Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015588.1 Corchorus olitorius cultivar O-4 contig15621, 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: 37314
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1928 original size:18 final size:18
Alignment explanation
Indices: 1905--1945 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1895 GTTCCCCGTT
1905 TCTGCTATTCTTGATTCA
1 TCTGCTATTCTTGATTCA
1923 TCTGCTATTCTTGATTCA
1 TCTGCTATTCTTGATTCA
1941 TCTGC
1 TCTGC
1946 AAGTACAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (18 bp):
TCTGCTATTCTTGATTCA
Found at i:3876 original size:56 final size:56
Alignment explanation
Indices: 3785--3898 Score: 194
Period size: 56 Copynumber: 2.0 Consensus size: 56
3775 TAGTGATTAG
*
3785 AACTAAAACTTTATATGATGAAAAGATTTCTTGTTTGTAAGCTATAATAAAGTAAA
1 AACTAAAACTTTATATGATGAAAAGATTTCTTGTTTGGAAGCTATAATAAAGTAAA
*
3841 AACTAAATCTTTATATGATGAAAAGATTT-TATGTTTGGAAGCTATAATAAAGTAAA
1 AACTAAAACTTTATATGATGAAAAGATTTCT-TGTTTGGAAGCTATAATAAAGTAAA
3897 AA
1 AA
3899 AAATGCTGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 1 0.02
56 54 0.98
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (56 bp):
AACTAAAACTTTATATGATGAAAAGATTTCTTGTTTGGAAGCTATAATAAAGTAAA
Found at i:8515 original size:21 final size:24
Alignment explanation
Indices: 8486--8536 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
8476 TTTTGAACTC
8486 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
*
8509 -TTATTATTTGTTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
8532 ATTAT
1 ATTAT
8537 ATCTAAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 12 0.50
23 8 0.33
24 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:10163 original size:107 final size:104
Alignment explanation
Indices: 9933--10194 Score: 348
Period size: 107 Copynumber: 2.5 Consensus size: 104
9923 AATTTTTGTA
** *
9933 ACCCTTAAAA-TAAAATTTTAATTTTAATTTA-GACTAAACTTAGTGAATTAGTTATATATTTTA
1 ACCCTTAAAATTAAAA-TAAAATTTTAATTTAGGACTAAACTTAGTAAATTAGTTATATATTTTA
*
9996 TTTCTAAAATCCTATAACAATATTATTAATTATGAAATTT
65 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
** * * *
10036 GTCCTTAAAATAAAAATAAAATTTTAATTTAGGACTAAACTTAGTAAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATTAAAATAAAATTTTAATTTAGGACTAAACTTAGT-AAATTAGTTATATATTTTA
*
10101 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
* * *
10143 ACCCTTAAAATTAAAATAAAATTTTAATTTGGGGCTAAACTTTGTGAAATTA
1 ACCCTTAAAATTAAAATAAAATTTTAATTTAGGACTAAACTTAGT-AAATTA
10195 AGTCTAAACT
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
103 21 0.15
104 17 0.12
105 36 0.26
107 63 0.46
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (104 bp):
ACCCTTAAAATTAAAATAAAATTTTAATTTAGGACTAAACTTAGTAAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:12548 original size:51 final size:51
Alignment explanation
Indices: 12468--12572 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
12458 TTAATCCTCA
*
12468 ATTTGGCTTTGAAGTAATTTCCATTGTCACTAAAAATAATATATAGTATAT
1 ATTTGGCTTTGAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
12519 ATTTGGCTTTGAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
1 ATTTGGCTTTGAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
12570 ATT
1 ATT
12573 ACATAATACT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (51 bp):
ATTTGGCTTTGAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
Found at i:12698 original size:16 final size:16
Alignment explanation
Indices: 12679--12719 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
12669 TTTTAATAGC
*
12679 TATTTTAATTAAAAAA
1 TATTTTAATAAAAAAA
*
12695 TATTATAATAAAAAAA
1 TATTTTAATAAAAAAA
12711 TA-TTTAATA
1 TATTTTAATA
12720 TTGGTCTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATTTTAATAAAAAAA
Found at i:15403 original size:22 final size:22
Alignment explanation
Indices: 15376--15448 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
15366 AAATCTGGAG
15376 GGAGGAGTTCCTGTTGAAAAAA
1 GGAGGAGTTCCTGTTGAAAAAA
15398 GGAGGAGTTCCTGTTGAAAAAAA
1 GGAGGAGTTCCTGTTG-AAAAAA
** *
15421 AAAGGAGTTTCTGTTGAAAAAA
1 GGAGGAGTTCCTGTTGAAAAAA
15443 GGAGGA
1 GGAGGA
15449 AGTCAGCGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
22 26 0.58
23 19 0.42
ACGTcount: A:0.40, C:0.07, G:0.32, T:0.22
