Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000656.1 Corchorus capsularis cultivar CVL-1 contig00656, 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: 8059
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Found at i:2077 original size:29 final size:31
Alignment explanation
Indices: 2034--2105 Score: 105
Period size: 29 Copynumber: 2.4 Consensus size: 31
2024 TTTTGAAATG
*
2034 TAAGGGATTAATTTAT-CCAAAA-AAAAACA
1 TAAGGGATTATTTTATCCCAAAAGAAAAACA
2063 TAAGGGATTATTTTATCCCAAAAGAAAAACA
1 TAAGGGATTATTTTATCCCAAAAGAAAAACA
*
2094 TAAAGGA-TATTT
1 TAAGGGATTATTT
2106 GTTGGTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 15 0.38
30 11 0.28
31 13 0.33
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (31 bp):
TAAGGGATTATTTTATCCCAAAAGAAAAACA
Found at i:2105 original size:30 final size:29
Alignment explanation
Indices: 2038--2105 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
2028 GAAATGTAAG
* *
2038 GGATTAATTTATCCAAAAAAAAACATAAG
1 GGATTATTTTATCCAAAAAAAAACATAAA
2067 GGATTATTTTATCCCAAAAGAAAAACATAAA
1 GGATTATTTTAT-CCAAAA-AAAAACATAAA
2098 GGA-TATTT
1 GGATTATTT
2106 GTTGGTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 11 0.31
30 11 0.31
31 13 0.37
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (29 bp):
GGATTATTTTATCCAAAAAAAAACATAAA
Found at i:2438 original size:45 final size:45
Alignment explanation
Indices: 2389--2537 Score: 176
Period size: 45 Copynumber: 3.5 Consensus size: 45
2379 TCTCTAGGTG
2389 ATTCATCAAAATAAAACTAATATTCTACTCCTCCATGTCTAGATA
1 ATTCATCAAAATAAAACTAATATTCTACTCCTCCATGTCTAGATA
* *
2434 ATTCATC-----AAAA-TAA-ATTCTACT--T-CATCTCTA-AGTG
1 ATTCATCAAAATAAAACTAATATTCTACTCCTCCATGTCTAGA-TA
*
2469 ATTCATCAAAACAAAACTAATATTCTACTCCTCCATGTCTAGATA
1 ATTCATCAAAATAAAACTAATATTCTACTCCTCCATGTCTAGATA
*
2514 ATTCATCAAAATAAAGCTAATATT
1 ATTCATCAAAATAAAACTAATATT
2538 AATTGTTGTT
Statistics
Matches: 86, Mismatches: 6, Indels: 24
0.74 0.05 0.21
Matches are distributed among these distances:
34 1 0.01
35 15 0.17
36 1 0.01
38 8 0.09
39 3 0.03
40 8 0.09
41 3 0.03
42 8 0.09
44 1 0.01
45 37 0.43
46 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.34
Consensus pattern (45 bp):
ATTCATCAAAATAAAACTAATATTCTACTCCTCCATGTCTAGATA
Found at i:2461 original size:80 final size:80
Alignment explanation
Indices: 2365--2528 Score: 310
Period size: 80 Copynumber: 2.0 Consensus size: 80
2355 GTGGATTACT
* *
2365 TAAATTCTACTTCATCTCTAGGTGATTCATCAAAATAAAACTAATATTCTACTCCTCCATGTCTA
1 TAAATTCTACTTCATCTCTAAGTGATTCATCAAAACAAAACTAATATTCTACTCCTCCATGTCTA
2430 GATAATTCATCAAAA
66 GATAATTCATCAAAA
2445 TAAATTCTACTTCATCTCTAAGTGATTCATCAAAACAAAACTAATATTCTACTCCTCCATGTCTA
1 TAAATTCTACTTCATCTCTAAGTGATTCATCAAAACAAAACTAATATTCTACTCCTCCATGTCTA
2510 GATAATTCATCAAAA
66 GATAATTCATCAAAA
2525 TAAA
1 TAAA
2529 GCTAATATTA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (80 bp):
TAAATTCTACTTCATCTCTAAGTGATTCATCAAAACAAAACTAATATTCTACTCCTCCATGTCTA
GATAATTCATCAAAA
Found at i:2476 original size:35 final size:36
Alignment explanation
Indices: 2365--2480 Score: 101
Period size: 35 Copynumber: 3.0 Consensus size: 36
2355 GTGGATTACT
*
