Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013853.1 Corchorus capsularis cultivar CVL-1 contig13874, 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: 9280
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Found at i:3897 original size:34 final size:36
Alignment explanation
Indices: 3858--3938 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 36
3848 AGAGGAAGTG
3858 ATCAGTA-G-AATTAAGAGTAAAAGTAAAAG-GAGTA
1 ATCAGTAGGTAATTAAGAGTAAAAGTAAAAGAG-GTA
3892 ATCAGTAAAATGGTAATTAAGAGTAAAAGTAAAAGAGGTA
1 ATCAGT---A-GGTAATTAAGAGTAAAAGTAAAAGAGGTA
3932 ATCAGTA
1 ATCAGTA
3939 AATCGGTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
34 6 0.15
37 2 0.05
39 1 0.03
40 30 0.75
41 1 0.03
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (36 bp):
ATCAGTAGGTAATTAAGAGTAAAAGTAAAAGAGGTA
Found at i:4028 original size:33 final size:33
Alignment explanation
Indices: 3985--4067 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
3975 AGTAATCGGT
3985 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
* *
4018 AAAGACTAAAAT-G-ACAAATGGTGATTAAATTC
1 AAAGAGTAAAATAGTA-AAATGGTAATTAAATTC
4050 AAAGAGTGAAAATAGTAA
1 AAAGAGT-AAAATAGTAA
4068 TTAAATTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 1 0.02
32 23 0.53
33 16 0.37
34 2 0.05
35 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (33 bp):
AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
Found at i:4070 original size:26 final size:26
Alignment explanation
Indices: 4041--4092 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
4031 ACAAATGGTG
4041 ATTAAATTCAA-AGAGTGAAAATAGTA
1 ATTAAATTCAAGAGAGT-AAAATAGTA
4067 ATTAAATTCAAGAGAGTAAAATAGTA
1 ATTAAATTCAAGAGAGTAAAATAGTA
4093 GTCAGTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.27
Consensus pattern (26 bp):
ATTAAATTCAAGAGAGTAAAATAGTA
Found at i:4127 original size:14 final size:14
Alignment explanation
Indices: 4089--4240 Score: 68
Period size: 14 Copynumber: 11.0 Consensus size: 14
4079 AGAGTAAAAT
*
4089 AGTAGTCAGTAAAG
1 AGTAATCAGTAAAG
* **
4103 AGGAAGAAGTAAAG
1 AGTAATCAGTAAAG
*
4117 AGTAATCAGTAAAA
1 AGTAATCAGTAAAG
* *
4131 ATGAAAAT-GGTAAA-
1 A-G-TAATCAGTAAAG
4145 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
*
4159 AGTAATCAGCGAAA-
1 AGTAATCAG-TAAAG
** *
4173 AGTAAAAATGGCAAAG
1 AGTAATCA--GTAAAG
4189 AGTAAT-A--AAAG
1 AGTAATCAGTAAAG
* *
4200 -GTATTCAGGCAAA-
1 AGTAATCA-GTAAAG
4213 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
*
4227 AGTGATCAGTAAAG
1 AGTAATCAGTAAAG
4241 GAAGAATAAT
Statistics
Matches: 103, Mismatches: 21, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
10 4 0.04
11 5 0.05
12 3 0.03
13 10 0.10
14 59 0.57
15 13 0.13
16 9 0.09
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:4127 original size:28 final size:27
Alignment explanation
Indices: 4089--4160 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
4079 AGAGTAAAAT
*
4089 AGTAGTCAGTAAAGAGGAAGAA-GTAAA
1 AGTAATCAGTAAAGAGGAA-AAGGTAAA
* *
