Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1042
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: 19902
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1607 original size:14 final size:14
Alignment explanation
Indices: 1588--1640 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
1578 TAATGACTAG
1588 TTTTTTTTT--CAA
1 TTTTTTTTTCACAA
1600 -TTTTTTTTCACAA
1 TTTTTTTTTCACAA
*
1613 TTTTTTTTTCAAAA
1 TTTTTTTTTCACAA
1627 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
1641 CTTGATATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
11 8 0.22
13 3 0.08
14 25 0.69
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:1696 original size:13 final size:13
Alignment explanation
Indices: 1678--1725 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 13
1668 TGGAAACTAG
1678 TTTTTTTTCGAA-
1 TTTTTTTTCGAAT
1690 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
* *
1702 TTTTTGTTCGAGT
1 TTTTTTTTCGAAT
1715 TTTTTTTTCGA
1 TTTTTTTTCGA
1726 GAAACTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 3 0.10
12 15 0.48
13 13 0.42
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.69
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:3404 original size:36 final size:39
Alignment explanation
Indices: 3364--3439 Score: 131
Period size: 36 Copynumber: 2.0 Consensus size: 39
3354 TTGTCCTCAA
3364 ATCGGGCCACTTGCTCGAG-AAAAA-TTT-AAGATCATG
1 ATCGGGCCACTTGCTCGAGAAAAAATTTTCAAGATCATG
3400 ATCGGGCCACTTGCTCGAGAAAAAATTTTCAAGATCATG
1 ATCGGGCCACTTGCTCGAGAAAAAATTTTCAAGATCATG
3439 A
1 A
3440 CCCCTTTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
36 19 0.51
37 5 0.14
38 3 0.08
39 10 0.27
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (39 bp):
ATCGGGCCACTTGCTCGAGAAAAAATTTTCAAGATCATG
Found at i:5904 original size:14 final size:13
Alignment explanation
Indices: 5881--5929 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
5871 ACTAGCTCTC
5881 TTTTTTTTCAATT
1 TTTTTTTTCAATT
*
5894 TTTTGTTTTCACAAT
1 TTTT-TTTTCA-ATT
5909 TTTTTTTTCAAATT
1 TTTTTTTTC-AATT
5923 TTTTTTT
1 TTTTTTT
5930 ACAACTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 4 0.13
14 20 0.65
15 7 0.23
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTTTTCAATT
Found at i:5912 original size:28 final size:26
Alignment explanation
Indices: 5881--5933 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
5871 ACTAGCTCTC
*
5881 TTTTTTTTCAATTTTTTGTTTTCACAAT
1 TTTTTTTTCAAATTTTT-TTTT-ACAAT
5909 TTTTTTTTCAAATTTTTTTTTACAA
1 TTTTTTTTCAAATTTTTTTTTACAA
5934 CTTGATATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.17
27 4 0.17
28 16 0.67
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTTTTTCAAATTTTTTTTTACAAT
Found at i:5998 original size:23 final size:23
Alignment explanation
Indices: 5972--6016 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5962 GGAAACTAGT
5972 TTTTTTTTCGAATTTTTTTTGAA
1 TTTTTTTTCGAATTTTTTTTGAA
* *
5995 TTTTTTTTTGAGTTTTTTTTGA
1 TTTTTTTTCGAATTTTTTTTGA
6017 GAAACTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.73
Consensus pattern (23 bp):
TTTTTTTTCGAATTTTTTTTGAA
Found at i:6002 original size:11 final size:11
Alignment explanation
Indices: 5972--6016 Score: 63
Period size: 12 Copynumber: 3.9 Consensus size: 11
5962 GGAAACTAGT
5972 TTTTTTTTCGAA
1 TTTTTTTT-GAA
5984 TTTTTTTTGAA
1 TTTTTTTTGAA
*
5995 TTTTTTTTTGAG
1 -TTTTTTTTGAA
6007 TTTTTTTTGA
1 TTTTTTTTGA
6017 GAAACTACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 13 0.42
12 18 0.58
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:16993 original size:10 final size:10
Alignment explanation
Indices: 16969--17017 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
16959 AGCTCGTTTC
*
16969 CAGCTCACTT
1 CAGCTCAATT
* *
16979 GAGCTCAAGT
1 CAGCTCAATT
16989 CAGCTC-ATT
1 CAGCTCAATT
16998 CGAGCTCAATT
1 C-AGCTCAATT
17009 CAGCTCAAT
1 CAGCTCAAT
17018 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:16994 original size:20 final size:20
Alignment explanation
Indices: 16969--17015 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
16959 AGCTCGTTTC
16969 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
16989 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
17009 CAGCTCA
1 CAGCTCA
17016 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Done.