2365 TAAATTCTACTTCATCTCTAGGTGATTCATCAAAATAAAAC
1 TAAATTCTACTTCATCTCTAAGTGATTCATC-----AAAAC
* *
2406 TAATATTCTACTCCTCCATGTCT-AGATAATTCATCAAAA-
1 TAA-ATTCTACT--T-CATCTCTAAG-TGATTCATCAAAAC
2445 TAAATTCTACTTCATCTCTAAGTGATTCATCAAAAC
1 TAAATTCTACTTCATCTCTAAGTGATTCATCAAAAC
2481 AAAACTAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
35 18 0.29
36 3 0.05
38 8 0.13
39 3 0.05
40 4 0.06
41 3 0.05
42 8 0.13
44 2 0.03
45 14 0.22
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (36 bp):
TAAATTCTACTTCATCTCTAAGTGATTCATCAAAAC
Found at i:3502 original size:38 final size:38
Alignment explanation
Indices: 3421--3502 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
3411 TTAACATTTA
** * *
3421 AATAATTTCCATAATCACTAAATTTAATATATACCTTT
1 AATAATTTCCATAATCACTAAAAATAATATATACATAT
* *
3459 AATAATTTTCATAGTCACTAAAAATAATATAT-CATAT
1 AATAATTTCCATAATCACTAAAAATAATATATACATAT
3496 ATATAAT
1 A-ATAAT
3503 AATAACAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
37 4 0.11
38 33 0.89
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.40
Consensus pattern (38 bp):
AATAATTTCCATAATCACTAAAAATAATATATACATAT
Found at i:3504 original size:3 final size:3
Alignment explanation
Indices: 3498--3544 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
3488 TATCATATAT
*
3498 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3545 TTAATACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3556 original size:14 final size:14
Alignment explanation
Indices: 3539--3565 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3529 TAATAATAAT
3539 AATAATTTAATACA
1 AATAATTTAATACA
3553 AATAATTTAATAC
1 AATAATTTAATAC
3566 GTACTAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAATTTAATACA
Found at i:5200 original size:51 final size:51
Alignment explanation
Indices: 5119--5216 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 51
5109 AAAAGAATGA
*
5119 GAGAGAGAGAAAAAAGAGAGAAT-AAAAAAAATAGAGGTTAGAAGCGGGAAT
1 GAGAGAGAGAAAAAAGAGAGAATAAAAAAAAAAAG-GGTTAGAAGCGGGAAT
5170 GAGAGAGAG-AAAAAGAGAGAATAAACAAAAAAAAGGGTTAGAAGCGG
1 GAGAGAGAGAAAAAAGAGAGAATAAA-AAAAAAAAGGGTTAGAAGCGG
5217 AAAGTTTTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
50 13 0.30
51 23 0.52
52 8 0.18
ACGTcount: A:0.57, C:0.03, G:0.32, T:0.08
Consensus pattern (51 bp):
GAGAGAGAGAAAAAAGAGAGAATAAAAAAAAAAAGGGTTAGAAGCGGGAAT
Found at i:6491 original size:17 final size:17
Alignment explanation
Indices: 6449--6493 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
6439 TTGAGAAATG
*
6449 TTACTAGTAATAAAACA
1 TTACTAGTCATAAAACA
* *
6466 TTACTAGTCCTAAATCA
1 TTACTAGTCATAAAACA
6483 TTACTAGTCAT
1 TTACTAGTCAT
6494 GTGTTATGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.36
Consensus pattern (17 bp):
TTACTAGTCATAAAACA
Found at i:7249 original size:25 final size:21
Alignment explanation
Indices: 7203--7245 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
7193 AATGCAGCAG
7203 GTGTAGAACAAATCGAATCAT
1 GTGTAGAACAAATCGAATCAT
7224 GTGTAGAACAAATCGAATCAT
1 GTGTAGAACAAATCGAATCAT
7245 G
1 G
7246 CATGGATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (21 bp):
GTGTAGAACAAATCGAATCAT
Done.