Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1146
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: 23295
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:9853 original size:30 final size:31
Alignment explanation
Indices: 9819--9915 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
9809 AGCTCACTCC
*
9819 TAGCTC-ACTTTCAACTTACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * * *
9849 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * *
9879 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
9909 TAGCTCA
1 TAGCTCA
9916 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 48 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTTACGAGCTAAACCT
Found at i:12684 original size:12 final size:12
Alignment explanation
Indices: 12669--12704 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
12659 AAAAAAAAAA
12669 AAAAAAAAATTG
1 AAAAAAAAATTG
12681 AAAAAAAAATTG
1 AAAAAAAAATTG
12693 AAAAAAAAATTG
1 AAAAAAAAATTG
12705 CATACGGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:12689 original size:24 final size:24
Alignment explanation
Indices: 12657--12704 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12647 AGATTCAAAA
12657 AAAAAAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAAAATTG
***
12681 AAAAAAAAATTGAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAAAATTG
12705 CATACGGTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAAAAAATTG
Found at i:12697 original size:1 final size:1
Alignment explanation
Indices: 12653--12677 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12643 TTGTAGATTC
12653 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12678 TTGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14976 original size:17 final size:18
Alignment explanation
Indices: 14937--14978 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
14927 AAGAAGAAAA
14937 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
14954 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
14971 TCAAAAGA
1 ACAAAAGA
14979 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:20336 original size:6 final size:5
Alignment explanation
Indices: 20312--20368 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
20302 ACGAGAAAAC
*
20312 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
20359 AAAGA AAAGA
1 AAAGA AAAGA
20369 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:20343 original size:15 final size:14
Alignment explanation
Indices: 20312--20368 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
20302 ACGAGAAAAC
20312 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
20328 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
20343 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
20359 AAAGAAAAGA
1 AAAGAAAAGA
20369 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:20455 original size:11 final size:12
Alignment explanation
Indices: 20423--20453 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20413 TTGAGAGAAC
20423 TTGAAAAAGCCT
1 TTGAAAAAGCCT
*
20435 TTGAAAAAGCTT
1 TTGAAAAAGCCT
20447 TTGAAAA
1 TTGAAAA
20454 GCAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:20490 original size:30 final size:31
Alignment explanation
Indices: 20456--20537 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
20446 TTTGAAAAGC
* *
20456 AAAAATAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
20486 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
20516 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
20538 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:22679 original size:30 final size:31
Alignment explanation
Indices: 22645--22741 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
22635 AGCTCACTCC
*
22645 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
22675 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
22705 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
22735 TAGCTCA
1 TAGCTCA
22742 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Done.