DoriC database

DoriC accession number ORI10010003
Organism Treponema pallidum subsp. pallidum str. Nichols
RefSeq NC_000919.1
Topology Circular
Lineage Bacteria, Spirochaetes, Spirochaetales, Spirochaetaceae, Treponema.
Chromosome size 1138011 nt
Chromosome GC content 0.5278
OriC length 242 nt
OriC AT content 0.6694
The number of DnaA box 3
The location of oriC region 1399..1640 nt
The location of dnaA gene 4..1398 nt
The extremes of GC disparity 2066 nt (minimum), 557777 nt (maximum)
Note -
OriC Sequence

ggcgtagacactgaattcgaTGGGGATAAgtGGTGGATAAaagaatataaattagtcattacactttactcacgaatatccccctttttttagagaaaaaatatactttcttcacaagcttgtgtgcggtttttgtttggtaattctcgagacataagcacTTATCCAGAtattcacagttactattatgtgatacgactacattctttatacttataagattaataaggaggaaactaact

The information of repeat
The following lines contain repeats found, one line each.
[1] - repeat length of the first part
[2] - starting position of the first part
[4] - repeat length of the second part
[5] - starting position of the second part
[6] - distance of this repeat
[7] - calculated evalue of this repeat
[8] - repeat sequence

For more details, please refer to The Manual of REPuter.

12 112 P 12 112 0 9.82e-04 cacaagcttgtg
12 66 R 12 153 -1 3.53e-02 ta[ct]tcacgaata
9 23 P 9 158 0 6.28e-02 ggataagtg
9 226 R 9 226 0 6.28e-02 aaggaggaa
11 79 F 11 80 -1 1.30e-01 cccc[ct]tttttt
8 144 P 8 144 0 2.51e-01 tctcgaga
8 212 P 8 212 0 2.51e-01 cttataag
10 25 R 10 29 -1 4.71e-01 ata[ag]gtggtg
10 39 F 10 95 -1 4.71e-01 aaa[ga]aatata
10 39 P 10 199 -1 4.71e-01 aaagaat[ag]ta
7 21 P 7 76 0 1.01e+00 ggggata
7 25 C 7 170 0 1.01e+00 ataagtg
7 33 P 7 161 0 1.01e+00 tggataa
7 41 R 7 214 0 1.01e+00 agaatat
7 43 R 7 43 0 1.01e+00 aatataa
7 44 R 7 98 0 1.01e+00 atataaa
7 73 P 7 168 0 1.01e+00 gaatatc
7 78 R 7 78 0 1.01e+00 tccccct
7 83 C 7 94 0 1.01e+00 ctttttt
7 84 R 7 84 0 1.01e+00 ttttttt
7 85 C 7 95 0 1.01e+00 tttttta
7 101 F 7 208 0 1.01e+00 tatactt
7 128 R 7 128 0 1.01e+00 gtttttg
7 131 R 7 131 0 1.01e+00 tttgttt
7 158 R 7 170 0 1.01e+00 cacttat
7 169 R 7 211 0 1.01e+00 atattca
9 10 C 9 150 -1 1.70e+00 ctg[at]attcg
9 36 R 9 40 -1 1.70e+00 ata[at]aagaa
9 36 C 9 103 -1 1.70e+00 at[ag]aaagaa
9 39 P 9 100 -1 1.70e+00 aaag[at]atat
9 43 C 9 207 -1 1.70e+00 aatat[ag]aat
9 55 R 9 61 -1 1.70e+00 tcatt[at]cac
9 78 C 9 227 -1 1.70e+00 tcc[ct]ccttt
9 95 C 9 203 -1 1.70e+00 aa[ag]aaatat
9 103 F 9 199 -1 1.70e+00 tac[ta]ttctt
9 151 R 9 194 -1 1.70e+00 acat[ac]agca
6 6 R 6 173 0 4.02e+00 gacact
6 12 P 6 12 0 4.02e+00 gaattc
6 23 F 6 34 0 4.02e+00 ggataa
6 25 P 6 211 0 4.02e+00 ataagt
6 36 R 6 97 0 4.02e+00 ataaaa
6 38 R 6 93 0 4.02e+00 aaaaga
6 42 F 6 73 0 4.02e+00 gaatat
6 42 C 6 212 0 4.02e+00 gaatat
6 42 P 6 169 0 4.02e+00 gaatat
6 43 F 6 99 0 4.02e+00 aatata
6 45 P 6 206 0 4.02e+00 tataaa
6 49 R 6 219 0 4.02e+00 aattag
6 56 R 6 56 0 4.02e+00 cattac
6 59 C 6 187 0 4.02e+00 tacact

Refseq NC_000919.1
Legend Figure1 shows the Z-curves for the original sequence. Figure2 shows the Z-curves for the rotated sequence beginning and ending in dif site or the maximum of the GC disparity curve. Short vertical red line indicates the indicator gene (such as dnaA, dnaN, gidA, hemE etc) location, and short up vertical dark blue arrow indicates the identified oriC location, short down vertical brown arrow indicates dif site location. Purple peaks with the diamonds indicates the DnaA box clusters.
Figure 1
zcurve
Figure 2
zcurve

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