Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1445
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: 27138
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:11801 original size:52 final size:51
Alignment explanation
Indices: 11723--11871 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
11713 CGAAATATGA
11723 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
11775 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
11827 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
11872 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:11878 original size:13 final size:13
Alignment explanation
Indices: 11860--11884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11850 CAAAGATCAG
11860 TGTATCGATACAA
1 TGTATCGATACAA
11873 TGTATCGATACA
1 TGTATCGATACA
11885 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11962 original size:33 final size:33
Alignment explanation
Indices: 11925--11991 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11915 AGTAGCGTAA
11925 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
11958 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
11991 A
1 A
11992 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:11965 original size:13 final size:13
Alignment explanation
Indices: 11947--11971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11937 CAAAAAAATA
11947 TGTATCGATACAT
1 TGTATCGATACAT
11960 TGTATCGATACA
1 TGTATCGATACA
11972 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:19590 original size:19 final size:18
Alignment explanation
Indices: 19545--19602 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
19535 ACTCCCAGTT
19545 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
*
19564 TCCATGTATCAATACAATG
1 T-CATGTATCGATACAATG
19583 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
19602 T
1 T
19603 ATGATACATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.54
20 15 0.43
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:21931 original size:45 final size:45
Alignment explanation
Indices: 21877--21992 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 45
21867 AAATATAAAT
* * *
21877 TAAACTTAAAAGTTAAACCC-ATTTAATAC-AAATTAAAAATCTATA
1 TAAACTTAAAACTCAAACCCAATTAAAT-CTAAA-TAAAAATCTATA
*
21922 TAAA-TTTAAACTCAAACCCAATTAAATCTAAATAAAAATCTATA
1 TAAACTTAAAACTCAAACCCAATTAAATCTAAATAAAAATCTATA
* *
21966 TGAAACTT-AAACCCAAACTCAATTAAA
1 T-AAACTTAAAACTCAAACCCAATTAAA
21993 ACTTAATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
44 26 0.43
45 33 0.54
46 2 0.03
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.28
Consensus pattern (45 bp):
TAAACTTAAAACTCAAACCCAATTAAATCTAAATAAAAATCTATA
Found at i:25387 original size:5 final size:5
Alignment explanation
Indices: 25367--25424 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
25357 CTGACATTAC
* * *
25367 TAAAA TATAA -AAAA TAAAA TAAAA TAAAA T--TA TAAAA TAAAAA TTAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA
25415 TAAAAA TAAA
1 T-AAAA TAAA
25425 TTTATTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
3 2 0.05
4 3 0.07
5 28 0.67
6 9 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:25396 original size:24 final size:25
Alignment explanation
Indices: 25367--25424 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
25357 CTGACATTAC
25367 TAAAATATAAAAAAT-AAAATAAAA
1 TAAAATATAAAAAATAAAAATAAAA
* *
25391 TAAAAT-TATAAAATAAAAATTAAA
1 TAAAATATAAAAAATAAAAATAAAA
25415 TAAAA-ATAAA
1 TAAAATATAAA
25425 TTTATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (25 bp):
TAAAATATAAAAAATAAAAATAAAA
Done.