Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1764
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: 22361
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Found at i:5326 original size:13 final size:13
Alignment explanation
Indices: 5308--5452 Score: 118
Period size: 13 Copynumber: 11.1 Consensus size: 13
5298 AAATAAGAAT
5308 TTAAAAAAAAAAA
1 TTAAAAAAAAAAA
5321 TTAAAAAAAAAAA
1 TTAAAAAAAAAAA
5334 TTTTTTAAAAAAAAAAAA
1 ----TT-AAAAAAAAAAA
**
5352 AAAAAAAAAAAAA
1 TTAAAAAAAAAAA
**
5365 AAAAAAAAAAAAA
1 TTAAAAAAAAAAA
* * *
5378 ATATAAAAAAAAG
1 TTAAAAAAAAAAA
*
5391 TTTAAAAAAAAAA
1 TTAAAAAAAAAAA
5404 -TAAAAAAAAAAA
1 TTAAAAAAAAAAA
5416 --AAAAAAAAAAA
1 TTAAAAAAAAAAA
*
5427 -GAAAAAAAAAAA
1 TTAAAAAAAAAAA
**
5439 AAAAAAAAAAAAA
1 TTAAAAAAAAAAA
5452 T
1 T
5453 AAATGGCTAG
Statistics
Matches: 113, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
11 11 0.10
12 22 0.19
13 67 0.59
17 2 0.02
18 11 0.10
ACGTcount: A:0.87, C:0.00, G:0.01, T:0.12
Consensus pattern (13 bp):
TTAAAAAAAAAAA
Found at i:5341 original size:30 final size:30
Alignment explanation
Indices: 5307--5452 Score: 115
Period size: 30 Copynumber: 4.9 Consensus size: 30
5297 TAAATAAGAA
**
5307 TTTAAAAAAAAAAATTAAAAAAAAAAATTT
1 TTTAAAAAAAAAAAAAAAAAAAAAAAATTT
5337 TTTAAAAAAAAAAAAAAAAAAAAAAAA---
1 TTTAAAAAAAAAAAAAAAAAAAAAAAATTT
5364 ---AAAAAAAAAAAAAAATATAAAAAAAAGTTT
1 TTTAAAAAAAAAAAAAAA-A-AAAAAAAA-TTT
*** ***
5394 AAAAAAAAAATAAAAAAAAAAAAAAAAAAAA
1 TTTAAAAAAA-AAAAAAAAAAAAAAAAATTT
***
5425 AAGAAAAAAAAAAAAAAAAAAAAAAAAT
1 TTTAAAAAAAAAAAAAAAAAAAAAAAAT
5453 AAATGGCTAG
Statistics
Matches: 99, Mismatches: 7, Indels: 20
0.79 0.06 0.16
Matches are distributed among these distances:
24 15 0.15
25 1 0.01
26 8 0.08
30 42 0.42
31 9 0.09
32 8 0.08
33 8 0.08
34 8 0.08
ACGTcount: A:0.86, C:0.00, G:0.01, T:0.12
Consensus pattern (30 bp):
TTTAAAAAAAAAAAAAAAAAAAAAAAATTT
Found at i:5344 original size:1 final size:1
Alignment explanation
Indices: 5340--5451 Score: 152
Period size: 1 Copynumber: 112.0 Consensus size: 1
5330 AAAATTTTTT
* * **** *
5340 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATAAAAAAAAGTTTAAAAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
5405 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5452 TAAATGGCTA
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 100 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:13785 original size:6 final size:6
Alignment explanation
Indices: 13774--13847 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
13764 GGGATCACTA
13774 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
13817 A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
13848 GAATAGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.05
5 22 0.38
6 27 0.47
8 6 0.10
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (6 bp):
ACTAAT
Found at i:13791 original size:5 final size:5
Alignment explanation
Indices: 13771--13832 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
13761 GCCGGGATCA
13771 CTAA- CTAAT ACTAAT CTAAT CTAA- CTAAT ACTAAT CTAAT ACTAAT
1 CTAAT CTAAT -CTAAT CTAAT CTAAT CTAAT -CTAAT CTAAT -CTAAT
**
13817 AGAAT ACTAAT CTAAT
1 CTAAT -CTAAT CTAAT
13833 ACTCTAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (5 bp):
CTAAT
Found at i:13809 original size:11 final size:11
Alignment explanation
Indices: 13770--13846 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
13760 AGCCGGGATC
13770 ACTAA-CTAAT
1 ACTAATCTAAT
13780 ACTAATCTAAT
1 ACTAATCTAAT
13791 -CTAA-CTAAT
1 ACTAATCTAAT
13800 ACTAATCTAAT
1 ACTAATCTAAT
**
13811 ACTAATAGAAT
1 ACTAATCTAAT
13822 ACTAATCTAAT
1 ACTAATCTAAT
13833 AC---TCTAAT
1 ACTAATCTAAT
13841 ACTAAT
1 ACTAAT
13847 AGAATAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:13825 original size:22 final size:21
Alignment explanation
Indices: 13770--13846 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
13760 AGCCGGGATC
13770 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
13791 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
13811 ACTAA-TAGAATACTAATCTAAT
1 ACTAACT--AATACTAATCTAAT
13833 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
13847 AGAATAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.17
20 21 0.40
21 5 0.10
22 17 0.33
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:13861 original size:14 final size:14
Alignment explanation
Indices: 13844--13871 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13834 CTCTAATACT
13844 AATAGAATAGAAAA
1 AATAGAATAGAAAA
13858 AATAGAATAGAAAA
1 AATAGAATAGAAAA
13872 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:22203 original size:18 final size:18
Alignment explanation
Indices: 22124--22217 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
22114 CAAGGTCACG
*
22124 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
22142 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
22160 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
22178 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
22196 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
22211 ATCAATA
1 ATCAATA
22218 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:22204 original size:9 final size:9
Alignment explanation
Indices: 22124--22204 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
22114 CAAGGTCACG
*
22124 ATCAATAGC
1 ATCAATATC
* *
22133 GTCACTATC
1 ATCAATATC
*
22142 ATCAATAGC
1 ATCAATATC
* * *
22151 GTCACTAGC
1 ATCAATATC
22160 ATCAATATC
1 ATCAATATC
* * *
22169 GTCACTAGC
1 ATCAATATC
22178 ATCAATATC
1 ATCAATATC
* *
22187 GTCACTATC
1 ATCAATATC
22196 ATCAATATC
1 ATCAATATC
22205 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Done.