Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007407.1 Corchorus capsularis cultivar CVL-1 contig07428, 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: 6324
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1440 original size:22 final size:20
Alignment explanation
Indices: 1405--1445 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
1395 ACAAAGGCGT
1405 CTTTTTTTTCTTTTTTTTTA
1 CTTTTTTTTCTTTTTTTTTA
1425 CTTTTCTTCTTCTTTTTTTTT
1 CTTTT-TT-TTCTTTTTTTTT
1446 TTTTGAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
CTTTTTTTTCTTTTTTTTTA
Found at i:1448 original size:19 final size:17
Alignment explanation
Indices: 1406--1449 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
1396 CAAAGGCGTC
1406 TTTTTTTTCTTTTTTTT
1 TTTTTTTTCTTTTTTTT
*
1423 TACTTTTCTTCTTCTTTTTT
1 T--TTTTTTTCTT-TTTTTT
1443 TTTTTTT
1 TTTTTTT
1450 GAGATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 1 0.05
18 5 0.23
19 9 0.41
20 7 0.32
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTTCTTTTTTTT
Found at i:4123 original size:22 final size:22
Alignment explanation
Indices: 4080--4140 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
4070 CATCGAAGTA
* *
4080 AATTGAAAGCATTGACATATTGG
1 AATTGAAAGCATTGAAAAATT-G
4103 AATTGAAA-CATTGAAAAATTG
1 AATTGAAAGCATTGAAAAATTG
*
4124 AATTTG-AAGTATTGAAA
1 AA-TTGAAAGCATTGAAA
4141 TTGAAGCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 5 0.15
22 20 0.61
23 8 0.24
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (22 bp):
AATTGAAAGCATTGAAAAATTG
Found at i:4143 original size:36 final size:36
Alignment explanation
Indices: 4097--4167 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
4087 AGCATTGACA
* *
4097 TATTGGAATTGAAACATTGAAAAATTGAATTTGAAG
1 TATTGAAATTGAAACATTGAAAAATTGAAATTGAAG
* *
4133 TATTGAAATTGAAGCATTGAAATATTGAAATTGAA
1 TATTGAAATTGAAACATTGAAAAATTGAAATTGAA
4168 ACATTGGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (36 bp):
TATTGAAATTGAAACATTGAAAAATTGAAATTGAAG
Found at i:4151 original size:58 final size:59
Alignment explanation
Indices: 4079--4193 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 59
4069 TCATCGAAGT
* * * *
4079 AAATTGAAAGCATTGACATATTGGAATTGAAACATT-GAAAAATTGAATTTGAAGTATTG
1 AAATTGAAAGCATTGAAATATTGAAATTGAAACATTGGAAAAA-GGAAATTGAAGTATTG
4138 AAATTG-AAGCATTGAAATATTGAAATTGAAACATTGGAAAAAGGAAATTGAAGTAT
1 AAATTGAAAGCATTGAAATATTGAAATTGAAACATTGGAAAAAGGAAATTGAAGTAT
4194 CAAAGAAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 39 0.76
59 12 0.24
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (59 bp):
AAATTGAAAGCATTGAAATATTGAAATTGAAACATTGGAAAAAGGAAATTGAAGTATTG
Found at i:4152 original size:22 final size:22
Alignment explanation
Indices: 4127--4173 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4117 AAAATTGAAT
* *
4127 TTGAAGTATTGAAATTGAAGCA
1 TTGAAATATTGAAATTGAAACA
4149 TTGAAATATTGAAATTGAAACA
1 TTGAAATATTGAAATTGAAACA
4171 TTG
1 TTG
4174 GAAAAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (22 bp):
TTGAAATATTGAAATTGAAACA
Found at i:4165 original size:14 final size:14
Alignment explanation
Indices: 4090--4173 Score: 50
Period size: 14 Copynumber: 5.9 Consensus size: 14
4080 AATTGAAAGC
* *
4090 ATTGACATATTGGA
1 ATTGAAATATTGAA
*
4104 ATTGAAACATTGAAAA
1 ATTGAAATATTG--AA
4120 ATTG-AAT-TTGAA
1 ATTGAAATATTGAA
4132 GTATTG-AA-ATTGAA
1 --ATTGAAATATTGAA
4146 GCATTGAAATATTGAA
1 --ATTGAAATATTGAA
*
4162 ATTGAAACATTG
1 ATTGAAATATTG
