Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2380
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: 48609
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:3161 original size:24 final size:25
Alignment explanation
Indices: 3134--3182 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
3124 AATCCAAAGG
3134 AAAT-CACCATTTTTGACAAACACA
1 AAATACACCATTTTTGACAAACACA
3158 AAATAACCACCATTTTTGACAAACA
1 AAAT-A-CACCATTTTTGACAAACA
3183 AATGGGTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
27 18 0.82
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (25 bp):
AAATACACCATTTTTGACAAACACA
Found at i:10920 original size:28 final size:28
Alignment explanation
Indices: 10888--10943 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
10878 TTATCAGGAG
*
10888 TATGTTATTATGTTTGTTTAAGCTAAAA
1 TATGTTATTATGTTTGTTTAAGATAAAA
10916 TATGTTATTATGTTTGTTTAAGATAAAA
1 TATGTTATTATGTTTGTTTAAGATAAAA
10944 ACTGTAGGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (28 bp):
TATGTTATTATGTTTGTTTAAGATAAAA
Found at i:24386 original size:128 final size:128
Alignment explanation
Indices: 24223--24483 Score: 513
Period size: 128 Copynumber: 2.0 Consensus size: 128
24213 AGTGTGAAGA
24223 CACTCTAAGGAGACTTGAAAGTCAATAGACAATTACAATTTTACAACTAATTGAATCATTGCAAA
1 CACTCTAAGGAGACTTGAAAGTCAATAGACAATTACAATTTTACAACTAATTGAATCATTGCAAA
24288 TTCTGGAAAGAACATCTAGCATGGTAGATGGATGATAGTTAAAGCAACAGAAACTAAACTTAC
66 TTCTGGAAAGAACATCTAGCATGGTAGATGGATGATAGTTAAAGCAACAGAAACTAAACTTAC
*
24351 CACTCTAAGGAGACTTGAAAGTCAATATACAATTACAATTTTACAACTAATTGAATCATTGCAAA
1 CACTCTAAGGAGACTTGAAAGTCAATAGACAATTACAATTTTACAACTAATTGAATCATTGCAAA
24416 TTCTGGAAAGAACATCTAGCATGGTAGATGGATGATAGTTAAAGCAACAGAAACTAAACTTAC
66 TTCTGGAAAGAACATCTAGCATGGTAGATGGATGATAGTTAAAGCAACAGAAACTAAACTTAC
24479 CACTC
1 CACTC
24484 CACTTCTTTA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 132 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (128 bp):
CACTCTAAGGAGACTTGAAAGTCAATAGACAATTACAATTTTACAACTAATTGAATCATTGCAAA
TTCTGGAAAGAACATCTAGCATGGTAGATGGATGATAGTTAAAGCAACAGAAACTAAACTTAC
Found at i:36254 original size:11 final size:11
Alignment explanation
Indices: 36238--36267 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
36228 TAATTATGTT
36238 ATATAAATATA
1 ATATAAATATA
*
36249 ATATAAAAATA
1 ATATAAATATA
36260 ATATAAAT
1 ATATAAAT
36268 TAAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAATATA
Found at i:40906 original size:18 final size:19
Alignment explanation
Indices: 40872--40907 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40862 AATATGATTA
*
40872 TTAAAAGATATTTTTTATC
1 TTAAAAGATAATTTTTATC
40891 TTAAAA-ATAATTTTTAT
1 TTAAAAGATAATTTTTAT
40908 TTATTGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
TTAAAAGATAATTTTTATC
Found at i:43756 original size:15 final size:14
Alignment explanation
Indices: 43731--43761 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
43721 TTGTTAATGT
43731 ATTATTTAAATATA
1 ATTATTTAAATATA
43745 ATTATATTAAATATA
1 ATTAT-TTAAATATA
43760 AT
1 AT
43762 ACGATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTATTTAAATATA
Found at i:44346 original size:21 final size:20
Alignment explanation
Indices: 44315--44359 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
44305 TACGATAAAA
44315 AAATTTATTAAAAATAATTT
1 AAATTTATTAAAAATAATTT
* *
44335 AAATTATATTAAAATTACTTT
1 AAATT-TATTAAAAATAATTT
44356 AAAT
1 AAAT
44360 AGTAAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTATTAAAAATAATTT
Found at i:45344 original size:20 final size:22
Alignment explanation
Indices: 45305--45346 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
45295 AGTTTTACCA
*
45305 TTAAAATAAATTAGTTAAAATT
1 TTAAAATAAATCAGTTAAAATT
45327 TTAAAA-AAATCA-TTAAAATT
1 TTAAAATAAATCAGTTAAAATT
45347 AACATATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TTAAAATAAATCAGTTAAAATT
Found at i:48383 original size:36 final size:36
Alignment explanation
Indices: 48336--48411 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
48326 TTTCATATGG
48336 ACACTACACTTTAATCAATATGAAATTAATGTATAA
1 ACACTACACTTTAATCAATATGAAATTAATGTATAA
48372 ACACTACACTTTAATCAATATGAAATTAATGTATAA
1 ACACTACACTTTAATCAATATGAAATTAATGTATAA
48408 ACAC
1 ACAC
48412 CGTATGATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (36 bp):
ACACTACACTTTAATCAATATGAAATTAATGTATAA
Done.