Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018464.1 Corchorus olitorius cultivar O-4 contig18497, 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: 42013
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1814 original size:2 final size:2
Alignment explanation
Indices: 1809--1848 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1799 TATAATTAAA
*
1809 AT AT AT AT A- AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1849 AGTGTCGAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3701 original size:2 final size:2
Alignment explanation
Indices: 3694--3720 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3684 CTTAACCACT
3694 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3721 TGGAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7596 original size:1 final size:1
Alignment explanation
Indices: 7590--7623 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
7580 GGTATGTTTC
*
7590 TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7624 AAAGGCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:14956 original size:80 final size:80
Alignment explanation
Indices: 14823--14985 Score: 308
Period size: 80 Copynumber: 2.0 Consensus size: 80
14813 ATCTTGATTC
14823 TTTATGCTTAATTTGATGATTTTCAAGTGCCTATCCTTTGAATTAATACTTAATTGCTTTGTTTT
1 TTTATGCTTAATTTGATGATTTTCAAGTGCCTATCCTTTGAATTAATACTTAATTGCTTTGTTTT
14888 TGTCTTATAGGTACT
66 TGTCTTATAGGTACT
* *
14903 TTTATGCTTAATTTGATGATTTTCAAGTGTCTATCCTTTGAATTAGTACTTAATTGCTTTGTTTT
1 TTTATGCTTAATTTGATGATTTTCAAGTGCCTATCCTTTGAATTAATACTTAATTGCTTTGTTTT
14968 TGTCTTATAGGTACT
66 TGTCTTATAGGTACT
14983 TTT
1 TTT
14986 GGAGATAATG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (80 bp):
TTTATGCTTAATTTGATGATTTTCAAGTGCCTATCCTTTGAATTAATACTTAATTGCTTTGTTTT
TGTCTTATAGGTACT
Found at i:16100 original size:21 final size:20
Alignment explanation
Indices: 16053--16102 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
16043 TGGGATTGGG
*
16053 TATTTATTTATCTTGTTGCT
1 TATTTATTTATCTTCTTGCT
* * *
16073 TAATTATATTATTTTCTTGTT
1 TATTTAT-TTATCTTCTTGCT
16094 TATTTATTT
1 TATTTATTT
16103 TTATTGTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.68
Consensus pattern (20 bp):
TATTTATTTATCTTCTTGCT
Found at i:23550 original size:21 final size:21
Alignment explanation
Indices: 23512--23553 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23502 TTCCTCTGCT
*
23512 TCCGCTTTAGTCTGCAACTCC
1 TCCGCTTTAGTCTCCAACTCC
**
23533 TCCGCTTTCTTCTCCAACTCC
1 TCCGCTTTAGTCTCCAACTCC
23554 CGCATCTCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.43, G:0.10, T:0.36
Consensus pattern (21 bp):
TCCGCTTTAGTCTCCAACTCC
Found at i:26188 original size:31 final size:30
Alignment explanation
Indices: 26120--26188 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
26110 TTATGGCAGT
*
26120 GGCAAAGTGTCCTTTATTTCATACTTTGGG
1 GGCAAAGTGTCCTTTATTTCATACTTAGGG
* *
26150 GGAAAAGTGTCCTTTATTTCATGCTTCAGGG
1 GGCAAAGTGTCCTTTATTTCATACTT-AGGG
26181 GGCAAAGT
1 GGCAAAGT
26189 TGGACAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (30 bp):
GGCAAAGTGTCCTTTATTTCATACTTAGGG
Found at i:32034 original size:32 final size:32
Alignment explanation
Indices: 31998--32085 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 32
31988 AAAAAGAATC
*
31998 AATCAAACCTAATACCCAAAATCCAGACCTAA
1 AATCAAACCTAAAACCCAAAATCCAGACCTAA
* *
32030 AATCAAACCTAAAACCCCAAAACCCAGACTTAA
1 AATCAAACCTAAAA-CCCAAAATCCAGACCTAA
* *
32063 AATCAAATCTAAAACCCTAAATC
1 AATCAAACCTAAAACCCAAAATC
32086 AATTAAAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 20 0.41
33 29 0.59
ACGTcount: A:0.51, C:0.31, G:0.02, T:0.16
Consensus pattern (32 bp):
AATCAAACCTAAAACCCAAAATCCAGACCTAA
Found at i:37434 original size:2 final size:2
Alignment explanation
Indices: 37427--37455 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37417 AAATGCCACA
37427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37456 CTAAATAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39546 original size:31 final size:31
Alignment explanation
Indices: 39405--39545 Score: 149
Period size: 31 Copynumber: 4.5 Consensus size: 31
39395 GCATGCCATG
** * * **
39405 TGTCACTTTTTGGTACACATGACGTGACATG
1 TGTCACTTTTTGGTACATGTGGCGTGCCACA
* *
39436 TGTCACTTTTTGGTACATGTGGCGTACCACT
1 TGTCACTTTTTGGTACATGTGGCGTGCCACA
*
39467 TGTCACTTTTTGGTACATGTGGTGTGCCACA
1 TGTCACTTTTTGGTACATGTGGCGTGCCACA
* *
39498 TGTCGCTTTTTGGTACACT-TGGCGTGTCACA
1 TGTCACTTTTTGGTACA-TGTGGCGTGCCACA
* *
39529 TGTCGCTTTTTAGTACA
1 TGTCACTTTTTGGTACA
39546 CATGGCATGC
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
31 94 0.99
32 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (31 bp):
TGTCACTTTTTGGTACATGTGGCGTGCCACA
Done.