Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold262
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: 15431
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Found at i:381 original size:20 final size:20
Alignment explanation
Indices: 356--398 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
346 TTCTGCCCGC
*
356 CTCCCTCGCTGCTGCCTCCG
1 CTCCCTCGCTGCTCCCTCCG
376 CTCCCTCGCTGCTCCCTCCG
1 CTCCCTCGCTGCTCCCTCCG
396 CTC
1 CTC
399 TAAGTTGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.00, C:0.58, G:0.16, T:0.26
Consensus pattern (20 bp):
CTCCCTCGCTGCTCCCTCCG
Found at i:389 original size:11 final size:11
Alignment explanation
Indices: 356--393 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
346 TTCTGCCCGC
356 CTCCCTCGCTG
1 CTCCCTCGCTG
*
367 CTGCCTC-C-G
1 CTCCCTCGCTG
376 CTCCCTCGCTG
1 CTCCCTCGCTG
387 CTCCCTC
1 CTCCCTC
394 CGCTCTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.30
10 2 0.09
11 14 0.61
ACGTcount: A:0.00, C:0.58, G:0.16, T:0.26
Consensus pattern (11 bp):
CTCCCTCGCTG
Found at i:5880 original size:40 final size:40
Alignment explanation
Indices: 5806--6027 Score: 312
Period size: 40 Copynumber: 5.6 Consensus size: 40
5796 AACCCAAGTA
* * *
5806 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
5845 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
5885 CCTTCGGGACTTAGCCCGG-TATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATG
*
5927 CCTTCGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
5967 CCTTCGGGACTTAG-CCGGATATGGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
6006 CCTTC-GGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
6028 CATCTGAATA
Statistics
Matches: 168, Mismatches: 6, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
38 9 0.05
39 59 0.35
40 62 0.37
41 1 0.01
42 27 0.16
43 9 0.05
44 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:5944 original size:82 final size:81
Alignment explanation
Indices: 5806--6027 Score: 332
Period size: 82 Copynumber: 2.8 Consensus size: 81
5796 AACCCAAGTA
* *
5806 CCTTCGGGATTTAGCCGGATATAGCA--ACTCGCACACATGCCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCGGATATAGCACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
5869 GTCACTAGCACAAATG
66 GTCACTAGCACAAATG
*
5885 CCTTCGGGACTTAGCCCGG-TATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAG-CCGGATATAGC-ACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
5949 TAGTCACTAGCACAAATG
64 TAGTCACTAGCACAAATG
*
5967 CCTTCGGGACTTAGCCGGATATGGTCACTA---GCACAAATGCCTTC-GGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCGGATATAG-CACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
6028 CATCTGAATA
Statistics
Matches: 132, Mismatches: 5, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
78 16 0.12
79 33 0.25
80 5 0.04
81 4 0.03
82 73 0.55
83 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (81 bp):
CCTTCGGGACTTAGCCGGATATAGCACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
GTCACTAGCACAAATG
Found at i:13744 original size:39 final size:40
Alignment explanation
Indices: 13690--13907 Score: 294
Period size: 40 Copynumber: 5.6 Consensus size: 40
13680 AACCCAAGTA
* *
13690 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
13729 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
13769 CCTTCGGGACTTAG--CGG-TATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATG
13809 CCTTC-GGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
13848 CCTTCGGGACTTAGCCCGGATAT-GTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
13887 CCTTC-GGACTTAG-CCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
13908 CATCCGAATA
Statistics
Matches: 164, Mismatches: 4, Indels: 24
0.85 0.02 0.12
Matches are distributed among these distances:
36 1 0.01
37 17 0.10
38 11 0.07
39 55 0.34
40 66 0.40
41 4 0.02
42 9 0.05
43 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:13822 original size:79 final size:79
Alignment explanation
Indices: 13690--13907 Score: 308
Period size: 79 Copynumber: 2.8 Consensus size: 79
13680 AACCCAAGTA
* *
13690 CCTTCGGGATTTAGCCGGATATAGCA--ACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCGG-TATAGCACTACTCGCACAAATGCCTTC-GGACTTAGCCCGGATATA
13753 GTCACTAGCACAAATG
64 GTCACTAGCACAAATG
13769 CCTTCGGGACTTAG-CGGTATAGCAACTACTCGCACAAATGCCTTCGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCGGTATAGC-ACTACTCGCACAAATGCCTTCGGACTTAGCCCGGATATAG
13833 TCACTAGCACAAATG
65 TCACTAGCACAAATG
13848 CCTTCGGGACTTAGCCCGG-ATATGTCACTA---GCACAAATGCCTTCGGACTTAG-CCGGATAT
1 CCTTCGGGACTTAG-CCGGTATA-G-CACTACTCGCACAAATGCCTTCGGACTTAGCCCGGATAT
13908 CATCCGAATA
Statistics
Matches: 130, Mismatches: 2, Indels: 16
0.88 0.01 0.11
Matches are distributed among these distances:
77 14 0.11
78 26 0.20
79 60 0.46
80 21 0.16
81 8 0.06
82 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCGGTATAGCACTACTCGCACAAATGCCTTCGGACTTAGCCCGGATATAGT
CACTAGCACAAATG
Done.