Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011003.1 Corchorus capsularis cultivar CVL-1 contig11024, 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: 5945
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2646 original size:38 final size:39
Alignment explanation
Indices: 2595--2669 Score: 134
Period size: 38 Copynumber: 1.9 Consensus size: 39
2585 TTGGAATATT
2595 AGAGAGTCATGGTTTTCAAAAATGCTTT-TTCAAAAAGA
1 AGAGAGTCATGGTTTTCAAAAATGCTTTCTTCAAAAAGA
*
2633 AGAGAGTCATGGTTTTCAAAAATGTTTTCTTCAAAAA
1 AGAGAGTCATGGTTTTCAAAAATGCTTTCTTCAAAAA
2670 ATGTTTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 27 0.77
39 8 0.23
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (39 bp):
AGAGAGTCATGGTTTTCAAAAATGCTTTCTTCAAAAAGA
Found at i:2710 original size:3 final size:3
Alignment explanation
Indices: 2704--2736 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2694 TTTTCAAAAA
2704 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2737 TTTTGAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4411 original size:24 final size:24
Alignment explanation
Indices: 4384--4430 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4374 ATAATCTCTT
4384 TCTTCAACTT-TTCAATGCTTCAAA
1 TCTTCAA-TTATTCAATGCTTCAAA
* *
4408 TCTTCCATTATTCAATTCTTCAA
1 TCTTCAATTATTCAATGCTTCAA
4431 TTCACTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.28, C:0.26, G:0.02, T:0.45
Consensus pattern (24 bp):
TCTTCAATTATTCAATGCTTCAAA
Found at i:4429 original size:8 final size:8
Alignment explanation
Indices: 4383--4433 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
4373 AATAATCTCT
4383 TTCTTCAA
1 TTCTTCAA
4391 CTT-TTCAA
1 -TTCTTCAA
*
4399 TGCTTCAA
1 TTCTTCAA
* *
4407 ATCTTCCA
1 TTCTTCAA
*
4415 TTATTCAA
1 TTCTTCAA
4423 TTCTTCAA
1 TTCTTCAA
4431 TTC
1 TTC
4434 ACTTCAATGA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
7 1 0.03
8 30 0.91
9 2 0.06
ACGTcount: A:0.25, C:0.25, G:0.02, T:0.47
Consensus pattern (8 bp):
TTCTTCAA
Found at i:4553 original size:8 final size:8
Alignment explanation
Indices: 4542--4612 Score: 57
Period size: 8 Copynumber: 9.8 Consensus size: 8
4532 TCCTCAAGTT
4542 TTCAATGC
1 TTCAATGC
4550 TTCAA--C
1 TTCAATGC
*
4556 TTCAATGT
1 TTCAATGC
4564 TTCAAT--
1 TTCAATGC
*
4570 TTCAATTC
1 TTCAATGC
4578 -TCAAT--
1 TTCAATGC
*
4583 TTCAATTC
1 TTCAATGC
4591 TTCAATGC
1 TTCAATGC
*
4599 TTCAATGT
1 TTCAATGC
4607 TTCAAT
1 TTCAAT
4613 TTCCATTCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
6 17 0.32
7 5 0.09
8 31 0.58
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (8 bp):
TTCAATGC
Found at i:4561 original size:14 final size:14
Alignment explanation
Indices: 4542--4611 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
4532 TCCTCAAGTT
4542 TTCAATGCTTCAAC
1 TTCAATGCTTCAAC
* *
4556 TTCAATGTTTCAAT
1 TTCAATGCTTCAAC
* *
4570 TTCAATTC-TCAAT
1 TTCAATGCTTCAAC
*
4583 TTCAATTCTTCAATGC
1 TTCAATGCTTCAA--C
*
4599 TTCAATGTTTCAA
1 TTCAATGCTTCAA
4612 TTTCCATTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
13 13 0.28
14 22 0.48
16 11 0.24
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (14 bp):
TTCAATGCTTCAAC
Found at i:4795 original size:14 final size:14
Alignment explanation
Indices: 4769--4815 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
4759 ACTTCTAGTC
*
4769 ATTCTTCAGTTTCA
1 ATTCTTCAATTTCA
4783 A-TCTTTCAATTTCA
1 ATTC-TTCAATTTCA
*
4797 ATTCTTCAAATTCA
1 ATTCTTCAATTTCA
4811 ATTCT
1 ATTCT
4816 ACAGTGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 2 0.07
14 25 0.86
15 2 0.07
ACGTcount: A:0.28, C:0.21, G:0.02, T:0.49
Consensus pattern (14 bp):
ATTCTTCAATTTCA
Found at i:5056 original size:22 final size:21
Alignment explanation
Indices: 5001--5083 Score: 105
Period size: 22 Copynumber: 3.9 Consensus size: 21
4991 CAATTTCAAA
5001 TTCAATTTCAATTCTTCAA-C
1 TTCAATTTCAATTCTTCAAGC
* *
5021 CTCAGTTTCAATTCTTCAATGC
1 TTCAATTTCAATTCTTCAA-GC
* *
5043 TTCAATTTCGATTCTTCAGCGC
1 TTCAATTTCAATTCTTCA-AGC
5065 TTCAATTTCAATTCTTCAA
1 TTCAATTTCAATTCTTCAA
5084 ATTTCAAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.33
22 35 0.67
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.43
Consensus pattern (21 bp):
TTCAATTTCAATTCTTCAAGC
Found at i:5143 original size:16 final size:16
Alignment explanation
Indices: 5122--5156 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5112 AATGTTTTAA
*
5122 TTTCAATTTTTCAATG
1 TTTCAATATTTCAATG
5138 TTTCAATATTTCAATG
1 TTTCAATATTTCAATG
5154 TTT
1 TTT
5157 TAGATCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTCAATATTTCAATG
Found at i:5167 original size:38 final size:38
Alignment explanation
Indices: 5095--5173 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
5085 TTTCAAATGC
* * *
5095 CAATGCTTCAATCCTTCAATGTTTTAATTTCAATTTTT
1 CAATGCTTCAATACTTCAATGTTTTAATTCCAATTCTT
* *
5133 CAATGTTTCAATATTTCAATGTTTTAGA-TCCAATTCTT
1 CAATGCTTCAATACTTCAATGTTTTA-ATTCCAATTCTT
5171 CAA
1 CAA
5174 ATTCCAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (38 bp):
CAATGCTTCAATACTTCAATGTTTTAATTCCAATTCTT
Found at i:5254 original size:14 final size:14
Alignment explanation
Indices: 5230--5277 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
5220 TCTTCCATTG
*
5230 CTTCAGTTTCAATT
1 CTTCAATTTCAATT
5244 CTTCGAA-TTCAATGT
1 CTTC-AATTTCAAT-T
5259 -TTCAATTTCAATT
1 CTTCAATTTCAATT
5272 CTTCAA
1 CTTCAA
5278 AGCCTCCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 3 0.10
14 24 0.83
15 2 0.07
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (14 bp):
CTTCAATTTCAATT
Found at i:5374 original size:18 final size:19
Alignment explanation
Indices: 5346--5392 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5336 CGATCGTGAT
5346 TTTTCCTCAAGATT-TTAAA
1 TTTT-CTCAAGATTCTTAAA
*
5365 TTTTCTCAAGGTTCTTAAA
1 TTTTCTCAAGATTCTTAAA
*
5384 GTTTCTCAA
1 TTTTCTCAA
5393 TAAAATGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (19 bp):
TTTTCTCAAGATTCTTAAA
Done.