4174 GAAAAAGGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.04
14 40 0.70
15 4 0.07
16 11 0.19
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (14 bp):
ATTGAAATATTGAA
Found at i:4184 original size:22 final size:22
Alignment explanation
Indices: 4137--4189 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
4127 TTGAAGTATT
* **
4137 GAAATTGAAGCATTGAAATATT
1 GAAATTGAAACATTGAAATAAG
4159 GAAATTGAAACATTGGAAA-AAG
1 GAAATTGAAACATT-GAAATAAG
4181 GAAATTGAA
1 GAAATTGAA
4190 GTATCAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.25
Consensus pattern (22 bp):
GAAATTGAAACATTGAAATAAG
Found at i:4262 original size:52 final size:51
Alignment explanation
Indices: 4225--4323 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 51
4215 TTGACATTTG
*
4225 GAATTTGAAGAATTGAAATTGAAGCATT-AAAATATTGACACATTGAAGGATC
1 GAATTTGAAGAATTGAAATTGAACCATTGAAAA-ATTGA-ACATTGAAGGATC
* *
4277 GAATTTGAGGAATTGAAATTGAACCATTGAAGAATTGAAACATTGAA
1 GAATTTGAAGAATTGAAATTGAACCATTGAAAAATTG-AACATTGAA
4324 ATTGAAACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
52 38 0.90
53 4 0.10
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.28
Consensus pattern (51 bp):
GAATTTGAAGAATTGAAATTGAACCATTGAAAAATTGAACATTGAAGGATC
Found at i:4305 original size:14 final size:14
Alignment explanation
Indices: 4288--4337 Score: 73
Period size: 14 Copynumber: 3.4 Consensus size: 14
4278 AATTTGAGGA
*
4288 ATTGAAATTGAACC
1 ATTGAAATTGAAAC
4302 ATTGAAGAATTGAAAC
1 ATTG-A-AATTGAAAC
4318 ATTGAAATTGAAAC
1 ATTGAAATTGAAAC
4332 ATTGAA
1 ATTGAA
4338 GGATTGAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
14 19 0.58
15 2 0.06
16 12 0.36
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (14 bp):
ATTGAAATTGAAAC
Found at i:4314 original size:16 final size:16
Alignment explanation
Indices: 4293--4345 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
4283 GAGGAATTGA
*
4293 AATTGAACCATTGAAG
1 AATTGAAACATTGAAG
4309 AATTGAAACATTG-A-
1 AATTGAAACATTGAAG
4323 AATTGAAACATTGAAG
1 AATTGAAACATTGAAG
*
4339 GATTGAA
1 AATTGAA
4346 TTTGGATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.39
15 2 0.06
16 18 0.55
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (16 bp):
AATTGAAACATTGAAG
Found at i:4343 original size:22 final size:21
Alignment explanation
Indices: 4235--4402 Score: 74
Period size: 22 Copynumber: 7.7 Consensus size: 21
4225 GAATTTGAAG
* *
4235 AATTG-AAATTGAAGCATTAAA
1 AATTGAAAATTGAAGGATT-GA
* *
4256 ATATTGACACATTGAAGGATCGA
1 A-ATTGA-AAATTGAAGGATTGA
* *
4279 ATTTGAGGAATTGAA--ATTGA
1 AATTGA-AAATTGAAGGATTGA
**
4299 ACCATTGAAGAATTGAAACATTGA
1 A--ATTGAA-AATTGAAGGATTGA
4323 AATTGAAACATTGAAGGATTGA
1 AATTGAAA-ATTGAAGGATTGA
* * **
4345 ATTTGGATAATTGAATAATTGA
1 AATT-GAAAATTGAAGGATTGA
* *
4367 AATTTGAAGCATCGAAGGATTGA
1 AA-TTGAA-AATTGAAGGATTGA
*
4390 ATTTG-AAATTGAA
1 AATTGAAAATTGAA
4403 ATTGAAGCGT
Statistics
Matches: 109, Mismatches: 26, Indels: 25
0.68 0.16 0.16
Matches are distributed among these distances:
20 10 0.09
21 3 0.03
22 62 0.57
23 18 0.17
24 16 0.15
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.30
Consensus pattern (21 bp):
AATTGAAAATTGAAGGATTGA
Found at i:4344 original size:52 final size:51
Alignment explanation
Indices: 4229--4382 Score: 118
Period size: 52 Copynumber: 3.0 Consensus size: 51
4219 CATTTGGAAT
* * * *
4229 TTGAAGAATTGAAATTGAAGCATT-AAAATATTGACACATTGAAGGATCGAAT
1 TTGAAGGATTGAAATTGAACCATTGAAAA-ATTGAAACATTGAA-GATCGAAA
