view test-data/motif_test1/homerResults/motif3.info.html @ 0:db456c398880 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
author iuc
date Mon, 13 Dec 2021 15:13:33 +0000
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<HTML><HEAD><TITLE>Motif 3</TITLE></HEAD>
<H2>Information for 3-CGAGGCTAACCC (Motif 3)</H2>
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Reverse Opposite:<BR/><svg width="305" height="50">
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<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>
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</TD></TR></TABLE>
</TD></TR>
<TR><TD>
<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>
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</TD></TR></TABLE>
</TD></TR>
<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>
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</TD></TR></TABLE>
</TD></TR>
<TR><TD>
<H4>bcd/dmmpmm(Bergman)/fly</H4>
<TABLE><TR><TD>
<TABLE>
<TR><TD>Match Rank:</TD><TD>4</TD></TR>
<TR><TD>Score:</TD><TD>0.59</TD</TR>
<TR><TD>Offset:</TD><TD>2</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">--CCNCTAATCCN</FONT></TD></TR></TABLE>
</TD><TD>
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</TD></TR></TABLE>
</TD></TR>
<TR><TD>
<H4>bcd/dmmpmm(Noyes_hd)/fly</H4>
<TABLE><TR><TD>
<TABLE>
<TR><TD>Match Rank:</TD><TD>5</TD></TR>
<TR><TD>Score:</TD><TD>0.59</TD</TR>
<TR><TD>Offset:</TD><TD>3</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">---GGTTAATCCN</FONT></TD></TR></TABLE>
</TD><TD>
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</TD></TR>
<TR><TD>
<H4>HOW(KH)/Drosophila_melanogaster-RNCMPT00118-PBM/HughesRNA</H4>
<TABLE><TR><TD>
<TABLE>
<TR><TD>Match Rank:</TD><TD>6</TD></TR>
<TR><TD>Score:</TD><TD>0.59</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">----ACTAACA-</FONT></TD></TR></TABLE>
</TD><TD>
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</TD></TR></TABLE>
</TD></TR>
<TR><TD>
<H4>GT-1/MA1020.1/Jaspar</H4>
<TABLE><TR><TD>
<TABLE>
<TR><TD>Match Rank:</TD><TD>7</TD></TR>
<TR><TD>Score:</TD><TD>0.59</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">----GTTAACCA</FONT></TD></TR></TABLE>
</TD><TD>
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</TD></TR>
<TR><TD>
<H4>Kr/dmmpmm(Papatsenko)/fly</H4>
<TABLE><TR><TD>
<TABLE>
<TR><TD>Match Rank:</TD><TD>8</TD></TR>
<TR><TD>Score:</TD><TD>0.58</TD</TR>
<TR><TD>Offset:</TD><TD>6</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">------TAACCCTTT</FONT></TD></TR></TABLE>
</TD><TD>
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</TD></TR>
<TR><TD>
<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>
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</TD></TR></TABLE>
</TD></TR>
<TR><TD>
<H4>bcd/dmmpmm(Papatsenko)/fly</H4>
<TABLE><TR><TD>
<TABLE>
<TR><TD>Match Rank:</TD><TD>10</TD></TR>
<TR><TD>Score:</TD><TD>0.58</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">----CCTAATCCC</FONT></TD></TR></TABLE>
</TD><TD>
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