Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1801
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: 16149
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Found at i:2195 original size:14 final size:14
Alignment explanation
Indices: 2159--2189 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2149 GTAGACTCTA
2159 ACTCTAAATTTTAG
1 ACTCTAAATTTTAG
*
2173 ACTCTAAATTTTTG
1 ACTCTAAATTTTAG
2187 ACT
1 ACT
2190 TCAAATCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (14 bp):
ACTCTAAATTTTAG
Found at i:3543 original size:23 final size:23
Alignment explanation
Indices: 3517--3592 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
3507 ATAAGTGCCA
3517 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3540 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3563 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3586 CACTGAT
1 CACTGAT
3593 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3692 original size:8 final size:8
Alignment explanation
Indices: 3679--3707 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3669 ACCCGGGACT
3679 CACTGTAA
1 CACTGTAA
3687 CACTGTAA
1 CACTGTAA
3695 CACTGTAA
1 CACTGTAA
3703 CACTG
1 CACTG
3708 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:3838 original size:18 final size:17
Alignment explanation
Indices: 3812--3850 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
3802 ATTTTCCTTC
3812 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
3829 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
3847 CACA
1 CACA
3851 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:10781 original size:23 final size:23
Alignment explanation
Indices: 10755--10830 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
10745 CATAAGTGCA
10755 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
10778 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
10801 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
10824 CACTGAT
1 CACTGAT
10831 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:10930 original size:8 final size:8
Alignment explanation
Indices: 10917--10945 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
10907 ACCCGGGACT
10917 CACTGTAA
1 CACTGTAA
10925 CACTGTAA
1 CACTGTAA
10933 CACTGTAA
1 CACTGTAA
10941 CACTG
1 CACTG
10946 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:11076 original size:18 final size:17
Alignment explanation
Indices: 11050--11088 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11040 ATTTTCCTTC
11050 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
11067 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
11085 CACA
1 CACA
11089 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Done.