Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021304.1 Corchorus olitorius cultivar O-4 contig21337, 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: 16325
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:6343 original size:28 final size:29
Alignment explanation
Indices: 6289--6355 Score: 118
Period size: 28 Copynumber: 2.3 Consensus size: 29
6279 GACTGGAATA
*
6289 CCCCTAGATGTGCAAAAATGACCAAAATG
1 CCCCTGGATGTGCAAAAATGACCAAAATG
6318 CCCCTGGATGTGC-AAAATGACCAAAATG
1 CCCCTGGATGTGCAAAAATGACCAAAATG
6346 CCCCTGGATG
1 CCCCTGGATG
6356 AGTGACCCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 25 0.68
29 12 0.32
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (29 bp):
CCCCTGGATGTGCAAAAATGACCAAAATG
Found at i:9885 original size:102 final size:102
Alignment explanation
Indices: 9709--9914 Score: 376
Period size: 102 Copynumber: 2.0 Consensus size: 102
9699 AGTTAAACTG
* *
9709 TCCCAAAATTGAGAATCAGAGAGCTTAATTGTCCCAATCGAAAGTCTAGGAGTCATTTTTTCCCT
1 TCCCAAAATTGAGAATCAGAGAGCATAAATGTCCCAATCGAAAGTCTAGGAGTCATTTTTTCCCT
9774 TTGGTGATAGCTCAAGGATCATTTTGTCTATTAATCC
66 TTGGTGATAGCTCAAGGATCATTTTGTCTATTAATCC
*
9811 TCCCAAAATTGAGAATCAGAGAGCATAAATGTCCCAATCGAAAGTTTAGGAGTCATTTTTTCCCT
1 TCCCAAAATTGAGAATCAGAGAGCATAAATGTCCCAATCGAAAGTCTAGGAGTCATTTTTTCCCT
*
9876 TTGGTGATAGTTCAAGGATCATTTTGTCTATTAATCC
66 TTGGTGATAGCTCAAGGATCATTTTGTCTATTAATCC
9913 TC
1 TC
9915 AACAAATTCA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (102 bp):
TCCCAAAATTGAGAATCAGAGAGCATAAATGTCCCAATCGAAAGTCTAGGAGTCATTTTTTCCCT
TTGGTGATAGCTCAAGGATCATTTTGTCTATTAATCC
Found at i:10412 original size:2 final size:2
Alignment explanation
Indices: 10407--10440 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10397 CTATAGAACT
10407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10441 ATAGAAGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11429 original size:52 final size:52
Alignment explanation
Indices: 11332--11620 Score: 401
Period size: 52 Copynumber: 5.6 Consensus size: 52
11322 ATTGAAAACT
* *
11332 AAAACTTGATGGGAACTTTCCCAATTTAATAAAAGAGCTAAATTGAATACTTTG
1 AAAAC-TGGTGGGAACTTTCCCAATTTGA-AAAAGAGCTAAATTGAATACTTTG
*
11386 AAAACTGGTAGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
* *
11438 AAGACTAGTGGGAACTTTCCCAATTTG-AAAA-A-CTTAAATTGAATACTTTG
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGC-TAAATTGAATACTTTG
* * * *
11488 AAAACTGATGGGAACTTTCCCAACTTGAAAAAGAGATAGATTGAATACTTTG
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
* *
11540 AAGACTGATGGGAACTTTCCCAATTTG-AAAA-A-CTTAAATTGAATACTTTG
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGC-TAAATTGAATACTTTG
11590 AAAACTGGTGGGAACTTTCCCAATTTGAAAA
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAA
11621 CTTAAACCTG
Statistics
Matches: 211, Mismatches: 18, Indels: 15
0.86 0.07 0.06
Matches are distributed among these distances:
49 1 0.00
50 81 0.38
51 15 0.07
52 89 0.42
53 20 0.09
54 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (52 bp):
AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
Found at i:11502 original size:102 final size:102
Alignment explanation
Indices: 11338--11620 Score: 453
Period size: 102 Copynumber: 2.7 Consensus size: 102
11328 AACTAAAACT
* *
11338 TGATGGGAACTTTCCCAATTTAATAAAAGAGC-TAAATTGAATACTTTGAAAACTGGTAGGAACT
1 TGATGGGAACTTTCCCAATTT--GAAAA-A-CTTAAATTGAATACTTTGAAAACTGGTGGGAACT
*
11402 TTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAGAC
62 TTCCCAATTTGAAAAAGAGATAAATTGAATACTTTGAAGAC
*
11443 T-AGTGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTTTGAAAACTGATGGGAACTTTC
1 TGA-TGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTTTGAAAACTGGTGGGAACTTTC
* *
11507 CCAACTTGAAAAAGAGATAGATTGAATACTTTGAAGAC
65 CCAATTTGAAAAAGAGATAAATTGAATACTTTGAAGAC
11545 TGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTTTGAAAACTGGTGGGAACTTTCC
1 TGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTTTGAAAACTGGTGGGAACTTTCC
11610 CAATTTGAAAA
66 CAATTTGAAAA
11621 CTTAAACCTG
Statistics
Matches: 167, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
101 1 0.01
102 141 0.84
103 5 0.03
104 1 0.01
105 19 0.11
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (102 bp):
TGATGGGAACTTTCCCAATTTGAAAAACTTAAATTGAATACTTTGAAAACTGGTGGGAACTTTCC
CAATTTGAAAAAGAGATAAATTGAATACTTTGAAGAC
Found at i:15790 original size:17 final size:17
Alignment explanation
Indices: 15768--15803 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15758 TGATTTGTAA
15768 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
15785 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
15802 AG
1 AG
15804 CTCTTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Done.