Mercurial > repos > iuc > homer_annotatepeaks

annotate test-data/motif_test1/homerResults/motif4.info.html @ 3:fa7c3a74acf2 draft

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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 16:24:36 +0000
parents adab852c8216
children
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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1 <HTML><HEAD><TITLE>Motif 4</TITLE></HEAD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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2 <H2>Information for 4-CTCCTGAGACTG (Motif 4)</H2>
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3 <svg width="305" height="50">
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4 <g font-family="Arial" font-weight="bold" font-size="66.5">
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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108 <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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109 <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,177,34)">A</text>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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111 <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,202,49)">A</text>
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112 <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,200,44)">C</text>
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128 <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,276,39)">T</text>
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129 <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,275,34)">G</text>
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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131 </g>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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132 </svg>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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133 <BR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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134 <TABLE border="1" cellpading="0" cellspacing="0">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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135 <TR><TD>p-value:</TD><TD>1e-1</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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136 <TR><TD>log p-value:</TD><TD>-2.912e+00</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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137 <TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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138 <TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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139 <TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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140 <TR><TD>Number of Background Sequences with motif</TD><TD>218.1</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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141 <TR><TD>Percentage of Background Sequences with motif</TD><TD>5.44%</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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142 <TR><TD>Average Position of motif in Targets</TD><TD>180.0 +/- 0.0bp</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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143 <TR><TD>Average Position of motif in Background</TD><TD>95.7 +/- 83.7bp</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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144 <TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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145 <TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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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>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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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>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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148 </TABLE>
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149 <H3>Matches to Known Motifs</H3>
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150 <TABLE border="1" cellpading="0" cellspacing="0">
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151 <TR><TD>
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152 <H4>RAV1(2)(AP2/EREBP)/Arabidopsis thaliana/AthaMap</H4>
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153 <TABLE><TR><TD>
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154 <TABLE>
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155 <TR><TD>Match Rank:</TD><TD>1</TD></TR>
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156 <TR><TD>Score:</TD><TD>0.66</TD</TR>
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157 <TR><TD>Offset:</TD><TD>-2</TD</TR>
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158 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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159 <TR><TD>Alignment:</TD><TD><FONT face="courier">--CTCCTGAGACTG</FONT><BR><FONT face="courier">ATCACCTGAGGC--</FONT></TD></TR></TABLE>
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160 </TD><TD>
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161 <svg width="355" height="50">
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162 <g font-family="Arial" font-weight="bold" font-size="66.5">
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310 </svg>
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312 </TD></TR></TABLE>
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313 </TD></TR>
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314 <TR><TD>
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315 <H4>RAV1(var.2)/MA0583.1/Jaspar</H4>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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316 <TABLE><TR><TD>
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317 <TABLE>
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318 <TR><TD>Match Rank:</TD><TD>2</TD></TR>
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319 <TR><TD>Score:</TD><TD>0.66</TD</TR>
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320 <TR><TD>Offset:</TD><TD>-2</TD</TR>
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321 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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322 <TR><TD>Alignment:</TD><TD><FONT face="courier">--CTCCTGAGACTG</FONT><BR><FONT face="courier">ATCACCTGAGGC--</FONT></TD></TR></TABLE>
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323 </TD><TD>
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324 <svg width="355" height="50">
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475 </TD></TR></TABLE>
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476 </TD></TR>
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477 <TR><TD>
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iuc
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478 <H4>CELF2(RRM)/JSL1-CELF2-CLIP-Seq(GSE71264)/Homer</H4>
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479 <TABLE><TR><TD>
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480 <TABLE>
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diff changeset
481 <TR><TD>Match Rank:</TD><TD>3</TD></TR>
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482 <TR><TD>Score:</TD><TD>0.64</TD</TR>
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483 <TR><TD>Offset:</TD><TD>3</TD</TR>
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iuc
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484 <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
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485 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">---CTGACACY-</FONT></TD></TR></TABLE>
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486 </TD><TD>
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616 </svg>
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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618 </TD></TR></TABLE>
