Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold463
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: 20776
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Found at i:2243 original size:28 final size:27
Alignment explanation
Indices: 2212--2269 Score: 100
Period size: 26 Copynumber: 2.1 Consensus size: 27
2202 TGTGGTTTTG
2212 TTGTTGTGTGATTGGGATTAGTGCAATA
1 TTGTT-TGTGATTGGGATTAGTGCAATA
2240 TTG-TTGTGATTGGGATTAGTGCAATA
1 TTGTTTGTGATTGGGATTAGTGCAATA
2266 TTGT
1 TTGT
2270 ATTGACTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 25 0.86
27 1 0.03
28 3 0.10
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.45
Consensus pattern (27 bp):
TTGTTTGTGATTGGGATTAGTGCAATA
Found at i:2251 original size:26 final size:26
Alignment explanation
Indices: 2218--2269 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2208 TTTGTTGTTG
2218 TGTGATTGGGATTAGTGCAATATTGT
1 TGTGATTGGGATTAGTGCAATATTGT
2244 TGTGATTGGGATTAGTGCAATATTGT
1 TGTGATTGGGATTAGTGCAATATTGT
2270 ATTGACTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.04, G:0.31, T:0.42
Consensus pattern (26 bp):
TGTGATTGGGATTAGTGCAATATTGT
Found at i:2404 original size:19 final size:19
Alignment explanation
Indices: 2377--2415 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2367 ATTGTGTGAC
*
2377 TCGATTTGGTGTTTTTTAA
1 TCGAGTTGGTGTTTTTTAA
2396 TCGAGTTGGTGTTTTTTAA
1 TCGAGTTGGTGTTTTTTAA
2415 T
1 T
2416 GTCATTTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.05, G:0.23, T:0.56
Consensus pattern (19 bp):
TCGAGTTGGTGTTTTTTAA
Found at i:3229 original size:75 final size:75
Alignment explanation
Indices: 3106--3258 Score: 288
Period size: 75 Copynumber: 2.0 Consensus size: 75
3096 ATGAAAGCTT
* *
3106 TGTATTGGTTGAGCTAACTATTGTTTTGGAGGAACCATTCAGATTGGGGAAGCATTTAGGGGTGA
1 TGTATTGGTTGAGCTAACTATCGTTTTGGAGGAACCATTCAGATTGGGGAAGCATTTAGGGGTAA
3171 GATATTGCTG
66 GATATTGCTG
3181 TGTATTGGTTGAGCTAACTATCGTTTTGGAGGAACCATTCAGATTGGGGAAGCATTTAGGGGTAA
1 TGTATTGGTTGAGCTAACTATCGTTTTGGAGGAACCATTCAGATTGGGGAAGCATTTAGGGGTAA
3246 GATATTGCTG
66 GATATTGCTG
3256 TGT
1 TGT
3259 TAAGATAATT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (75 bp):
TGTATTGGTTGAGCTAACTATCGTTTTGGAGGAACCATTCAGATTGGGGAAGCATTTAGGGGTAA
GATATTGCTG
Found at i:13062 original size:28 final size:28
Alignment explanation
Indices: 13029--13087 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
13019 TACACAAGAG
13029 AAAGGACATTACATATCTAAAAGAACAT
1 AAAGGACATTACATATCTAAAAGAACAT
13057 AAAGGACATTACATATCTAAAAGAACAT
1 AAAGGACATTACATATCTAAAAGAACAT
13085 AAA
1 AAA
13088 AGGCTTTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.20
Consensus pattern (28 bp):
AAAGGACATTACATATCTAAAAGAACAT
Found at i:15710 original size:11 final size:11
Alignment explanation
Indices: 15681--15711 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
15671 ACCTGGAGCA
*
15681 ATATTCAAATG
1 ATATTCAGATG
15692 ATATTCAGATG
1 ATATTCAGATG
15703 ATATTCAGA
1 ATATTCAGA
15712 ACTTAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (11 bp):
ATATTCAGATG
Found at i:17011 original size:20 final size:20
Alignment explanation
Indices: 16983--17026 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16973 ACTACAAAGG
16983 AAATGAATTCAGATTAAAAA-
1 AAATGAATT-AGATTAAAAAT
* *
17003 AAATTAATTATATTAAAAAT
1 AAATGAATTAGATTAAAAAT
17023 AAAT
1 AAAT
17027 CAAATAACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATGAATTAGATTAAAAAT
Done.