Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2306
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: 36727
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:9105 original size:54 final size:54
Alignment explanation
Indices: 9003--9110 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
8993 TGGATTTATA
* * * *
9003 CACTTAATAATTTTAAATCAAATTTTATTTAAAAAAGGTATTTTAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
* *
9057 CACTTAATAATCTTAAATCGAATTTGA-TTAGAAACAGGGATTTCAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTA-AAAAAGGGATTTCAATCTTAAAT
9111 TAGTGACGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 3 0.06
54 44 0.94
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (54 bp):
CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
Found at i:10907 original size:17 final size:17
Alignment explanation
Indices: 10886--10919 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
10876 TTATTATTAA
10886 ATAT-ATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
10903 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
10920 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17991 original size:16 final size:16
Alignment explanation
Indices: 17970--18015 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
17960 ACTTGAGCTC
17970 TTTTTTTCTTTTTCTT
1 TTTTTTTCTTTTTCTT
* *
17986 TTTTTTTCTTTTCCCT
1 TTTTTTTCTTTTTCTT
18002 TTTTTTT-TTTTTCT
1 TTTTTTTCTTTTTCT
18016 ACTATTGGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTCTTTTTCTT
Found at i:18397 original size:6 final size:6
Alignment explanation
Indices: 18388--18461 Score: 53
Period size: 6 Copynumber: 11.7 Consensus size: 6
18378 TTGCTCTTCT
* * *
18388 TTTTTC TTTTTA TTTTTC TTTCTTTC TTTTGT- TTTCTCTC TCTTTC TTCTTCC
1 TTTTTC TTTTTC TTTTTC -TT-TTTC TTTT-TC TTT-T-TC TTTTTC TT-TTTC
18441 TTTTTC TTTTTC TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTT
18462 CAAACCCTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
5 4 0.07
6 32 0.58
7 13 0.24
8 6 0.11
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:18397 original size:19 final size:20
Alignment explanation
Indices: 18375--18417 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
18365 ATATTTTTAT
*
18375 TTTTTGCTCTTCTTT-TTTC
1 TTTTTACTCTTCTTTCTTTC
* *
18394 TTTTTATTTTTCTTTCTTTC
1 TTTTTACTCTTCTTTCTTTC
18414 TTTT
1 TTTT
18418 GTTTTCTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTACTCTTCTTTCTTTC
Found at i:19120 original size:29 final size:30
Alignment explanation
Indices: 19067--19185 Score: 118
Period size: 29 Copynumber: 4.0 Consensus size: 30
19057 TAGAGGACAC
* *
19067 AAAACTTTTGAGGTCAAAATGTAATTTTAAG
1 AAAA-TTTAGAGGTCAAAATATAATTTTAAG
19098 AAAATTTAG-GGTCAAAATATAATTTTAAG
1 AAAATTTAGAGGTCAAAATATAATTTTAAG
* * *
19127 AAAGTTGAGATGTCAAAATATAATTTT-A-
1 AAAATTTAGAGGTCAAAATATAATTTTAAG
* * *
19155 AAAAGTTAGGTGGTCAAAATGTAAATTTTAA
1 AAAATTTA-GAGGTCAAAATAT-AATTTTAA
19186 ATTTTATATT
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
28 5 0.07
29 37 0.51
30 26 0.36
31 5 0.07
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.34
Consensus pattern (30 bp):
AAAATTTAGAGGTCAAAATATAATTTTAAG
Found at i:29355 original size:27 final size:27
Alignment explanation
Indices: 29316--29378 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
29306 TAGGGTTTGA
* *
29316 AAAAAAGAAAAAGGAAGAAGAAAGAGAT
1 AAAAAAGAAAAAGAAAGAAAAAAGA-AT
* *
29344 AAAAAAG-GAAAGAAAGAAAAAATAAT
1 AAAAAAGAAAAAGAAAGAAAAAAGAAT
29370 AAAAAAGAA
1 AAAAAAGAA
29379 GAGAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 9 0.31
27 13 0.45
28 7 0.24
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (27 bp):
AAAAAAGAAAAAGAAAGAAAAAAGAAT
Found at i:29371 original size:26 final size:22
Alignment explanation
Indices: 29352--29395 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
29342 ATAAAAAAGG
29352 AAAGAA-AGAAAAAATAATAAA
1 AAAGAAGAGAAAAAATAATAAA
29373 AAAGAAGAGAAAAAATAA-AAA
1 AAAGAAGAGAAAAAATAATAAA
29394 AA
1 AA
29396 TATAGTCGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (22 bp):
AAAGAAGAGAAAAAATAATAAA
Found at i:29783 original size:6 final size:6
Alignment explanation
Indices: 29746--29800 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
29736 GTCCAACAGT
* * *
29746 AGAAAA A-AAAGA AAAAAA AGATAAA GGGAAA AGAAAA A-AAAA AGAAAA
1 AGAAAA AGAAA-A AGAAAA AGA-AAA AGAAAA AGAAAA AGAAAA AGAAAA
29794 AGAAAA A
1 AGAAAA A
29801 AAGAGCTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
5 8 0.20
6 25 0.62
7 7 0.17
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:29801 original size:24 final size:24
Alignment explanation
Indices: 29746--29802 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
29736 GTCCAACAGT
29746 AGAAAAAAAAGAAAAAAAAGATAAA
1 AGAAAAAAAAGAAAAAAAAGA-AAA
* * *
29771 GGGAAAAGAA-AAAAAAAAGAAAA
1 AGAAAAAAAAGAAAAAAAAGAAAA
29794 AGAAAAAAA
1 AGAAAAAAA
29803 GAGCTCAAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 9 0.35
24 10 0.38
25 7 0.27
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (24 bp):
AGAAAAAAAAGAAAAAAAAGAAAA
Done.