Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011624.1 Corchorus capsularis cultivar CVL-1 contig11645, 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: 29548
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:180 original size:2 final size:2
Alignment explanation
Indices: 168--201 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
158 TAAGTTGAAC
*
168 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
202 ATGACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6493 original size:26 final size:27
Alignment explanation
Indices: 6458--6509 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
6448 AGACGTCACT
6458 CTCTAGTATGGGAGACGGA-AATTTCC
1 CTCTAGTATGGGAGACGGATAATTTCC
*
6484 CTCTAGTATGGGTGACGGATAATTTC
1 CTCTAGTATGGGAGACGGATAATTTC
6510 TCTTTCTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (27 bp):
CTCTAGTATGGGAGACGGATAATTTCC
Found at i:7018 original size:156 final size:156
Alignment explanation
Indices: 6808--7097 Score: 404
Period size: 156 Copynumber: 1.9 Consensus size: 156
6798 TCATCATGAG
* * * *
6808 ACTATGGTAAAAATTTCAAGTGAAACCGAGCTCTCCATCATGGTGAACTTGGTTTCACTCCCTAA
1 ACTATGGTAAAAATTTCAAGTAAAACCGAGCTCTCCATCATGGTGAACATGGTTTCACACCCCAA
* * * * *
6873 ATTTTCCTTAACTGAAAAACATTCATAAGTTTTTCATTCTAAGTCGAATTGAGATGAAACTTGGC
66 ACTGTCCTTAAATGAAAAACATGCATAAATTTTTCATTCTAAGTCGAATTGAGATGAAACTTGGC
6938 CAAGGGACTTAAATTATCTCCATAAA
131 CAAGGGACTTAAATTATCTCCATAAA
* * *
6964 ACTATGG-AAATAA-TTCTAAGTAAAACCGAGCTCTCCTTGATGGTGAACATGGTTTCTCACCCC
1 ACTATGGTAAA-AATTTC-AAGTAAAACCGAGCTCTCCATCATGGTGAACATGGTTTCACACCCC
* ***
7027 AAACTGTCCTTAAATGAAAAACGTGCATAAATTTTTCATTCTAAGTCTCTTTGAGATGAAACTTG
64 AAACTGTCCTTAAATGAAAAACATGCATAAATTTTTCATTCTAAGTCGAATTGAGATGAAACTTG
7092 GCCAAG
129 GCCAAG
7098 ATGATCTTCA
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
155 6 0.05
156 110 0.95
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (156 bp):
ACTATGGTAAAAATTTCAAGTAAAACCGAGCTCTCCATCATGGTGAACATGGTTTCACACCCCAA
ACTGTCCTTAAATGAAAAACATGCATAAATTTTTCATTCTAAGTCGAATTGAGATGAAACTTGGC
CAAGGGACTTAAATTATCTCCATAAA
Found at i:8184 original size:3 final size:3
Alignment explanation
Indices: 8176--8201 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8166 GTGAAATTGG
8176 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
8202 ATACTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9209 original size:2 final size:2
Alignment explanation
Indices: 9202--9226 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9192 GGGTGAGTCT
9202 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 T
9227 GCAATTTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10318 original size:53 final size:53
Alignment explanation
Indices: 10255--10361 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
10245 CCGCTGTTTT
* * *
10255 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGGAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAAATTTGTTGTGA
*
10308 ATTTTTTAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAAATTTGTTGTGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAAATTTGTTGTGA
10361 A
1 A
10362 ATGATAACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (53 bp):
ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAAATTTGTTGTGA
Found at i:11183 original size:59 final size:59
Alignment explanation
Indices: 11091--11208 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
11081 TTTGTGGTAT
11091 GATAGATAAAAACAATATCAAAATGTACATTGTCACTATATTTAACTAATTAATTATAG
1 GATAGATAAAAACAATATCAAAATGTACATTGTCACTATATTTAACTAATTAATTATAG
11150 GATAGATAAAAACAATATCAAAATGTACATTGTCACTATATTTAACTAATTAATTATAG
1 GATAGATAAAAACAATATCAAAATGTACATTGTCACTATATTTAACTAATTAATTATAG
11209 ATTTTTATAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (59 bp):
GATAGATAAAAACAATATCAAAATGTACATTGTCACTATATTTAACTAATTAATTATAG
Found at i:16143 original size:2 final size:2
Alignment explanation
Indices: 16136--16167 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16126 TTGGTGCAAC
16136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16168 AGAAACAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23509 original size:13 final size:13
Alignment explanation
Indices: 23491--23525 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
23481 TTAATTATTG
23491 TTTGCTTTATTAA
1 TTTGCTTTATTAA
23504 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
23517 TTTGATTTA
1 TTTGCTTTA
23526 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.23, C:0.06, G:0.09, T:0.63
Consensus pattern (13 bp):
TTTGCTTTATTAA
Done.