Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013720.1 Corchorus capsularis cultivar CVL-1 contig13741, 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: 27392
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Found at i:1211 original size:18 final size:18
Alignment explanation
Indices: 1180--1219 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1170 GAATCCATCC
*
1180 AATCCGCCTAACCCACAA
1 AATCCACCTAACCCACAA
* *
1198 AATCCACCTCACCCCCAA
1 AATCCACCTAACCCACAA
1216 AATC
1 AATC
1220 AACCAAGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.47, G:0.03, T:0.12
Consensus pattern (18 bp):
AATCCACCTAACCCACAA
Found at i:3735 original size:360 final size:360
Alignment explanation
Indices: 3074--3796 Score: 1392
Period size: 360 Copynumber: 2.0 Consensus size: 360
3064 AGCCTGAAGA
*
3074 CAATCAGCCAAGGTGGATCCCTCTCTCAGGTGGTGGCACCACTTTTACAAATGCGAGACTAGTCA
1 CAATCAGCCAAGGTGGATCCCTCTCCCAGGTGGTGGCACCACTTTTACAAATGCGAGACTAGTCA
*
3139 CCAATGTGGCTGACAGGCCAGAAAGTAGTGCGATGGGCGAGAGGAGGGGAGAAATTTTGGAGGCC
66 CCAATGTGGCTGACAGACCAGAAAGTAGTGCGATGGGCGAGAGGAGGGGAGAAATTTTGGAGGCC
3204 ACCAGAAGAAGAGAAGCCCAATTTCAATTGAGCCTTGTTATCAACAATAATTCAGTTGAAAACTG
131 ACCAGAAGAAGAGAAGCCCAATTTCAATTGAGCCTTGTTATCAACAATAATTCAGTTGAAAACTG
*
3269 GAAAGAAGTGGGAGAAAGCTTGCACAACTTCAATGTAACAAACCCTCCATACTCCAATGTACAGC
196 GAAAGAAGTGGGAGAAAGCTTGCAAAACTTCAATGTAACAAACCCTCCATACTCCAATGTACAGC
3334 AAACGGCAACGGATGTTGTTCAAATGCAGGATCCACCACCTACACAGGATCTTGAATTGGCACAG
261 AAACGGCAACGGATGTTGTTCAAATGCAGGATCCACCACCTACACAGGATCTTGAATTGGCACAG
*
3399 GAGGCTCAGAAACCAGATGAAGGTCCATCTCATGG
326 GAGGCTCAGAAACCAGATGAAGGTCCATCCCATGG
3434 CAATCAGCCAAGGTGGATCCCTCTCCCAGGTGGTGGCACCACTTTTACAAATGCGAGACTAGTCA
1 CAATCAGCCAAGGTGGATCCCTCTCCCAGGTGGTGGCACCACTTTTACAAATGCGAGACTAGTCA
3499 CCAATGTGGCTGACAGACCAGAAAGTAGTGCGATGGGCGAGAGGAGGGGAGAAATTTTGGAGGCC
66 CCAATGTGGCTGACAGACCAGAAAGTAGTGCGATGGGCGAGAGGAGGGGAGAAATTTTGGAGGCC
3564 ACCAGAAGAAGAGAAGCCCAATTTCAATTGAGCCTTGTTATCAACAATAATTCAGTTGAAAACTG
131 ACCAGAAGAAGAGAAGCCCAATTTCAATTGAGCCTTGTTATCAACAATAATTCAGTTGAAAACTG
3629 GAAAGAAGTGGGAGAAAGCTTGCAAAACTTCAATGTAACAAACCCTCCATACTCCAATGTACAGC
196 GAAAGAAGTGGGAGAAAGCTTGCAAAACTTCAATGTAACAAACCCTCCATACTCCAATGTACAGC
3694 AAACGGCAACGGATGTTGTTCAAATGCAGGATCCACCACCTACACAGGATCTTGAATTGGCACAG
261 AAACGGCAACGGATGTTGTTCAAATGCAGGATCCACCACCTACACAGGATCTTGAATTGGCACAG
**
3759 GAGGCTCAGAAACTGGATGAAGGTCCATCCCATGG
326 GAGGCTCAGAAACCAGATGAAGGTCCATCCCATGG
3794 CAA
1 CAA
3797 CAACTCCCCA
Statistics
Matches: 357, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
360 357 1.00
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (360 bp):
CAATCAGCCAAGGTGGATCCCTCTCCCAGGTGGTGGCACCACTTTTACAAATGCGAGACTAGTCA
CCAATGTGGCTGACAGACCAGAAAGTAGTGCGATGGGCGAGAGGAGGGGAGAAATTTTGGAGGCC
ACCAGAAGAAGAGAAGCCCAATTTCAATTGAGCCTTGTTATCAACAATAATTCAGTTGAAAACTG
GAAAGAAGTGGGAGAAAGCTTGCAAAACTTCAATGTAACAAACCCTCCATACTCCAATGTACAGC
AAACGGCAACGGATGTTGTTCAAATGCAGGATCCACCACCTACACAGGATCTTGAATTGGCACAG
GAGGCTCAGAAACCAGATGAAGGTCCATCCCATGG
Found at i:8611 original size:27 final size:28
Alignment explanation
Indices: 8551--8603 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
8541 ATACAAAATT
*
8551 AATTAAAAAATCAGATATGATGTCAAAA
1 AATTAAAAAATCAGATAAGATGTCAAAA
*
