Mercurial > repos > iuc > homer_gtf_to_annotations
comparison test-data/motif_test1/homerResults/motif4.info.html @ 0:8ebb6520eef4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
author | iuc |
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date | Sun, 08 Aug 2021 11:04:17 +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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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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312 </TD></TR></TABLE> | |
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> | |
323 </TD><TD> | |
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474 | |
475 </TD></TR></TABLE> | |
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> | |
486 </TD><TD> | |
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618 </TD></TR></TABLE> | |
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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771 </TD></TR></TABLE> | |
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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944 </TD></TR></TABLE> | |
945 </TD></TR> | |
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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1087 </TD></TR></TABLE> | |
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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1229 | |
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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1432 | |
1433 </TD></TR></TABLE> | |
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> | |
1444 </TD><TD> | |
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1586 </TD></TR></TABLE> | |
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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