Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013154.1 Corchorus capsularis cultivar CVL-1 contig13175, 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: 22525
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4471 original size:3 final size:3
Alignment explanation
Indices: 4463--4495 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4453 AATCTTTAGG
4463 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
4496 GGAGAAGGAG
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:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4660 original size:3 final size:3
Alignment explanation
Indices: 4654--4679 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4644 TCCTTTTTTA
4654 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
4680 TAAAGGTTTT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:9110 original size:2 final size:2
Alignment explanation
Indices: 9103--9144 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
9093 ACATGTTTAA
*
9103 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9145 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12170 original size:30 final size:31
Alignment explanation
Indices: 12097--12176 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
12087 CAAAGGATCA
12097 AATGGCA-TCTTTGGTGCGATTCCTCCATCC
1 AATGGCATTCTTTGGTGCGATTCCTCCATCC
*
12127 AATGGCATT-TTTGGTGCGATTCCTTCA-CC
1 AATGGCATTCTTTGGTGCGATTCCTCCATCC
* *
12156 CATTG-ATGTCTTTGGTGCGAT
1 AATGGCAT-TCTTTGGTGCGAT
12177 CCCATCTCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.05
29 6 0.14
30 35 0.80
31 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.38
Consensus pattern (31 bp):
AATGGCATTCTTTGGTGCGATTCCTCCATCC
Found at i:18812 original size:13 final size:13
Alignment explanation
Indices: 18794--18842 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
18784 CAGGTCTCTT
18794 CCTTCCTTTTCTC
1 CCTTCCTTTTCTC
18807 CCTTCCTTTTCTC
1 CCTTCCTTTTCTC
*
18820 CTTTCCTTTTCTC
1 CCTTCCTTTTCTC
*
18833 CTTTCCTTTT
1 CCTTCCTTTT
18843 ATCTTACTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (13 bp):
CCTTCCTTTTCTC
Found at i:18827 original size:17 final size:15
Alignment explanation
Indices: 18788--18832 Score: 53
Period size: 13 Copynumber: 3.3 Consensus size: 15
18778 TTTTCGCAGG
18788 TCTCTTCCTTCCTTT
1 TCTCTTCCTTCCTTT
18803 TCTC--CCTTCCTTT
1 TCTCTTCCTTCCTTT
*
18816 TCTC--CTTTCCTTT
1 TCTCTTCCTTCCTTT
18829 TCTC
1 TCTC
18833 CTTTCCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 25 0.86
15 4 0.14
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (15 bp):
TCTCTTCCTTCCTTT
Found at i:20270 original size:27 final size:27
Alignment explanation
Indices: 20234--20323 Score: 164
Period size: 27 Copynumber: 3.3 Consensus size: 27
20224 TCCGACTCTC
20234 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
20261 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
20288 CCCACTTCGACCCCAGCAA-TGGATCCT
1 CCCACTTCGACCCCAG-AAGTGGATCCT
20315 CCCACTTCG
1 CCCACTTCG
20324 CCTCGGGTGG
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
27 60 0.97
28 2 0.03
ACGTcount: A:0.21, C:0.43, G:0.17, T:0.19
Consensus pattern (27 bp):
CCCACTTCGACCCCAGAAGTGGATCCT
Found at i:22501 original size:2 final size:2
Alignment explanation
Indices: 22494--22525 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
22484 AACAATTTTC
*
22494 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.