Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2706
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: 30537
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Found at i:11812 original size:40 final size:40
Alignment explanation
Indices: 11729--11991 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
11719 TTGAATGCTG
* * * * * *
11729 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
11769 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
11809 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
11849 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
11889 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
11929 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
11968 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
11992 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:12011 original size:79 final size:80
Alignment explanation
Indices: 11768--12026 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
11758 AAGTGAATAT
* * * * * * *
11768 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
11832 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
11848 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
11913 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
11928 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
11992 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
12007 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
12027 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:17937 original size:40 final size:40
Alignment explanation
Indices: 17854--18116 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
17844 TTGAATGCTG
* * * * * *
17854 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
17894 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
17934 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17974 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
18014 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
18054 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
18093 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
18117 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:18136 original size:79 final size:80
Alignment explanation
Indices: 17893--18151 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
17883 AAGTGAATAT
* * * * * * *
17893 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
17957 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
17973 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
18038 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
18053 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
18117 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
18132 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
18152 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:24145 original size:33 final size:33
Alignment explanation
Indices: 24098--24168 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
24088 GTTACTGCAA
*
24098 AAGAATGTTTCGTTTGTTTGGAGTGAACAGTGT
1 AAGAATGTTCCGTTTGTTTGGAGTGAACAGTGT
24131 AAGAATGTTCCGTTTGTTTGGAGTGAACAGTGT
1 AAGAATGTTCCGTTTGTTTGGAGTGAACAGTGT
24164 AAGAA
1 AAGAA
24169 AAGTTTTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.35
Consensus pattern (33 bp):
AAGAATGTTCCGTTTGTTTGGAGTGAACAGTGT
Found at i:27411 original size:40 final size:40
Alignment explanation
Indices: 27344--27569 Score: 275
Period size: 40 Copynumber: 5.7 Consensus size: 40
27334 ATGGTTATTC
*
27344 GACTGATATCCGGGCTAAG-TCCAGAAGGCTTTTGTGCTAGT
1 GACT-ATATCCGGGCTAAGATCC-GAAGGCATTTGTGCTAGT
* *
27385 GACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTT
1 GACTATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-T
* *
27426 G-CTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGC
1 GACTATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGT
*
27465 GACTATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGT
1 GACTATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGT
* *
27505 GACTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTT
1 GACTATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-T
*
27546 G-TTATATCC-GGCTAA-ATCCCGAAG
1 GACTATATCCGGGCTAAGAT-CCGAAG
27570 ATACTTGGGT
Statistics
Matches: 163, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.01
39 13 0.08
40 138 0.85
41 11 0.07
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GACTATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGT
Found at i:27837 original size:22 final size:22
Alignment explanation
Indices: 27797--27838 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27787 GAATGTGCAT
*
27797 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
27819 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
27839 TCGAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Done.