
39368 AGAAAC AGAAAC AGAAAC AGAAAC AGAA
1 AGAAAC AGAAAC AGAAAC AGAAAC AGAA
39396 TCTTTGTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.14, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAC
Found at i:49150 original size:14 final size:14
Alignment explanation
Indices: 49131--49159 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
49121 GACAAATTAG
49131 TAGTATGCTTAAGA
1 TAGTATGCTTAAGA
49145 TAGTATGCTTAAGA
1 TAGTATGCTTAAGA
49159 T
1 T
49160 TTTAATCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (14 bp):
TAGTATGCTTAAGA
Done.