Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4626
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: 14134
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1741 original size:28 final size:29
Alignment explanation
Indices: 1700--1763 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
1690 GAAATGAAAG
* *
1700 AAAAGAAAAAGAGATTG-AGAGAGAGTGA
1 AAAAGAAAAAGAGATTGAAAAGAGAATGA
*
1728 AAAAGAAAATGAGATTGAAAAAGAGAATGA
1 AAAAGAAAAAGAGATTG-AAAAGAGAATGA
1758 AAAAGA
1 AAAAGA
1764 GTTTGAGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 16 0.52
30 15 0.48
ACGTcount: A:0.62, C:0.00, G:0.27, T:0.11
Consensus pattern (29 bp):
AAAAGAAAAAGAGATTGAAAAGAGAATGA
Found at i:1746 original size:18 final size:18
Alignment explanation
Indices: 1720--1757 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1710 GAGATTGAGA
1720 GAGAGTGAAAAAGAAAAT
1 GAGAGTGAAAAAGAAAAT
* *
1738 GAGATTGAAAAAGAGAAT
1 GAGAGTGAAAAAGAAAAT
1756 GA
1 GA
1758 AAAAGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.29, T:0.13
Consensus pattern (18 bp):
GAGAGTGAAAAAGAAAAT
Found at i:7078 original size:16 final size:17
Alignment explanation
Indices: 7059--7094 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
7049 GAAAAAGGAT
7059 TGAGAGTGAAAAGA-AA
1 TGAGAGTGAAAAGAGAA
*
7075 TGAGATTGAAAAGAGAA
1 TGAGAGTGAAAAGAGAA
7092 TGA
1 TGA
7095 AAAAGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.31, T:0.17
Consensus pattern (17 bp):
TGAGAGTGAAAAGAGAA
Found at i:7130 original size:18 final size:17
Alignment explanation
Indices: 7109--7148 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
7099 GGTTTGAGAG
*
7109 AGAAAAAGAATGTGAACA
1 AGAAAAAGAATG-GAAAA
*
7127 AGAAAAAGAGTGGAAAA
1 AGAAAAAGAATGGAAAA
7144 AGAAA
1 AGAAA
7149 TTGAGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (17 bp):
AGAAAAAGAATGGAAAA
Found at i:10565 original size:26 final size:24
Alignment explanation
Indices: 10532--10600 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 24
10522 ATCACAACTC
10532 TTTTTTCTTTTCTCTCACATTTTCT
1 TTTTTTCTTTTCTCTCAC-TTTTCT
*
10557 TCTTTTTCTTCTTCGTCT-TCTTTTCT
1 T-TTTTTCTT-TTC-TCTCACTTTTCT
10583 TTTACTTTCTTTTCTCTC
1 TTT--TTTCTTTTCTCTC
10601 TCCAAGGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
25 6 0.16
26 18 0.49
27 10 0.27
28 3 0.08
ACGTcount: A:0.04, C:0.26, G:0.01, T:0.68
Consensus pattern (24 bp):
TTTTTTCTTTTCTCTCACTTTTCT
Found at i:13965 original size:30 final size:30
Alignment explanation
Indices: 13880--13976 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
13870 TAAACTAAAA
* * *
13880 TGAGCTAAGCTTTAGCTCGTGAACTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
13910 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
13940 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
13969 ATGAGCTA
1 -TGAGCTA
13977 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:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Done.