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ScanWM-PL: search for weight matrix patterns of plant regulatory sequencesPROGRAM
OUTPUT
Program ScanWM (Softberry Inc.) Search for motifs by Weight Matrixes of Regulatory Elements Version 1.2004 SET of WMs: derived from subsection of REGSITE DB (Plants; version IV) ____________________________________________________________ File with QUERY Sequences: TEST_SEQ.seq Search PARAMETERS: Threshold type : 2 Threshold value : 0.90 Search for motifs on "+" strand : yes Search for motifs on "-" strand : yes NOTE: WM - Weight Matrix of Regulatory Element AC - Accession No of Regulatory Element in a given DB OS - Organism/Species BF - Binding Factors or One of them ============================================================ QUERY: >At4g00160 [-300,+50] region of F-box family protein Length of Query Sequence: 350 ............................................................ WM: >151. AC: RSP00151//OS: tomato, Lycopersicon esculentum /GENE: Lhcb1*1, Lhcb1*2, Lhca3, Lhca4/RE: CRE, consensus /BF:unknown Motifs on "+" strand (in DIR orientation): Found 1 79 CAAGTACATC 88 7.76 ............................................................ WM: >174. AC: RSP00174//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: ATCATC motif /BF:unknown Motifs on "+" strand (in DIR orientation): Found 2 21 ATCATC 26 7.98 102 ATCATC 107 7.98 ............................................................ WM: >359. AC: RSP00359//OS: barley, Hordeum vulgare /GENE: GCCGAC motif/RE: HVA1s /BF: HvCBF1 Motifs on "-" strand (in INV orientation): Found 1 103 ATCGAC 98 4.73 ............................................................ WM: >707. AC: RSP00707//OS: /GENE: /RE: W-box (consensus 1) /BF: transcription factors of WRKY family Motifs on "-" strand (in INV orientation): Found 3 120 AATGACC 114 4.56 137 AATGACC 131 4.56 286 AATGACT 280 4.42 ............................................................ WM: >722. AC: RSP00722//OS: Nicotiana plumbaginifolia /GENE: rbcS 8B/RE: I-box /BF: unknown transcription factor Motifs on "-" strand (in INV orientation): Found 1 251 GATAAGA 245 9.12 ............................................................ Totally 8 motifs of 5 different WMs have been found ------------------------------------------------------------ MORE INFO
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