Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1569
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: 29932
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:2768 original size:40 final size:40
Alignment explanation
Indices: 2720--2986 Score: 471
Period size: 40 Copynumber: 6.7 Consensus size: 40
2710 GCAAACACAT
* *
2720 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
2760 TTGCCTTCGGGTCTTAGCCCGGATATATCATCCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
2800 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCACATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
2840 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
2880 TTACCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
2920 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
2960 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
2987 ATCCAATGTT
Statistics
Matches: 215, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 215 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:9401 original size:42 final size:42
Alignment explanation
Indices: 9291--9455 Score: 152
Period size: 43 Copynumber: 3.9 Consensus size: 42
9281 TTCCGATATG
* ** *
9291 TGATTTCATGTAAGACCACATCTGGGACATTGGCA-CCGATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCCTATT
*
9332 TGAGATTTACGCGTAAGACCATGTCTGGGACATTGGCATCCTATT
1 T--GATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCCTATT
* * * * *
9377 TGATTTTGTGTAAGACCTTGTCTGGGACAGTGGAATCGATATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC-CTATT
* ** **
9420 TGATTACGTGTAAGACCACATCTGGGATGTTGGCAT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCAT
9456 TGTACAAGCT
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 1 0.01
42 26 0.26
43 41 0.41
44 25 0.25
45 6 0.06
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCCTATT
Found at i:9733 original size:21 final size:20
Alignment explanation
Indices: 9687--9734 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
9677 ACTATATGGT
*
9687 TTATGATAGTATTTGATTATG
1 TTAT-ATAGTATTTGATGATG
* *
9708 GTATATATGTATTTTATGATG
1 TTATATA-GTATTTGATGATG
9729 TTATAT
1 TTATAT
9735 GCTTAAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (20 bp):
TTATATAGTATTTGATGATG
Found at i:13064 original size:40 final size:40
Alignment explanation
Indices: 13009--13230 Score: 356
Period size: 40 Copynumber: 5.6 Consensus size: 40
12999 ATTTGAATAC
13009 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
13049 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
13089 ATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
13129 ATCCGGGCTAAGACCCGAAGGCAATTG-GCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * * *
13168 ATCCGGGCTAAGACCCAAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
13208 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
13231 ATTGAGCTTG
Statistics
Matches: 168, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 36 0.21
40 132 0.79
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:13214 original size:79 final size:80
Alignment explanation
Indices: 13009--13234 Score: 364
Period size: 79 Copynumber: 2.8 Consensus size: 80
12999 ATTTGAATAC
*
13009 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
*
13074 TGTGCGAGTTGATAT
66 TGTGCAAGTTGATAT
*
13089 ATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
13154 TG-GCAAGTTGATAT
66 TGTGCAAGTTGATAT
* * * * * *
13168 ATCCGGGCTAAGACCCAAAGGCATTCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
13233 TG
66 TG
13235 AGCTTGTGGT
Statistics
Matches: 136, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
79 71 0.52
80 65 0.48
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTTGATAT
Found at i:13221 original size:119 final size:120
Alignment explanation
Indices: 13009--13230 Score: 374
Period size: 119 Copynumber: 1.9 Consensus size: 120
12999 ATTTGAATAC
* *
13009 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCAAAGGCATT
* *
13074 TGTGCGAGTTGATATATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
66 CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
13129 ATCCGGGCTAAGACCCGAAGGCAATTG-GCAAGTTGATATATCCGGGCTAAGACCCAAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCAAAGGCATT
* * *
13193 CGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCA
66 CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCA
13231 ATTGAGCTTG
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
119 69 0.73
120 26 0.27
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (120 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCAAAGGCATT
CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:21460 original size:40 final size:40
Alignment explanation
Indices: 21405--21627 Score: 383
Period size: 40 Copynumber: 5.6 Consensus size: 40
21395 ATTTGAATAC
21405 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
21445 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
21485 ATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
21525 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
21565 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
21605 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
21628 ATTGAGCTTG
Statistics
Matches: 174, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 174 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:21646 original size:120 final size:120
Alignment explanation
Indices: 21405--21654 Score: 394
Period size: 120 Copynumber: 2.1 Consensus size: 120
21395 ATTTGAATAC
21405 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * * *
21470 TGTGCGAGTTGATATATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
66 CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
21525 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * ** *
21590 CGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGAGCTTGTGGTTAT
66 CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
21645 ATCC-GGCTAA
1 ATCCGGGCTAA
21655 ATTCCAAAGA
Statistics
Matches: 119, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
119 6 0.05
120 113 0.95
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (120 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
Done.