Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3616
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: 18068
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Found at i:1883 original size:28 final size:27
Alignment explanation
Indices: 1842--1931 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
1832 AGGAAGCGTC
1842 CTGGTGGCTA-TGCCAAAAATTATCTGTT
1 CTGGTGGC-ACTGCCAAAAA-TATCTGTT
* * *
1870 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCAAAAATATCTGTT
*
1897 CTGGTGGCACTGCCATAACATATCTGTAT
1 CTGGTGGCACTGCCA-AAAATATCTGT-T
1926 CTGGTG
1 CTGGTG
1932 ACTCTGTCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 22 0.42
28 24 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCAAAAATATCTGTT
Found at i:1900 original size:27 final size:28
Alignment explanation
Indices: 1862--1931 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
1852 TGCCAAAAAT
* * *
1862 TATCTGTTCTGGTGGCCCTGCCA-CATA
1 TATCTGTTCTGGTGGCACTGCCATAACA
1889 TATCTGTTCTGGTGGCACTGCCATAACA
1 TATCTGTTCTGGTGGCACTGCCATAACA
1917 TATCTGTATCTGGTG
1 TATCTGT-TCTGGTG
1932 ACTCTGTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 22 0.58
28 9 0.24
29 7 0.18
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (28 bp):
TATCTGTTCTGGTGGCACTGCCATAACA
Found at i:10132 original size:32 final size:32
Alignment explanation
Indices: 10091--10152 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
10081 CTTACTTCTG
10091 ATATCTGTTCTGGGCCTATGGGCTTTATTCCT
1 ATATCTGTTCTGGGCCTATGGGCTTTATTCCT
10123 ATATCTGTTCTGGGCCTATGGGCTTTATTC
1 ATATCTGTTCTGGGCCTATGGGCTTTATTC
10153 TGATACCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.44
Consensus pattern (32 bp):
ATATCTGTTCTGGGCCTATGGGCTTTATTCCT
Found at i:11979 original size:46 final size:46
Alignment explanation
Indices: 11912--12133 Score: 290
Period size: 46 Copynumber: 4.8 Consensus size: 46
11902 TGTAACCCGC
* * * *
11912 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
11958 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
12008 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
12051 CCGTAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
12097 CCGTAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
12134 TGCTAGTTAC
Statistics
Matches: 157, Mismatches: 10, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
44 2 0.01
45 2 0.01
46 109 0.69
47 29 0.18
48 2 0.01
49 2 0.01
50 3 0.02
51 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:12032 original size:93 final size:93
Alignment explanation
Indices: 11919--12087 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 93
11909 CGCCCATAAG
* *
11919 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
11984 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
12012 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCGTAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
12077 ACGAGTTCGGA
66 ACGAGTTCGGA
12088 CATTCGCATC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:12214 original size:28 final size:30
Alignment explanation
Indices: 12156--12214 Score: 68
Period size: 33 Copynumber: 1.9 Consensus size: 30
12146 CTCACGACTC
*
12156 ACTCAACTCAACGAGTTCATGCCTATTCTCATG
1 ACTCAACTCAACGAGTTCA-G-C-ATGCTCATG
12189 ACTCAACTCAACGAGTTC-G-ATGCTCA
1 ACTCAACTCAACGAGTTCAGCATGCTCA
12215 AATCCTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 6 0.24
31 1 0.04
33 18 0.72
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.27
Consensus pattern (30 bp):
ACTCAACTCAACGAGTTCAGCATGCTCATG
Done.