Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012059.1 Corchorus olitorius cultivar O-4 contig12092, 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: 13404
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3526 original size:24 final size:23
Alignment explanation
Indices: 3473--3527 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
3463 GCCAGCTATC
**
3473 TTCTTCTCTTCATTTTTTGATTT
1 TTCTTCTCTTCATTTTTTGAGGT
* *
3496 TTCCTTCTCTTTATTTTCTTTAGGT
1 TT-CTTCTCTTCATTTT-TTGAGGT
3521 TTCTTCT
1 TTCTTCT
3528 AATATTTGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 18 0.69
25 6 0.23
ACGTcount: A:0.07, C:0.20, G:0.05, T:0.67
Consensus pattern (23 bp):
TTCTTCTCTTCATTTTTTGAGGT
Found at i:4247 original size:12 final size:12
Alignment explanation
Indices: 4230--4260 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4220 ATGTAAAAAC
4230 AAAAAAAAACAA
1 AAAAAAAAACAA
4242 AAAAAAAAACAA
1 AAAAAAAAACAA
*
4254 AACAAAA
1 AAAAAAA
4261 TGCAAATGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:4250 original size:17 final size:17
Alignment explanation
Indices: 4224--4260 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4214 GCTTAGATGT
*
4224 AAAAACAAAAAAAAACA
1 AAAAAAAAAAAAAAACA
*
4241 AAAAAAAAAACAAAACA
1 AAAAAAAAAAAAAAACA
4258 AAA
1 AAA
4261 TGCAAATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAACA
Found at i:4255 original size:10 final size:10
Alignment explanation
Indices: 4224--4248 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4214 GCTTAGATGT
4224 AAAAACAAAA
1 AAAAACAAAA
4234 AAAAACAAAA
1 AAAAACAAAA
4244 AAAAA
1 AAAAA
4249 AACAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:5313 original size:16 final size:16
Alignment explanation
Indices: 5292--5322 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5282 TTAACTAAAT
*
5292 TAGATTTGAGCTACAC
1 TAGATTTGAACTACAC
5308 TAGATTTGAACTACA
1 TAGATTTGAACTACA
5323 TGAATGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (16 bp):
TAGATTTGAACTACAC
Found at i:8037 original size:24 final size:24
Alignment explanation
Indices: 7965--8037 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
7955 AACAGAAAAA
* * * *
7965 CACAAGCAATCAATATAAAAAAGC
1 CACAAACAATCAACATTAAAAATC
*
7989 CACAAACATTCAACA-T--AAATC
1 CACAAACAATCAACATTAAAAATC
8010 CACAAACAATCAACATTAAAAATC
1 CACAAACAATCAACATTAAAAATC
8034 CACA
1 CACA
8038 TAAATGGGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
21 18 0.45
22 1 0.03
24 21 0.52
ACGTcount: A:0.56, C:0.26, G:0.03, T:0.15
Consensus pattern (24 bp):
CACAAACAATCAACATTAAAAATC
Found at i:8591 original size:26 final size:26
Alignment explanation
Indices: 8556--8605 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
8546 ATCTAGATGA
*
8556 CTAAAAATGAATTAGCTAATCTAAGC
1 CTAAAAATGAATTAGCTAAACTAAGC
* *
8582 CTAAATATGAGTTAGCTAAACTAA
1 CTAAAAATGAATTAGCTAAACTAA
8606 AAGTGGTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (26 bp):
CTAAAAATGAATTAGCTAAACTAAGC
Found at i:11018 original size:55 final size:54
Alignment explanation
Indices: 10952--11059 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 54
10942 TTATCAATAT
*
10952 AAAAATTCTCATTTTGGTTGAAATAAAGCTAATTTGGTCAGGATTATGCTTTAAG
1 AAAAATTCTCATTTTGGTTGAAACAAAGCTAATTTGGTCAGGATTATG-TTTAAG
* *
11007 AAAAATTCTCATTTTGGTTGCAACAAAGCTATTTTGGTCAGGATTATGTTTAA
1 AAAAATTCTCATTTTGGTTGAAACAAAGCTAATTTGGTCAGGATTATGTTTAA
11060 TTGGTATCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
54 5 0.10
55 45 0.90
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (54 bp):
AAAAATTCTCATTTTGGTTGAAACAAAGCTAATTTGGTCAGGATTATGTTTAAG
Found at i:12003 original size:36 final size:37
Alignment explanation
Indices: 11953--12024 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
11943 CATTTATAAG
*
11953 GCTACTTTCTCTTCCA-TCTCGAACCAACTGGCTTGA
1 GCTACTTTCCCTTCCATTCTCGAACCAACTGGCTTGA
* *
11989 GCTACTTTCCCTTCCATTTTCGAACCAATTGGCTTG
1 GCTACTTTCCCTTCCATTCTCGAACCAACTGGCTTG
12025 GAACTCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.18, C:0.32, G:0.14, T:0.36
Consensus pattern (37 bp):
GCTACTTTCCCTTCCATTCTCGAACCAACTGGCTTGA
Found at i:12034 original size:37 final size:36
Alignment explanation
Indices: 11954--12034 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 36
11944 ATTTATAAGG
* *
11954 CTACTTTCTCTTCCATCTCGAACCAACTGGCTTGAG
1 CTACTTTCCCTTCCATCTCGAACCAACTGGCTTGAA
* *
11990 CTACTTTCCCTTCCATTTTCGAACCAATTGGCTTGGAA
1 CTACTTTCCCTTCCA-TCTCGAACCAACTGGCTT-GAA
12028 CT-CTTTC
1 CTACTTTC
12035 ACCCGTTGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 14 0.36
37 21 0.54
38 4 0.10
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.37
Consensus pattern (36 bp):
CTACTTTCCCTTCCATCTCGAACCAACTGGCTTGAA
Done.