Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2128
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: 8773
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Found at i:7899 original size:32 final size:31
Alignment explanation
Indices: 7846--7940 Score: 102
Period size: 36 Copynumber: 2.8 Consensus size: 31
7836 CTATATCCGG
*
7846 GCTAAGTCCCGAAGGCATTGTGCGAGTACTAT-
1 GCTAAGT-CCGAAGGCTTTGTGCGAGTA-TATC
7878 GCTAAGTCCGAAGGCGTTTGTGCGAGCTTTATATC
1 GCTAAGTCCGAAGGC-TTTGTGCGAG---TATATC
7913 GGCTAAGTCCGAAGGCATTTGTGCGAGT
1 -GCTAAGTCCGAAGGC-TTTGTGCGAGT
7941 TATTATACCG
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
31 8 0.15
32 16 0.29
33 1 0.02
34 3 0.05
35 2 0.04
36 25 0.45
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (31 bp):
GCTAAGTCCGAAGGCTTTGTGCGAGTATATC
Found at i:7937 original size:68 final size:72
Alignment explanation
Indices: 7806--8009 Score: 231
Period size: 71 Copynumber: 2.8 Consensus size: 72
7796 ACTATTCCGG
7806 GCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTGTGCGA
1 GCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTGTGCGA
7871 GTACTAT
66 GTACTAT
* * *
7878 GCTAAGT-CCGAAGGCGTTTGTGCGAGCT-TTATAT-C-GGCTAAGT-CCGAAGGCATTTGTGCG
1 GCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCG
*
7938 AGTTATTAT
65 AG-TACTAT
* * * *
7947 ACCGGGCTAAGTCCCGAA-GCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATT
1 -----GCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATT
8010 TGAGCTAGTG
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
67 9 0.08
68 17 0.15
69 6 0.05
70 5 0.05
71 19 0.17
72 7 0.06
74 19 0.17
75 9 0.08
76 1 0.01
77 10 0.09
78 9 0.08
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (72 bp):
GCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTGTGCGA
GTACTAT
Found at i:7969 original size:38 final size:39
Alignment explanation
Indices: 7789--8011 Score: 263
Period size: 39 Copynumber: 6.0 Consensus size: 39
7779 GCTTAGCTTC
* *
7789 GCGAGCTACTATTCCGGGCTAAGTCCCGAAGGCATTCGT
1 GCGAGCTACTATACCGGGCTAAGTCCCGAAGGCATTTGT
7828 GCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCA-TTGT
1 GCGAGCTACTATA-CCGGGCTAAGTCCCGAAGGCATTTGT
*
7867 GCGAG-TACTAT-----GCTAAGT-CCGAAGGCGTTTGT
1 GCGAGCTACTATACCGGGCTAAGTCCCGAAGGCATTTGT
* *
7899 GCGAGCT-TTATATC-GGCTAAGT-CCGAAGGCATTTGT
1 GCGAGCTACTATACCGGGCTAAGTCCCGAAGGCATTTGT
* *
7935 GCGAGTTATTATACCGGGCTAAGTCCCGAA-GCATTTGT
1 GCGAGCTACTATACCGGGCTAAGTCCCGAAGGCATTTGT
* *
7973 GCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
1 GCGAGCTACTAT-ACCGGGCTAAGTCCCGAAGGCATTTG
8012 AGCTAGTGGC
Statistics
Matches: 163, Mismatches: 9, Indels: 23
0.84 0.05 0.12
Matches are distributed among these distances:
31 8 0.05
32 19 0.12
33 1 0.01
36 26 0.16
37 6 0.04
38 32 0.20
39 43 0.26
40 28 0.17
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (39 bp):
GCGAGCTACTATACCGGGCTAAGTCCCGAAGGCATTTGT
Found at i:8033 original size:39 final size:40
Alignment explanation
Indices: 7878--8034 Score: 161
Period size: 39 Copynumber: 4.1 Consensus size: 40
7868 CGAGTACTAT
* *
7878 GCTAAGT-CCGAAGGCGTTTGTGCGAGCTT--TATAT-C-G
1 GCTAAGTCCCGAAGGCATTTGTGCAAG-TTACTATATCCGG
* *
7914 GCTAAGT-CCGAAGGCATTTGTGCGAGTTATTATA-CCGG
1 GCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGG
*
7952 GCTAAGTCCCGAA-GCATTTGTGCAAGTTACTATAACCGG
1 GCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGG
* * **
7991 GCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGG
8030 GCTAA
1 GCTAA
8035 ACTCCGAAGG
Statistics
Matches: 106, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
35 2 0.02
36 25 0.24
37 5 0.05
38 27 0.25
39 28 0.26
40 19 0.18
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGG
Done.