Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3703
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: 17508
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:3055 original size:22 final size:20
Alignment explanation
Indices: 3018--3088 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 20
3008 GTAATTGAAC
*
3018 AAAAAAA-TCAAAAAAAAAG
1 AAAAAAATTGAAAAAAAAAG
* *
3037 AAGAGAAATTCGAAAAAAAATCG
1 AA-AAAAATT-GAAAAAAAA-AG
3060 AAAAAAATTGAAAAAAAAATTG
1 AAAAAAATTGAAAAAAAAA--G
3082 AAAAAAA
1 AAAAAAA
3089 ATTCGAAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 2 0.05
20 4 0.10
21 10 0.24
22 22 0.54
23 3 0.07
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.11
Consensus pattern (20 bp):
AAAAAAATTGAAAAAAAAAG
Found at i:3085 original size:10 final size:10
Alignment explanation
Indices: 3050--3088 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
3040 AGAAATTCGA
*
3050 AAAAAAATCG
1 AAAAAAATTG
3060 AAAAAAATTG
1 AAAAAAATTG
3070 AAAAAAAAATTG
1 --AAAAAAATTG
3082 AAAAAAA
1 AAAAAAA
3089 ATTCGAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 16 0.62
12 10 0.38
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:3091 original size:11 final size:11
Alignment explanation
Indices: 3010--3091 Score: 69
Period size: 12 Copynumber: 7.4 Consensus size: 11
3000 AGCATATTGT
3010 AATTGAACAAAA
1 AATTGAA-AAAA
* *
3022 AAATCAAAAAA
1 AATTGAAAAAA
* * *
3033 AA-AGAAGAGA
1 AATTGAAAAAA
3043 AATTCGAAAAAA
1 AATT-GAAAAAA
*
3055 AATCG-AAAAA
1 AATTGAAAAAA
3065 AATTGAAAAAAA
1 AATTG-AAAAAA
3077 AATTGAAAAAA
1 AATTGAAAAAA
3088 AATT
1 AATT
3092 CGAAGTATTA
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
10 15 0.27
11 17 0.31
12 23 0.42
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.15
Consensus pattern (11 bp):
AATTGAAAAAA
Found at i:9811 original size:20 final size:20
Alignment explanation
Indices: 9788--9834 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
9778 GGGTTAAGAT
*
9788 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
9808 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
9828 TGAGCTG
1 TGAGCTG
9835 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:11513 original size:14 final size:14
Alignment explanation
Indices: 11494--11521 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11484 CAATTTCTTT
11494 TTCATTTTCTTTTC
1 TTCATTTTCTTTTC
11508 TTCATTTTCTTTTC
1 TTCATTTTCTTTTC
11522 ACTACAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCATTTTCTTTTC
Done.