Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1999
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: 14196
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:940 original size:13 final size:13
Alignment explanation
Indices: 922--947 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
912 TACAGCAAGT
922 ATGTATCGATACA
1 ATGTATCGATACA
935 ATGTATCGATACA
1 ATGTATCGATACA
948 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3796 original size:12 final size:12
Alignment explanation
Indices: 3775--3825 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
3765 TTAGAAACTC
3775 AAGA-AAAAAAA
1 AAGAGAAAAAAA
3786 AAGAGAAAAAAA
1 AAGAGAAAAAAA
*
3798 AAGAGAAAGTAAA
1 AAGAGAAA-AAAA
*
3811 AA-AGAAAAAAT
1 AAGAGAAAAAAA
3822 AAGA
1 AAGA
3826 AAACTAGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 8 0.24
12 21 0.62
13 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (12 bp):
AAGAGAAAAAAA
Found at i:8784 original size:19 final size:19
Alignment explanation
Indices: 8760--8827 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
8750 AATTCAACGA
8760 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
8779 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
8794 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
8811 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
8828 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:8798 original size:32 final size:32
Alignment explanation
Indices: 8762--8824 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
8752 TTCAACGATT
*
8762 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
8794 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
8825 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:8799 original size:13 final size:13
Alignment explanation
Indices: 8781--8805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8771 ACATAAGTTT
8781 TGTATCGATACAA
1 TGTATCGATACAA
8794 TGTATCGATACA
1 TGTATCGATACA
8806 TAAGTATTGT
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:11322 original size:52 final size:52
Alignment explanation
Indices: 11203--11335 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 52
11193 TTGAGTTTCT
* * * *
11203 CAATTCTCCACAATCGGGGATATTCCAA-TCCCGATTTTATTTTCAAAACGC
1 CAATTTTCCACAATCGGGGATACTCCAACTCCCGATTTTATTTCCAAAACAC
** *
11254 CAATTTTCCTTTAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAATAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACTCCCGATTTTATTTCC-AAAACAC
* *
11307 CAATTTTTCACAATCGAGGATACTCCAAC
1 CAATTTTCCACAATCGGGGATACTCCAAC
11336 CTCGTTATGA
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
51 8 0.12
52 46 0.68
53 14 0.21
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (52 bp):
CAATTTTCCACAATCGGGGATACTCCAACTCCCGATTTTATTTCCAAAACAC
Found at i:13990 original size:19 final size:18
Alignment explanation
Indices: 13966--14033 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
13956 CAGTAGCTAA
13966 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
13985 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
14000 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
14017 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
14034 TCGTTGATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:14006 original size:13 final size:13
Alignment explanation
Indices: 13988--14012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13978 ACAATACTTA
13988 TGTATCGATACAT
1 TGTATCGATACAT
14001 TGTATCGATACA
1 TGTATCGATACA
14013 AAACTTATGT
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:14010 original size:32 final size:32
Alignment explanation
Indices: 13969--14031 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
13959 TAGCTAATTA
*
13969 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
14001 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
14032 AATCGTTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Done.