Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold645
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: 25641
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1105 original size:2 final size:2
Alignment explanation
Indices: 1098--1130 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1088 TGCTCTTGTC
1098 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1131 GTCTTGTGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5950 original size:27 final size:27
Alignment explanation
Indices: 5880--5978 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 27
5870 TTAGCTACCA
*
5880 ATTTTTGACAAACAAC-AA-G--CCACA
1 ATTTTTGACAAA-AACAAAGGAACCACC
* **
5904 ATTTTTGACAAACAAAAAAGGATTCACC
1 ATTTTTGACAAA-AACAAAGGAACCACC
* *
5932 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTGACAAAAACAAAGGAACCACC
*
5959 ATTTTTGACAAACACAAAGG
1 ATTTTTGACAAAAACAAAGG
5979 GTGGTTTTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
24 15 0.25
25 2 0.03
26 1 0.02
27 28 0.46
28 15 0.25
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.24
Consensus pattern (27 bp):
ATTTTTGACAAAAACAAAGGAACCACC
Found at i:10969 original size:12 final size:12
Alignment explanation
Indices: 10937--10988 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
10927 TTAATGTATT
10937 TATATTT-AATA
1 TATATTTAAATA
*
10948 TTTATGTTAAATA
1 TATAT-TTAAATA
10961 TATATTTAAATA
1 TATATTTAAATA
* * *
10973 TAAATATAAAAA
1 TATATTTAAATA
10985 TATA
1 TATA
10989 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 4 0.12
12 21 0.64
13 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (12 bp):
TATATTTAAATA
Found at i:13489 original size:22 final size:23
Alignment explanation
Indices: 13464--13510 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
13454 TACTTTTTTT
*
13464 ATAAAAGAAATT-TCAA-ATTAAG
1 ATAAAA-AAATTATAAATATTAAG
13486 ATAAAAAAATTATAAATATTAAG
1 ATAAAAAAATTATAAATATTAAG
13509 AT
1 AT
13511 TTTAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 9 0.41
23 8 0.36
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (23 bp):
ATAAAAAAATTATAAATATTAAG
Found at i:16965 original size:2 final size:2
Alignment explanation
Indices: 16958--16987 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16948 ATTAAAGTCG
16958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16988 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22580 original size:16 final size:16
Alignment explanation
Indices: 22547--22592 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
22537 CAAAAACAAG
22547 AATAAAATATAAAAAATA
1 AATAAAATAT--AAAATA
*
22565 ACTAAAATATAAAATA
1 AATAAAATATAAAATA
22581 AATAAAA-ATAAA
1 AATAAAATATAAA
22593 TTATCATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 5 0.19
16 12 0.46
18 9 0.35
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAAATATAAAATA
Found at i:23199 original size:17 final size:16
Alignment explanation
Indices: 23148--23190 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
23138 AATTGAAATT
23148 AAAATCTTAAAATAA-A
1 AAAAT-TTAAAATAATA
* *
23164 TATATTTAAAATAATA
1 AAAATTTAAAATAATA
23180 AAAATTTAAAA
1 AAAATTTAAAA
23191 ATATGAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTTAAAATAATA
Found at i:24803 original size:4 final size:4
Alignment explanation
Indices: 24794--24820 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
24784 AGTTTGTTAA
24794 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
24821 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Done.