Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009042.1 Corchorus capsularis cultivar CVL-1 contig09063, 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: 17274
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Found at i:8418 original size:13 final size:13
Alignment explanation
Indices: 8400--8424 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8390 TTTACAACTA
8400 GATTCGTATCAAT
1 GATTCGTATCAAT
8413 GATTCGTATCAA
1 GATTCGTATCAA
8425 CATGTCCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GATTCGTATCAAT
Found at i:9048 original size:12 final size:12
Alignment explanation
Indices: 9017--9048 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
9007 AACCCTAGCT
*
9017 ACAACTTACAAC
1 ACAACTTTCAAC
9029 ACAACTTTCAAC
1 ACAACTTTCAAC
9041 ACAACTTT
1 ACAACTTT
9049 TCTTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (12 bp):
ACAACTTTCAAC
Found at i:11354 original size:16 final size:15
Alignment explanation
Indices: 11322--11389 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 15
11312 ACCCTAGAGC
11322 TTTTTTCTCTC-TCTTT
1 TTTTTTCT-TCAT-TTT
11338 TTTTTTCATTCATTTT
1 TTTTTTC-TTCATTTT
*
11354 TTTATTTCCTCATTTT
1 TTT-TTTCTTCATTTT
11370 TTCATTTT-TTCATTTT
1 TT--TTTTCTTCATTTT
11386 TTTT
1 TTTT
11390 CATTGCACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
14 2 0.04
16 33 0.73
17 9 0.20
18 1 0.02
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTTCTTCATTTT
Found at i:11385 original size:7 final size:8
Alignment explanation
Indices: 11346--11387 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
11336 TTTTTTTTCA
11346 TTCATTTT
1 TTCATTTT
* *
11354 TTTATTTC
1 TTCATTTT
*
11362 CTCATTTT
1 TTCATTTT
11370 TTCATTTT
1 TTCATTTT
11378 TTCATTTT
1 TTCATTTT
11386 TT
1 TT
11388 TTCATTGCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (8 bp):
TTCATTTT
Found at i:12068 original size:12 final size:12
Alignment explanation
Indices: 12045--12081 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
12035 TTCGAAAATT
12045 ATTTTTGAAAAAC
1 ATTTTTG-AAAAC
12058 ATTTTTGAAAAC
1 ATTTTTGAAAAC
12070 ATTTTTGAAAAC
1 ATTTTTGAAAAC
12082 CATGATTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:12097 original size:20 final size:19
Alignment explanation
Indices: 12072--12136 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
12062 TTGAAAACAT
12072 TTTTGAAAACCATGATTCTC
1 TTTTGAAAACCATGA-TCTC
*
12092 TTTTGAAAAACATG---T-
1 TTTTGAAAACCATGATCTC
12107 TTTTGAAAAACCATGACTCTC
1 TTTTG-AAAACCATGA-TCTC
12128 TTTTGAAAA
1 TTTTGAAAA
12137 ACATTTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
15 5 0.14
16 9 0.24
20 18 0.49
21 5 0.14
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TTTTGAAAACCATGATCTC
Found at i:12101 original size:21 final size:20
Alignment explanation
Indices: 12072--12138 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
12062 TTGAAAACAT
12072 TTTTG-AAAACCATGATTCTC
1 TTTTGAAAAACCATGA-TCTC
12092 TTTTGAAAAA-CATG---T-
1 TTTTGAAAAACCATGATCTC
12107 TTTTGAAAAACCATGACTCTC
1 TTTTGAAAAACCATGA-TCTC
12128 TTTTGAAAAAC
1 TTTTGAAAAAC
12139 ATTTTTGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
15 10 0.25
16 5 0.12
20 10 0.25
21 15 0.38
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (20 bp):
TTTTGAAAAACCATGATCTC
Found at i:12121 original size:16 final size:15
Alignment explanation
Indices: 12046--12117 Score: 55
Period size: 20 Copynumber: 4.8 Consensus size: 15
12036 TCGAAAATTA
12046 TTTTTGAAAAACA--
1 TTTTTGAAAAACATG
12059 TTTTTG-AAAACA--
1 TTTTTGAAAAACATG
*
12071 TTTTTGAAAACCATG
1 TTTTTGAAAAACATG
12086 ATTCTCTTTTGAAAAACATG
1 ----T-TTTTGAAAAACATG
12106 TTTTTGAAAAAC
1 TTTTTGAAAAAC
12118 CATGACTCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
12 12 0.24
13 11 0.22
15 11 0.22
16 1 0.02
19 1 0.02
20 13 0.27
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (15 bp):
TTTTTGAAAAACATG
Found at i:12155 original size:33 final size:33
Alignment explanation
Indices: 12060--12161 Score: 161
Period size: 36 Copynumber: 3.0 Consensus size: 33
12050 TGAAAAACAT
*
12060 TTTTG-AAAACATTTTTGAAAACCATGATTCTC
1 TTTTGAAAAACATTTTTGAAAACCATGACTCTC
12092 TTTTGAAAAACATGTTTTTGAAAAACCATGACTCTC
1 TTTTGAAAAACA--TTTTTG-AAAACCATGACTCTC
12128 TTTTGAAAAACATTTTTGAAAACCATGACTCTC
1 TTTTGAAAAACATTTTTGAAAACCATGACTCTC
12161 T
1 T
12162 ACCATTCCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
32 5 0.08
33 22 0.34
34 6 0.09
35 6 0.09
36 26 0.40
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (33 bp):
TTTTGAAAAACATTTTTGAAAACCATGACTCTC
Found at i:14323 original size:21 final size:18
Alignment explanation
Indices: 14285--14325 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
14275 GGAATATTCT
14285 TGCTTCCAATGACTTCAA
1 TGCTTCCAATGACTTCAA
14303 TGCTCTCCAATTGATCTTCAA
1 TGCT-TCCAA-TGA-CTTCAA
14324 TG
1 TG
14326 GTCTTCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 3 0.15
21 8 0.40
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (18 bp):
TGCTTCCAATGACTTCAA
Done.