Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_58 ID=scaffold_58-JGI_221_v2.0
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: 21663
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.28
Warning! 2563 characters in sequence are not A, C, G, or T
Found at i:919 original size:30 final size:30
Alignment explanation
Indices: 870--931 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 30
860 ATTGTATTGG
870 ATTAAAAAAAGAAAGAAAATCGA-AAAAAA
1 ATTAAAAAAAGAAAGAAAATCGACAAAAAA
899 ATTAAAAAAAGTGAAA-AAAATCGAGCAAAAAA
1 ATTAAAAAAA--GAAAGAAAATCGA-CAAAAAA
931 A
1 A
932 AGNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.34
30 8 0.28
31 4 0.14
32 7 0.24
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.11
Consensus pattern (30 bp):
ATTAAAAAAAGAAAGAAAATCGACAAAAAA
Found at i:6979 original size:11 final size:11
Alignment explanation
Indices: 6965--7010 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
6955 ATTAAAAAAA
*
6965 GAAAGAAAATC
1 GAAAAAAAATC
*
6976 GAAAAAAAATT
1 GAAAAAAAATC
6987 GAAAAAAAAGT-
1 GAAAAAAAA-TC
6998 GAAAAAAAATC
1 GAAAAAAAATC
7009 GA
1 GA
7011 GCAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 1 0.03
11 29 0.94
12 1 0.03
ACGTcount: A:0.70, C:0.04, G:0.15, T:0.11
Consensus pattern (11 bp):
GAAAAAAAATC
Found at i:6990 original size:22 final size:21
Alignment explanation
Indices: 6958--7007 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
6948 GTATTGGATT
*
6958 AAAAAAA-GAAAGAAAA-TCGA
1 AAAAAAATGAAAAAAAAGT-GA
6978 AAAAAAATTGAAAAAAAAGTGA
1 AAAAAAA-TGAAAAAAAAGTGA
7000 AAAAAAAT
1 AAAAAAAT
7008 CGAGCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.27
21 1 0.04
22 17 0.65
23 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (21 bp):
AAAAAAATGAAAAAAAAGTGA
Found at i:7016 original size:22 final size:22
Alignment explanation
Indices: 6976--7019 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
6966 AAAGAAAATC
*
6976 GAAAAAAAATTGAAAAAAAAGT
1 GAAAAAAAATCGAAAAAAAAGT
6998 GAAAAAAAATCGAGCAAAAAAA
1 GAAAAAAAATCGA--AAAAAAA
7020 AGAGAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.09
Consensus pattern (22 bp):
GAAAAAAAATCGAAAAAAAAGT
Found at i:20930 original size:20 final size:20
Alignment explanation
Indices: 20907--20953 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20897 GGGTTGAGGT
20907 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
20927 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
20947 TGAGCTG
1 TGAGCTG
20954 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Done.