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619 </TD></TR>
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620 <TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
621 <H4>YML081W(MacIsaac)/Yeast</H4>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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622 <TABLE><TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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623 <TABLE>
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iuc
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diff changeset
624 <TR><TD>Match Rank:</TD><TD>4</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
625 <TR><TD>Score:</TD><TD>0.61</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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diff changeset
626 <TR><TD>Offset:</TD><TD>3</TD</TR>
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iuc
parents:
diff changeset
627 <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
628 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG-</FONT><BR><FONT face="courier">---TTCAGACTGG</FONT></TD></TR></TABLE>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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629 </TD><TD>
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771 </TD></TR></TABLE>
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772 </TD></TR>
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773 <TR><TD>
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iuc
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diff changeset
774 <H4>SRSF2(RRM)/Homo_sapiens-RNCMPT00072-PBM/HughesRNA</H4>
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775 <TABLE><TR><TD>
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776 <TABLE>
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777 <TR><TD>Match Rank:</TD><TD>5</TD></TR>
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778 <TR><TD>Score:</TD><TD>0.59</TD</TR>
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779 <TR><TD>Offset:</TD><TD>-3</TD</TR>
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780 <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
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781 <TR><TD>Alignment:</TD><TD><FONT face="courier">---CTCCTGAGACTG</FONT><BR><FONT face="courier">CNTCTCCT-------</FONT></TD></TR></TABLE>
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782 </TD><TD>
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944 </TD></TR></TABLE>
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945 </TD></TR>
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947 <H4>REI1/MA0364.1/Jaspar</H4>
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948 <TABLE><TR><TD>
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949 <TABLE>
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diff changeset
950 <TR><TD>Match Rank:</TD><TD>6</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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diff changeset
951 <TR><TD>Score:</TD><TD>0.59</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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952 <TR><TD>Offset:</TD><TD>0</TD</TR>
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diff changeset
953 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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954 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">CCCCTGA-----</FONT></TD></TR></TABLE>
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955 </TD><TD>
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1087 </TD></TR></TABLE>
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1088 </TD></TR>
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1090 <H4>REI1/MA0364.1/Jaspar</H4>
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1091 <TABLE><TR><TD>
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1092 <TABLE>
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diff changeset
1093 <TR><TD>Match Rank:</TD><TD>7</TD></TR>
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1094 <TR><TD>Score:</TD><TD>0.59</TD</TR>
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1095 <TR><TD>Offset:</TD><TD>0</TD</TR>
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1096 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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1097 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">CCCCTGA-----</FONT></TD></TR></TABLE>
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1098 </TD><TD>
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1230 </TD></TR></TABLE>
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1231 </TD></TR>
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1232 <TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
1233 <H4>AT5G05550(Trihelix)/col-AT5G05550-DAP-Seq(GSE60143)/Homer</H4>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
1234 <TABLE><TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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1235 <TABLE>
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iuc
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diff changeset
1236 <TR><TD>Match Rank:</TD><TD>8</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
1237 <TR><TD>Score:</TD><TD>0.59</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
1238 <TR><TD>Offset:</TD><TD>-6</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
1239 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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diff changeset
1240 <TR><TD>Alignment:</TD><TD><FONT face="courier">------CTCCTGAGACTG</FONT><BR><FONT face="courier">HDNHDTCKCCGGMGA---</FONT></TD></TR></TABLE>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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1241 </TD><TD>
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1242 <svg width="455" height="50">
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1431 </svg>
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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diff changeset
1433 </TD></TR></TABLE>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1434 </TD></TR>
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1435 <TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1436 <H4>GFX(?)/Promoter/Homer</H4>
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iuc
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diff changeset
1437 <TABLE><TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
1438 <TABLE>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1439 <TR><TD>Match Rank:</TD><TD>9</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1440 <TR><TD>Score:</TD><TD>0.58</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
1441 <TR><TD>Offset:</TD><TD>-1</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
1442 <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1443 <TR><TD>Alignment:</TD><TD><FONT face="courier">-CTCCTGAGACTG</FONT><BR><FONT face="courier">TCTCGCGAGAAT-</FONT></TD></TR></TABLE>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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diff changeset
1444 </TD><TD>
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1586 </TD></TR></TABLE>
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1587 </TD></TR>
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1589 <H4>ZmHOX2a(1)(HD-HOX)/Zea mays/AthaMap</H4>
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1590 <TABLE><TR><TD>
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1591 <TABLE>
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1592 <TR><TD>Match Rank:</TD><TD>10</TD></TR>
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1593 <TR><TD>Score:</TD><TD>0.58</TD</TR>
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1594 <TR><TD>Offset:</TD><TD>0</TD</TR>
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diff changeset
1595 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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1596 <TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">GTCCTAA-----</FONT></TD></TR></TABLE>
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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