Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006041.1 Corchorus capsularis cultivar CVL-1 contig06059, 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: 23100
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1487 original size:27 final size:28
Alignment explanation
Indices: 1444--1501 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
1434 AAGCAAATTC
*
1444 AAAGCTAAAAGGTCCAAATGCAAGT-CA
1 AAAGCTAAAAGGCCCAAATGCAAGTCCA
* *
1471 AAAGCTAAAATGCCCAAGTGCAAGTCCA
1 AAAGCTAAAAGGCCCAAATGCAAGTCCA
1499 AAA
1 AAA
1502 TTAACCTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (28 bp):
AAAGCTAAAAGGCCCAAATGCAAGTCCA
Found at i:4134 original size:13 final size:13
Alignment explanation
Indices: 4118--4159 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
4108 AAGATGATAG
4118 CAAAACTTGATCA
1 CAAAACTTGATCA
4131 C-AAACTTGAT-A
1 CAAAACTTGATCA
4142 GCAAAACTTGATCA
1 -CAAAACTTGATCA
4156 CAAA
1 CAAA
4160 CCATTTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.04
12 10 0.38
13 14 0.54
14 1 0.04
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (13 bp):
CAAAACTTGATCA
Found at i:4137 original size:12 final size:12
Alignment explanation
Indices: 4120--4160 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
4110 GATGATAGCA
4120 AAACTTGATCAC
1 AAACTTGATCAC
4132 AAACTTGAT-AGC
1 AAACTTGATCA-C
4144 AAAACTTGATCAC
1 -AAACTTGATCAC
4157 AAAC
1 AAAC
4161 CATTTTACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.04
12 14 0.54
13 10 0.38
14 1 0.04
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.22
Consensus pattern (12 bp):
AAACTTGATCAC
Found at i:4146 original size:25 final size:25
Alignment explanation
Indices: 4112--4160 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
4102 CTTCTGAAGA
4112 TGATAGCAAAACTTGATCACAAACT
1 TGATAGCAAAACTTGATCACAAACT
4137 TGATAGCAAAACTTGATCACAAAC
1 TGATAGCAAAACTTGATCACAAAC
4161 CATTTTACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (25 bp):
TGATAGCAAAACTTGATCACAAACT
Found at i:11775 original size:13 final size:12
Alignment explanation
Indices: 11752--11792 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
11742 TTAATACAGG
11752 TATCGATGGATA
1 TATCGATGGATA
11764 TATCGAATGGATA
1 TATCG-ATGGATA
*
11777 TATCGACGGATA
1 TATCGATGGATA
11789 TATC
1 TATC
11793 AAGGTATCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (12 bp):
TATCGATGGATA
Found at i:19097 original size:11 final size:11
Alignment explanation
Indices: 19081--19106 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19071 GTTTTTGAAC
19081 CCGATACCGAA
1 CCGATACCGAA
19092 CCGATACCGAA
1 CCGATACCGAA
19103 CCGA
1 CCGA
19107 CTATTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.38, G:0.19, T:0.08
Consensus pattern (11 bp):
CCGATACCGAA
Found at i:19173 original size:16 final size:19
Alignment explanation
Indices: 19135--19174 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
19125 TATTTTTCAG
19135 ATATATATAAATTATA-AT
1 ATATATATAAATTATATAT
*
19153 ATATATAATAAATTATTTAT
1 ATATAT-ATAAATTATATAT
19173 AT
1 AT
19175 GCGTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATATATAAATTATATAT
Found at i:19196 original size:15 final size:16
Alignment explanation
Indices: 19178--19210 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19168 TTTATATGCG
*
19178 TTTTA-TATTTATAAT
1 TTTTATTATTAATAAT
19193 TTTTATTATTAATAAT
1 TTTTATTATTAATAAT
19209 TT
1 TT
19211 AGAAATACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATTATTAATAAT
Done.