Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022047.1 Corchorus olitorius cultivar O-4 contig22080, 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: 7592
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Found at i:292 original size:21 final size:20
Alignment explanation
Indices: 251--299 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
241 GATTATGTAA
**
251 ATGCAAAATGTGAAATTAAT
1 ATGCAAAATGTGAAACAAAT
*
271 ATGCGAAAATGTGATACAAAT
1 ATGC-AAAATGTGAAACAAAT
292 ATGCAAAA
1 ATGCAAAA
300 GAACACAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.24
Consensus pattern (20 bp):
ATGCAAAATGTGAAACAAAT
Found at i:457 original size:28 final size:28
Alignment explanation
Indices: 390--496 Score: 114
Period size: 27 Copynumber: 3.9 Consensus size: 28
380 ACTTGAGCAA
* *
390 TGGA-GTAGAAATGACCATAATGCCCCC
1 TGGATGTAAAAATGACCAAAATGCCCCC
* * * *
417 T-GAAGCACAAATGACTAAAATGCCCCC
1 TGGATGTAAAAATGACCAAAATGCCCCC
444 TAGG-TGTAAAAATGACCAAAATG-CCCC
1 T-GGATGTAAAAATGACCAAAATGCCCCC
*
471 TGGATGTGAAAATGACCAAAATGCCC
1 TGGATGTAAAAATGACCAAAATGCCC
497 TTAGGTGATC
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
26 4 0.06
27 44 0.67
28 17 0.26
29 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (28 bp):
TGGATGTAAAAATGACCAAAATGCCCCC
Found at i:2240 original size:16 final size:16
Alignment explanation
Indices: 2188--2250 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
2178 CACGAATCCG
* *
2188 AAATTACCCAAATCC-
1 AAATGACCCAAACCCA
* *
2203 AAACGACCCGAACCCGA
1 AAATGACCCAAACCC-A
2220 AAATGACCCAAACCCA
1 AAATGACCCAAACCCA
*
2236 AAATGACCCGAACCC
1 AAATGACCCAAACCC
2251 GATCAACCCG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 11 0.28
16 15 0.38
17 13 0.33
ACGTcount: A:0.44, C:0.38, G:0.10, T:0.08
Consensus pattern (16 bp):
AAATGACCCAAACCCA
Found at i:2249 original size:33 final size:32
Alignment explanation
Indices: 2180--2252 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 32
2170 TTTGGGTACA
* * *
2180 CGAATCCG-AAATTACCCAAATCCAAACGACC
1 CGAACCCGAAAATGACCCAAACCCAAACGACC
*
2211 CGAACCCGAAAATGACCCAAACCCAAAATGACC
1 CGAACCCGAAAATGACCCAAACCC-AAACGACC
2244 CGAACCCGA
1 CGAACCCGA
2253 TCAACCCGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 7 0.19
32 13 0.36
33 16 0.44
ACGTcount: A:0.42, C:0.37, G:0.12, T:0.08
Consensus pattern (32 bp):
CGAACCCGAAAATGACCCAAACCCAAACGACC
Found at i:4130 original size:21 final size:21
Alignment explanation
Indices: 4106--4172 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
4096 AATTCTCTGT
4106 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
4127 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
4148 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
4169 AAAT
1 AAAT
4173 CCTAATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:4152 original size:42 final size:42
Alignment explanation
Indices: 4093--4173 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
4083 GCTAAGTCTT
4093 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
4135 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
4174 CTAATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:4311 original size:56 final size:56
Alignment explanation
Indices: 4239--4407 Score: 311
Period size: 56 Copynumber: 3.0 Consensus size: 56
4229 TTTATTTTGT
* *
4239 AGAATAATTAAGTAGAGATATGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
*
4295 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAATATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
4351 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
4407 A
1 A
4408 AGGAAACGAA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 109 1.00
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.36
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:5646 original size:15 final size:16
Alignment explanation
Indices: 5619--5675 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
5609 TCCGAACCGT
5619 ATGACCCGAAACCAAAA
1 ATGACCCG-AACCAAAA
*
5636 ATGACCC-AACCCAGAA
1 ATGACCCGAA-CCAAAA
* *
5652 TTGACCCGAACC-CAA
1 ATGACCCGAACCAAAA
5667 ATGACCCGA
1 ATGACCCGA
5676 CATTTGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.35
16 13 0.38
17 9 0.26
ACGTcount: A:0.42, C:0.35, G:0.14, T:0.09
Consensus pattern (16 bp):
ATGACCCGAACCAAAA
Found at i:5658 original size:16 final size:15
Alignment explanation
Indices: 5619--5675 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 15
5609 TCCGAACCGT
*
5619 ATGACCCGAAACCAAAA
1 ATGACCCG-AACC-CAA
5636 ATGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
5651 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
5667 ATGACCCGA
1 ATGACCCGA
5676 CATTTGAACG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.39
16 8 0.22
17 13 0.36
ACGTcount: A:0.42, C:0.35, G:0.14, T:0.09
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:6823 original size:30 final size:30
Alignment explanation
Indices: 6789--6867 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
6779 AGATTAAATC
6789 AGTCAACAATGTATTTATAGTGGAATCCAA
1 AGTCAACAATGTATTTATAGTGGAATCCAA
* * *
6819 AGTCAACAATGTATTTACAGTGGGATTCAA
1 AGTCAACAATGTATTTATAGTGGAATCCAA
* * *
6849 AATCAACAGTTTATTTATA
1 AGTCAACAATGTATTTATA
6868 ATAGGATCCA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (30 bp):
AGTCAACAATGTATTTATAGTGGAATCCAA
Found at i:7368 original size:25 final size:25
Alignment explanation
Indices: 7340--7390 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
7330 CCTATAAGAT
7340 CTCATTAAAATCACCAATACATGCC
1 CTCATTAAAATCACCAATACATGCC
7365 CTCATTAAAATCACCAATACATGCC
1 CTCATTAAAATCACCAATACATGCC
7390 C
1 C
7391 GAGAGTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.33, G:0.04, T:0.24
Consensus pattern (25 bp):
CTCATTAAAATCACCAATACATGCC
Done.