Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008263.1 Corchorus capsularis cultivar CVL-1 contig08284, 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: 14793
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:22 original size:2 final size:2
Alignment explanation
Indices: 15--52 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5 CTTGACAACC
15 AT AT AT 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 AT AT AT A
53 AGCCATGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2830 original size:17 final size:18
Alignment explanation
Indices: 2807--2849 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2797 AACCCAAAAC
2807 AAACATGGCT-ACTAATT
1 AAACATGGCTAACTAATT
*
2824 GAACATGGCTAACTAATT
1 AAACATGGCTAACTAATT
2842 AAACATGG
1 AAACATGG
2850 TTATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (18 bp):
AAACATGGCTAACTAATT
Found at i:12384 original size:27 final size:26
Alignment explanation
Indices: 12263--12542 Score: 153
Period size: 27 Copynumber: 10.1 Consensus size: 26
12253 TTATTTTTGA
12263 TTACTAATTACCATTCTTTTTCACTCTTT
1 TTACTAATTACCA--CTTTTT-ACTCTTT
* *
12292 ATACTGATTACCA-TATTTTACTCTTT
1 TTACTAATTACCACT-TTTTACTCTTT
* * *
12318 TTACTGATTACCCCTTTTCT-TTCTGTT
1 TTACTAATTACCACTTTT-TACTCT-TT
*
12345 TTGACTAAATACCACTTTTTACTCTTT
1 TT-ACTAATTACCACTTTTTACTCTTT
12372 TTACTTAATTACCA-TTTTTACTCTCCTTTTT
1 TTAC-TAATTACCACTTTTTA--CT-C--TTT
* *
12403 TTACTTAA-TACCA-TTTATATCCCTTT
1 TTAC-TAATTACCACTTTTTA-CTCTTT
12429 TTACTGAA-TACCACTTTTTACTCTTTT
1 TTACT-AATTACCACTTTTTACTC-TTT
* *
12456 TTACTGATCACCA-TTTCTTACTCTTAT
1 TTACTAATTACCACTTT-TTACTCTT-T
** *
12483 TTACTAATTA-CTTTTTTTCACCTTTTT
1 TTACTAATTACCACTTTTT-A-CTCTTT
12510 TTATCTTACTGATTACCACTTTTTACTCTTT
1 TTA-C-TA---ATTACCACTTTTTACTCTTT
12541 TT
1 TT
12543 CTTTTCCTCT
Statistics
Matches: 201, Mismatches: 23, Indels: 52
0.73 0.08 0.19
Matches are distributed among these distances:
25 1 0.00
26 58 0.29
27 63 0.31
28 24 0.12
29 16 0.08
30 10 0.05
31 18 0.09
32 5 0.02
33 6 0.03
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.54
Consensus pattern (26 bp):
TTACTAATTACCACTTTTTACTCTTT
Found at i:12769 original size:19 final size:19
Alignment explanation
Indices: 12745--12806 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
12735 TCTTTAATTA
12745 CTGATTACTATCTTTTTAC
1 CTGATTACTATCTTTTTAC
12764 CTGATTACTGA----TTTA-
1 CTGATTACT-ATCTTTTTAC
12779 CTGATTACTATCTTTTTAC
1 CTGATTACTATCTTTTTAC
12798 CTGATTACT
1 CTGATTACT
12807 GATTTACTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.03
15 9 0.24
16 4 0.11
18 4 0.11
19 18 0.49
20 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (19 bp):
CTGATTACTATCTTTTTAC
Found at i:12784 original size:15 final size:16
Alignment explanation
Indices: 12759--12821 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 16
12749 TTACTATCTT
12759 TTTACCTGATTACTGA
1 TTTACCTGATTACTGA
12775 TTTA-CTGATTACT-A
1 TTTACCTGATTACTGA
12789 TCTTTTTACCTGATTACTGA
1 ----TTTACCTGATTACTGA
12809 TTTA-CTGATTACT
1 TTTACCTGATTACT
12822 ATTATCTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.02
15 18 0.44
16 8 0.20
18 4 0.10
19 9 0.22
20 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (16 bp):
TTTACCTGATTACTGA
Found at i:12785 original size:34 final size:34
Alignment explanation
Indices: 12706--12823 Score: 170
Period size: 34 Copynumber: 3.5 Consensus size: 34
12696 CTTAATTATC
*
12706 GATTTACTGATTACTA--TTTTTACCTAGACT-CTT
1 GATTTACTGATTACTATCTTTTTACCT-GATTAC-T
* *
12739 TAATTACTGATTACTATCTTTTTACCTGATTACT
1 GATTTACTGATTACTATCTTTTTACCTGATTACT
12773 GATTTACTGATTACTATCTTTTTACCTGATTACT
1 GATTTACTGATTACTATCTTTTTACCTGATTACT
12807 GATTTACTGATTACTAT
1 GATTTACTGATTACTAT
12824 TATCTTGACT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
33 14 0.18
34 53 0.69
35 10 0.13
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49
Consensus pattern (34 bp):
GATTTACTGATTACTATCTTTTTACCTGATTACT
Found at i:13099 original size:55 final size:55
Alignment explanation
Indices: 12779--13096 Score: 438
Period size: 55 Copynumber: 5.8 Consensus size: 55
12769 TACTGATTTA
* * * * * *
12779 CTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTATCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
* **
12834 CTGATTAATCTCTTTTTTCTTAATTACTGATTTACTGATTACTATTACCTTGTCT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
*
12889 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
*
12944 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
* * * * * * *
12999 TTGATTAATCTCTTTTCACTTAATTACTGATTGACTGGTTACTGTTGCTTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
* * * *
13054 TTGATTAATCTCTTTTCACTTAATTACTGATTGACTGGTTACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACT
13097 GTTCGGACTG
Statistics
Matches: 244, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 244 1.00
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
Found at i:14032 original size:49 final size:49
Alignment explanation
Indices: 13953--14088 Score: 166
Period size: 49 Copynumber: 2.8 Consensus size: 49
13943 ACTAATTACT
* * * * *
13953 CTAAAAA-TCAATCTTTTGCTCTAAGGTGACATCTTTACTTGCTAATCA
1 CTAAAAATTCAATCTTTTACTCAAAGATGACATTTTTACTTACTAATCA
** * *
14001 CTAAAGTTTCAATCTTTCACTCAAAGATGACATTTTTACTTACTAATTA
1 CTAAAAATTCAATCTTTTACTCAAAGATGACATTTTTACTTACTAATCA
* *
14050 CTAAAAATTCAATCTTTTACCCAAAGATGGCATTTTTAC
1 CTAAAAATTCAATCTTTTACTCAAAGATGACATTTTTAC
14089 AAAAAGCTTC
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
48 5 0.07
49 68 0.93
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (49 bp):
CTAAAAATTCAATCTTTTACTCAAAGATGACATTTTTACTTACTAATCA
Done.