Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012364.1 Corchorus capsularis cultivar CVL-1 contig12385, 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: 19655
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1012 original size:51 final size:51
Alignment explanation
Indices: 882--1081 Score: 286
Period size: 51 Copynumber: 4.0 Consensus size: 51
872 ACAGGTAATC
* *
882 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGAT-A--AG
1 TCTCTAAGATTTCCTTGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
*
930 ---CTAAGATTTCCTTGCAAATTTCCTCTAGCAATTGACTATGATGAGTTG
1 TCTCTAAGATTTCCTTGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
* * *
978 TCTCTAAGATTTCCGTACAAATTTCCTTTGGCAATTGACTATGATGAGTTG
1 TCTCTAAGATTTCCTTGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
* *
1029 TCTCTAAAATTTCCTTGCAAATTTCCTCTGGTAATTGACTATGATGAGTTG
1 TCTCTAAGATTTCCTTGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
1080 TC
1 TC
1082 ATATTTTTTA
Statistics
Matches: 134, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
45 40 0.30
46 1 0.01
48 1 0.01
51 92 0.69
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (51 bp):
TCTCTAAGATTTCCTTGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
Found at i:8003 original size:27 final size:31
Alignment explanation
Indices: 7938--8003 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 31
7928 CTCAGATTCG
* *
7938 AAAAGAACTGAGACTAGACTCGAAACTGACT
1 AAAAGAACTGAGACTAGACTCAAAACTAACT
*
7969 CAAA-AACT-A-ACT-GACTCAAAAC-AACT
1 AAAAGAACTGAGACTAGACTCAAAACTAACT
7995 AAAAGAACT
1 AAAAGAACT
8004 CAAATAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
26 6 0.20
27 13 0.43
28 3 0.10
29 1 0.03
30 4 0.13
31 3 0.10
ACGTcount: A:0.52, C:0.21, G:0.12, T:0.15
Consensus pattern (31 bp):
AAAAGAACTGAGACTAGACTCAAAACTAACT
Found at i:10677 original size:51 final size:51
Alignment explanation
Indices: 10601--10797 Score: 241
Period size: 51 Copynumber: 4.0 Consensus size: 51
10591 ACAGGTAATC
* * * **
10601 TCTCTAGGATTTCTATGCAAATTTCCTCTGGCAAGTGAGGATGATGAGTTG
1 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
10652 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
1 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
10703 --TC-------TCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
1 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
* * * * *
10745 TCTCTAAGGTCTCCTTGCAAATTTCCTCCGACAATTGACTATGATGAGTTG
1 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
10796 TC
1 TC
10798 ATATTTTTTA
Statistics
Matches: 129, Mismatches: 8, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
42 40 0.31
44 2 0.02
49 2 0.02
51 85 0.66
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (51 bp):
TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
Found at i:10722 original size:42 final size:42
Alignment explanation
Indices: 10663--10748 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
10653 CTCTAAGATT
10663 TCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTGTC
1 TCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTGTC
10705 TCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTGTC
1 TCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTGTC
10747 TC
1 TC
10749 TAAGGTCTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (42 bp):
TCCATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTGTC
Found at i:10780 original size:93 final size:93
Alignment explanation
Indices: 10615--10797 Score: 294
Period size: 93 Copynumber: 2.0 Consensus size: 93
10605 TAGGATTTCT
* *
10615 ATGCAAATTTCCTCTGGCAAGTGAGGATGATGAGTTGTCTCTAAGATTTCCATGCAAATTTCCTC
1 ATGCAAATTTCCTCTGGCAAGTGACGATGATGAGTTGTCTCTAAGATCTCCATGCAAATTTCCTC
* *
10680 TGGCAATTGACTATGATGAGTTGTCTCC
66 CGACAATTGACTATGATGAGTTGTCTCC
* * * *
10708 ATGCAAATTTCCTCTGGCAATTGACTATGATGAGTTGTCTCTAAGGTCTCCTTGCAAATTTCCTC
1 ATGCAAATTTCCTCTGGCAAGTGACGATGATGAGTTGTCTCTAAGATCTCCATGCAAATTTCCTC
10773 CGACAATTGACTATGATGAGTTGTC
66 CGACAATTGACTATGATGAGTTGTC
10798 ATATTTTTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (93 bp):
ATGCAAATTTCCTCTGGCAAGTGACGATGATGAGTTGTCTCTAAGATCTCCATGCAAATTTCCTC
CGACAATTGACTATGATGAGTTGTCTCC
Found at i:12817 original size:3 final size:3
Alignment explanation
Indices: 12811--12850 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12801 TTTTTTTTTT
12811 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
12851 AATCTTTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:14601 original size:51 final size:51
Alignment explanation
Indices: 14525--14679 Score: 265
Period size: 51 Copynumber: 3.0 Consensus size: 51
14515 ACAGGTAATC
14525 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATAAGTTG
1 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATAAGTTG
* *
14576 TCTCTAAGATTTCCGTGCAAATTTCCTCTGGCAATTGACTATGATGAGTTG
1 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATAAGTTG
* * *
14627 TCTCTAAGATTTCCTTGCAAATTTCCTCTGGTAATTGACTATGATTAGTTG
1 TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATAAGTTG
14678 TC
1 TC
14680 ATATTTTTTA
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 99 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (51 bp):
TCTCTAAGATTTCCATGCAAATTTCCTCTGGCAATTGACTATGATAAGTTG
Found at i:18977 original size:32 final size:32
Alignment explanation
Indices: 18936--19036 Score: 103
Period size: 38 Copynumber: 3.0 Consensus size: 32
18926 CTCTAAGATT
* * *
18936 TCCATGCAAATTTGCTCTGGCAATTGACTATA
1 TCCATGCAAATTTCCTCCGACAATTGACTATA
*
18968 TCCATGCAAATTTCCTCCGATAATTGACTATTAA
1 TCCATGCAAATTTCCTCCGACAATTGACTA-T-A
*
19002 GGTTTCCTTGCAAATTTCCTCCGACAATTGACTAT
1 ----TCCATGCAAATTTCCTCCGACAATTGACTAT
19037 GATGAGTTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
32 26 0.46
33 1 0.02
34 1 0.02
37 1 0.02
38 28 0.49
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (32 bp):
TCCATGCAAATTTCCTCCGACAATTGACTATA
Found at i:19279 original size:2 final size:2
Alignment explanation
Indices: 19272--19307 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19262 TATTATTCTA
19272 AT AT AT AT AT AT AT 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 AT AT
19308 TTGAAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.