Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1561
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: 68779
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:3299 original size:20 final size:22
Alignment explanation
Indices: 3258--3306 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
3248 TAAATAATAG
3258 TTATATTTGTATAAATTGTGAA
1 TTATATTTGTATAAATTGTGAA
*
3280 TTATATTTG-ATAGA-TGTGAA
1 TTATATTTGTATAAATTGTGAA
3300 TTATATT
1 TTATATT
3307 GAGATGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 13 0.50
21 4 0.15
22 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TTATATTTGTATAAATTGTGAA
Found at i:3313 original size:17 final size:19
Alignment explanation
Indices: 3274--3316 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3264 TTGTATAAAT
3274 TGTGAATTATATTTGATAGA
1 TGTGAATTATATTTGA-AGA
3294 TGTGAATTATA-TTG-AGA
1 TGTGAATTATATTTGAAGA
3311 TGTGAA
1 TGTGAA
3317 GGAAAATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
19 3 0.13
20 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (19 bp):
TGTGAATTATATTTGAAGA
Found at i:3430 original size:8 final size:8
Alignment explanation
Indices: 3417--3445 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3407 CACTAGAGAC
3417 CAGTGTTA
1 CAGTGTTA
3425 CAGTGTTA
1 CAGTGTTA
3433 CAGTGTTA
1 CAGTGTTA
3441 CAGTG
1 CAGTG
3446 AGTCCGGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:3563 original size:22 final size:22
Alignment explanation
Indices: 3532--3574 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3522 GTGTTATTGA
*
3532 TCAGTTGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
3554 TCAGTGGTAGCTTCGGCTACA
1 TCAGTGGTAGCTTCGGCTACA
3575 ATCGAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (22 bp):
TCAGTGGTAGCTTCGGCTACAT
Found at i:8051 original size:17 final size:17
Alignment explanation
Indices: 8029--8062 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8019 ATCCACTAAT
*
8029 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
8046 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
8063 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:16696 original size:20 final size:20
Alignment explanation
Indices: 16671--16720 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
16661 TGGCTTAAAA
16671 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
16691 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
16708 GTGGTAGTGGATT
1 TTGGTAGTGGATT
16721 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:21335 original size:20 final size:20
Alignment explanation
Indices: 21310--21359 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
21300 TGGCTTAAAA
21310 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
21330 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
21347 GTGGTAGTGGATT
1 TTGGTAGTGGATT
21360 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:42766 original size:21 final size:21
Alignment explanation
Indices: 42740--42780 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42730 ATCTGCTCAA
* *
42740 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
42761 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
42781 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:53553 original size:20 final size:20
Alignment explanation
Indices: 53528--53577 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
53518 TGGCTTAAAA
53528 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
53548 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
53565 GTGGTAGTGGATT
1 TTGGTAGTGGATT
53578 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:58182 original size:20 final size:20
Alignment explanation
Indices: 58157--58206 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
58147 TGGCTTAAAA
58157 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
58177 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
58194 GTGGTAGTGGATT
1 TTGGTAGTGGATT
58207 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Done.