Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023496.1 Corchorus olitorius cultivar O-4 contig23529, 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: 39688
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1251 original size:28 final size:28
Alignment explanation
Indices: 1219--1276 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
1209 TTAATTGGCA
*
1219 TTGCACACCCGGGGGGCATTTTGGTCAT
1 TTGCACACCCAGGGGGCATTTTGGTCAT
**
1247 TTGCACAGTCAGGGGGCATTTTGGTCAT
1 TTGCACACCCAGGGGGCATTTTGGTCAT
1275 TT
1 TT
1277 TAAGTTCACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.16, C:0.21, G:0.31, T:0.33
Consensus pattern (28 bp):
TTGCACACCCAGGGGGCATTTTGGTCAT
Found at i:1787 original size:20 final size:20
Alignment explanation
Indices: 1762--1801 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1752 AAAATACAAT
1762 GCATTTAATTTACAAATTGG
1 GCATTTAATTTACAAATTGG
* *
1782 GCATTTGATTTGCAAATTGG
1 GCATTTAATTTACAAATTGG
1802 TGCTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (20 bp):
GCATTTAATTTACAAATTGG
Found at i:2550 original size:11 final size:11
Alignment explanation
Indices: 2528--2557 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2518 ACACCAAAAT
2528 CAGAGTCAATTA
1 CAGAG-CAATTA
2540 CAGAGCAATTA
1 CAGAGCAATTA
2551 CAGAGCA
1 CAGAGCA
2558 TCAATATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (11 bp):
CAGAGCAATTA
Found at i:5098 original size:14 final size:15
Alignment explanation
Indices: 5079--5109 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5069 AAGAGGTAAT
5079 AAAAGGTTTTT-TCA
1 AAAAGGTTTTTCTCA
5093 AAAAGGTTTTTCTCA
1 AAAAGGTTTTTCTCA
5108 AA
1 AA
5110 TCATGTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (15 bp):
AAAAGGTTTTTCTCA
Found at i:6255 original size:15 final size:15
Alignment explanation
Indices: 6235--6268 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
6225 GAAGTTGAAG
6235 ATGATGATGTTCCAA
1 ATGATGATGTTCCAA
6250 ATGATGATGTTCCAA
1 ATGATGATGTTCCAA
6265 ATGA
1 ATGA
6269 AGTTGTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (15 bp):
ATGATGATGTTCCAA
Found at i:6275 original size:15 final size:15
Alignment explanation
Indices: 6235--6277 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
6225 GAAGTTGAAG
*
6235 ATGATGATGTTCCAA
1 ATGAAGATGTTCCAA
*
6250 ATGATGATGTTCCAA
1 ATGAAGATGTTCCAA
*
6265 ATGAAGTTGTTCC
1 ATGAAGATGTTCC
6278 TCAAAGTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (15 bp):
ATGAAGATGTTCCAA
Found at i:6972 original size:7 final size:7
Alignment explanation
Indices: 6960--6984 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6950 AGTGATTTTG
6960 TTTTGTT
1 TTTTGTT
6967 TTTTGTT
1 TTTTGTT
6974 TTTTGTT
1 TTTTGTT
6981 TTTT
1 TTTT
6985 TTTGGTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:7230 original size:15 final size:16
Alignment explanation
Indices: 7210--7241 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7200 GAAGGATATA
7210 AATAAAC-TGAACAAG
1 AATAAACATGAACAAG
7225 AATAAACATGAACAAG
1 AATAAACATGAACAAG
7241 A
1 A
7242 CTCAGGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (16 bp):
AATAAACATGAACAAG
Found at i:7683 original size:20 final size:21
Alignment explanation
Indices: 7648--7697 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
7638 TATTTTGATA
7648 AACGAACACAAACAAACACTT
1 AACGAACACAAACAAACACTT
*
7669 AACGAACGC-AACAAACACTT
1 AACGAACACAAACAAACACTT
7689 AACGAACAC
1 AACGAACAC
7698 GAACCGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.54, C:0.30, G:0.08, T:0.08
Consensus pattern (21 bp):
AACGAACACAAACAAACACTT
Found at i:13189 original size:36 final size:36
Alignment explanation
Indices: 13146--13216 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
13136 TTGTGCAATG
13146 TTGTACAGTTTTGAGTTTTGAAGTTTCTACTTACTT
1 TTGTACAGTTTTGAGTTTTGAAGTTTCTACTTACTT
*
13182 TTGTACAGTTTTGTGTTTTGAAGTTTCTACTTACT
1 TTGTACAGTTTTGAGTTTTGAAGTTTCTACTTACT
13217 CCGATTTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.18, C:0.11, G:0.17, T:0.54
Consensus pattern (36 bp):
TTGTACAGTTTTGAGTTTTGAAGTTTCTACTTACTT
Found at i:21886 original size:2 final size:2
Alignment explanation
Indices: 21879--21906 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21869 GGTAATTCCA
21879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21907 TTGTCGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37948 original size:12 final size:12
Alignment explanation
Indices: 37931--37955 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37921 ATATTAAATG
37931 TGGTACAAAGAT
1 TGGTACAAAGAT
37943 TGGTACAAAGAT
1 TGGTACAAAGAT
37955 T
1 T
37956 TACTAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (12 bp):
TGGTACAAAGAT
Done.