Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2936
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: 22323
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Found at i:4941 original size:31 final size:31
Alignment explanation
Indices: 4900--4960 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
4890 TTTCATATTT
*
4900 CATATTTCATAACACTAGGCCGAAACCTTTC
1 CATATCTCATAACACTAGGCCGAAACCTTTC
** * *
4931 CATATCTCATATTACTGGGCCGAAGCCTTT
1 CATATCTCATAACACTAGGCCGAAACCTTT
4961 ACTGTAAACG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (31 bp):
CATATCTCATAACACTAGGCCGAAACCTTTC
Found at i:5217 original size:24 final size:24
Alignment explanation
Indices: 5153--5248 Score: 142
Period size: 24 Copynumber: 4.0 Consensus size: 24
5143 TGCTTTTCAT
*
5153 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
5178 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
5201 ATAATTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
5225 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
5249 CACTTCCTCC
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.26
24 41 0.62
25 8 0.12
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:5322 original size:20 final size:20
Alignment explanation
Indices: 5297--5343 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
5287 TTATGAATAC
5297 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
5317 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
5337 ACCATGT
1 ATCATGT
5344 TTATCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:10174 original size:27 final size:28
Alignment explanation
Indices: 10090--10187 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
10080 CATGAGATTG
* * *
10090 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
10119 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
10147 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
10174 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
10188 GACTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:10201 original size:29 final size:27
Alignment explanation
Indices: 10118--10202 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 27
10108 TAAATTGTTC
* *
10118 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
10146 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
10173 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
10202 A
1 A
10203 TTTTTGAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.45
28 22 0.43
29 6 0.12
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:18166 original size:27 final size:28
Alignment explanation
Indices: 18082--18179 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
18072 CATGAGATTG
* * *
18082 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
18111 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
18139 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
18166 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
18180 GACTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:18193 original size:29 final size:27
Alignment explanation
Indices: 18110--18194 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 27
18100 TAAATTGTTC
* *
18110 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
18138 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
18165 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
18194 A
1 A
18195 TTTTTGAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.45
28 22 0.43
29 6 0.12
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Done.