Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4429
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: 14875
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:1672 original size:46 final size:46
Alignment explanation
Indices: 1622--1794 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
1612 TGGTTGAGCA
1622 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
1668 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
1713 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
1761 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1795 GGGCGGGTTA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:1778 original size:93 final size:93
Alignment explanation
Indices: 1619--1789 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
1609 GGATGGTTGA
* *
1619 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1684 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
1712 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1777 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
1790 ACTTAGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:9156 original size:46 final size:45
Alignment explanation
Indices: 9106--9278 Score: 136
Period size: 46 Copynumber: 3.8 Consensus size: 45
9096 GTTGAGCATC
* *
9106 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTT
1 CGAACTCATTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATGAT
* * * * * *
9152 CGAACTCGTTGAGTTGAGTTCGGGTTC-GTGA-GATG-TAACTAGGCAT
1 CGAACTCATTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G-AT
* * **
9198 CTGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCC
1 C-GAACTCATTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATGAT
**
9245 CGGGCTCATTGAGTTGAGTCCGAGTTCACTTAGG
1 CGAACTCATTGAGTTGAGTCCGAGTTCACTTAGG
9279 GGCGGGTTAC
Statistics
Matches: 99, Mismatches: 19, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 55 0.56
47 23 0.23
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (45 bp):
CGAACTCATTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATGAT
Found at i:12990 original size:14 final size:14
Alignment explanation
Indices: 12969--13009 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
12959 TTGCAACTTG
12969 CACAACTTGCACAT
1 CACAACTTGCACAT
** *
12983 TGCAACTTGCAAAT
1 CACAACTTGCACAT
12997 CACAACTTGCACA
1 CACAACTTGCACA
13010 ATCAGGTTAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (14 bp):
CACAACTTGCACAT
Found at i:14283 original size:4 final size:4
Alignment explanation
Indices: 14043--14275 Score: 396
Period size: 4 Copynumber: 58.5 Consensus size: 4
14033 GAAATCAAAT
14043 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
14091 ATAC ATAT ATAC ATAC ATAC ATAC ATA- ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
14138 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
14186 ATAC ATAC ATAC ATAC ATAT ATAC ATGC ATGC ATAC ATAC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
14234 ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
14276 GCATGCATAT
Statistics
Matches: 220, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
3 3 0.01
4 217 0.99
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:14724 original size:19 final size:19
Alignment explanation
Indices: 14689--14730 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
14679 TATGGTTAAC
14689 ATTAGTTAATTATTAATTA
1 ATTAGTTAATTATTAATTA
14708 ATTATGTTAATTA-TAATTA
1 ATTA-GTTAATTATTAATTA
14727 ATTA
1 ATTA
14731 AAGTTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
ATTAGTTAATTATTAATTA
Done.