Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: evm.model.Scaffold103.187
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: 2328
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Found at i:771 original size:36 final size:36
Alignment explanation
Indices: 718--1009 Score: 274
Period size: 36 Copynumber: 8.3 Consensus size: 36
708 GCCGGATACA
*
718 TTGCGCAGATCTATTGAGATACTTCCTCAGGAGACT
1 TTGCGCAGACCTATTGAGATACTTCCTCAGGAGACT
* * ** *
754 TGGCGCAGACCTGTTGAGATACTTCCTTGGGAGCCT
1 TTGCGCAGACCTATTGAGATACTTCCTCAGGAGACT
* * *
790 TTGCGCAGACATATTGACATACTTCCCCAGGAGACT
1 TTGCGCAGACCTATTGAGATACTTCCTCAGGAGACT
* * *
826 TTGCACAGACCTATCGAGGTACTTCCTCAGGAGACT
1 TTGCGCAGACCTATTGAGATACTTCCTCAGGAGACT
* *
862 TTGCGCAGA-C----G-TATACTTCCCCAGGAGACT
1 TTGCGCAGACCTATTGAGATACTTCCTCAGGAGACT
* * * *
892 TTGCGCCGACCTACTGAGGTACTTCCTCGGGCA-ACT
1 TTGCGCAGACCTATTGAGATACTTCCTCAGG-AGACT
* * * * *
928 TTGCGTAGGCATATTGAGATACTTCCCCAGGAGAAT
1 TTGCGCAGACCTATTGAGATACTTCCTCAGGAGACT
* * * *
964 TTGCGCAGACCTATTGAGTTGCCTCCACAGGAGACT
1 TTGCGCAGACCTATTGAGATACTTCCTCAGGAGACT
*
1000 TTGCACAGAC
1 TTGCGCAGAC
1010 ATACAGAGGT
Statistics
Matches: 201, Mismatches: 47, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
30 24 0.12
31 2 0.01
35 3 0.01
36 171 0.85
37 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (36 bp):
TTGCGCAGACCTATTGAGATACTTCCTCAGGAGACT
Found at i:835 original size:72 final size:71
Alignment explanation
Indices: 718--1009 Score: 308
Period size: 72 Copynumber: 4.1 Consensus size: 71
708 GCCGGATACA
* * * * *
718 TTGCGCAGATCTATTGAGATACTTCCTCAGGAGACTTGGCGCAGACCTGTTGAGATACTTCCTTG
1 TTGCGCAGA-CTATTGAGATACTTCCCCAGGAGACTTTGCGCAGACCTATTGAGGTACTTCCTCG
*
783 GGAGCCT
65 GGAGACT
* * * *
790 TTGCGCAGACATATTGACATACTTCCCCAGGAGACTTTGCACAGACCTATCGAGGTACTTCCTCA
1 TTGCGCAGAC-TATTGAGATACTTCCCCAGGAGACTTTGCGCAGACCTATTGAGGTACTTCCTCG
855 GGAGACT
65 GGAGACT
* * *
862 TTGCGCAGAC----G-TATACTTCCCCAGGAGACTTTGCGCCGACCTACTGAGGTACTTCCTCGG
1 TTGCGCAGACTATTGAGATACTTCCCCAGGAGACTTTGCGCAGACCTATTGAGGTACTTCCTCGG
922 GCA-ACT
66 G-AGACT
* * * * * * * *
928 TTGCGTAGGCATATTGAGATACTTCCCCAGGAGAATTTGCGCAGACCTATTGAGTTGCCTCCACA
1 TTGCGCAGAC-TATTGAGATACTTCCCCAGGAGACTTTGCGCAGACCTATTGAGGTACTTCCTCG
993 GGAGACT
65 GGAGACT
*
1000 TTGCACAGAC
1 TTGCGCAGAC
1010 ATACAGAGGT
Statistics
Matches: 181, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
66 55 0.30
67 2 0.01
71 3 0.02
72 121 0.67
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (71 bp):
TTGCGCAGACTATTGAGATACTTCCCCAGGAGACTTTGCGCAGACCTATTGAGGTACTTCCTCGG
GAGACT
Found at i:995 original size:138 final size:138
Alignment explanation
Indices: 736--1009 Score: 361
Period size: 138 Copynumber: 2.0 Consensus size: 138
726 ATCTATTGAG
* ** * *
736 ATACTTCCTCAGGAGACTTGGCGCAGACCTGTTGAGATACTTCCTTGGGAGCCTTTGCGCAGACA
1 ATACTTCCCCAGGAGACTTGGCGCAGACCTACTGAGATACTTCCTCGGGAGACTTTGCGCAGACA
* * *
801 TATTGACATACTTCCCCAGGAGACTTTGCACAGACCTATCGAGGTACTTCCTCAGGAGACTTTGC
66 TATTGACATACTTCCCCAGGAGAATTTGCACAGACCTATCGAGGTACCTCCACAGGAGACTTTGC
*
866 GCAGACGT
131 ACAGACGT
* * * * *
874 ATACTTCCCCAGGAGACTTTGCGCCGACCTACTGAGGTACTTCCTCGGGCA-ACTTTGCGTAGGC
1 ATACTTCCCCAGGAGACTTGGCGCAGACCTACTGAGATACTTCCTCGGG-AGACTTTGCGCAGAC
* * * * *
938 ATATTGAGATACTTCCCCAGGAGAATTTGCGCAGACCTATTGAGTTGCCTCCACAGGAGACTTTG
65 ATATTGACATACTTCCCCAGGAGAATTTGCACAGACCTATCGAGGTACCTCCACAGGAGACTTTG
1003 CACAGAC
130 CACAGAC
1010 ATACAGAGGT
Statistics
Matches: 116, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
138 115 0.99
139 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (138 bp):
ATACTTCCCCAGGAGACTTGGCGCAGACCTACTGAGATACTTCCTCGGGAGACTTTGCGCAGACA
TATTGACATACTTCCCCAGGAGAATTTGCACAGACCTATCGAGGTACCTCCACAGGAGACTTTGC
ACAGACGT
Found at i:1031 original size:36 final size:36
Alignment explanation
Indices: 877--1045 Score: 88
Period size: 36 Copynumber: 4.7 Consensus size: 36
867 CAGACGTATA
* * * * *
877 CTTCCCCAGGAGACTTTGCGCCGACCTACTGAGGTA
1 CTTCCCCAGGAGACTTTGCACAGACATACAGAGGTG
* * ** * ** * *
913 CTTCCTCGGGCA-ACTTTGCGTAGGCATATTGAGATA
1 CTTCCCCAGG-AGACTTTGCACAGACATACAGAGGTG
* * * ** *
949 CTTCCCCAGGAGAATTTGCGCAGACCTATTGAGTTG
1 CTTCCCCAGGAGACTTTGCACAGACATACAGAGGTG
* *
985 CCTCCACAGGAGACTTTGCACAGACATACAGAGGTG
1 CTTCCCCAGGAGACTTTGCACAGACATACAGAGGTG
* ** *
1021 GTTCCCCAGGACCCATTGCACAGAC
1 CTTCCCCAGGAGACTTTGCACAGAC
1046 CTATTAGCAT
Statistics
Matches: 101, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
35 1 0.01
36 99 0.98
37 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (36 bp):
CTTCCCCAGGAGACTTTGCACAGACATACAGAGGTG
Done.