Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022364.1 Corchorus olitorius cultivar O-4 contig22397, 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: 19706
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:5896 original size:13 final size:13
Alignment explanation
Indices: 5878--5903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5868 ATTGTACCAA
5878 TTTCATTAATCAT
1 TTTCATTAATCAT
5891 TTTCATTAATCAT
1 TTTCATTAATCAT
5904 ATACCTACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTCATTAATCAT
Found at i:6040 original size:13 final size:13
Alignment explanation
Indices: 6022--6047 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6012 ATTATACCAA
6022 TTTCATTAATCAT
1 TTTCATTAATCAT
6035 TTTCATTAATCAT
1 TTTCATTAATCAT
6048 ATGCCTAGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTCATTAATCAT
Found at i:6131 original size:69 final size:67
Alignment explanation
Indices: 6049--6184 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 67
6039 ATTAATCATA
* *
6049 TGCCTAGACATTTTAATTTCTTTCACCCAATTACTTTATTATTATAATTGACTTTTTAGCTTCGA
1 TGCCTACACATTTTAATTCCTTTCACCCAATTACTTTATTATTAT-A-TGACTTTTTAGCTTCGA
6114 TTTT
64 TTTT
*
6118 TGCCTACACATTTTAATTCCTTTCACCCAATTACTTTATTATTATATGACTTTTTAGCTTGGATT
1 TGCCTACACATTTTAATTCCTTTCACCCAATTACTTTATTATTATATGACTTTTTAGCTTCGATT
6183 TT
66 TT
6185 AAATCTTTTG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
67 20 0.31
68 1 0.02
69 43 0.67
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.50
Consensus pattern (67 bp):
TGCCTACACATTTTAATTCCTTTCACCCAATTACTTTATTATTATATGACTTTTTAGCTTCGATT
TT
Found at i:6372 original size:74 final size:75
Alignment explanation
Indices: 6284--6434 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
6274 ACCTTTTACT
* *
6284 TAAGTGGTGTCAATATTCCTATTTTATTCATTAA-CTATCAGCTATTAACCGTTTAATCCTAATT
1 TAAGTGGTGTCAATATTCCTATTTTATTCATTAACCTACCAACTATTAACCGTTTAATCCTAATT
6348 TTAGGAGTTC
66 TTAGGAGTTC
*
6358 TAAGTGGTGTCAATATTCCTATTTTATTCATTAACCTACCAACTATTAATCGTTTAATCCTAATT
1 TAAGTGGTGTCAATATTCCTATTTTATTCATTAACCTACCAACTATTAACCGTTTAATCCTAATT
6423 TTAGGAGTTC
66 TTAGGAGTTC
6433 TA
1 TA
6435 TGGCTATTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 34 0.47
75 39 0.53
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (75 bp):
TAAGTGGTGTCAATATTCCTATTTTATTCATTAACCTACCAACTATTAACCGTTTAATCCTAATT
TTAGGAGTTC
Found at i:6450 original size:36 final size:35
Alignment explanation
Indices: 6410--6482 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
6400 CTATTAATCG
*
6410 TTTAATC-CTAATTTTAGGAGTTCTATGGCTATTTTA
1 TTTAATCTC-AATTTTAGGA-TTATATGGCTATTTTA
**
6446 TTTAATCTCGCTTTTAGGATTATATGGCTATTTTA
1 TTTAATCTCAATTTTAGGATTATATGGCTATTTTA
6481 TT
1 TT
6483 CAATTAACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 17 0.52
36 15 0.45
37 1 0.03
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (35 bp):
TTTAATCTCAATTTTAGGATTATATGGCTATTTTA
Found at i:6638 original size:11 final size:10
Alignment explanation
Indices: 6623--6674 Score: 65
Period size: 9 Copynumber: 5.4 Consensus size: 10
6613 TGGATTTGGG
6623 TTTTGTTTTT
1 TTTTGTTTTT
6633 GTTTTG-TTTT
1 -TTTTGTTTTT
*
6643 TTGT-TTTTT
1 TTTTGTTTTT
6652 TTTTG-TTTT
1 TTTTGTTTTT
6661 TTTTGTTTTT
1 TTTTGTTTTT
6671 TTTT
1 TTTT
6675 TCTCTATGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 19 0.53
10 12 0.33
11 5 0.14
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:6643 original size:1 final size:1
Alignment explanation
Indices: 6623--6675 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
6613 TGGATTTGGG
* * * * * *
6623 TTTTGTTTTTGTTTTGTTTTTTGTTTTTTTTTTGTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6676 CTCTATGGGC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:6648 original size:23 final size:22
Alignment explanation
Indices: 6622--6664 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
6612 CTGGATTTGG
6622 GTTTTGTTTTTGTTTTGTTTTTT
1 GTTTTGTTTTTGTTTT-TTTTTT
*
6645 GTTTTTTTTTTGTTTTTTTT
1 GTTTTGTTTTTGTTTTTTTT
6665 GTTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (22 bp):
GTTTTGTTTTTGTTTTTTTTTT
Found at i:6675 original size:11 final size:11
Alignment explanation
Indices: 6622--6675 Score: 76
Period size: 11 Copynumber: 5.0 Consensus size: 11
6612 CTGGATTTGG
*
6622 GTTTTGTTTTT
1 GTTTTTTTTTT
6633 GTTTTGTTTTTT
1 GTTTT-TTTTTT
6645 GTTTTTTTTTT
1 GTTTTTTTTTT
6656 G--TTTTTTTT
1 GTTTTTTTTTT
6665 GTTTTTTTTTT
1 GTTTTTTTTTT
6676 CTCTATGGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
9 9 0.23
11 20 0.51
12 10 0.26
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:16674 original size:15 final size:16
Alignment explanation
Indices: 16647--16676 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16637 CTCTGCTTTG
16647 TTTTCTAGTTTAATTA
1 TTTTCTAGTTTAATTA
16663 TTTTCT-GTTTAATT
1 TTTTCTAGTTTAATT
16677 GCTTTCTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTTCTAGTTTAATTA
Done.