Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1152
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: 35814
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:15230 original size:174 final size:174
Alignment explanation
Indices: 14915--15245 Score: 504
Period size: 176 Copynumber: 1.9 Consensus size: 174
14905 ATCATGAGAT
* * * * *
14915 TGGCACTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGCGGTTGATTATTAAGCACTA
1 TGGCACTAAGTGTGCGAGTTTAAAGTGCACAGCACTAAGTGTGCGCGGTTGATTACTAAACACTA
* *
14980 TGTGTGCGAACCCAATATATATATTTTCTATAATTATTTACATTAAGGGTGCGACTTTACCGAGT
66 TGCGTGCGAACCC-ATATATATATTTTCTATAATTATTTACATGAAGGGTGCGACTTTACCGAGT
*
15045 CGATTTTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCA
130 CAATTTTGGACAGCGG-AAAAGGTAAGTGTGCGAACTTGAAATGCA
* ** * *
15091 TGGCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTA
1 TGGCACTAAGTGTGCGAGTTTAAAGTGCACAGCACTAAGTGTGCGCGGTTGATTACTAAACACTA
15156 TGCGTGC-AACCC-TATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGT
66 TGCGTGCGAACCCATATATATATTTTCTAT-AATTATTTACATGAAGGGTGCGACTTTACCGAGT
15219 CAATTTTGGACAGCGGAAAAGGTAAGT
130 CAATTTTGGACAGCGGAAAAGGTAAGT
15246 ACCTTGAGTT
Statistics
Matches: 141, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
173 27 0.19
174 48 0.34
175 5 0.04
176 61 0.43
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.32
Consensus pattern (174 bp):
TGGCACTAAGTGTGCGAGTTTAAAGTGCACAGCACTAAGTGTGCGCGGTTGATTACTAAACACTA
TGCGTGCGAACCCATATATATATTTTCTATAATTATTTACATGAAGGGTGCGACTTTACCGAGTC
AATTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCA
Found at i:22842 original size:40 final size:40
Alignment explanation
Indices: 22787--23010 Score: 288
Period size: 40 Copynumber: 5.5 Consensus size: 40
22777 TATTCGGATG
22787 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
22827 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
22870 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
22910 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
22950 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCCAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
22990 ACATCC-GGCTAAATCTCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
23011 ATACTTGGGT
Statistics
Matches: 162, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 11 0.07
40 113 0.70
41 1 0.01
43 37 0.23
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:22930 original size:83 final size:80
Alignment explanation
Indices: 22791--23010 Score: 291
Period size: 83 Copynumber: 2.7 Consensus size: 80
22781 CGGATGATAT
**
22791 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCA
22856 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
* *
22874 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
22939 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * * * * *
22954 CCGGGCTAAGACCTGAAGGCATTTGTGCCAGTTACTACATCC-GGCTAAATCTCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAG
23011 ATACTTGGGT
Statistics
Matches: 124, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
79 15 0.12
80 45 0.36
83 64 0.52
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:27357 original size:13 final size:13
Alignment explanation
Indices: 27339--27375 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27329 CTAAGTTATA
27339 GCAGGCACACGGT
1 GCAGGCACACGGT
27352 GCAGGCACACGGT
1 GCAGGCACACGGT
* *
27365 CCAGTCACACG
1 GCAGGCACACG
27376 CCCGTGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.24, C:0.35, G:0.32, T:0.08
Consensus pattern (13 bp):
GCAGGCACACGGT
Found at i:29775 original size:43 final size:43
Alignment explanation
Indices: 29722--29845 Score: 194
Period size: 43 Copynumber: 2.9 Consensus size: 43
29712 TTTATCGAGA
*
29722 TGTGAATACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
*
29765 TGTGATTACATGTAAGACCATGTCTGAGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * * *
29808 TGTAATTACGTGTAAGACCGTGTCTGGGATATTGGCAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT
29846 CGTTATATGA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:29867 original size:43 final size:41
Alignment explanation
Indices: 29732--29881 Score: 158
Period size: 43 Copynumber: 3.5 Consensus size: 41
29722 TGTGAATACA
*
29732 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATTGTA-T-TGATTACG
*
29775 TGTAAGACCATGTCTGAGACATTGGCATTGTATTGTAATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTG--ATTACG
* * * *
29818 TGTAAGACCGTGTCTGGGATATTGGCATCGTTATATGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATTG-TAT-TGATTACG
* *
29861 TATAAGACTC-TGTCTGAGACA
1 TGTAAGAC-CATGTCTGGGACA
29882 GAGGCATCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 83 0.90
44 4 0.04
45 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATTGGCATTGTATTGATTACG
Found at i:29908 original size:86 final size:85
Alignment explanation
Indices: 29721--29914 Score: 196
Period size: 86 Copynumber: 2.3 Consensus size: 85
29711 ATTTATCGAG
* * *
29721 ATGTGA-ATACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGATTACATGTAAGACCA
1 ATGTGATA-ACATGTAAGACCATGTCTGGGACATTGGCATCGTATTATGATTACATATAAGACCA
** **
29785 TGTCTGAGACATTGGCATTGT
65 TGTCTGAGACAGAGGCATAAT
* * * * * * *
29806 ATTGTAATTACGTGTAAGACCGTGTCTGGGATATTGGCATCGT-TATATGATTTCGTATAAGACT
1 A-TGTGATAACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-TATGATTACATATAAGAC-
29870 C-TGTCTGAGACAGAGGCATCAAT
63 CATGTCTGAGACAGAGGCAT-AAT
29893 ATGTGATAACATGTAAGACCAT
1 ATGTGATAACATGTAAGACCAT
29915 ATTCGGGATA
Statistics
Matches: 86, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
85 2 0.02
86 81 0.94
87 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.32
Consensus pattern (85 bp):
ATGTGATAACATGTAAGACCATGTCTGGGACATTGGCATCGTATTATGATTACATATAAGACCAT
GTCTGAGACAGAGGCATAAT
Found at i:33670 original size:16 final size:17
Alignment explanation
Indices: 33636--33686 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
33626 AATCTTACTA
*
33636 TATTATTAATAAATTTT
1 TATTATTAATAAATATT
*
33653 TATTTTTAA-AAATATT
1 TATTATTAATAAATATT
**
33669 TAAAATTAATAAAATATT
1 TATTATTAAT-AAATATT
33687 ATGATTTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 12 0.44
17 8 0.30
18 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATTAATAAATATT
Done.