Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g00385.P3
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: 8263
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:175 original size:6 final size:6
Alignment explanation
Indices: 157--193 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
147 CAACCGAACA
* *
157 TTCACC TTTACC TTCACC TTCACC TTCACT TTCACC T
1 TTCACC TTCACC TTCACC TTCACC TTCACC TTCACC T
194 GCTCCTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.16, C:0.43, G:0.00, T:0.41
Consensus pattern (6 bp):
TTCACC
Found at i:3985 original size:33 final size:33
Alignment explanation
Indices: 3943--4028 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
3933 CAAACCTTCC
**
3943 ACGGAAACCGCTGATTCGGAACCGCCGGCGACA
1 ACGGAAACCGCTGATTCCAAACCGCCGGCGACA
* *
3976 ACGGAAACCGCTGGTTCCAAACCGCCGGCGACG
1 ACGGAAACCGCTGATTCCAAACCGCCGGCGACA
* *
4009 ACGGAAACCGCCGACTCCAA
1 ACGGAAACCGCTGATTCCAA
4029 GCAACCGGCG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.28, C:0.36, G:0.28, T:0.08
Consensus pattern (33 bp):
ACGGAAACCGCTGATTCCAAACCGCCGGCGACA
Found at i:4037 original size:33 final size:33
Alignment explanation
Indices: 3967--4042 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
3957 TTCGGAACCG
* * ** **
3967 CCGGCGACAACGGAAACCGCTGGTTCCAAACCG
1 CCGGCGACGACGGAAACCGCCGACTCCAAACAA
*
4000 CCGGCGACGACGGAAACCGCCGACTCCAAGCAA
1 CCGGCGACGACGGAAACCGCCGACTCCAAACAA
4033 CCGGCGACGA
1 CCGGCGACGA
4043 AACCATCGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.38, G:0.29, T:0.05
Consensus pattern (33 bp):
CCGGCGACGACGGAAACCGCCGACTCCAAACAA
Found at i:4053 original size:39 final size:39
Alignment explanation
Indices: 4009--4127 Score: 141
Period size: 39 Copynumber: 2.9 Consensus size: 39
3999 GCCGGCGACG
* *
4009 ACGGAAACCGCCGACTCCAAGCAACCGGCGACGAAACCAT
1 ACGGAAACC-CCGAATCCAAACAACCGGCGACGAAACCAT
* * *
4049 -CGGAAAACCCGGAATCCAAAAAACCGGCGACGAAACCTT
1 ACGG-AAACCCCGAATCCAAACAACCGGCGACGAAACCAT
4088 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACC
1 --ACGGAAACCCC-GAATCCAAACAACCGGCGACGAAACC
4128 TTTGAAAGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
39 28 0.42
40 5 0.07
41 6 0.09
42 28 0.42
ACGTcount: A:0.38, C:0.35, G:0.22, T:0.05
Consensus pattern (39 bp):
ACGGAAACCCCGAATCCAAACAACCGGCGACGAAACCAT
Found at i:4107 original size:42 final size:42
Alignment explanation
Indices: 4007--4178 Score: 181
Period size: 42 Copynumber: 4.2 Consensus size: 42
3997 CCGCCGGCGA
* * *
4007 CGACGGAAACCGCC-GACTCCAAGCAACCGGCGACGAAACCAT
1 CGACGGAAACC-CCGGAATCCAAACAACCGGCGACGAAACCTT
* *
4049 ---CGGAAAACCCGGAATCCAAAAAACCGGCGACGAAACCTT
1 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT
4088 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT
1 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT
* ** * * *** *
4130 TGAAAGAAACCTCGGAATCTAAACAATTAGCGACGAAACCGT
1 CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT
4172 CGACGGA
1 CGACGGA
4179 CACATCAGAA
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
38 2 0.02
39 31 0.29
42 74 0.69
ACGTcount: A:0.38, C:0.31, G:0.22, T:0.09
Consensus pattern (42 bp):
CGACGGAAACCCCGGAATCCAAACAACCGGCGACGAAACCTT
Found at i:6120 original size:16 final size:17
Alignment explanation
Indices: 6093--6132 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
6083 GTTTAATGTG
6093 TAATTAATTTAAAATTC
1 TAATTAATTTAAAATTC
*
6110 TAATTAA-TTAAAATTT
1 TAATTAATTTAAAATTC
6126 TAATTAA
1 TAATTAA
6133 AAATCTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTAATTTAAAATTC
Found at i:6217 original size:13 final size:13
Alignment explanation
Indices: 6194--6226 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
6184 TAACCACTTT
6194 ATAACAACATATTA
1 ATAA-AACATATTA
6208 ATAAAACATATTA
1 ATAAAACATATTA
6221 ATAAAA
1 ATAAAA
6227 GTGACTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (13 bp):
ATAAAACATATTA
Done.