Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1592
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: 20322
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1211 original size:5 final size:5
Alignment explanation
Indices: 1201--1231 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1191 CACCAACAAC
1201 AAATA AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
1232 TATACAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:4535 original size:15 final size:15
Alignment explanation
Indices: 4515--4549 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4505 CTATTTATAT
* *
4515 AATTTGTGTATATTA
1 AATTTGAGTAAATTA
4530 AATTTGAGTAAATTA
1 AATTTGAGTAAATTA
4545 AATTT
1 AATTT
4550 TTTAATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (15 bp):
AATTTGAGTAAATTA
Found at i:4697 original size:21 final size:21
Alignment explanation
Indices: 4673--4722 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
4663 GTAATGAATG
* *
4673 TAATTATTTTGTTAAATTTAA
1 TAATTATTTTATTAAATATAA
*
4694 TAATTAATTTATTAAATATAA
1 TAATTATTTTATTAAATATAA
4715 TAAATTAT
1 T-AATTAT
4723 AAAATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TAATTATTTTATTAAATATAA
Found at i:4727 original size:17 final size:17
Alignment explanation
Indices: 4702--4736 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4692 AATAATTAAT
* *
4702 TTATTAAATATAATAAA
1 TTATAAAATATAAAAAA
4719 TTATAAAATATAAAAAA
1 TTATAAAATATAAAAAA
4736 T
1 T
4737 CAATTACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTATAAAATATAAAAAA
Found at i:5260 original size:7 final size:7
Alignment explanation
Indices: 5248--5276 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5238 ATTAACATAT
5248 AATTATG
1 AATTATG
5255 AATTATG
1 AATTATG
5262 AATTATG
1 AATTATG
5269 AATTATG
1 AATTATG
5276 A
1 A
5277 TGACCAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (7 bp):
AATTATG
Found at i:5528 original size:14 final size:14
Alignment explanation
Indices: 5487--5532 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
5477 AAGAGATAAA
*
5487 AAATATTAATATTT
1 AAATATTAATTTTT
*
5501 AAATTTTAAATTTTT
1 AAATATT-AATTTTT
*
5516 AAATATTATTTTTT
1 AAATATTAATTTTT
5530 AAA
1 AAA
5533 AATAATTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AAATATTAATTTTT
Found at i:5761 original size:18 final size:18
Alignment explanation
Indices: 5718--5770 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
5708 ATATGATTTG
*
5718 AATTAATATTTTATTAATA
1 AATTAATATTTTAAT-ATA
* *
5737 AA-AAATATATTAATATA
1 AATTAATATTTTAATATA
5754 AATTAATATTTTAATAT
1 AATTAATATTTTAATAT
5771 TTTAATAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 5 0.18
18 21 0.75
19 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTAATATTTTAATATA
Found at i:6571 original size:35 final size:35
Alignment explanation
Indices: 6513--6586 Score: 114
Period size: 34 Copynumber: 2.1 Consensus size: 35
6503 TTATGCCTTA
6513 TAATTGTTTTTAAAAATTATATATTTATATAAATTT
1 TAATTGTTTTTAAAAATTATATA-TTATATAAATTT
* *
6549 TAATT-TTTTTAATAATTTTATATTATATAAATTT
1 TAATTGTTTTTAAAAATTATATATTATATAAATTT
6583 TAAT
1 TAAT
6587 ATATGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 16 0.44
35 15 0.42
36 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
TAATTGTTTTTAAAAATTATATATTATATAAATTT
Found at i:14438 original size:15 final size:16
Alignment explanation
Indices: 14395--14438 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
14385 ATATGTGATA
*
14395 TAAAAATTAATAAGCT
1 TAAAAATTAAAAAGCT
14411 TAAATATATTAAAAAGC-
1 TAAA-A-ATTAAAAAGCT
14428 TAAAAATTAAA
1 TAAAAATTAAA
14439 TTTAACTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 6 0.24
16 5 0.20
17 5 0.20
18 9 0.36
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (16 bp):
TAAAAATTAAAAAGCT
Found at i:17378 original size:14 final size:14
Alignment explanation
Indices: 17359--17385 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17349 TACGTTAGAC
17359 TGGATGAAATTTTG
1 TGGATGAAATTTTG
17373 TGGATGAAATTTT
1 TGGATGAAATTTT
17386 TTTTATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (14 bp):
TGGATGAAATTTTG
Found at i:19108 original size:11 final size:11
Alignment explanation
Indices: 19092--19116 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19082 CATAAAATTA
19092 TTATTATTATT
1 TTATTATTATT
19103 TTATTATTATT
1 TTATTATTATT
19114 TTA
1 TTA
19117 GTGATTACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTATT
Found at i:20046 original size:15 final size:16
Alignment explanation
Indices: 20020--20050 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
20010 ATTTTTTAAA
20020 TTAAATTAAATTATAT
1 TTAAATTAAATTATAT
20036 TTAAA-TAAATTATAT
1 TTAAATTAAATTATAT
20051 GATCAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAATTAAATTATAT
Done.