Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2188
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: 26831
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:11686 original size:22 final size:22
Alignment explanation
Indices: 11655--11719 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
11645 ACCTTTTTGA
*
11655 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
11678 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
11700 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
11720 TTCCTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:14896 original size:12 final size:12
Alignment explanation
Indices: 14881--14923 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
14871 ACGAGATTGT
*
14881 AAAAAAAATTGA
1 AAAAAAAATTCA
*
14893 AAAAAAAATTCT
1 AAAAAAAATTCA
14905 AAAAAAAATTCA
1 AAAAAAAATTCA
14917 AAAAAAA
1 AAAAAAA
14924 GTTTGTATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:17042 original size:15 final size:14
Alignment explanation
Indices: 17006--17060 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
16996 TCTATTGAGC
17006 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
17020 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
17034 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
17049 GAAAGAAAAGAA
1 GAGA-AAAAGAA
17061 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:19668 original size:10 final size:10
Alignment explanation
Indices: 19653--19692 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
19643 TAGTAGTTTC
19653 TTCAAAAAAA
1 TTCAAAAAAA
19663 TTCAAAAAAAA
1 TTC-AAAAAAA
*
19674 AT-AAAAAAA
1 TTCAAAAAAA
19683 TTCAAAAAAA
1 TTCAAAAAAA
19693 ATTTTTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 8 0.31
10 10 0.38
11 8 0.31
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:19672 original size:11 final size:11
Alignment explanation
Indices: 19656--19695 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
19646 TAGTTTCTTC
19656 AAAAAAATTCA
1 AAAAAAATTCA
*
19667 AAAAAAAAT--
1 AAAAAAATTCA
19676 AAAAAAATTCA
1 AAAAAAATTCA
19687 AAAAAAATT
1 AAAAAAATT
19696 TTTCCATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:19681 original size:20 final size:20
Alignment explanation
Indices: 19656--19693 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19646 TAGTTTCTTC
19656 AAAAAAATTCAAAAAAAAAT
1 AAAAAAATTCAAAAAAAAAT
19676 AAAAAAATTCAAAAAAAA
1 AAAAAAATTCAAAAAAAA
19694 TTTTTCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAAAATTCAAAAAAAAAT
Found at i:19748 original size:14 final size:13
Alignment explanation
Indices: 19729--19777 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 13
19719 GATATCAAGT
19729 TGAAAAAAAATTCG
1 TGAAAAAAAATT-G
19743 TGAAAAAAAAATTG
1 TG-AAAAAAAATTG
*
19757 TGAAAAAAAAAT-
1 TGAAAAAAAATTG
19769 TGAAAAAAA
1 TGAAAAAAA
19778 GAAGAAGCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
12 9 0.27
13 9 0.27
14 5 0.15
15 10 0.30
ACGTcount: A:0.67, C:0.02, G:0.12, T:0.18
Consensus pattern (13 bp):
TGAAAAAAAATTG
Found at i:19751 original size:15 final size:14
Alignment explanation
Indices: 19731--19770 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
19721 TATCAAGTTG
19731 AAAAAAAATTCGTGA
1 AAAAAAAATT-GTGA
19746 AAAAAAAATTGTGA
1 AAAAAAAATTGTGA
19760 AAAAAAAATTG
1 AAAAAAAATTG
19771 AAAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (14 bp):
AAAAAAAATTGTGA
Done.