Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3597
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: 17980
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:3323 original size:13 final size:13
Alignment explanation
Indices: 3305--3329 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3295 TGGTCATCAT
3305 GGTGTGAACACAA
1 GGTGTGAACACAA
3318 GGTGTGAACACA
1 GGTGTGAACACA
3330 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:3892 original size:30 final size:30
Alignment explanation
Indices: 3807--3903 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
3797 TAAACTAAAA
* *
3807 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * * *
3837 TGAGTTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
3867 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
3896 ATGAGCTA
1 -TGAGCTA
3904 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:5320 original size:14 final size:14
Alignment explanation
Indices: 5273--5320 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
5263 GTACGAATGG
*
5273 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
5287 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
5301 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
5315 ATTGGT
1 AATGGT
5321 CAGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:12569 original size:17 final size:17
Alignment explanation
Indices: 12510--12569 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
12500 GAGACAGCCA
* * *
12510 CCATACATGCACTTGAG
1 CCATTCATGCATTTGAT
12527 CCATTCATGCATTCT-AT
1 CCATTCATGCATT-TGAT
*
12544 -CATCCCATGCATTTGAT
1 CCAT-TCATGCATTTGAT
12561 CCATTCATG
1 CCATTCATG
12570 ACTAGCCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 26 0.76
18 4 0.12
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (17 bp):
CCATTCATGCATTTGAT
Found at i:13031 original size:30 final size:30
Alignment explanation
Indices: 12946--13042 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
12936 TTAAACAAAA
* *
12946 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
* * * * * *
12976 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
*
13006 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
13035 ATGAGCTA
1 -TGAGCTA
13043 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
Found at i:15360 original size:33 final size:32
Alignment explanation
Indices: 15309--15376 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
15299 TCTTACTGCC
*
15309 TCTTCTCTCTTTTCTTTTTTATTTCGTTTCTTT
1 TCTTCTCTCTTTTCTTTTTTATTTC-TTTATTT
* *
15342 TCTTCTTTACTTTT-TTTTTTTTTTCTTTATTT
1 TCTTCTCT-CTTTTCTTTTTTATTTCTTTATTT
15374 TCT
1 TCT
15377 CTTACAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 9 0.29
33 17 0.55
34 5 0.16
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (32 bp):
TCTTCTCTCTTTTCTTTTTTATTTCTTTATTT
Found at i:16305 original size:10 final size:10
Alignment explanation
Indices: 16292--16326 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
16282 TTTTTCTTTC
16292 TTTTCGAATT
1 TTTTCGAATT
*
16302 TTTTTGAATTT
1 TTTTCGAA-TT
16313 TTTTCGAATT
1 TTTTCGAATT
16323 TTTT
1 TTTT
16327 TTGACTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.17, C:0.06, G:0.09, T:0.69
Consensus pattern (10 bp):
TTTTCGAATT
Found at i:16306 original size:11 final size:11
Alignment explanation
Indices: 16292--16327 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
16282 TTTTTCTTTC
16292 TTTTCGAATTT
1 TTTTCGAATTT
16303 TTTT-GAATTT
1 TTTTCGAATTT
16313 TTTTCGAATTT
1 TTTTCGAATTT
16324 TTTT
1 TTTT
16328 TGACTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCGAATTT
Found at i:16356 original size:19 final size:19
Alignment explanation
Indices: 16321--16358 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
16311 TTTTTTCGAA
16321 TTTTTTTTGACTTGTATAAC
1 TTTTTTTTGAC-TGTATAAC
16341 TTTTTTTTGTAC-GTATAA
1 TTTTTTTTG-ACTGTATAA
16359 TTGACAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 9 0.53
21 2 0.12
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.61
Consensus pattern (19 bp):
TTTTTTTTGACTGTATAAC
Done.