Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015296.1 Corchorus olitorius cultivar O-4 contig15329, 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: 9014
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Found at i:126 original size:16 final size:16
Alignment explanation
Indices: 105--135 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
95 CTTATTCCCC
*
105 AAAAAAGAACTACTTA
1 AAAAAAAAACTACTTA
121 AAAAAAAAACTACTT
1 AAAAAAAAACTACTT
136 CGGTTCTTGA
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:0.65, C:0.13, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAAAAAACTACTTA
Found at i:2173 original size:3 final size:3
Alignment explanation
Indices: 2167--2192 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2157 AATATAAAAA
2167 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
2193 AGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2283 original size:35 final size:35
Alignment explanation
Indices: 2229--2322 Score: 143
Period size: 35 Copynumber: 2.7 Consensus size: 35
2219 GCCAGCCTGG
* *
2229 CGCGGCCCAACGCCTAGGCCAGGCGCGCGGGCCAA
1 CGCGGCCCAGCGCCTAGGCCAGGCGCACGGGCCAA
*
2264 CGCGGCCCAGCGCCCAGGCCAGGCGCACGGGCCAA
1 CGCGGCCCAGCGCCTAGGCCAGGCGCACGGGCCAA
**
2299 CATGGCCCAGCGCCTAGGCCAGGC
1 CGCGGCCCAGCGCCTAGGCCAGGC
2323 TTGGGCCCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.17, C:0.44, G:0.36, T:0.03
Consensus pattern (35 bp):
CGCGGCCCAGCGCCTAGGCCAGGCGCACGGGCCAA
Found at i:3374 original size:28 final size:28
Alignment explanation
Indices: 3333--3407 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
3323 TTAAGATGTC
** *
3333 AAAATTACTGTTTTGCCCTTGGTAGGCT
1 AAAATTACCATTTTGCCCTTGGTAGACT
* * *
3361 AAAATTACCATTTTACCCCTGGTTGACT
1 AAAATTACCATTTTGCCCTTGGTAGACT
3389 -AAATTA-CAGTTTTGCCCTT
1 AAAATTACCA-TTTTGCCCTT
3408 AAATGCCGGA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.05
27 14 0.37
28 22 0.58
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCTTGGTAGACT
Found at i:8395 original size:3 final size:3
Alignment explanation
Indices: 8389--8435 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
8379 ATAATATAAA
8389 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
8436 AGAAAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:8619 original size:20 final size:21
Alignment explanation
Indices: 8590--8639 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
8580 GAGGAAAAAG
*
8590 AAAAAGGAAAAAT-AAATAAAT
1 AAAAA-GAAAAATAAAAGAAAT
8611 AAAAAG-AAAATAAAAGAAAT
1 AAAAAGAAAAATAAAAGAAAT
8631 -AAAAGAAAA
1 AAAAAGAAAA
8640 GTTTTAGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAAAGAAAAATAAAAGAAAT
Found at i:8622 original size:19 final size:19
Alignment explanation
Indices: 8598--8639 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
8588 AGAAAAAGGA
*
8598 AAAAT-AAATAAATAAAAAG
1 AAAATAAAAGAAAT-AAAAG
8617 AAAATAAAAGAAATAAAAG
1 AAAATAAAAGAAATAAAAG
8636 AAAA
1 AAAA
8640 GTTTTAGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAATAAAAGAAATAAAAG
Found at i:8627 original size:10 final size:10
Alignment explanation
Indices: 8607--8639 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
8597 AAAAATAAAT
8607 AAATAAAAAGA
1 AAAT-AAAAGA
8618 AAATAAAAG-
1 AAATAAAAGA
8627 AAATAAAAGA
1 AAATAAAAGA
8637 AAA
1 AAA
8640 GTTTTAGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 8 0.38
11 4 0.19
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (10 bp):
AAATAAAAGA
Done.