Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2126
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: 25191
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:5106 original size:27 final size:27
Alignment explanation
Indices: 5035--5175 Score: 153
Period size: 27 Copynumber: 5.3 Consensus size: 27
5025 AGCATGGCTG
* *
5035 CCAGAACAGATA-ATGTGAC-GAGTCA
1 CCAGAACAGATATATGTGGCAGAGCCA
*
5060 CAAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGA-ACAGATATAT-GTGGCAGAGCCA
5088 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* *
5115 CCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* ** * *
5142 CTAGATTAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
5169 CCAGAAC
1 CCAGAAC
5176 GCTTCCTCCA
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
25 4 0.04
26 9 0.09
27 76 0.76
28 11 0.11
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
CCAGAACAGATATATGTGGCAGAGCCA
Found at i:6854 original size:25 final size:26
Alignment explanation
Indices: 6819--6925 Score: 166
Period size: 25 Copynumber: 4.2 Consensus size: 26
6809 AAGACATGAA
6819 ATCAT-GAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAACCCATT
6843 ATCATGGAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAACCCATT
*
6868 ATCATGGAACATTTACCTAATCCTATT
1 ATCATGGAACATTTACCTAA-CCCATT
6895 ATCATTGGAACATTTACCTAACCCATT
1 ATCA-TGGAACATTTACCTAACCCATT
6922 ATCA
1 ATCA
6926 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
24 5 0.06
25 39 0.51
27 17 0.22
28 16 0.21
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:6913 original size:53 final size:50
Alignment explanation
Indices: 6819--6925 Score: 171
Period size: 53 Copynumber: 2.1 Consensus size: 50
6809 AAGACATGAA
6819 ATCATGAACATTTACCTAACCATTATCATGGAACATTTACCTAA-CCATT
1 ATCATGAACATTTACCTAACCATTATCATGGAACATTTACCTAACCCATT
6868 ATCATGGAACATTTACCTAATCCTATTATCATTGGAACATTTACCTAACCCATT
1 ATCAT-GAACATTTACCTAA-CC-ATTATCA-TGGAACATTTACCTAACCCATT
6922 ATCA
1 ATCA
6926 ATTTGTACCA
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
49 5 0.09
50 14 0.26
51 2 0.04
52 7 0.13
53 16 0.30
54 9 0.17
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.34
Consensus pattern (50 bp):
ATCATGAACATTTACCTAACCATTATCATGGAACATTTACCTAACCCATT
Found at i:9746 original size:23 final size:23
Alignment explanation
Indices: 9715--9766 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
9705 TGACTTGAGA
*
9715 ATTAATTTAAGATTTTTTGAATT
1 ATTAATTTAAGATTTATTGAATT
* *
9738 ATTATTTTAAGGTTTATTGAATT
1 ATTAATTTAAGATTTATTGAATT
9761 A-TAATT
1 ATTAATT
9767 AAATAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.56
Consensus pattern (23 bp):
ATTAATTTAAGATTTATTGAATT
Found at i:13886 original size:20 final size:22
Alignment explanation
Indices: 13863--13907 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
13853 TTTTCAATAA
13863 TTTAATATT-AATT-TAGTATT
1 TTTAATATTAAATTGTAGTATT
*
13883 TTT-ATCTTAAATTGTAGTATT
1 TTTAATATTAAATTGTAGTATT
13904 TTTA
1 TTTA
13908 TTTTTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 10 0.48
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTAATATTAAATTGTAGTATT
Done.