Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold574
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: 38991
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6416 original size:15 final size:15
Alignment explanation
Indices: 6396--6443 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
6386 TCAAAGATGG
6396 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
6411 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
6425 GTTTATGGATATAAA
1 GTTTATGGATATGAA
6440 GTTT
1 GTTT
6444 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:6430 original size:14 final size:14
Alignment explanation
Indices: 6390--6433 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
6380 AAGGATTCAA
6390 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
6404 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
6419 AGATGGGTTTATGG
1 AGATGGGTTTATGG
6433 A
1 A
6434 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:6459 original size:29 final size:29
Alignment explanation
Indices: 6390--6449 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
6380 AAGGATTCAA
*
6390 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
6419 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
6448 AG
1 AG
6450 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:7463 original size:14 final size:14
Alignment explanation
Indices: 7421--7465 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
7411 TTAAAGAAGC
7421 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
7435 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
7448 AACTCATTTAATTA
1 AACTCATTAAATTA
7462 AACT
1 AACT
7466 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:10719 original size:10 final size:10
Alignment explanation
Indices: 10704--10730 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
10694 TAAGTTGAAG
10704 TTGAGCTGAT
1 TTGAGCTGAT
10714 TTGAGCTGAT
1 TTGAGCTGAT
10724 TTGAGCT
1 TTGAGCT
10731 TGAAGGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:11166 original size:6 final size:6
Alignment explanation
Indices: 11157--11181 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11147 GGAGTTTTTT
11157 TTTTAG TTTTAG TTTTAG TTTTAG T
1 TTTTAG TTTTAG TTTTAG TTTTAG T
11182 GTTCTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTAG
Found at i:19289 original size:22 final size:22
Alignment explanation
Indices: 19261--19307 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
19251 CCTTTTTGAA
19261 CCCTTACCATTTCGTACCAAAT
1 CCCTTACCATTTCGTACCAAAT
*
19283 CCCTTACCATTTCGTACCAATT
1 CCCTTACCATTTCGTACCAAAT
19305 CCC
1 CCC
19308 AAATACCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.40, G:0.04, T:0.32
Consensus pattern (22 bp):
CCCTTACCATTTCGTACCAAAT
Found at i:22235 original size:12 final size:11
Alignment explanation
Indices: 22218--22248 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
22208 TTGGAGTAAC
22218 AAAAAAAATTGA
1 AAAAAAAATT-A
22230 AAAAAAAATTA
1 AAAAAAAATTA
22241 AAAAAAAA
1 AAAAAAAA
22249 GAAGTGACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:23180 original size:12 final size:13
Alignment explanation
Indices: 23142--23185 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
23132 CAAAAAGTGA
*
23142 GAGAAAAGAAAAT
1 GAGAAAAGAAATT
23155 GAAGAAAAGAAAATT
1 G-AGAAAAG-AAATT
23170 GA-AAAAGAAATT
1 GAGAAAAGAAATT
23182 GAGA
1 GAGA
23186 TTGAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.26
13 7 0.26
14 8 0.30
15 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (13 bp):
GAGAAAAGAAATT
Found at i:23199 original size:17 final size:18
Alignment explanation
Indices: 23167--23200 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23157 AGAAAAGAAA
23167 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
*
23185 ATTGAGAAA-AAATTGA
1 ATTGAAAAAGAAATTGA
23201 AAAAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:32744 original size:23 final size:22
Alignment explanation
Indices: 32693--32744 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
32683 CCTCGTCTTT
*
32693 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
32715 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
32738 TTCTTTT
1 TTCTTTT
32745 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Done.