Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5761.1
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: 18156
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Found at i:1291 original size:22 final size:22
Alignment explanation
Indices: 1266--1307 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1256 TGAAGAGTAT
1266 AGTATGTG-AAGATTGATGTACG
1 AGTAT-TGAAAGATTGATGTACG
*
1288 AGTATTGAAATATTGATGTA
1 AGTATTGAAAGATTGATGTA
1308 TGGCTGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (22 bp):
AGTATTGAAAGATTGATGTACG
Found at i:3415 original size:18 final size:18
Alignment explanation
Indices: 3373--3415 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3363 GTATTTAATG
3373 GTGGTGGAAGGCTCCGTT
1 GTGGTGGAAGGCTCCGTT
*
3391 GTAGTGGAAGGCT-CGATT
1 GTGGTGGAAGGCTCCG-TT
3409 GTGGTGG
1 GTGGTGG
3416 TTAGAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.14, C:0.12, G:0.47, T:0.28
Consensus pattern (18 bp):
GTGGTGGAAGGCTCCGTT
Found at i:5217 original size:79 final size:79
Alignment explanation
Indices: 5100--6191 Score: 1930
Period size: 79 Copynumber: 13.8 Consensus size: 79
5090 GCTCCTCGTT
* * *
5100 CAAATGCCTTCGGGA-CATAGCCCGG-TTATATTAACTCGCACAAATGCCTTCGGGACTTCA-CC
1 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAATAACTCGCACAAATGCCTTCGGG-CTT-AGCC
* * *
5162 CGG-ATTTAATAACTCACA
62 CGGAATTT-GTATCTCGCA
* * * * *
5180 CAAATGCCTTCGG-GCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5244 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5258 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5323 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5337 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5402 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5416 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5481 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5495 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5560 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5574 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5639 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5653 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5718 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5732 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5797 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5811 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5876 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5890 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
5955 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
5969 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
6034 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
6048 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
6113 ATTTGTATCTCGCA
66 ATTTGTATCTCGCA
* * *
6127 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGATCTTAGTCCGGAT-TTAATAAC-TCGCACAAATGCCTTCGGG-CTTAGCCC
6189 GGA
63 GGA
6192 CATCATTCAA
Statistics
Matches: 989, Mismatches: 15, Indels: 17
0.97 0.01 0.02
Matches are distributed among these distances:
77 1 0.00
78 37 0.04
79 932 0.94
80 19 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (79 bp):
CAAATGCCTTCGGATCTTAGTCCGGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGGA
ATTTGTATCTCGCA
Found at i:16726 original size:28 final size:28
Alignment explanation
Indices: 16687--16747 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
16677 TTGATACTGA
* *
16687 TTCTGTAATGGGCTTAGGTCCACT-TGT
1 TTCTGTAATGGGCTCAGGCCCACTCTGT
*
16714 TTCTGTTAATGGGCTCAGGCCCAGTCTGT
1 TTCTG-TAATGGGCTCAGGCCCACTCTGT
16743 TTCTG
1 TTCTG
16748 CATACCGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.17
28 16 0.55
29 8 0.28
ACGTcount: A:0.13, C:0.21, G:0.26, T:0.39
Consensus pattern (28 bp):
TTCTGTAATGGGCTCAGGCCCACTCTGT
Found at i:17552 original size:13 final size:12
Alignment explanation
Indices: 17529--17563 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
17519 TCTCATCTAT
17529 CATTCCCTTTTC
1 CATTCCCTTTTC
17541 CATTCTCCTTTTC
1 CATTC-CCTTTTC
*
17554 CTTTCCCTTT
1 CATTCCCTTT
17564 GCATAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.06, C:0.40, G:0.00, T:0.54
Consensus pattern (12 bp):
CATTCCCTTTTC
Done.