Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015288.1 Kokia drynarioides strain JFW-HI SEQ_130333, whole genome shotgun sequence
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: 637797
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 464 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:636833 original size:30 final size:30
Alignment explanation
Indices: 636698--636975 Score: 136
Period size: 30 Copynumber: 9.3 Consensus size: 30
636688 CATTAAAATC
* * * * *
636698 GGTCAATTTTGAATTTTTGGAAACTTCAAG
1 GGTCAAATTTGAATTTTTAGAAAGTTTAGG
** * *
636728 GGTCAAA-TAAAATTTTTTGGAAA-TTTTGAG
1 GGTCAAATTTGAA-TTTTTAGAAAGTTTAG-G
* ** * *
636758 GGTCAAATTGGAAAATTTGGAAAATTT-GG
1 GGTCAAATTTGAATTTTTAGAAAGTTTAGG
**
636787 GGATCAAATTCAAATTTTTAGAAAGTTTAGG
1 GG-TCAAATTTGAATTTTTAGAAAGTTTAGG
* * * *
636818 TGTCAATTTTGAATTTTTGGAAAATTTAGG
1 GGTCAAATTTGAATTTTTAGAAAGTTTAGG
* * *
636848 GGTTAAATTTGAATTTAT-GAAAAGGTTAGG
1 GGTCAAATTTGAATTTTTAG-AAAGTTTAGG
** * *
636878 GGTCAAATTCAAATTTTTAGATAGTTT-GT
1 GGTCAAATTTGAATTTTTAGAAAGTTTAGG
* * * *
636907 GGTCAAATTCGAATTTTTTGGAAAATTTAAG
1 GGTCAAATTTGAA-TTTTTAGAAAGTTTAGG
** * * *
636938 GGTCAAAACAT-AATTTTTTGACAGTTTAAG
1 GGTC-AAATTTGAATTTTTAGAAAGTTTAGG
636968 GGTCAAAT
1 GGTCAAAT
636976 AATAATTTTA
Statistics
Matches: 189, Mismatches: 48, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
29 25 0.13
30 145 0.77
31 16 0.08
32 3 0.02
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (30 bp):
GGTCAAATTTGAATTTTTAGAAAGTTTAGG
Found at i:636835 original size:90 final size:88
Alignment explanation
Indices: 636738--636944 Score: 233
Period size: 90 Copynumber: 2.3 Consensus size: 88
636728 GGTCAAATAA
* *
636738 AATTTTTTGGAAATTTTGAGGGTCAAATTGGAAAATTT-GGAAAA-TTTGGGGATCAAATTCAAA
1 AATTTTTTGGAAAATTT-AGGGTCAAATTGG--AATTTAGGAAAAGTTAGGGG-TCAAATTCAAA
* *
636801 TTTTTAGAAAGTTTAG-GTGTCAATTTTG
62 TTTTTAGAAAGTTT-GTG-GTCAAATTCG
* * *
636829 AA-TTTTTGGAAAATTTAGGGGTTAAATTTGAATTTATGAAAAGGTTAGGGGTCAAATTCAAATT
1 AATTTTTTGGAAAATTTA-GGGTCAAATTGGAATTTAGGAAAA-GTTAGGGGTCAAATTCAAATT
*
636893 TTTAGATAGTTTGTGGTCAAATTCG
64 TTTAGAAAGTTTGTGGTCAAATTCG
636918 AATTTTTTGGAAAATTTAAGGGTCAAA
1 AATTTTTTGGAAAATTT-AGGGTCAAA
636945 ACATAATTTT
Statistics
Matches: 100, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
88 5 0.05
89 17 0.17
90 69 0.69
91 9 0.09
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (88 bp):
AATTTTTTGGAAAATTTAGGGTCAAATTGGAATTTAGGAAAAGTTAGGGGTCAAATTCAAATTTT
TAGAAAGTTTGTGGTCAAATTCG
Found at i:636856 original size:60 final size:61
Alignment explanation
Indices: 636698--636856 Score: 173
Period size: 60 Copynumber: 2.6 Consensus size: 61
636688 CATTAAAATC
