Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2221
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: 46442
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:8774 original size:15 final size:16
Alignment explanation
Indices: 8754--8785 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
8744 AGAAAATGAA
8754 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
8769 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
8785 A
1 A
8786 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:8918 original size:21 final size:18
Alignment explanation
Indices: 8894--8938 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
8884 ACGAGAGTAC
8894 AAAAGAAATGAGTGATGTGA
1 AAAAGAAA-GAG-GATGTGA
*
8914 TAAAAGAAAGAGGATTTGA
1 -AAAAGAAAGAGGATGTGA
8933 AAAAGA
1 AAAAGA
8939 GTTTGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.18
Consensus pattern (18 bp):
AAAAGAAAGAGGATGTGA
Found at i:15295 original size:27 final size:27
Alignment explanation
Indices: 15217--15295 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
15207 AACAAGTGAG
* * *
15217 GAAAAGGAAAAAGGAGAAGAGAAAAAT
1 GAAAATGAAAAAGGAGAAAAGGAAAAT
*
15244 -AAAAGTG-AAAAGGAAGAAAATGAAAAT
1 GAAAA-TGAAAAAGG-AGAAAAGGAAAAT
*
15271 GAAAATGAAAAAGGCGAAAAGGAAA
1 GAAAATGAAAAAGGAGAAAAGGAAA
15296 GCGAGAGAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
26 10 0.24
27 22 0.52
28 10 0.24
ACGTcount: A:0.66, C:0.01, G:0.27, T:0.06
Consensus pattern (27 bp):
GAAAATGAAAAAGGAGAAAAGGAAAAT
Found at i:17744 original size:10 final size:10
Alignment explanation
Indices: 17720--17768 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
17710 AGCTCGTTTC
*
17720 CAGCTCACTT
1 CAGCTCAATT
* *
17730 GAGCTCAAGT
1 CAGCTCAATT
17740 CAGCTC-ATT
1 CAGCTCAATT
17749 CGAGCTCAATT
1 C-AGCTCAATT
17760 CAGCTCAAT
1 CAGCTCAAT
17769 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:17745 original size:20 final size:20
Alignment explanation
Indices: 17720--17766 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
17710 AGCTCGTTTC
17720 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
17740 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
17760 CAGCTCA
1 CAGCTCA
17767 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:21776 original size:10 final size:10
Alignment explanation
Indices: 21761--21809 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
21751 TTGGGTTAAG
21761 ATTGAGCTGA
1 ATTGAGCTGA
21771 ATTGAGCTCGA
1 ATTGAGCT-GA
21782 A-TGAGCTGA
1 ATTGAGCTGA
* *
21791 CTTGAGCTCA
1 ATTGAGCTGA
*
21801 AGTGAGCTG
1 ATTGAGCTG
21810 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:21786 original size:20 final size:20
Alignment explanation
Indices: 21763--21809 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
21753 GGGTTAAGAT
21763 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
21783 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
21803 TGAGCTG
1 TGAGCTG
21810 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:34028 original size:12 final size:11
Alignment explanation
Indices: 33986--34028 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
33976 ATTGTAGTTC
33986 AAAAAAAA-T-
1 AAAAAAAATTG
*
33995 AAAAAAAATCG
1 AAAAAAAATTG
34006 AAAAAAAATTG
1 AAAAAAAATTG
34017 AAAAAAATATTG
1 AAAAAAA-ATTG
34029 CATACGGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 8 0.28
11 17 0.59
12 4 0.14
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:39624 original size:24 final size:24
Alignment explanation
Indices: 39583--39646 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
39573 CATTAAGCTT
* *
39583 TTAAATATGTCTTAATTAATTAAG
1 TTAAATATGTCTTGATTAATTAAA
* *
39607 TGTTAATAT-TCTTGATTAGTTAAA
1 T-TAAATATGTCTTGATTAATTAAA
39631 TTAAATATGTCTTGAT
1 TTAAATATGTCTTGAT
39647 GTCATTTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 6 0.18
24 21 0.64
25 6 0.18
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (24 bp):
TTAAATATGTCTTGATTAATTAAA
Found at i:40837 original size:12 final size:11
Alignment explanation
Indices: 40810--40852 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
40800 ATTGAGTTTT
40810 TGAAAAAAAAA
1 TGAAAAAAAAA
40821 T--AAAAAAAA
1 TGAAAAAAAAA
40830 TCGAAAAAAAAA
1 T-GAAAAAAAAA
40842 TTGAAAAAAAA
1 -TGAAAAAAAA
40853 TATATTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 9 0.32
11 1 0.04
12 17 0.61
13 1 0.04
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (11 bp):
TGAAAAAAAAA
Found at i:40853 original size:11 final size:11
Alignment explanation
Indices: 40809--40853 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
40799 AATTGAGTTT
40809 TTGAAAAAAAA
1 TTGAAAAAAAA
*
40820 AT-AAAAAAAA
1 TTGAAAAAAAA
*
40830 TCGAAAAAAAAA
1 TTG-AAAAAAAA
40842 TTGAAAAAAAA
1 TTGAAAAAAAA
40853 T
1 T
40854 ATATTACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 8 0.29
11 10 0.36
12 10 0.36
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (11 bp):
TTGAAAAAAAA
Done.