Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1683
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: 33556
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Found at i:4390 original size:17 final size:18
Alignment explanation
Indices: 4370--4412 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
4360 AATGAGACAT
*
4370 AAAAAAATAAAT-TATAA
1 AAAAAAATAAATACATAA
*
4387 AAAATAATAAATACATAA
1 AAAAAAATAAATACATAA
4405 AAATAAAA
1 AAA-AAAA
4413 ATTTATGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 11 0.52
18 7 0.33
19 3 0.14
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAAAATAAATACATAA
Found at i:7287 original size:15 final size:15
Alignment explanation
Indices: 7257--7285 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
7247 GGAAATGATT
7257 TAGATTGGAATGAAA
1 TAGATTGGAATGAAA
7272 TAGA-TGGAATGAAA
1 TAGATTGGAATGAAA
7286 ATTTTAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (15 bp):
TAGATTGGAATGAAA
Found at i:10820 original size:21 final size:21
Alignment explanation
Indices: 10802--10848 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
10792 TATTAAAAGT
*
10802 TGCATTTTTTCATCCAAAAAA
1 TGCATTTTTTAATCCAAAAAA
**
10823 TGCATTTTTTAATCCAACCAA
1 TGCATTTTTTAATCCAAAAAA
10844 TGCAT
1 TGCAT
10849 CATTTCATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.38
Consensus pattern (21 bp):
TGCATTTTTTAATCCAAAAAA
Found at i:14178 original size:51 final size:51
Alignment explanation
Indices: 14015--14194 Score: 193
Period size: 51 Copynumber: 3.5 Consensus size: 51
14005 TGTGAGTTAC
* * *
14015 TTATGAATATTATTATGTTCATTATGAGATCATGTAAATTCATGTTTTTAT
1 TTATGAATATTATTGTGTTGATTATAAGATCATGTAAATTCATGTTTTTAT
* ** * * * **
14066 TTGTGAATATGGTTGTATTGATTATGAGATTC-TATAAATTCATGTTTCAAT
1 TTATGAATATTATTGTGTTGATTATAAGA-TCATGTAAATTCATGTTTTTAT
* * *
14117 TTGT-AGATATTTTTGTGTTGGTTATAAGATCATGTAAATTCATGTTTTTAT
1 TTATGA-ATATTATTGTGTTGATTATAAGATCATGTAAATTCATGTTTTTAT
*
14168 TTATGAATATTATCGTGTTGATTATAA
1 TTATGAATATTATTGTGTTGATTATAA
14195 AGTTATATAA
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
50 3 0.03
51 98 0.94
52 3 0.03
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (51 bp):
TTATGAATATTATTGTGTTGATTATAAGATCATGTAAATTCATGTTTTTAT
Found at i:28067 original size:1 final size:1
Alignment explanation
Indices: 28057--28186 Score: 89
Period size: 1 Copynumber: 130.0 Consensus size: 1
28047 TGGCAATTGG
* * * ** * * * * *
28057 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAGAAAAAAACAAAACAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * ** * *
28122 GAAAAAGAAAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28187 GTGAAGATTT
Statistics
Matches: 97, Mismatches: 32, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 97 1.00
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:28087 original size:29 final size:29
Alignment explanation
Indices: 28057--28185 Score: 102
Period size: 32 Copynumber: 4.2 Consensus size: 29
28047 TGGCAATTGG
* *
28057 AAAAA-GAAAAA-AACAAAACAAAAAAAA
1 AAAAAGGAAAAAGAAAAAAACAAAACAAA
*
28084 GGAAAAAGAAAAAAAGAAAAAAACAAAACAAA
1 --AAAAAG-GAAAAAGAAAAAAACAAAACAAA
*
28116 AAAAAGGAAAAAGAAAAAAGAAAAAAACAAA
1 AAAAAGGAAAAAG-AAAAA-AACAAAACAAA
28147 ACAAAAAAAAAGGAAAAAGAAAAAAA-AAAACAAA
1 A-AAAA-----GGAAAAAGAAAAAAACAAAACAAA
28181 AAAAA
1 AAAAA
28186 AGTGAAGATT
Statistics
Matches: 84, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
29 11 0.13
30 11 0.13
31 16 0.19
32 18 0.21
33 4 0.05
34 9 0.11
35 2 0.02
36 5 0.06
37 8 0.10
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (29 bp):
AAAAAGGAAAAAGAAAAAAACAAAACAAA
Found at i:28104 original size:36 final size:37
Alignment explanation
Indices: 28057--28186 Score: 217
Period size: 37 Copynumber: 3.5 Consensus size: 37
28047 TGGCAATTGG
28057 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
1 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
28094 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAG-A
1 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
28130 AAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAA
1 AAAAAGAAAAAAACAAAAC-AAAAAAAAGGAAAAAGAA
* *
28168 AAAAAAAAACAAAAAAAAA
1 AAAAAGAAA-AAAACAAAA
28187 GTGAAGATTT
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
36 20 0.23
37 51 0.58
38 9 0.10
39 8 0.09
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (37 bp):
AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
Found at i:31392 original size:57 final size:60
Alignment explanation
Indices: 31291--31404 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 60
31281 GAAATTTCTC
* *
31291 GAGATAATAGAAGCAAAAATTTTCGTAGCCATGATGGTTTGAAATTTCATGAGATAACAT
1 GAGATAATAGAAGCAAAAATTTTCATAGCCATGATGGTTAGAAATTTCATGAGATAACAT
* * *
31351 GAGATAATAGATGC-CAAA-TTTCATAG-CATGATGGTTAGAAATTTCATTAGATAA
1 GAGATAATAGAAGCAAAAATTTTCATAGCCATGATGGTTAGAAATTTCATGAGATAA
31405 TAGAGGCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 26 0.53
58 7 0.14
59 3 0.06
60 13 0.27
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (60 bp):
GAGATAATAGAAGCAAAAATTTTCATAGCCATGATGGTTAGAAATTTCATGAGATAACAT
Done.