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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 16a919905f336e34e237388c1921d0f4f8a368af
| author | iuc |
|---|---|
| date | Thu, 06 Apr 2023 16:23:06 +0000 |
| parents | 8ebb6520eef4 |
| children |
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<HTML><HEAD><TITLE>Motif 6</TITLE></HEAD> <H2>Information for 3-GTTGCTGCCA (Motif 6)</H2> <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="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,0,34)">G</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="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,39)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,26,34)">T</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" 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y="0" transform="matrix(0.59,0,0,0.700,150,34)">C</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,175,49)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,175,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,177,34)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,200,49)">C</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="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,202,34)">A</text> <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,227,49)">A</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,225,44)">G</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,226,39)">T</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,225,34)">C</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>-2.907e+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>219.9</TD></TR> <TR><TD>Percentage of Background Sequences with motif</TD><TD>5.49%</TD></TR> <TR><TD>Average Position of motif in Targets</TD><TD>140.0 +/- 0.0bp</TD></TR> <TR><TD>Average Position of motif in Background</TD><TD>103.4 +/- 83.3bp</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="motif6.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif6RV.motif">reverse opposite</A></TD></TR> <TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif6.logo.svg">forward logo</A><BR/><A HREF="motif6RV.logo.svg">reverse opposite</A></TD></TR> </TABLE> <H3>Matches to Known Motifs</H3> <TABLE border="1" cellpading="0" cellspacing="0"> <TR><TD> <H4>DEL1(E2FDP)/colamp-DEL1-DAP-Seq(GSE60143)/Homer</H4> <TABLE><TR><TD> <TABLE> <TR><TD>Match Rank:</TD><TD>1</TD></TR> <TR><TD>Score:</TD><TD>0.66</TD</TR> <TR><TD>Offset:</TD><TD>1</TD</TR> <TR><TD>Orientation:</TD><TD>forward strand</TD></TR> <TR><TD>Alignment:</TD><TD><FONT face="courier">GTTGCTGCCA-</FONT><BR><FONT face="courier">-TTCCCGCCAA</FONT></TD></TR></TABLE> </TD><TD> <svg width="280" 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="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> <text fill="#DD0000" x="0" 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<TR><TD>Match Rank:</TD><TD>4</TD></TR> <TR><TD>Score:</TD><TD>0.65</TD</TR> <TR><TD>Offset:</TD><TD>-4</TD</TR> <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR> <TR><TD>Alignment:</TD><TD><FONT face="courier">----GTTGCTGCCA-</FONT><BR><FONT face="courier">AGATGCTRCTRCCHT</FONT></TD></TR></TABLE> </TD><TD> <svg width="380" 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(0.53,0,0,0.25,27,49)">A</text> <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.25,25,36.5)">C</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.25,25,24)">G</text> <text fill="#DD0000" 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<TR><TD>Score:</TD><TD>0.64</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">GTTGCTGCCA--</FONT><BR><FONT face="courier">---CGTGCCAAG</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="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,0,34)">G</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="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,39)">G</text> <text fill="#DD0000" x="0" y="0" 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