Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2008
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: 28828
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Found at i:746 original size:40 final size:40
Alignment explanation
Indices: 672--853 Score: 305
Period size: 40 Copynumber: 4.6 Consensus size: 40
662 AACCCAAGTA
* *
672 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
711 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
751 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
791 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
831 CCTTCGGGACTTAGCCAGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
854 CATTCGAATA
Statistics
Matches: 136, Mismatches: 5, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
39 12 0.09
40 123 0.90
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:7374 original size:17 final size:17
Alignment explanation
Indices: 7352--7403 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
7342 AAAACTTAAT
7352 TTCATTTATTTACACAG
1 TTCATTTATTTACACAG
7369 TTCA-TT-TTT--A-A-
1 TTCATTTATTTACACAG
*
7380 TTCATTTATTTACACGG
1 TTCATTTATTTACACAG
7397 TTCATTT
1 TTCATTT
7404 TAAATTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 12
0.68 0.02 0.29
Matches are distributed among these distances:
11 4 0.14
12 3 0.11
13 4 0.14
15 4 0.14
16 2 0.07
17 11 0.39
ACGTcount: A:0.25, C:0.15, G:0.06, T:0.54
Consensus pattern (17 bp):
TTCATTTATTTACACAG
Found at i:7388 original size:28 final size:28
Alignment explanation
Indices: 7347--7409 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
7337 GTGTTAAAAC
7347 TTAATTTCATTTATTTACACAGTTCATTT
1 TTAA-TTCATTTATTTACACAGTTCATTT
*
7376 TTAATTCATTTATTTACACGGTTCATTT
1 TTAATTCATTTATTTACACAGTTCATTT
*
7404 TAAATT
1 TTAATT
7410 TCAGACAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.54
Consensus pattern (28 bp):
TTAATTCATTTATTTACACAGTTCATTT
Found at i:8709 original size:40 final size:40
Alignment explanation
Indices: 8652--8831 Score: 237
Period size: 40 Copynumber: 4.5 Consensus size: 40
8642 ACCCAAGTAT
* *
8652 CTTC-GGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
8690 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
8730 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
8770 CTTCGGGACTTAG-CCGG-TATAG-CAACTACTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA--GCACAAATGC
8810 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
8832 CATCCGAATA
Statistics
Matches: 126, Mismatches: 8, Indels: 12
0.86 0.05 0.08
Matches are distributed among these distances:
37 1 0.01
38 13 0.10
39 10 0.08
40 94 0.75
41 5 0.04
42 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:17923 original size:1 final size:1
Alignment explanation
Indices: 17917--17983 Score: 71
Period size: 1 Copynumber: 67.0 Consensus size: 1
17907 CACACGGATC
* * * * * * *
17917 AAAAAAAAAATAAATAAAAGAACAAAATAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17982 AA
1 AA
17984 GTGCCTCAAC
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.90, C:0.03, G:0.03, T:0.04
Consensus pattern (1 bp):
A
Found at i:20524 original size:10 final size:10
Alignment explanation
Indices: 20511--20539 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
20501 TAAAAAGCAA
20511 AAAAAAAAAT
1 AAAAAAAAAT
20521 AAAAAAAAAT
1 AAAAAAAAAT
20531 AAAAAAAAA
1 AAAAAAAAA
20540 AATACTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:20524 original size:12 final size:12
Alignment explanation
Indices: 20509--20543 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
20499 TCTAAAAAGC
20509 AAAAAAAAAAAT
1 AAAAAAAAAAAT
20521 --AAAAAAAAAT
1 AAAAAAAAAAAT
20531 AAAAAAAAAAAT
1 AAAAAAAAAAAT
20543 A
1 A
20544 CTGTTGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.48
12 11 0.52
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (12 bp):
AAAAAAAAAAAT
Done.