Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023097.1 Corchorus olitorius cultivar O-4 contig23130, 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: 24593
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:1238 original size:13 final size:12
Alignment explanation
Indices: 1220--1249 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1210 GATCAAGTGT
1220 AAAAATAAAAACG
1 AAAAATAAAAA-G
1233 AAAAATAAAAAG
1 AAAAATAAAAAG
1245 AAAAA
1 AAAAA
1250 CAACTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAATAAAAAG
Found at i:3949 original size:30 final size:29
Alignment explanation
Indices: 3913--3970 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
3903 ACAGAATGTT
3913 AGTTTTCTTTGTAATTTATTTGTTTGTGTG
1 AGTTTTCTTTGTAATTTATTT-TTTGTGTG
3943 AGTTTTCTTTGTAATTTATTTTTTGTGT
1 AGTTTTCTTTGTAATTTATTTTTTGTGT
3971 ATTTAGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.14, C:0.03, G:0.17, T:0.66
Consensus pattern (29 bp):
AGTTTTCTTTGTAATTTATTTTTTGTGTG
Found at i:4534 original size:12 final size:12
Alignment explanation
Indices: 4518--4550 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
4508 ATAATTACTG
4518 AAATTAAAAAAT
1 AAATTAAAAAAT
*
4530 GAATTAAAAAAT
1 AAATTAAAAAAT
4542 AAATTAAAA
1 AAATTAAAA
4551 CTTTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AAATTAAAAAAT
Found at i:4602 original size:13 final size:13
Alignment explanation
Indices: 4581--4623 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
4571 TTTACTCTTA
4581 TTTTCTTCTTTTC
1 TTTTCTTCTTTTC
*
4594 TTTTTTTCTTTTC
1 TTTTCTTCTTTTC
*
4607 TTCTTCCTCTTCTTC
1 TT-TTCTTCTT-TTC
4622 TT
1 TT
4624 CTCCCTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 14 0.56
14 6 0.24
15 5 0.20
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTCTTCTTTTC
Found at i:6334 original size:19 final size:18
Alignment explanation
Indices: 6295--6339 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
6285 TCACTTGTCT
*
6295 TTTTCTT-TTTCCTTTTT
1 TTTTCTTCTTTCCTTTTC
*
6312 TTTTCTTCTTTTCTTTCTC
1 TTTTCTTCTTTCCTTT-TC
6331 TTTTCTTCT
1 TTTTCTTCT
6340 CGAACCCCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 10 0.42
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTCTTTCCTTTTC
Found at i:13304 original size:15 final size:15
Alignment explanation
Indices: 13252--13307 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
13242 GTCGGGTCAA
*
13252 ATTTGGG-TCGGATTG
1 ATTTGGGTTAGGA-TG
* *
13267 ATTTGGGTTCAGGTTAA
1 ATTTGGGTT-AGGAT-G
13284 ATTTGGGTTAGGATG
1 ATTTGGGTTAGGATG
13299 ATTTGGGTT
1 ATTTGGGTT
13308 CGAGTCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 16 0.48
16 6 0.18
17 11 0.33
ACGTcount: A:0.18, C:0.04, G:0.36, T:0.43
Consensus pattern (15 bp):
ATTTGGGTTAGGATG
Found at i:13321 original size:32 final size:33
Alignment explanation
Indices: 13246--13341 Score: 99
Period size: 32 Copynumber: 3.0 Consensus size: 33
13236 AGTCAGGTCG
*
13246 GGTCAAATTTGGG-TCGGATTGATTTGGGTTC-A
1 GGTCAAATTTGGGTTAGGA-TGATTTGGGTTCGA
*
13278 GGTTAAATTTGGGTTAGGATGATTTGGGTTCGA
1 GGTCAAATTTGGGTTAGGATGATTTGGGTTCGA
* * * * *
13311 -GTCAATTTTGGGTCAGGTTAATTCGGGTTCG
1 GGTCAAATTTGGGTTAGGATGATTTGGGTTCG
13342 GGCTGGGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 49 0.91
33 5 0.09
ACGTcount: A:0.19, C:0.08, G:0.34, T:0.39
Consensus pattern (33 bp):
GGTCAAATTTGGGTTAGGATGATTTGGGTTCGA
Found at i:13333 original size:16 final size:17
Alignment explanation
Indices: 13268--13333 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
