Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_292 ID=scaffold_292-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: 9120
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.25
Warning! 580 characters in sequence are not A, C, G, or T
Found at i:7984 original size:11 final size:11
Alignment explanation
Indices: 7966--8018 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
7956 TTATGCCTGA
7966 AAAAAAAAGAGAC
1 AAAAAAAA-A-AC
7979 AAAAAAAAAAC
1 AAAAAAAAAAC
* *
7990 AAAAAAACAAG
1 AAAAAAAAAAC
*
8001 AAAAAAAACAAG
1 AAAAAAAA-AAC
8013 AAAAAA
1 AAAAAA
8019 GGAAAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 18 0.50
12 10 0.28
13 8 0.22
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:8005 original size:12 final size:11
Alignment explanation
Indices: 7964--8018 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 11
7954 TATTATGCCT
7964 GAAAAAAAAAGA
1 GAAAAAAAAA-A
7976 GACAAAAAAAAA
1 GA-AAAAAAAAA
7988 -ACAAAAAAACAA
1 GA-AAAAAAA-AA
8000 GAAAAAAAACAA
1 GAAAAAAAA-AA
8012 GAAAAAA
1 GAAAAAA
8019 GGAAAAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.22
12 22 0.55
13 9 0.22
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:8024 original size:19 final size:19
Alignment explanation
Indices: 7981--8036 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
7971 AAAGAGACAA
*
7981 AAAAAAAACAAAAAAACAAG
1 AAAAAAAACAAGAAAA-AAG
8001 AAAAAAAACAAGAAAAAAGG
1 AAAAAAAACAAGAAAAAA-G
*
8021 AAAAAAGA-AAGAAAAA
1 AAAAAAAACAAGAAAAA
8037 TCAAGATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 10 0.30
20 23 0.70
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAAAAACAAGAAAAAAG
Found at i:9001 original size:79 final size:79
Alignment explanation
Indices: 8894--9120 Score: 341
Period size: 79 Copynumber: 2.8 Consensus size: 79
8884 TCAAGAAATA
*
8894 TTTTTAAAA-TTCTGTTTTTTTTTCAAAAAATCAACTCATAATACAGATGTGAGTTGAGCCTCGG
1 TTTTTAAAATTTCTG---TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
8958 GTCACGCTGAGGTA-TT
63 GTCACGCTGAGGTATTT
8974 TTTTTAAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAAATTTCTG-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
9039 CACGCTGAGGTATTT
65 CACGCTGAGGTATTT
*
9054 TTTTTAAAATTTAATTTCTGTTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
1 TTTTT--AA---AATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTC
9119 GG
61 GG
Statistics
Matches: 137, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
79 60 0.44
80 16 0.12
81 5 0.04
82 2 0.01
84 46 0.34
85 8 0.06
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (79 bp):
TTTTTAAAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
ACGCTGAGGTATTT
Done.