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comparison test-data/motif_test1/homerResults/motif4.info.html @ 0:db456c398880 draft

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"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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1 <HTML><HEAD><TITLE>Motif 4</TITLE></HEAD>
2 <H2>Information for 4-CTCCTGAGACTG (Motif 4)</H2>
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68 <BR>
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133 <BR>
134 <TABLE border="1" cellpading="0" cellspacing="0">
135 <TR><TD>p-value:</TD><TD>1e-1</TD></TR>
136 <TR><TD>log p-value:</TD><TD>-2.912e+00</TD></TR>
137 <TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR>
138 <TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR>
139 <TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR>
140 <TR><TD>Number of Background Sequences with motif</TD><TD>218.1</TD></TR>
141 <TR><TD>Percentage of Background Sequences with motif</TD><TD>5.44%</TD></TR>
142 <TR><TD>Average Position of motif in Targets</TD><TD>180.0 +/- 0.0bp</TD></TR>
143 <TR><TD>Average Position of motif in Background</TD><TD>95.7 +/- 83.7bp</TD></TR>
144 <TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR>
145 <TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR>
146 <TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif4.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif4RV.motif">reverse opposite</A></TD></TR>
147 <TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif4.logo.svg">forward logo</A><BR/><A HREF="motif4RV.logo.svg">reverse opposite</A></TD></TR>
148 </TABLE>
149 <H3>Matches to Known Motifs</H3>
150 <TABLE border="1" cellpading="0" cellspacing="0">
151 <TR><TD>
152 <H4>RAV1(2)(AP2/EREBP)/Arabidopsis thaliana/AthaMap</H4>
153 <TABLE><TR><TD>
154 <TABLE>
155 <TR><TD>Match Rank:</TD><TD>1</TD></TR>
156 <TR><TD>Score:</TD><TD>0.66</TD</TR>
157 <TR><TD>Offset:</TD><TD>-2</TD</TR>
158 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
159 <TR><TD>Alignment:</TD><TD><FONT face="courier">--CTCCTGAGACTG</FONT><BR><FONT face="courier">ATCACCTGAGGC--</FONT></TD></TR></TABLE>
160 </TD><TD>
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313 </TD></TR>
314 <TR><TD>
315 <H4>RAV1(var.2)/MA0583.1/Jaspar</H4>
316 <TABLE><TR><TD>
317 <TABLE>
318 <TR><TD>Match Rank:</TD><TD>2</TD></TR>
319 <TR><TD>Score:</TD><TD>0.66</TD</TR>
320 <TR><TD>Offset:</TD><TD>-2</TD</TR>
321 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
322 <TR><TD>Alignment:</TD><TD><FONT face="courier">--CTCCTGAGACTG</FONT><BR><FONT face="courier">ATCACCTGAGGC--</FONT></TD></TR></TABLE>
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476 </TD></TR>
477 <TR><TD>
478 <H4>CELF2(RRM)/JSL1-CELF2-CLIP-Seq(GSE71264)/Homer</H4>
479 <TABLE><TR><TD>
480 <TABLE>
481 <TR><TD>Match Rank:</TD><TD>3</TD></TR>
482 <TR><TD>Score:</TD><TD>0.64</TD</TR>
483 <TR><TD>Offset:</TD><TD>3</TD</TR>
484 <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
485 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">---CTGACACY-</FONT></TD></TR></TABLE>
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619 </TD></TR>
620 <TR><TD>
621 <H4>YML081W(MacIsaac)/Yeast</H4>
622 <TABLE><TR><TD>
623 <TABLE>
624 <TR><TD>Match Rank:</TD><TD>4</TD></TR>
625 <TR><TD>Score:</TD><TD>0.61</TD</TR>
626 <TR><TD>Offset:</TD><TD>3</TD</TR>
627 <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
628 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG-</FONT><BR><FONT face="courier">---TTCAGACTGG</FONT></TD></TR></TABLE>
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772 </TD></TR>
773 <TR><TD>
774 <H4>SRSF2(RRM)/Homo_sapiens-RNCMPT00072-PBM/HughesRNA</H4>
775 <TABLE><TR><TD>
776 <TABLE>
777 <TR><TD>Match Rank:</TD><TD>5</TD></TR>
778 <TR><TD>Score:</TD><TD>0.59</TD</TR>
779 <TR><TD>Offset:</TD><TD>-3</TD</TR>
780 <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
781 <TR><TD>Alignment:</TD><TD><FONT face="courier">---CTCCTGAGACTG</FONT><BR><FONT face="courier">CNTCTCCT-------</FONT></TD></TR></TABLE>
782 </TD><TD>
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946 <TR><TD>
947 <H4>REI1/MA0364.1/Jaspar</H4>
948 <TABLE><TR><TD>
949 <TABLE>
950 <TR><TD>Match Rank:</TD><TD>6</TD></TR>
951 <TR><TD>Score:</TD><TD>0.59</TD</TR>
952 <TR><TD>Offset:</TD><TD>0</TD</TR>
953 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
954 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">CCCCTGA-----</FONT></TD></TR></TABLE>
955 </TD><TD>
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1088 </TD></TR>
1089 <TR><TD>
1090 <H4>REI1/MA0364.1/Jaspar</H4>
1091 <TABLE><TR><TD>
1092 <TABLE>
1093 <TR><TD>Match Rank:</TD><TD>7</TD></TR>
1094 <TR><TD>Score:</TD><TD>0.59</TD</TR>
1095 <TR><TD>Offset:</TD><TD>0</TD</TR>
1096 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
1097 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">CCCCTGA-----</FONT></TD></TR></TABLE>
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1230 </TD></TR></TABLE>
1231 </TD></TR>
1232 <TR><TD>
1233 <H4>AT5G05550(Trihelix)/col-AT5G05550-DAP-Seq(GSE60143)/Homer</H4>
1234 <TABLE><TR><TD>
1235 <TABLE>
1236 <TR><TD>Match Rank:</TD><TD>8</TD></TR>
1237 <TR><TD>Score:</TD><TD>0.59</TD</TR>
1238 <TR><TD>Offset:</TD><TD>-6</TD</TR>
1239 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
1240 <TR><TD>Alignment:</TD><TD><FONT face="courier">------CTCCTGAGACTG</FONT><BR><FONT face="courier">HDNHDTCKCCGGMGA---</FONT></TD></TR></TABLE>
1241 </TD><TD>
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1434 </TD></TR>
1435 <TR><TD>
1436 <H4>GFX(?)/Promoter/Homer</H4>
1437 <TABLE><TR><TD>
1438 <TABLE>
1439 <TR><TD>Match Rank:</TD><TD>9</TD></TR>
1440 <TR><TD>Score:</TD><TD>0.58</TD</TR>
1441 <TR><TD>Offset:</TD><TD>-1</TD</TR>
1442 <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
1443 <TR><TD>Alignment:</TD><TD><FONT face="courier">-CTCCTGAGACTG</FONT><BR><FONT face="courier">TCTCGCGAGAAT-</FONT></TD></TR></TABLE>
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1587 </TD></TR>
1588 <TR><TD>
1589 <H4>ZmHOX2a(1)(HD-HOX)/Zea mays/AthaMap</H4>
1590 <TABLE><TR><TD>
1591 <TABLE>
1592 <TR><TD>Match Rank:</TD><TD>10</TD></TR>
1593 <TR><TD>Score:</TD><TD>0.58</TD</TR>
1594 <TR><TD>Offset:</TD><TD>0</TD</TR>
1595 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
1596 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">GTCCTAA-----</FONT></TD></TR></TABLE>
1597 </TD><TD>
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