8579 AATTAAAAAATGAGATAAG-TGTCAA
1 AATTAAAAAATCAGATAAGATGTCAA
8604 CACCTTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.25
Consensus pattern (28 bp):
AATTAAAAAATCAGATAAGATGTCAAAA
Found at i:9258 original size:20 final size:21
Alignment explanation
Indices: 9221--9263 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
9211 AACCCGTTAA
*
9221 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
9242 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
9262 TT
1 TT
9264 GACACGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:10078 original size:21 final size:22
Alignment explanation
Indices: 10035--10079 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
10025 ATCTTTGAGA
*
10035 AGATATTAAAATCCTCCTGAATTT
1 AGATATTAAAA--CTCCTAAATTT
10059 AGATATTAAAA-TCCTAAATTT
1 AGATATTAAAACTCCTAAATTT
10080 GTATCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
24 11 0.55
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (22 bp):
AGATATTAAAACTCCTAAATTT
Found at i:13748 original size:1 final size:1
Alignment explanation
Indices: 13727--13772 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
13717 CACCTCCTTG
* * *
13727 TTTTGTTTTGTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13773 GCTATATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:16081 original size:3 final size:3
Alignment explanation
Indices: 16073--16097 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16063 CCAAAAACAG
16073 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
16098 TGTGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:24439 original size:31 final size:30
Alignment explanation
Indices: 24372--24470 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 30
24362 CAAAAAGTCG
24372 TGCCACATGTATCAAAAAGTGACACATGTG-A
1 TGCCACATGTATCAAAAAGTG--ACATGTGCA
* * *
24403 CGCCACGTGTACCAAAAAGTGACATGTGCCA
1 TGCCACATGTATCAAAAAGTGACATGTG-CA
* * * *
24434 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTATCAAAAAGTGACATGT-GCA
24465 TGCCAC
1 TGCCAC
24471 GTGCACAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
29 7 0.13
31 47 0.85
32 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.20
Consensus pattern (30 bp):
TGCCACATGTATCAAAAAGTGACATGTGCA
Found at i:25187 original size:25 final size:25
Alignment explanation
Indices: 25154--25226 Score: 137
Period size: 25 Copynumber: 2.9 Consensus size: 25
25144 AGGAGATGAA
25154 GAATATAATAGGAGGCATGAAATCT
1 GAATATAATAGGAGGCATGAAATCT
25179 GAATATAATAGGAGGCATGAAATCT
1 GAATATAATAGGAGGCATGAAATCT
*
25204 GAATATAATAGGATGCATGAAAT
1 GAATATAATAGGAGGCATGAAAT
25227 TTCTCTGCAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (25 bp):
GAATATAATAGGAGGCATGAAATCT
Found at i:25722 original size:2 final size:2
Alignment explanation
Indices: 25715--25747 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25705 AAATGTATGT
25715 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25748 GGTATAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27361 original size:2 final size:2
Alignment explanation
Indices: 27354--27390 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
27344 AAATGTATGT
27354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27391 TA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.