4116 GAGTAATCAGTAAAAATGAAAATGGTAAA
1 -AGTAATCAGTAAAGAGGAAAA-GGTAAA
4145 AGTAATCAGTAAAGAG
1 AGTAATCAGTAAAGAG
4161 TAATCAGCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.05
28 30 0.81
29 5 0.14
ACGTcount: A:0.53, C:0.04, G:0.25, T:0.18
Consensus pattern (27 bp):
AGTAATCAGTAAAGAGGAAAAGGTAAA
Found at i:4163 original size:42 final size:44
Alignment explanation
Indices: 4110--4194 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 44
4100 AAGAGGAAGA
* * *
4110 AGTAAAGAGTAATCAG-TAAAAATGAAAATGGTAAA-AGTAATC
1 AGTAAAGAGTAATCAGCGAAAAATAAAAATGGCAAAGAGTAATC
*
4152 AGTAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGTAAT
1 AGTAAAGAGTAATCAGCGAAAAATAAAAATGGCAAAGAGTAAT
4195 AAAAGGTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 16 0.43
43 15 0.41
44 6 0.16
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (44 bp):
AGTAAAGAGTAATCAGCGAAAAATAAAAATGGCAAAGAGTAATC
Found at i:4287 original size:21 final size:22
Alignment explanation
Indices: 4262--4313 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
4252 AAGAGTAAAG
*
4262 GGTAATCAGT-AAGAGCAAGAT
1 GGTAATCAGTAAAGAGCAAAAT
*
4283 GGTAATCAGTAAAGAGTAAAAT
1 GGTAATCAGTAAAGAGCAAAAT
*
4305 AGTAATCAG
1 GGTAATCAG
4314 CAAAAAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.21
Consensus pattern (22 bp):
GGTAATCAGTAAAGAGCAAAAT
Found at i:4294 original size:35 final size:35
Alignment explanation
Indices: 4213--4301 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
4203 TTCAGGCAAA
* *
4213 AGTAATCAGTAAAGAGTGATCAGTAAAGGAAGAAT
1 AGTAATCAGTAAAGAGTAATCAGTAAAGCAAGAAT
* ** *
4248 AATAAAGAGTAAAGGGTAATCAGTAAGAGCAAG-AT
1 AGTAATCAGTAAAGAGTAATCAGTAA-AGCAAGAAT
*
4283 GGTAATCAGTAAAGAGTAA
1 AGTAATCAGTAAAGAGTAA
4302 AATAGTAATC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
35 37 0.88
36 5 0.12
ACGTcount: A:0.49, C:0.06, G:0.26, T:0.19
Consensus pattern (35 bp):
AGTAATCAGTAAAGAGTAATCAGTAAAGCAAGAAT
Found at i:4396 original size:14 final size:14
Alignment explanation
Indices: 4357--4406 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
4347 AATATTAAGA
4357 GTAAAAAGGTAAAATG
1 GTAAAAA-GTAAAA-G
4373 GTAAAAAGTAAAAG
1 GTAAAAAGTAAAAG
** *
4387 GTAATCAGTAAAGG
1 GTAAAAAGTAAAAG
4401 GTAAAA
1 GTAAAA
4407 TGGTAACTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 16 0.55
15 6 0.21
16 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.24, T:0.18
Consensus pattern (14 bp):
GTAAAAAGTAAAAG
Found at i:4411 original size:22 final size:22
Alignment explanation
Indices: 4373--4441 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
4363 AGGTAAAATG
4373 GTAAAAAGTAAAA-GGTAATCA
1 GTAAAAAGTAAAATGGTAATCA
**
4394 GTAAAGGGTAAAATGGTAA-CTA
1 GTAAAAAGTAAAATGGTAATC-A
* *
4416 GTAAAAAGTAAGATGGCAATCA
1 GTAAAAAGTAAAATGGTAATCA
4438 GTAA
1 GTAA
4442 GAAGAGGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 12 0.31
22 26 0.67
23 1 0.03
ACGTcount: A:0.51, C:0.06, G:0.23, T:0.20
Consensus pattern (22 bp):
GTAAAAAGTAAAATGGTAATCA
Done.