Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2579
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: 38029
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:6729 original size:26 final size:26
Alignment explanation
Indices: 6700--6759 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
6690 TCCCTTTGAA
* * *
6700 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
6726 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
6754 CCATTC
1 TCATTC
6760 TCAATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:6775 original size:28 final size:28
Alignment explanation
Indices: 6707--6785 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
6697 GAATCATTCG
*
6707 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
* *
6735 ATATCTCGCACACTAAGTGCCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
* * *
6763 ATATTTTGTACACTGAGTACCAT
1 ATATTTTGCACACTAAGTGCCAT
6786 ATGTGATTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
ATATTTTGCACACTAAGTGCCATTCTCA
Found at i:12716 original size:9 final size:10
Alignment explanation
Indices: 12677--12709 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12667 AACTTAATAA
12677 AAGA-AAAAT
1 AAGATAAAAT
*
12686 AAAATAAAAT
1 AAGATAAAAT
12696 AAGATAAAAT
1 AAGATAAAAT
12706 AAGA
1 AAGA
12710 CAAATAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 3 0.14
10 18 0.86
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (10 bp):
AAGATAAAAT
Found at i:21290 original size:41 final size:40
Alignment explanation
Indices: 21163--21307 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
21153 CTCGCACAAG
** * * * *
21163 GCCTTCGGTTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
21203 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
21243 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
21284 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
21308 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 58 0.64
41 27 0.30
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:32162 original size:5 final size:5
Alignment explanation
Indices: 32152--32247 Score: 81
Period size: 6 Copynumber: 18.2 Consensus size: 5
32142 TATGTCTTTC
* *
32152 AAAAT AAAAT AATAAT AAAATT GAAAT GAAAAT AAAAAT CAAAAA AAAAT
1 AAAAT AAAAT AA-AAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT AAAAT
32202 AAAAAT AAAAT -AAA- AAAAT AAAAAT AAGAAT -AAAT AAAAT AAAAT
1 -AAAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAAT AAAAT
32247 A
1 A
32248 GGAGGATTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
4 9 0.12
5 32 0.42
6 35 0.46
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:32200 original size:17 final size:16
Alignment explanation
Indices: 32152--32245 Score: 73
Period size: 17 Copynumber: 5.6 Consensus size: 16
32142 TATGTCTTTC
*
32152 AAAATAAAATAATAATA
1 AAAATAAAA-AAAAATA
* **
32169 AAATTGAAATGAAAATA
1 AAAAT-AAAAAAAAATA
32186 AAAATCAAAAAAAAATA
1 AAAAT-AAAAAAAAATA
32203 AAAATAAAATAAAAAAATA
1 AAAAT--AA-AAAAAAATA
* *
32222 AAAATAAGAATAAAT-
1 AAAATAAAAAAAAATA
32237 AAAATAAAA
1 AAAATAAAA
32246 TAGGAGGATT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
15 8 0.13
16 6 0.10
17 29 0.47
18 5 0.08
19 14 0.23
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAATAAAAAAAAATA
Found at i:32201 original size:40 final size:36
Alignment explanation
Indices: 32150--32246 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 36
32140 GATATGTCTT
*
32150 TCAAAATAAAATAATAATAAAATTGAAATGAAAATAAAAA
1 TCAAAAAAAAATAA-AATAAAATT-AAA--AAAATAAAAA
32190 TCAAAAAAAAATAAAAATAAAA-TAAAAAAATAAAAA
1 TCAAAAAAAAAT-AAAATAAAATTAAAAAAATAAAAA
* *
32226 T-AAGAATAAATAAAATAAAAT
1 TCAAAAAAAAATAAAATAAAAT
32247 AGGAGGATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
34 9 0.17
35 8 0.15
36 11 0.21
38 3 0.06
39 1 0.02
40 18 0.35
41 2 0.04
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (36 bp):
TCAAAAAAAAATAAAATAAAATTAAAAAAATAAAAA
Found at i:32218 original size:29 final size:28
Alignment explanation
Indices: 32157--32245 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 28
32147 CTTTCAAAAT
*
32157 AAAATAATAATAA-AATTGAAATGAAAAT-A
1 AAAATAAAAATAAGAA-T-AAAT-AAAATAA
32186 AAAATCAAAAA-AA-AATAAAAATAAAATAAA
1 AAAAT-AAAAATAAGAAT--AAATAAAAT-AA
32216 AAAATAAAAATAAGAATAAATAAAATAA
1 AAAATAAAAATAAGAATAAATAAAATAA
32244 AA
1 AA
32246 TAGGAGGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
28 10 0.19
29 27 0.52
30 12 0.23
31 3 0.06
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (28 bp):
AAAATAAAAATAAGAATAAATAAAATAA
Done.