Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008166.1 Corchorus capsularis cultivar CVL-1 contig08187, 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: 40031
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:1946 original size:12 final size:13
Alignment explanation
Indices: 1921--1954 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1911 ATAATTATTG
1921 TTTGCTTTATTAA
1 TTTGCTTTATTAA
1934 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
1946 TCTGCTTTA
1 TTTGCTTTA
1955 GATTTAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:11230 original size:20 final size:20
Alignment explanation
Indices: 11205--11242 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11195 GGATTTTAAG
*
11205 AAAGCAAATTAAACTAAAAC
1 AAAGCAAAGTAAACTAAAAC
*
11225 AAAGCAAAGTAAATTAAA
1 AAAGCAAAGTAAACTAAA
11243 TCTAAATCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.11, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAGCAAAGTAAACTAAAAC
Found at i:12823 original size:22 final size:21
Alignment explanation
Indices: 12791--12841 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
12781 CTAAAAACAC
*
12791 AAATACTTATAAAATAGGGTAA
1 AAATACATATAAAA-AGGGTAA
*
12813 AAATACATATAAAAATGGTAA
1 AAATACATATAAAAAGGGTAA
12834 AAA-ACATA
1 AAATACATA
12842 GGAAAATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 5 0.19
21 9 0.33
22 13 0.48
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.24
Consensus pattern (21 bp):
AAATACATATAAAAAGGGTAA
Found at i:12847 original size:21 final size:21
Alignment explanation
Indices: 12808--12848 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12798 TATAAAATAG
*
12808 GGTAAAAATACATATAAAAAT
1 GGTAAAAATACATAGAAAAAT
*
12829 GGTAAAAA-ACATAGGAAAAT
1 GGTAAAAATACATAGAAAAAT
12849 AACTATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.61, C:0.05, G:0.15, T:0.20
Consensus pattern (21 bp):
GGTAAAAATACATAGAAAAAT
Found at i:18248 original size:20 final size:20
Alignment explanation
Indices: 18223--18260 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18213 GGATTTTAAG
*
18223 AAAGCAAATTAAACTAAAAC
1 AAAGCAAAGTAAACTAAAAC
*
18243 AAAGCAAAGTAAATTAAA
1 AAAGCAAAGTAAACTAAA
18261 TCTAAATCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.11, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAGCAAAGTAAACTAAAAC
Found at i:35677 original size:15 final size:16
Alignment explanation
Indices: 35637--35677 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
35627 TACATAGATC
*
35637 TATATATATATATATA
1 TATATATATGTATATA
*
35653 TAT-TAGATGTATATA
1 TATATATATGTATATA
35668 T-TATATATGT
1 TATATATATGT
35678 GGAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 17 0.81
16 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (16 bp):
TATATATATGTATATA
Found at i:36821 original size:108 final size:108
Alignment explanation
Indices: 36567--36845 Score: 443
Period size: 108 Copynumber: 2.5 Consensus size: 108
36557 ACTATTATAT
* *
36567 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATTAAATTTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAA-TTAATATTTTTATAATTACTT
36632 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
60 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
36681 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATTTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TAATATTTTTATAATTACTTTATTT
*
36746 TTACCAAAAAATTTGGATATA-TTAAATTTTTTCTAATATACAA
65 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
36789 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTATATAATT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATT-AATATTTT-TATAATT
36846 TTTTTTTTAT
Statistics
Matches: 159, Mismatches: 3, Indels: 11
0.92 0.02 0.06
Matches are distributed among these distances:
107 1 0.01
108 69 0.43
109 62 0.39
110 3 0.02
111 2 0.01
114 22 0.14
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.50
Consensus pattern (108 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTAATATTTTTATAATTACTTTATTTT
TACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:37792 original size:19 final size:17
Alignment explanation
Indices: 37768--37802 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
37758 TAATAATAAT
37768 TTTTTAAGTATAATATTTA
1 TTTTTAA-T-TAATATTTA
37787 TTTTTAATTAATATTT
1 TTTTTAATTAATATTT
37803 TTTAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTTAATTAATATTTA
Done.