Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold594
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: 32089
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:8511 original size:13 final size:12
Alignment explanation
Indices: 8478--8533 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
8468 AGGAATGTGA
*
8478 AAAAAGAAATTG
1 AAAAAGAAGTTG
8490 AAAAAGAAGTTG
1 AAAAAGAAGTTG
*
8502 AAGAAAGAAG-AG
1 AA-AAAGAAGTTG
*
8514 AAAATGAA-TTAG
1 AAAAAGAAGTT-G
8526 AAAAAGAA
1 AAAAAGAA
8534 ACAAAAGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
11 5 0.14
12 24 0.67
13 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:15286 original size:52 final size:52
Alignment explanation
Indices: 15203--15303 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
15193 TAAGGAAAAG
*
15203 TAATGGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
15255 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
15304 TATGTGCATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:22660 original size:23 final size:24
Alignment explanation
Indices: 22633--22677 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
22623 CCTTAGCTTG
22633 ACACATTAAAACATT-ATTTAAGA
1 ACACATTAAAACATTGATTTAAGA
* *
22656 ACACATTTAAACTTTGATTTAA
1 ACACATTAAAACATTGATTTAA
22678 TTTGTTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (24 bp):
ACACATTAAAACATTGATTTAAGA
Found at i:25913 original size:31 final size:31
Alignment explanation
Indices: 25878--25944 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
25868 ATCATGCATG
* * *
25878 AACCTTGCTAAATGAATCTCCACATTCGGCT
1 AACCTTGCTAAATGAACCCCCACATTCGGCC
25909 AACCTTGCTAAATGAACCCCCACATTCGGCC
1 AACCTTGCTAAATGAACCCCCACATTCGGCC
25940 AACCT
1 AACCT
25945 ACATAAATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.24
Consensus pattern (31 bp):
AACCTTGCTAAATGAACCCCCACATTCGGCC
Found at i:25952 original size:31 final size:31
Alignment explanation
Indices: 25878--25952 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
25868 ATCATGCATG
* * * *
25878 AACCTTGCTAAATGAATCTCCACATTCGGCT
1 AACCTTACTAAATGAACCCCCACATTCGGCC
*
25909 AACCTTGCTAAATGAACCCCCACATTCGGCC
1 AACCTTACTAAATGAACCCCCACATTCGGCC
25940 AACC-TACATAAAT
1 AACCTTAC-TAAAT
25953 AGGATGAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.05
31 37 0.95
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.24
Consensus pattern (31 bp):
AACCTTACTAAATGAACCCCCACATTCGGCC
Found at i:27974 original size:20 final size:19
Alignment explanation
Indices: 27951--28003 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
27941 TAGTTTTCCC
*
27951 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTC-CATG
* **
27971 AGCTTAATTTAGCTCGTTG
1 AGCTCAATTTAGCTCCATG
27990 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
28004 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (19 bp):
AGCTCAATTTAGCTCCATG
Done.