Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013686.1 Corchorus olitorius cultivar O-4 contig13719, 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: 28988
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Found at i:3421 original size:106 final size:103
Alignment explanation
Indices: 3198--3447 Score: 358
Period size: 106 Copynumber: 2.4 Consensus size: 103
3188 TTTTTCTAAT
* **
3198 CCTTAAAATAAAATTTTAATTTTAATTTGGGCT-AACTTAGTGAATTAGTTATATATTTTATTTC
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAATTAGTTATATATTTTATTTC
* **
3262 TAAAACCCTATAATAATATTATTAATTATGGAATTTAC
66 TAAAACCCTATAACAATATTATTAATTATCAAATTTAC
* * * *
3300 TCTTAAAATAAAAATAAAATTTTAATTTGGGTTAAACTTAGTGAAATTAGTTTTGTATTTTATTT
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATATTTTATTT
*
3365 CTAAAACCCTATAACAATAAATTATTAATTTTCAAATTTAC
65 CTAAAACCCTATAACAAT--ATTATTAATTATCAAATTTAC
3406 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAG
1 CCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAG
3448 GTTCTGTTTG
Statistics
Matches: 130, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
102 28 0.22
103 9 0.07
104 36 0.28
106 45 0.35
107 12 0.09
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (103 bp):
CCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAATTAGTTATATATTTTATTTC
TAAAACCCTATAACAATATTATTAATTATCAAATTTAC
Found at i:6350 original size:8 final size:9
Alignment explanation
Indices: 6337--6395 Score: 62
Period size: 8 Copynumber: 7.4 Consensus size: 9
6327 GGATTTTTAT
6337 TACTAT-TA
1 TACTATATA
6345 TACTATATA
1 TACTATATA
6354 TA-TATA-A
1 TACTATATA
6361 TA-TATATA
1 TACTATATA
6369 TA-TATATA
1 TACTATATA
6377 TA-TATATA
1 TACTATATA
6385 TA-TATAT-
1 TACTATATA
6392 TACT
1 TACT
6396 TCTCTATATA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
7 9 0.19
8 35 0.73
9 4 0.08
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (9 bp):
TACTATATA
Found at i:6405 original size:2 final size:2
Alignment explanation
Indices: 6343--6391 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
6333 TTATTACTAT
6343 TA TA CTA TA TA TA TA TA -A 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 TA TA TA TA
6385 TA TA TA T
1 TA TA TA T
6392 TACTTCTCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13811 original size:131 final size:132
Alignment explanation
Indices: 13635--13898 Score: 494
Period size: 131 Copynumber: 2.0 Consensus size: 132
13625 AAAGTTAAAT
13635 CCCGTCAAAAGTATGCGGCTAGATATATATATGAAATCCTAATTTATTGTTTTGGCAAATTTACA
1 CCCGTCAAAAGTATGCGGCTAGATATATATATGAAATCCTAATTTATTGTTTTGGCAAATTTACA
13700 ATTTTACCATCTAAAGAAACAAATAAAATGGCATG-GTCATCTTCTTTTCTTCCAAAGCCCAAAT
66 ATTTTACCATCTAAAGAAACAAATAAAATGGCATGAGTCATCTTCTTTTCTTCCAAAGCCCAAAT
13764 CA
131 CA
* *
13766 CCCGTCAAAAGTATGCGGCTAGATATATATATGAAATCTTTATTTATTGTTTTGGCAAATTTACA
1 CCCGTCAAAAGTATGCGGCTAGATATATATATGAAATCCTAATTTATTGTTTTGGCAAATTTACA
*
13831 ATTTTGCCATCTAAAGAAACAAATAAAATGGCATGAGTCATCTTCTTTTCTTCCAAAGCCCAAAT
66 ATTTTACCATCTAAAGAAACAAATAAAATGGCATGAGTCATCTTCTTTTCTTCCAAAGCCCAAAT
13896 CA
131 CA
13898 C
1 C
13899 ATTAATTCTG
Statistics
Matches: 129, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
131 97 0.75
132 32 0.25
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (132 bp):
CCCGTCAAAAGTATGCGGCTAGATATATATATGAAATCCTAATTTATTGTTTTGGCAAATTTACA
ATTTTACCATCTAAAGAAACAAATAAAATGGCATGAGTCATCTTCTTTTCTTCCAAAGCCCAAAT
CA
Found at i:27200 original size:15 final size:15
Alignment explanation
Indices: 27180--27220 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
27170 ACAGAGATTG
*
27180 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
*
27195 ACAGAAAACGATTAA
1 ACAGAAAACAATTAA
27210 ACTAGAAAACA
1 AC-AGAAAACA
27221 GAGCAGAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.61, C:0.15, G:0.12, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:27998 original size:11 final size:11
Alignment explanation
Indices: 27982--28007 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27972 CCTTTGCCTA
27982 AAAACTAGAAG
1 AAAACTAGAAG
27993 AAAACTAGAAG
1 AAAACTAGAAG
28004 AAAA
1 AAAA
28008 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Done.