Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009796.1 Corchorus capsularis cultivar CVL-1 contig09817, 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: 9515
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Found at i:26 original size:19 final size:18
Alignment explanation
Indices: 2--52 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
1 T
*
2 TTTTTTCTTCTTCTTCTTC
1 TTTTTTCTTCTTCTT-TCC
*
21 TTTTTTTTTCTT-TTTCC
1 TTTTTTCTTCTTCTTTCC
38 TTTTTTCTT-TTCTTT
1 TTTTTTCTTCTTCTTT
53 GGATGCGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 2 0.07
17 13 0.46
18 2 0.07
19 11 0.39
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTCTTCTTCTTTCC
Found at i:42 original size:8 final size:7
Alignment explanation
Indices: 2--48 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
1 T
2 TTTTTTC
1 TTTTTTC
9 TTCTTCTTC
1 TT-TT-TTC
*
18 TTCTTT-
1 TTTTTTC
24 TTTTTTC
1 TTTTTTC
*
31 TTTTTCC
1 TTTTTTC
38 TTTTTTC
1 TTTTTTC
45 TTTT
1 TTTT
49 CTTTGGATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 5 0.15
7 20 0.61
8 3 0.09
9 5 0.15
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:734 original size:14 final size:13
Alignment explanation
Indices: 690--734 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 13
680 AAAAACTCAT
690 AAACCTTTTTTGA
1 AAACCTTTTTTGA
*
703 AAACTCATTTTTTAA
1 AAAC-C-TTTTTTGA
718 AAACCTTTTCTTGA
1 AAACCTTTT-TTGA
732 AAA
1 AAA
735 TAATTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 8 0.30
14 8 0.30
15 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (13 bp):
AAACCTTTTTTGA
Found at i:1959 original size:42 final size:42
Alignment explanation
Indices: 1859--1959 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
1849 TATACAAGCG
** * *
1859 AATGCATGATGGATGCATGGGCACATATACCAATGAAAGGAT
1 AATGCATGATGGATGCATGAACACATATACCAAAGAAAGGAC
* ** *
1901 AATGCATAATCAATGCATGAACATATATA-CAAAGAAATGGAC
1 AATGCATGATGGATGCATGAACACATATACCAAAGAAA-GGAC
1943 AATGCATGATGGATGCA
1 AATGCATGATGGATGCA
1960 CCATATACAA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
41 7 0.15
42 40 0.85
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (42 bp):
AATGCATGATGGATGCATGAACACATATACCAAAGAAAGGAC
Found at i:2895 original size:14 final size:13
Alignment explanation
Indices: 2875--2928 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 13
2865 ATACCTTTTC
2875 ACTTTTACTGATT
1 ACTTTTACTGATT
**
2888 ACCTTTTACTTTTT
1 A-CTTTTACTGATT
2902 ACTGTTTACT-ATT
1 ACT-TTTACTGATT
2915 ACTTCTTACTGATT
1 ACTT-TTACTGATT
2929 TCTATTACTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 1 0.03
13 13 0.38
14 20 0.59
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.56
Consensus pattern (13 bp):
ACTTTTACTGATT
Found at i:2900 original size:20 final size:20
Alignment explanation
Indices: 2866--2992 Score: 105
Period size: 20 Copynumber: 6.0 Consensus size: 20
2856 CCCTTTCAGA
2866 TACCTTTTCACTTTTACTGAT
1 TACCTTTT-ACTTTTACTGAT
*
2887 TACCTTTTACTTTTTACTGTT
1 TACCTTTTAC-TTTTACTGAT
*
2908 TA-CTATTACTTCTTACTGAT
1 TACCTTTTACTT-TTACTGAT
* *
2928 T-TCTATTACTCTTTACTGAT
1 TACCTTTTACT-TTTACTGAT
*
2948 TACCATTTTACTCTTTACTAAT
1 TACC-TTTTACT-TTTACTGAT
* *
2970 TGCCATTATACCTTTTACTGAT
1 TACC-TTTTA-CTTTTACTGAT
2992 T
1 T
2993 GCATCTTTCT
Statistics
Matches: 90, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.02
20 33 0.37
21 21 0.23
22 32 0.36
23 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (20 bp):
TACCTTTTACTTTTACTGAT
Found at i:2993 original size:22 final size:22
Alignment explanation
Indices: 2934--2994 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
2924 TGATTTCTAT
* *
2934 TACTCTTTACTGATTACCATTT
1 TACTCTTTACTGATTGCCATTA
*
2956 TACTCTTTACTAATTGCCATTA
1 TACTCTTTACTGATTGCCATTA
2978 TAC-CTTTTACTGATTGC
1 TACTC-TTTACTGATTGC
2995 ATCTTTCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.48
Consensus pattern (22 bp):
TACTCTTTACTGATTGCCATTA
Found at i:6423 original size:28 final size:29
Alignment explanation
Indices: 6365--6439 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
6355 GTAGATTAAG
*
6365 AATGACCAAAATACCCCCCTAAATGC-AAA
1 AATGACCAAAAT-GCCCCCTAAATGCAAAA
* **
6394 AATGACCAAAATGCCCCCTAGATGTGAAA
1 AATGACCAAAATGCCCCCTAAATGCAAAA
6423 AATGACCAAAATGCCCC
1 AATGACCAAAATGCCCC
6440 TGGATGACTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 10 0.24
29 32 0.76
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (29 bp):
AATGACCAAAATGCCCCCTAAATGCAAAA
Found at i:8686 original size:23 final size:22
Alignment explanation
Indices: 8638--8703 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
8628 TACCTTTATC
**
8638 TTTTTATTTTTCGTTATT-TTCC
1 TTTTTATTTTTCGTT-TTATTTA
8660 TTTTTATTTTTCGTTTTATTTA
1 TTTTTATTTTTCGTTTTATTTA
8682 TTTTTATTCTTTC-TATTTATTT
1 TTTTTATT-TTTCGT-TTTATTT
8704 TCTTTGGTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.05
22 26 0.67
23 11 0.28
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (22 bp):
TTTTTATTTTTCGTTTTATTTA
Done.