Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013716.1 Corchorus capsularis cultivar CVL-1 contig13737, 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: 31139
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:254 original size:6 final size:6
Alignment explanation
Indices: 238--277 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
228 TGAGATAGAA
* *
238 AAAAAC CAAAAC AAAAA- AAACAC AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
278 TGGCCCGCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:265 original size:17 final size:15
Alignment explanation
Indices: 236--271 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
226 CGTGAGATAG
236 AAAAAAACCAAAACA
1 AAAAAAACCAAAACA
251 AAAAAAACACAAAAACA
1 AAAAAAAC-C-AAAACA
268 AAAA
1 AAAA
272 CAAAAATGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAACCAAAACA
Found at i:4553 original size:69 final size:69
Alignment explanation
Indices: 4480--4614 Score: 252
Period size: 69 Copynumber: 2.0 Consensus size: 69
4470 CCCGCTCCTT
4480 CTCATCACGATGCCTCCTATCAGAATTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCC
1 CTCATCACGATGCCTCCTATCAGAATTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCC
4545 GCTC
66 GCTC
* *
4549 CTCATCACGATGCCTTCTATCAGAGTTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCC
1 CTCATCACGATGCCTCCTATCAGAATTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCC
4614 G
66 G
4615 AGAGGCAACA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.20, C:0.39, G:0.14, T:0.27
Consensus pattern (69 bp):
CTCATCACGATGCCTCCTATCAGAATTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCC
GCTC
Found at i:4634 original size:69 final size:69
Alignment explanation
Indices: 4485--4634 Score: 212
Period size: 69 Copynumber: 2.2 Consensus size: 69
4475 TCCTTCTCAT
* ***
4485 CACGATGCCTCCTATCAGAATTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCCGCTCC
1 CACGATGCCTTCTATCAGAATTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCCGAGAC
* *
4550 TCAT
66 GCAA
* *
4554 CACGATGCCTTCTATCAGAGTTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCCGAGAG
1 CACGATGCCTTCTATCAGAATTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCCGAGAC
4619 GCAA
66 GCAA
4623 CA-GATGACCTTC
1 CACGATG-CCTTC
4635 CCTTTTCATG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
68 4 0.06
69 68 0.94
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.25
Consensus pattern (69 bp):
CACGATGCCTTCTATCAGAATTGCCTGACCACTCACGCTCAGAAACCCGCTCTTTTTCCCGAGAC
GCAA
Found at i:19725 original size:13 final size:13
Alignment explanation
Indices: 19707--19731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19697 CTAGTTTTTC
19707 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
19720 AAAAAAAAAAAA
1 AAAAAAAAAAAA
19732 CCTCTCACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:20082 original size:5 final size:6
Alignment explanation
Indices: 20067--20102 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
20057 ACGAGCTAGT
*
20067 TTTTTC TTTTTC TTTTTC TTTTTCC TTTTTG TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTT-C TTTTTC TTTTT
20103 AAGTAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:22722 original size:37 final size:36
Alignment explanation
Indices: 22664--22734 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 36
22654 TAATGTACAC
* *
22664 CATTACAACAATTACTAAAATATAATAATGCTATAA
1 CATTACAAAAATTACTAAAATATAATAATACTATAA
22700 CATTACAAAAAATTACTAAAATATAATAATACTAT
1 CATTAC-AAAAATTACTAAAATATAATAATACTAT
22735 TACTATTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (36 bp):
CATTACAAAAATTACTAAAATATAATAATACTATAA
Found at i:30435 original size:3 final size:3
Alignment explanation
Indices: 30427--30481 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
30417 TATCAATAAC
* * * *
30427 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CCT CAT CCT CTT CCT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
30475 CTT CTT C
1 CTT CTT C
30482 CCCCATCTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (3 bp):
CTT
Done.