Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013418.1 Corchorus olitorius cultivar O-4 contig13451, 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: 7431
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1052 original size:39 final size:37
Alignment explanation
Indices: 938--1138 Score: 245
Period size: 34 Copynumber: 5.5 Consensus size: 37
928 TGAAAATGAC
* * *
938 GGGAACTTTCCCTAAATTG-AAAAC-T-AAAACCTGGT
1 GGGAACTTTCCC-AATTTGAAAAACTTAAAAACTTGAT
* *
973 GGGAACTTTCCCAAATTG-AAAACTTAAAAACTTGGT
1 GGGAACTTTCCCAATTTGAAAAACTTAAAAACTTGAT
1009 GGGAACTTTCCCAATTTGAAAAACTTAAAAAAACTTGAT
1 GGGAACTTTCCCAATTTGAAAAACTT--AAAAACTTGAT
1048 GGGAACTTTCCCAATTTGAAAAACTTAAAAAACTTGAT
1 GGGAACTTTCCCAATTTGAAAAACTT-AAAAACTTGAT
* *
1086 GGGAACTTTCCAAATTTG-AAAAC-T-AAAACCTGAT
1 GGGAACTTTCCCAATTTGAAAAACTTAAAAACTTGAT
*
1120 GGGAACTTTCCTAATTTGA
1 GGGAACTTTCCCAATTTGA
1139 CTTTTGAGTT
Statistics
Matches: 154, Mismatches: 6, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
34 37 0.24
35 13 0.08
36 27 0.18
37 12 0.08
38 29 0.19
39 36 0.23
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (37 bp):
GGGAACTTTCCCAATTTGAAAAACTTAAAAACTTGAT
Found at i:2323 original size:14 final size:14
Alignment explanation
Indices: 2288--2325 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2278 GGACCCTCCG
2288 CTTCTTGCTTCCCTT
1 CTTCTT-CTTCCCTT
2303 -TTC-TCTTCCCTT
1 CTTCTTCTTCCCTT
2315 CTTCTTCTTCC
1 CTTCTTCTTCC
2326 TCCTTGCGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.38
13 4 0.19
14 9 0.43
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (14 bp):
CTTCTTCTTCCCTT
Found at i:2523 original size:15 final size:15
Alignment explanation
Indices: 2512--2541 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2502 CCCAAATCTC
2512 AACCTCCAAAATTCG
1 AACCTCCAAAATTCG
2527 AACCTCCCAAAATTC
1 AACCT-CCAAAATTC
2542 TCTACTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.37, G:0.03, T:0.20
Consensus pattern (15 bp):
AACCTCCAAAATTCG
Found at i:2538 original size:16 final size:15
Alignment explanation
Indices: 2500--2541 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
2490 AAACTTCCCT
2500 CTCCC-AAATCTCAAC
1 CTCCCAAAAT-TCAAC
2515 CT-CCAAAATTCGAAC
1 CTCCCAAAATTC-AAC
2530 CTCCCAAAATTC
1 CTCCCAAAATTC
2542 TCTACTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.17
15 11 0.46
16 9 0.38
ACGTcount: A:0.36, C:0.40, G:0.02, T:0.21
Consensus pattern (15 bp):
CTCCCAAAATTCAAC
Found at i:5396 original size:27 final size:27
Alignment explanation
Indices: 5362--5417 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5352 ATAATAAATG
5362 AACATGAATATGACCAAAGTAACTAAT
1 AACATGAATATGACCAAAGTAACTAAT
5389 AACATGAATATGACCAAAGTAACTAAT
1 AACATGAATATGACCAAAGTAACTAAT
5416 AA
1 AA
5418 AAACATGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (27 bp):
AACATGAATATGACCAAAGTAACTAAT
Found at i:5430 original size:30 final size:30
Alignment explanation
Indices: 5353--5431 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 30
5343 GTATGCCCAA
5353 TAATAAATGAACATGAATATGACCAAAGTAAC
1 TAATAAA--AACATGAATATGACCAAAGTAAC
5385 TAAT---AACATGAATATGACCAAAGTAAC
1 TAATAAAAACATGAATATGACCAAAGTAAC
*
5412 TAATAAAAACATGCATATGA
1 TAATAAAAACATGAATATGA
5432 TTGATGTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
27 27 0.63
30 12 0.28
32 4 0.09
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.23
Consensus pattern (30 bp):
TAATAAAAACATGAATATGACCAAAGTAAC
Done.