Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold754
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: 22168
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:11813 original size:88 final size:88
Alignment explanation
Indices: 11714--11891 Score: 320
Period size: 88 Copynumber: 2.0 Consensus size: 88
11704 AAAAATATTA
*
11714 AATAAAATATGAATTTTAAATTTCATTTTTCATAAAAATAAAGAAAGAAGACAATATTATCTTAT
1 AATAAAATATGAATTTTAAATTTCATTTTTCATAAAAATAAAGAAAGAAAACAATATTATCTTAT
11779 AATTGACAAACAACATTTGAAAC
66 AATTGACAAACAACATTTGAAAC
*
11802 AATAAAATATGAATTTTAAATTTCATTTTTCATAAAAATAAAGATAGAAAACAATATTATCTTAT
1 AATAAAATATGAATTTTAAATTTCATTTTTCATAAAAATAAAGAAAGAAAACAATATTATCTTAT
* *
11867 AATTGATAAACAATATTTGAAAC
66 AATTGACAAACAACATTTGAAAC
11890 AA
1 AA
11892 ATATCTAATG
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (88 bp):
AATAAAATATGAATTTTAAATTTCATTTTTCATAAAAATAAAGAAAGAAAACAATATTATCTTAT
AATTGACAAACAACATTTGAAAC
Found at i:13031 original size:17 final size:16
Alignment explanation
Indices: 13009--13041 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
12999 GACTTATTTG
13009 AAAAAATACAAAAAAAT
1 AAAAAATA-AAAAAAAT
13026 AAAAAATAAAAAAAAT
1 AAAAAATAAAAAAAAT
13042 GAATGGCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:13700 original size:49 final size:50
Alignment explanation
Indices: 13644--13742 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 50
13634 AAATATCAAA
*
13644 ACAATTCTTTTAAGCCATTATTTAACTAAATGATTGC-AAGTTGAATGGC
1 ACAATTCTTTTAAGCCATTATTTAACTAAATGATTGCAAAATTGAATGGC
* *
13693 ACAATTCTTTTAAGCCATTATTTCAGTAAATGATTGCAAAATTGAATGGC
1 ACAATTCTTTTAAGCCATTATTTAACTAAATGATTGCAAAATTGAATGGC
13743 CTGGGTTTCG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 35 0.76
50 11 0.24
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (50 bp):
ACAATTCTTTTAAGCCATTATTTAACTAAATGATTGCAAAATTGAATGGC
Found at i:20990 original size:52 final size:52
Alignment explanation
Indices: 20850--20978 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
20840 CGAAATATGA
20850 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
20902 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
20954 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
20979 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:21038 original size:19 final size:19
Alignment explanation
Indices: 21014--21072 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
21004 ACATTATATT
21014 GATACAAAACTTATGTATC
1 GATACAAAACTTATGTATC
21033 GATAC---A--T-TGTATC
1 GATACAAAACTTATGTATC
* *
21046 GATACAACACTTATGTATG
1 GATACAAAACTTATGTATC
21065 GATACAAA
1 GATACAAA
21073 TCGTTGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 11 0.34
14 1 0.03
16 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (19 bp):
GATACAAAACTTATGTATC
Found at i:21045 original size:13 final size:13
Alignment explanation
Indices: 21027--21051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21017 ACAAAACTTA
21027 TGTATCGATACAT
1 TGTATCGATACAT
21040 TGTATCGATACA
1 TGTATCGATACA
21052 ACACTTATGT
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:21050 original size:32 final size:32
Alignment explanation
Indices: 21000--21070 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
20990 AGCTTCGTAG
*
21000 CGATACATTATATTGATACAAAACTTATGTAT
1 CGATACATTATATCGATACAAAACTTATGTAT
* *
21032 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTATATCGATACAAAACTTATGTAT
*
21064 GGATACA
1 CGATACA
21071 AATCGTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTATATCGATACAAAACTTATGTAT
Done.