Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008074.1 Corchorus capsularis cultivar CVL-1 contig08095, 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: 33042
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:3593 original size:2 final size:2
Alignment explanation
Indices: 3586--3663 Score: 71
Period size: 2 Copynumber: 41.0 Consensus size: 2
3576 CTTTTGTCTC
3586 AT AT AT AT AT AT AT AT -T AT -T AT AT AT ACT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
*
3626 AT AT TT AT -T AT AT ACT A- AT AT -T AT ACT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT
3664 TTTTCTTTGA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
1 7 0.11
2 51 0.80
3 6 0.09
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3622 original size:30 final size:31
Alignment explanation
Indices: 3588--3664 Score: 104
Period size: 30 Copynumber: 2.5 Consensus size: 31
3578 TTTGTCTCAT
*
3588 ATATATATATATATTATTATATA-TACTATA
1 ATATATATATATATTATTATATACTAATATA
*
3618 ATATATATATAT-TTATTATATACTAATATT
1 ATATATATATATATTATTATATACTAATATA
3648 ATACTAATATATATATT
1 ATA-T-ATATATATATT
3665 TTTCTTTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
29 10 0.24
30 20 0.49
31 1 0.02
32 8 0.20
33 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (31 bp):
ATATATATATATATTATTATATACTAATATA
Found at i:3664 original size:34 final size:32
Alignment explanation
Indices: 3586--3665 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 32
3576 CTTTTGTCTC
*
3586 ATATATATATATATATTATTATATATACTATA
1 ATATATATATATTTATTATTATATATACTATA
*
3618 ATATATATATATTTATTA-TATACTAATATTATA
1 ATATATATATATTTATTATTATA-T-ATACTATA
*
3651 CTAATATATATATTT
1 AT-ATATATATATTT
3666 TTCTTTGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 18 0.43
33 8 0.19
34 12 0.29
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATATATATATTTATTATTATATATACTATA
Found at i:12794 original size:15 final size:15
Alignment explanation
Indices: 12774--12804 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12764 GTCAATAGGG
*
12774 TTCTTTTTTTTCTTT
1 TTCTTTTATTTCTTT
12789 TTCTTTTATTTCTTT
1 TTCTTTTATTTCTTT
12804 T
1 T
12805 ATAGATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTTTTATTTCTTT
Found at i:14124 original size:2 final size:2
Alignment explanation
Indices: 14117--14155 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
14107 GCCAGTGGGG
14117 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
14156 TTTGTGTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:17160 original size:47 final size:47
Alignment explanation
Indices: 17106--17200 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
17096 GCTGCAGCTC
*
17106 ATTGAATGTTGATGGAAGTTTTGGTACAAGCCTCTCTTGTGGAAAAT
1 ATTGAATGTTGATGGAAGTTTTGGTACAAGCCTCTCTTGTGAAAAAT
17153 ATTGAATGTTGATGGAAGTTTTGGTACAAGCCTCTCTTGTGAAAAAT
1 ATTGAATGTTGATGGAAGTTTTGGTACAAGCCTCTCTTGTGAAAAAT
17200 A
1 A
17201 GACAATCACG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (47 bp):
ATTGAATGTTGATGGAAGTTTTGGTACAAGCCTCTCTTGTGAAAAAT
Found at i:23567 original size:1 final size:1
Alignment explanation
Indices: 23561--23590 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
23551 ACTGCTTTAA
*
23561 CCCCCCCCCCCCCCCCCCCCCCTCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
23591 TTCCTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:25295 original size:43 final size:42
Alignment explanation
Indices: 25197--25310 Score: 156
Period size: 43 Copynumber: 2.7 Consensus size: 42
25187 TCTAGATGAG
* *
25197 AAGTGTCGTAAAATACATCATTTTCTAACGTAAAATTGGTGAA
1 AAGTGTCATAAAATACATCA-TTTCTAACATAAAATTGGTGAA
* * *
25240 AAATGTCCTAAAATACATCATTTGTAACATAAAATTGGTGACA
1 AAGTGTCATAAAATACATCATTTCTAACATAAAATTGGTGA-A
*
25283 AAGTGTCATAAAATACATCATCTCTAAC
1 AAGTGTCATAAAATACATCATTTCTAAC
25311 GTATATAACT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 19 0.31
43 43 0.69
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (42 bp):
AAGTGTCATAAAATACATCATTTCTAACATAAAATTGGTGAA
Found at i:29105 original size:20 final size:20
Alignment explanation
Indices: 29080--29122 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
29070 GTGAAATTTC
29080 ACACATTGCATTGTTTTGTT
1 ACACATTGCATTGTTTTGTT
29100 ACACATTGCATTGTTTTGTT
1 ACACATTGCATTGTTTTGTT
29120 ACA
1 ACA
29123 ATATATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (20 bp):
ACACATTGCATTGTTTTGTT
Done.