Consensus pattern (22 bp):
GGAGGAGTTCCTGTTGAAAAAA
Found at i:15426 original size:23 final size:23
Alignment explanation
Indices: 15378--15442 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
15368 ATCTGGAGGG
**
15378 AGGAGTTCCTGTTG-AAAAAAGG
1 AGGAGTTCCTGTTGAAAAAAAAA
15400 AGGAGTTCCTGTTGAAAAAAAAA
1 AGGAGTTCCTGTTGAAAAAAAAA
*
15423 AGGAGTTTCTGTTGAAAAAA
1 AGGAGTTCCTGTTGAAAAAA
15443 GGAGGAAGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 14 0.36
23 25 0.64
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.25
Consensus pattern (23 bp):
AGGAGTTCCTGTTGAAAAAAAAA
Found at i:21278 original size:25 final size:25
Alignment explanation
Indices: 21250--21307 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
21240 TAAGCGGTTT
21250 TTAAACGGATTTGGATAATGGATAA
1 TTAAACGGATTTGGATAATGGATAA
*
21275 TTAAACGGATTTGGATAGTGGATAA
1 TTAAACGGATTTGGATAATGGATAA
21300 TTAAACGG
1 TTAAACGG
21308 TTTCAGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (25 bp):
TTAAACGGATTTGGATAATGGATAA
Found at i:23302 original size:14 final size:14
Alignment explanation
Indices: 23283--23310 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23273 GTTGAAACAA
23283 CATTTAATAAAATT
1 CATTTAATAAAATT
23297 CATTTAATAAAATT
1 CATTTAATAAAATT
23311 TCTGAAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
CATTTAATAAAATT
Found at i:25766 original size:2 final size:2
Alignment explanation
Indices: 25759--25795 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25749 GTATACATAC
25759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25796 CTACGTCCCA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26894 original size:18 final size:17
Alignment explanation
Indices: 26867--26900 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
26857 CATTTTCAAC
26867 TTTAATATATATTTATA
1 TTTAATATATATTTATA
26884 TTTATATATATATTTAT
1 TTTA-ATATATATTTAT
26901 TTATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATATATATTTATA
Found at i:27253 original size:35 final size:35
Alignment explanation
Indices: 27213--27282 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
27203 ATATTTTATG
*
27213 AGAAAAAGTAACACTATGCATATATATTTAGTTTT
1 AGAAAAAGTAACAATATGCATATATATTTAGTTTT
27248 AGAAAAAGTAACAATATGCATATATATTTAGTTTT
1 AGAAAAAGTAACAATATGCATATATATTTAGTTTT
27283 TGAACTCCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (35 bp):
AGAAAAAGTAACAATATGCATATATATTTAGTTTT
Found at i:27847 original size:14 final size:14
Alignment explanation
Indices: 27828--27856 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27818 TCGAGGCTAA
27828 ATCACACATATAAT
1 ATCACACATATAAT
27842 ATCACACATATAAT
1 ATCACACATATAAT
27856 A
1 A
27857 ATATATTTAT
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:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (14 bp):
ATCACACATATAAT
Found at i:29894 original size:4 final size:4
Alignment explanation
Indices: 29877--29939 Score: 75
Period size: 4 Copynumber: 17.2 Consensus size: 4
29867 TTTTTTTTTT
*
29877 TTTC TTT- TTAC TTTC TTTC TTTC TTTC TTTC TTTC -TTC -TTC -TTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
29921 -TTC -TTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC T
29940 GCTGCTGCTG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 17 0.31
4 38 0.69
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:31343 original size:31 final size:31
Alignment explanation
Indices: 31274--31375 Score: 136
Period size: 31 Copynumber: 3.4 Consensus size: 31
31264 TTACACATGG
31274 CACTTTTTGGTACATGTGGCATGCCAC--GT
1 CACTTTTTGGTACATGTGGCATGCCACGTGT
*
31303 CACTTTTTGGTACATGTGGCATGACACGTGT
1 CACTTTTTGGTACATGTGGCATGCCACGTGT
* * * * *
31334 CACTCTTTGGCACATATGGCGTGCCATGTGT
1 CACTTTTTGGTACATGTGGCATGCCACGTGT
31365 CACTTTTTGGT
1 CACTTTTTGGT
31376 GATTTTTGGT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 26 0.42
31 36 0.58
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.36
Consensus pattern (31 bp):
CACTTTTTGGTACATGTGGCATGCCACGTGT
Found at i:37288 original size:2 final size:2
Alignment explanation
Indices: 37281--37310 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
37271 ATTTCCTTTA
37281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37311 GTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.