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NSITE-PL

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    Recognition of PLANT Regulatory motifs with statistics

    Program   NSITE  (Softberry Inc.)    | Version 2.2004
    Search for motifs of   1432 Regulatory Elements (REs)     | SET of REs: REGSITE DB: Plant Transcription Regulatory Sites [Last Update: April 10, 2007]
    ____________________________________________________________
    Search PARAMETRS:
         Expected  Mean  Number                      :  0.0100000
         Statistical Siginicance Level               :  0.9500000
         Level of homology between known RE and motif:   80%
         Variation of Distance between RE Blocks     :   20%
    NOTE: RE - Regulatory Element/Consensus   | AC - Accession No of RE in a given DB
           OS - Organism/Species   | BF - Binding Factor or One of them
           Mism. - Mismatches   | Mean. Exp. Number - Mean Expected Number   | Up.Conf.Int. - Upper Confidence Interval
    ============================================================
    QUERY: > test sequence
    Length of Query Sequence:      96116 bp     | Nucleotide Frequencies:  A -  0.26   G -  0.24   T -  0.26   C -  0.24

    ............................................................
    RE:   213. AC: RSP00213//OS: rice (Oryza sativa), Oryza sativa /GENE: rab16B/RE: ABRE-motif III /BF: unknown bZIP proteins
    Motifs on "-" Strand: Mean Exp. Number   0.00515     Up.Conf.Int.  1     Found   1
        5184  AGgAgGTGGC     5175  --15--     5159  GCCGCGTaGC     5150 (Mism.= 2/ 1)
    ............................................................
    RE:   310. AC: RSP00310//OS: pea, Pisum sativum /GENE: rbcS-3A/RE: BOX II** /BF: GT-1
    Motifs on "-" Strand: Mean Exp. Number   0.00481     Up.Conf.Int.  1     Found   1
       60303  AATGTTACtCATACA    60289 (Mism.= 1)
    ............................................................
    RE:   589. AC: RSP00589//OS: tomato (Lycopersicon esculentum), Lycopersicon esculentum /GENE: rbcS3A/RE: G-box DD /BF: unknown nuclear factor
    Motifs on "+" Strand: Mean Exp. Number   0.00972     Up.Conf.Int.  1     Found   1
       88205  ccaCTGcCACGTGGCACCCTT    88225 (Mism.= 4)
    ............................................................
    RE:   636. AC: RSP00636//OS: soybean (Glycine max) /GENE: SAUR 15A/RE: DUE region /BF: unknown nuclear factor
    Motifs on "+" Strand: Mean Exp. Number   0.00205     Up.Conf.Int.  1     Found   1
       93104  CcTAAGAAtGTCCTCaAAGgCA    93125 (Mism.= 4)
    ............................................................
    RE:   711. AC: RSP00711//OS: pea (Pisum sativum) /GENE: PSPAL2/RE: Box 1 homolog /BF: epicotyl-specific nuclear factor
    Motifs on "+" Strand: Mean Exp. Number   0.00649     Up.Conf.Int.  1     Found   1
       78989  TCTCACCAACTA    79000 (Mism.= 0)
    ............................................................
    RE:   760. AC: RSP00760//OS: potato (Solanum tuberosum) /GENE: S2-RNase/RE: motif III /BF: unknown transcription factor
    Motifs on "-" Strand: Mean Exp. Number   0.00659     Up.Conf.Int.  1     Found   1
       54777  ACATAAT    54771  --30--    54740  ATTATAT    54734 (Mism.= 0/ 0)
    ............................................................
    RE:   802. AC: RSP00802//OS: potato (Solanum tuberosum) /GENE: patatin 21/RE: Box A-1 /BF: BABF
    Motifs on "-" Strand: Mean Exp. Number   0.00534     Up.Conf.Int.  1     Found   1
       64264  ATATtTATATAcTATATAAa    64245 (Mism.= 3)
    ............................................................
    Totally       7 motifs of     7 different REs have been found

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