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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e6639e130c5bf50f489dd09e38a1cbc712280fff
| author | iuc |
|---|---|
| date | Fri, 07 Apr 2023 15:03:57 +0000 |
| parents | adab852c8216 |
| children |
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<HTML><HEAD><TITLE>Motif 3</TITLE></HEAD> <H2>Information for 3-CGAGGCTAACCC (Motif 3)</H2> <svg width="305" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,0,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,25,34)">G</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,49)">C</text> <text fill="#F9A500" x="0" y="0" 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x="0" y="0" transform="matrix(0.59,0,0,0.700,175,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,202,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,200,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,201,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,200,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,227,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,225,44)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,225,39)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,226,34)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,252,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,250,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,251,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,250,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,277,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,275,44)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,276,39)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,275,34)">G</text> </g> </svg> <BR> <TABLE border="1" cellpading="0" cellspacing="0"> <TR><TD>p-value:</TD><TD>1e-1</TD></TR> <TR><TD>log p-value:</TD><TD>-2.916e+00</TD></TR> <TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> <TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> <TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> <TR><TD>Number of Background Sequences with motif</TD><TD>217.8</TD></TR> <TR><TD>Percentage of Background Sequences with motif</TD><TD>5.43%</TD></TR> <TR><TD>Average Position of motif in Targets</TD><TD>91.0 +/- 0.0bp</TD></TR> <TR><TD>Average Position of motif in Background</TD><TD>101.8 +/- 65.4bp</TD></TR> <TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> <TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> <TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif3.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif3RV.motif">reverse opposite</A></TD></TR> <TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif3.logo.svg">forward logo</A><BR/><A HREF="motif3RV.logo.svg">reverse opposite</A></TD></TR> </TABLE> <H3>Matches to Known Motifs</H3> <TABLE border="1" cellpading="0" cellspacing="0"> <TR><TD> <H4>PH0015.1_Crx/Jaspar</H4> <TABLE><TR><TD> <TABLE> <TR><TD>Match Rank:</TD><TD>1</TD></TR> <TR><TD>Score:</TD><TD>0.63</TD</TR> <TR><TD>Offset:</TD><TD>2</TD</TR> <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR> <TR><TD>Alignment:</TD><TD><FONT face="courier">CGAGGCTAACCC------</FONT><BR><FONT face="courier">--AGGCTAATCCCCAANG</FONT></TD></TR></TABLE> </TD><TD> <svg width="455" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,0,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,25,34)">G</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,50,44)">G</text> <text 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<H4>CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer</H4> <TABLE><TR><TD> <TABLE> <TR><TD>Match Rank:</TD><TD>2</TD></TR> <TR><TD>Score:</TD><TD>0.62</TD</TR> <TR><TD>Offset:</TD><TD>4</TD</TR> <TR><TD>Orientation:</TD><TD>forward strand</TD></TR> <TR><TD>Alignment:</TD><TD><FONT face="courier">CGAGGCTAACCC</FONT><BR><FONT face="courier">----GCTAATCC</FONT></TD></TR></TABLE> </TD><TD> <svg width="305" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,0,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> <text fill="#DD0000" x="0" 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<TR><TD> <H4>ttk/dmmpmm(Noyes)/fly</H4> <TABLE><TR><TD> <TABLE> <TR><TD>Match Rank:</TD><TD>3</TD></TR> <TR><TD>Score:</TD><TD>0.61</TD</TR> <TR><TD>Offset:</TD><TD>0</TD</TR> <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR> <TR><TD>Alignment:</TD><TD><FONT face="courier">CGAGGCTAACCC--</FONT><BR><FONT face="courier">CAAGGATAATCNAA</FONT></TD></TR></TABLE> </TD><TD> <svg width="355" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,0,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> <text fill="#DD0000" x="0" y="0" 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<H4>HNRNPK(KH)/Homo_sapiens-RNCMPT00026-PBM/HughesRNA</H4> <TABLE><TR><TD> <TABLE> <TR><TD>Match Rank:</TD><TD>9</TD></TR> <TR><TD>Score:</TD><TD>0.58</TD</TR> <TR><TD>Offset:</TD><TD>5</TD</TR> <TR><TD>Orientation:</TD><TD>forward strand</TD></TR> <TR><TD>Alignment:</TD><TD><FONT face="courier">CGAGGCTAACCC</FONT><BR><FONT face="courier">-----CCAACCC</FONT></TD></TR></TABLE> </TD><TD> <svg width="305" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,0,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> <text fill="#DD0000" x="0" 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