Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013947.1 Corchorus capsularis cultivar CVL-1 contig13968, 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: 6218
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Found at i:3627 original size:9 final size:9
Alignment explanation
Indices: 3615--3644 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3605 AAAAAAAGTT
3615 TGAAAAAAA
1 TGAAAAAAA
3624 TG-AAAAAA
1 TGAAAAAAA
3632 TGAAAAAAA
1 TGAAAAAAA
3641 TGAA
1 TGAA
3645 TGAATGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (9 bp):
TGAAAAAAA
Found at i:3760 original size:17 final size:15
Alignment explanation
Indices: 3732--3787 Score: 62
Period size: 17 Copynumber: 3.7 Consensus size: 15
3722 AGAGTCGCGG
3732 TTTTCAAAAAAATGAT
1 TTTTC-AAAAAATGAT
3748 GATTTTCAAAAAATGAT
1 --TTTTCAAAAAATGAT
*
3765 TTTTC-AAAGATG-T
1 TTTTCAAAAAATGAT
3778 TTTTCAAAAA
1 TTTTCAAAAA
3788 TGGTTTTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 6 0.17
14 9 0.26
15 5 0.14
17 10 0.29
18 5 0.14
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (15 bp):
TTTTCAAAAAATGAT
Found at i:3765 original size:14 final size:14
Alignment explanation
Indices: 3746--3787 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3736 CAAAAAAATG
3746 ATGATTTTCAAAAA
1 ATGATTTTCAAAAA
*
3760 ATGATTTTTC-AAAG
1 ATGA-TTTTCAAAAA
*
3774 ATGTTTTTCAAAAA
1 ATGATTTTCAAAAA
3788 TGGTTTTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 5 0.22
14 13 0.57
15 5 0.22
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (14 bp):
ATGATTTTCAAAAA
Found at i:3793 original size:14 final size:14
Alignment explanation
Indices: 3750--3794 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
3740 AAAATGATGA
*
3750 TTTTCAAAAAATGAT
1 TTTTC-AAAAATGGT
*
3765 TTTTCAAAGAT-GT
1 TTTTCAAAAATGGT
3778 TTTTCAAAAATGGT
1 TTTTCAAAAATGGT
3792 TTT
1 TTT
3795 CGAACACGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 11 0.42
14 10 0.38
15 5 0.19
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (14 bp):
TTTTCAAAAATGGT
Found at i:4102 original size:22 final size:22
Alignment explanation
Indices: 4077--4136 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
4067 AAAAGAAAAG
*
4077 AAAAAAATCAATCAAAATCAATA
1 AAAAAAATCAA-AAAAATCAATA
*
4100 AAAAAAATCAAAAAAATCAAAA
1 AAAAAAATCAAAAAAATCAATA
4122 ATATAAAAAT-AAAAA
1 A-A-AAAAATCAAAAA
4137 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 10 0.30
23 17 0.52
24 6 0.18
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAAAAATCAAAAAAATCAATA
Found at i:4121 original size:19 final size:19
Alignment explanation
Indices: 4086--4134 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
4076 GAAAAAAATC
*
4086 AATCAAAATCAATAAAAAA
1 AATCAAAATAAATAAAAAA
*
4105 AATCAAAA-AAATCAAAAA
1 AATCAAAATAAATAAAAAA
* *
4123 TATAAAAATAAA
1 AATCAAAATAAA
4135 AAGAGAGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (19 bp):
AATCAAAATAAATAAAAAA
Found at i:4445 original size:12 final size:13
Alignment explanation
Indices: 4417--4445 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4407 TGGTCAAAAC
4417 TTTTGAAAAGAGT
1 TTTTGAAAAGAGT
4430 TTTTGAAAAGAGT
1 TTTTGAAAAGAGT
4443 TTT
1 TTT
4446 CGGGTTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (13 bp):
TTTTGAAAAGAGT
Found at i:6080 original size:22 final size:22
Alignment explanation
Indices: 6052--6126 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
6042 ATTGGTAAGT
6052 CCTCCGGGCTCAAATTCAGAAA
1 CCTCCGGGCTCAAATTCAGAAA
** ** *
6074 CCTCCGGATTTTAATTCTGACAA
1 CCTCCGGGCTCAAATTCAGA-AA
*
6097 GTCCTCCGGGCACAAATTCAGAAA
1 --CCTCCGGGCTCAAATTCAGAAA
6121 CCTCCG
1 CCTCCG
6127 TGTATTAATT
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
22 21 0.54
23 2 0.05
24 2 0.05
25 14 0.36
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (22 bp):
CCTCCGGGCTCAAATTCAGAAA
Found at i:6117 original size:47 final size:47
Alignment explanation
Indices: 6048--6140 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
6038 TTGCATTGGT
* *
6048 AAGTCCTCCGGGCTCAAATTCAGAAACCTCCG-GATTTTAATTCTGAC
1 AAGTCCTCCGGGCACAAATTCAGAAACCTCCGTG-TATTAATTCTGAC
6095 AAGTCCTCCGGGCACAAATTCAGAAACCTCCGTGTATTAATTCTGA
1 AAGTCCTCCGGGCACAAATTCAGAAACCTCCGTGTATTAATTCTGA
6141 TATATAAGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 42 0.98
48 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (47 bp):
AAGTCCTCCGGGCACAAATTCAGAAACCTCCGTGTATTAATTCTGAC
Done.