13258 GTCGGATTGA
*
13268 TTTGGGTTCAGGTTAAA
1 TTTGGGTTCAGGTTAAT
* *
13285 TTTGGGTT-AGGATGA-
1 TTTGGGTTCAGGTTAAT
*
13300 TTTGGGTTC-GAGTCAAT
1 TTTGGGTTCAG-GTTAAT
13317 TTTGGG-TCAGGTTAAT
1 TTTGGGTTCAGGTTAAT
13333 T
1 T
13334 CGGGTTCGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 9 0.23
16 15 0.38
17 15 0.38
ACGTcount: A:0.20, C:0.06, G:0.32, T:0.42
Consensus pattern (17 bp):
TTTGGGTTCAGGTTAAT
Found at i:13545 original size:22 final size:22
Alignment explanation
Indices: 13515--13560 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
13505 AATATTAGTA
*
13515 TTGAATTCGGGTTTTTTCAGGT
1 TTGAATTCGAGTTTTTTCAGGT
* *
13537 TTGAGTTCGAGTTTTTTCGGGT
1 TTGAATTCGAGTTTTTTCAGGT
13559 TT
1 TT
13561 CAGATTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.09, G:0.28, T:0.52
Consensus pattern (22 bp):
TTGAATTCGAGTTTTTTCAGGT
Found at i:14996 original size:57 final size:57
Alignment explanation
Indices: 14920--15033 Score: 147
Period size: 57 Copynumber: 2.0 Consensus size: 57
14910 GGGATCAAGG
* * **
14920 CATCTTCTCTTTTTTTTGGACTGGAGTACTCTCTTGATGTCAGTTCTGTGTTAATAT
1 CATCTTCTATCTTTTTTGGACTAAAGTACTCTCTTGATGTCAGTTCTGTGTTAATAT
* * ** *
14977 CATCTTCTATCTTTTTTGGACTAAAGTGCTTTCTTGATGTGGGTTTTGTGTTAATAT
1 CATCTTCTATCTTTTTTGGACTAAAGTACTCTCTTGATGTCAGTTCTGTGTTAATAT
15034 TACGAATGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (57 bp):
CATCTTCTATCTTTTTTGGACTAAAGTACTCTCTTGATGTCAGTTCTGTGTTAATAT
Found at i:16627 original size:11 final size:11
Alignment explanation
Indices: 16611--16667 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
16601 GTTCTGACTG
16611 TTTTTTTCTCT
1 TTTTTTTCTCT
*
16622 TTTTTTTCCCT
1 TTTTTTTCTCT
*
16633 TTTTTTTGGTCT
1 TTTTTTT-CTCT
16645 TCTTTGTTTC-CT
1 T-TTT-TTTCTCT
*
16657 TTTTCTTCTCT
1 TTTTTTTCTCT
16668 GATGTTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
10 3 0.08
11 22 0.59
12 6 0.16
13 3 0.08
14 3 0.08
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:16654 original size:25 final size:21
Alignment explanation
Indices: 16611--16667 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
16601 GTTCTGACTG
16611 TTTTTTTCTCTTTTTTTTCCCT
1 TTTTTTTCTCTTTTTTTT-CCT
*
16633 TTTTTTTGGTCTTCTTTGTTTCCT
1 TTTTTTT-CTCTT-TTT-TTTCCT
*
16657 TTTTCTTCTCT
1 TTTTTTTCTCT
16668 GATGTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.24
23 7 0.24
24 12 0.41
25 3 0.10
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTTTTCTCTTTTTTTTCCT
Found at i:21270 original size:11 final size:11
Alignment explanation
Indices: 21254--21279 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21244 AGATAATTTA
21254 TTTTCTTCTAG
1 TTTTCTTCTAG
21265 TTTTCTTCTAG
1 TTTTCTTCTAG
21276 TTTT
1 TTTT
21280 TTGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:22069 original size:15 final size:15
Alignment explanation
Indices: 22043--22080 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
22033 TTTGCTTTGT
22043 TTTCTAGTTTAATTGC
1 TTTCT-GTTTAATTGC
22059 TTTCTGTTTAATTGC
1 TTTCTGTTTAATTGC
22074 TTTCTGT
1 TTTCTGT
22081 CAATCTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTGTTTAATTGC
Found at i:22913 original size:13 final size:13
Alignment explanation
Indices: 22895--22921 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22885 TTTTTTTTTG
22895 AAAGTATTCACCT
1 AAAGTATTCACCT
22908 AAAGTATTCACCT
1 AAAGTATTCACCT
22921 A
1 A
22922 TTTCCTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
AAAGTATTCACCT
Done.