Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1789
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: 37514
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5644 original size:11 final size:12
Alignment explanation
Indices: 5623--5657 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5613 ATAGTAGTTT
5623 CTCGAAAAAAAA
1 CTCGAAAAAAAA
5635 CTCGAAAAAAAA
1 CTCGAAAAAAAA
*
5647 TTC-AAAAAAAA
1 CTCGAAAAAAAA
5658 ATTTTTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.11
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:5713 original size:14 final size:14
Alignment explanation
Indices: 5694--5734 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
5684 GGATATCAAG
5694 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
5708 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
5722 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
5735 GAGAGCTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:10174 original size:13 final size:13
Alignment explanation
Indices: 10156--10191 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
10146 ACGAGATTGT
*
10156 AAAAAAAATTTGA
1 AAAAAAAATTCGA
10169 AAAAAAAATTCGA
1 AAAAAAAATTCGA
10182 AAAAAAAATT
1 AAAAAAAATT
10192 GTTTAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:12276 original size:15 final size:14
Alignment explanation
Indices: 12232--12276 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
12222 TCTATTGAGC
*
12232 GAGAAAAAGAAAAG
1 GAGAAAAAGAAAAA
*
12246 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
12260 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
12275 GA
1 GA
12277 AAGAAACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:12282 original size:15 final size:15
Alignment explanation
Indices: 12232--12282 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
12222 TCTATTGAGC
*
12232 GAGA-AAAAGAAAAG
1 GAGAGAAAAGAAAAA
*
12246 GAGA-AAAACAAAAA
1 GAGAGAAAAGAAAAA
*
12260 GAGTGAAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
12275 GAAAGAAA
1 GAGAGAAA
12283 CGAATGATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 15 0.50
15 15 0.50
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (15 bp):
GAGAGAAAAGAAAAA
Found at i:18849 original size:11 final size:11
Alignment explanation
Indices: 18832--18861 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
18822 ACAAAATATT
18832 TTTTTTTTGAA
1 TTTTTTTTGAA
18843 CTTTTTTTTGAA
1 -TTTTTTTTGAA
18855 TTTTTTT
1 TTTTTTT
18862 ACAATCTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:20705 original size:12 final size:12
Alignment explanation
Indices: 20690--20738 Score: 73
Period size: 12 Copynumber: 4.1 Consensus size: 12
20680 AGGAAATTCG
*
20690 AAAAAAAA-TCA
1 AAAAAAAATTGA
20701 AAAAAAAATTTGA
1 AAAAAAAA-TTGA
20714 AAAAAAAATTGA
1 AAAAAAAATTGA
20726 AAAAAAAATTGA
1 AAAAAAAATTGA
20738 A
1 A
20739 GTATTAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
11 8 0.23
12 17 0.49
13 10 0.29
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:20733 original size:36 final size:34
Alignment explanation
Indices: 20649--20734 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 34
20639 AGCATATTGT
* **
20649 AATTGAACAAAAAAATCAAAAAAAGAAGAAGAGGA
1 AATTGAA-AAAAAAATCAAAAAAAGAAGAAAAAAA
20684 AATTCG-AAAAAAAATCAAAAAAA-AATTTGAAAAAAA
1 AATT-GAAAAAAAAATCAAAAAAAGAA---GAAAAAAA
20720 AATTGAAAAAAAAAT
1 AATTGAAAAAAAAAT
20735 TGAAGTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
33 2 0.05
34 16 0.37
35 6 0.14
36 19 0.44
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.14
Consensus pattern (34 bp):
AATTGAAAAAAAAATCAAAAAAAGAAGAAAAAAA
Found at i:28625 original size:15 final size:15
Alignment explanation
Indices: 28605--28659 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
28595 ACTCTCCTCA
*
28605 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
28620 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
28635 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
28649 TTCTTTT-TCTC
1 TTCTTTTCTCTC
28660 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Done.