* * * * *
636698 GGTCAATTTTGAATTTTTGGAAACTTCAAGGGTCAAA-TAAAATTTTTTGGAAATTTTGAG
1 GGTCAATTTTGAATTTTTGGAAAATTTAGGGGTCAAATTAAAATTTTTTAGAAAGTTTGAG
* * ** *
636758 GGTCAAATTGGAAAATTTGGAAAATTT-GGGGATCAAATTCAAA-TTTTTAGAAAGTTT-AG
1 GGTCAATTTTGAATTTTTGGAAAATTTAGGGG-TCAAATTAAAATTTTTTAGAAAGTTTGAG
*
636817 GTGTCAATTTTGAATTTTTGGAAAATTTAGGGGTTAAATT
1 G-GTCAATTTTGAATTTTTGGAAAATTTAGGGGTCAAATT
636857 TGAATTTATG
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
59 6 0.08
60 66 0.82
61 8 0.10
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (61 bp):
GGTCAATTTTGAATTTTTGGAAAATTTAGGGGTCAAATTAAAATTTTTTAGAAAGTTTGAG
Found at i:636971 original size:90 final size:90
Alignment explanation
Indices: 636790--636975 Score: 209
Period size: 90 Copynumber: 2.1 Consensus size: 90
636780 AATTTGGGGA
* * * *
636790 TCAAATTCAAATTTTTAGAAAGTTTAGGTGTCAATTTTGAATTTTTGGAAAATTTAGGGGTTAAA
1 TCAAATTCAAATTTTTAGAAAGTTTAGGTGTCAAATTCGAATTTTTGGAAAATTTAAGGGTAAAA
** *
636855 TTTGAATTTATGAAAAGGTTAGGGG
66 CATGAATTTATGAAAAGGTTAAGGG
*
636880 TCAAATTCAAATTTTTAGATAGTTT--GTGGTCAAATTCGAATTTTTTGGAAAATTTAAGGGTCA
1 TCAAATTCAAATTTTTAGAAAGTTTAGGT-GTCAAATTCGAA-TTTTTGGAAAATTTAAGGGT-A
* * *
636943 AAACAT-AATTTTTTG-ACAGTTTAAGGG
63 AAACATGAA-TTTATGAAAAGGTTAAGGG
636970 TCAAAT
1 TCAAAT
636976 AATAATTTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
88 2 0.02
89 10 0.12
90 60 0.74
91 9 0.11
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (90 bp):
TCAAATTCAAATTTTTAGAAAGTTTAGGTGTCAAATTCGAATTTTTGGAAAATTTAAGGGTAAAA
CATGAATTTATGAAAAGGTTAAGGG
Found at i:636981 original size:30 final size:31
Alignment explanation
Indices: 636918--636984 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
636908 GTCAAATTCG
636918 AATTTTTTGGAAAATTTAAGGGTCAAAACAT
1 AATTTTTTGGAAAATTTAAGGGTCAAAACAT
* *
636949 AATTTTTT-GACAGTTTAAGGGTCAAATA-AT
1 AATTTTTTGGAAAATTTAAGGGTCAAA-ACAT
636979 AATTTT
1 AATTTT
636985 AAAATAACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (31 bp):
AATTTTTTGGAAAATTTAAGGGTCAAAACAT
Found at i:637758 original size:16 final size:15
Alignment explanation
Indices: 637718--637770 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
637708 AAATAATAAT
637718 AATATAATATCAAATA
1 AATATAATAT-AAATA
* *
637734 AGTAAAATATAAAGTA
1 AATATAATATAAA-TA
*
637750 AATATAATATATATA
1 AATATAATATAAATA
*
637765 TATATA
1 AATATA
637771 TATGTGTGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (15 bp):
AATATAATATAAATA
Found at i:637778 original size:2 final size:2
Alignment explanation
Indices: 637773--637797 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
637763 TATATATATA
637773 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.