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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 15:02:25 +0000 |
| parents | 8ebb6520eef4 |
| children |
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<HTML><HEAD><TITLE>Motif 7</TITLE></HEAD> <H2>Information for 1-CCCTAATG (Motif 7)</H2> <svg width="205" 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="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,25,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,50,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,51,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,50,34)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,77,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,44)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,75,39)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,76,34)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,100,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,100,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,102,34)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,125,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,125,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,126,39)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,127,34)">A</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,150,44)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,150,39)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,151,34)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,177,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,175,44)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,175,34)">G</text> </g> </svg> <BR> Reverse Opposite:<BR/><svg width="205" 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="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,27,34)">A</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,44)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,50,39)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,51,34)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,77,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,44)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,75,39)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,76,34)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,100,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,100,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,102,34)">A</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,127,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,125,44)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,126,39)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,125,34)">G</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,150,44)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,151,39)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,150,34)">G</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,177,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,175,44)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,175,34)">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>-2.898e+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>221.6</TD></TR> <TR><TD>Percentage of Background Sequences with motif</TD><TD>5.53%</TD></TR> <TR><TD>Average Position of motif in Targets</TD><TD>98.0 +/- 0.0bp</TD></TR> <TR><TD>Average Position of motif in Background</TD><TD>97.0 +/- 70.2bp</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="motif7.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif7RV.motif">reverse opposite</A></TD></TR> <TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif7.logo.svg">forward logo</A><BR/><A HREF="motif7RV.logo.svg">reverse opposite</A></TD></TR> </TABLE> <H3>Matches to Known Motifs</H3> <TABLE border="1" cellpading="0" cellspacing="0"> <TR><TD> <H4>HNRNPA1L2(RRM)/Homo_sapiens-RNCMPT00023-PBM/HughesRNA</H4> <TABLE><TR><TD> <TABLE> <TR><TD>Match Rank:</TD><TD>1</TD></TR> <TR><TD>Score:</TD><TD>0.81</TD</TR> <TR><TD>Offset:</TD><TD>-1</TD</TR> <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR> <TR><TD>Alignment:</TD><TD><FONT face="courier">-CCCTAATG</FONT><BR><FONT face="courier">TCCCTAA--</FONT></TD></TR></TABLE> </TD><TD> <svg width="230" height="50"> <g font-family="Arial" font-weight="bold" font-size="66.5"> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.25,2,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.25,0,36.5)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.25,0,24)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.25,1,11.5)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> <text fill="#DD0000" x="0" 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x="0" y="0" transform="matrix(0.59,0,0,0.961,75,47.05)">C</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.013,102,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.013,100,48.35)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.013,100,47.7)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.961,101,47.05)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.013,125,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.013,125,48.35)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.013,126,47.7)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.961,127,47.05)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.086,150,49)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.178,151,44.7)">T</text> <text fill="#0000EE" x="0" y="0" 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<TR><TD>Offset:</TD><TD>0</TD</TR> <TR><TD>Orientation:</TD><TD>forward strand</TD></TR> <TR><TD>Alignment:</TD><TD><FONT face="courier">CCCTAATG--</FONT><BR><FONT face="courier">CCCTAATGAA</FONT></TD></TR></TABLE> </TD><TD> <svg width="255" 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="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,25,34)">C</text> <text fill="#00BB00" 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