* *
4281 TTG-AGGAATTGAAATTGAACCATTGAAGAATTGAAACATTGAA-ATTGAAACA
1 TTGAAGG-ATTGAAATTGAACCATTGAAAAATTGAAACATTGAAGATCG-AA-A
* * ** * *
4333 TTGAAGGATTGAATTTGGATAATTGAATAATTGAAA-TTTGAAGCATCGAA
1 TTGAAGGATTGAAATTGAACCATTGAAAAATTGAAACATTGAAG-ATCGAA
4383 GGATTGAATT
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
50 3 0.04
51 9 0.11
52 61 0.74
53 9 0.11
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (51 bp):
TTGAAGGATTGAAATTGAACCATTGAAAAATTGAAACATTGAAGATCGAAA
Found at i:4359 original size:30 final size:30
Alignment explanation
Indices: 4288--4345 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
4278 AATTTGAGGA
*
4288 ATTGAAATTGAACCATTGAAGAATTGAAAC
1 ATTGAAATTGAAACATTGAAGAATTGAAAC
*
4318 ATTGAAATTGAAACATTGAAGGATTGAA
1 ATTGAAATTGAAACATTGAAGAATTGAA
4346 TTTGGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (30 bp):
ATTGAAATTGAAACATTGAAGAATTGAAAC
Found at i:4473 original size:8 final size:8
Alignment explanation
Indices: 4460--4586 Score: 61
Period size: 8 Copynumber: 16.2 Consensus size: 8
4450 CGTTGAAGTA
4460 AATTGAAG
1 AATTGAAG
4468 AATTGAA-
1 AATTGAAG
*
4475 ACGTTG-AG
1 A-ATTGAAG
*
4483 TAATTGAAA
1 -AATTGAAG
4492 AATTGAAG
1 AATTGAAG
* *
4500 CAA-TAAAT
1 -AATTGAAG
*
4508 AATTAAAG
1 AATTGAAG
4516 AATTGAAG
1 AATTGAAG
*
4524 AAAT--A-
1 AATTGAAG
4529 AATTGAAG
1 AATTGAAG
*
4537 TATTGAAG
1 AATTGAAG
*
4545 AATTGAAT
1 AATTGAAG
*
4553 AATAGAAG
1 AATTGAAG
4561 -ATTCGAAG
1 AATT-GAAG
* *
4569 CATTGAAT
1 AATTGAAG
*
4577 AGTTGAAG
1 AATTGAAG
4585 AA
1 AA
4587 AGAGATTATT
Statistics
Matches: 87, Mismatches: 21, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 7 0.08
8 69 0.79
9 7 0.08
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.27
Consensus pattern (8 bp):
AATTGAAG
Found at i:4489 original size:24 final size:26
Alignment explanation
Indices: 4450--4498 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
4440 CACCCTGGGT
*
4450 CGTTGAAGTAAATTGAAGAATTGAAA
1 CGTTGAAGTAAATTGAAAAATTGAAA
4476 CGTTG-AGT-AATTGAAAAATTGAA
1 CGTTGAAGTAAATTGAAAAATTGAA
4499 GCAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 3 0.14
26 5 0.23
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (26 bp):
CGTTGAAGTAAATTGAAAAATTGAAA
Found at i:4510 original size:24 final size:24
Alignment explanation
Indices: 4483--4531 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
4473 AAACGTTGAG
*
4483 TAATTGAAA-AATTGAAGCAATAAA
1 TAATT-AAAGAATTGAAGAAATAAA
4507 TAATTAAAGAATTGAAGAAATAAA
1 TAATTAAAGAATTGAAGAAATAAA
4531 T
1 T
4532 TGAAGTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.27
Consensus pattern (24 bp):
TAATTAAAGAATTGAAGAAATAAA
Found at i:4584 original size:24 final size:23
Alignment explanation
Indices: 4529--4585 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
4519 TGAAGAAATA
4529 AATTGAAGTATTGAAGAATTGAAT
1 AATTGAAG-ATTGAAGAATTGAAT
* *
4553 AATAGAAGATTCGAAGCATTGAAT
1 AATTGAAGATT-GAAGAATTGAAT
*
4577 AGTTGAAGA
1 AATTGAAGA
4586 AAGAGATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.28
Consensus pattern (23 bp):
AATTGAAGATTGAAGAATTGAAT
Found at i:4627 original size:16 final size:16
Alignment explanation
Indices: 4606--4636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4596 TTTGATATAA
*
4606 ATTGAAGCATTGAAGG
1 ATTGAAGAATTGAAGG
4622 ATTGAAGAATTGAAG
1 ATTGAAGAATTGAAG
4637 CTAATTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (16 bp):
ATTGAAGAATTGAAGG
Done.