Mercurial > repos > iuc > homer_annotatepeaks

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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 15:03:57 +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 1</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 1-ATGAGCTTAATC (Motif 1)</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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107 <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,175,44)">G</text>
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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="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,175,34)">C</text>
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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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118 <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,226,39)">T</text>
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128 <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,275,39)">G</text>
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129 <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,276,34)">T</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>-2.921e+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>216.0</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>5.39%</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>105.0 +/- 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>97.7 +/- 71.4bp</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="motif1.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif1RV.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="motif1.logo.svg">forward logo</A><BR/><A HREF="motif1RV.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>Oc/dmmpmm(Noyes_hd)/fly</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>0.65</TD</TR>
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157 <TR><TD>Offset:</TD><TD>4</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">ATGAGCTTAATC--</FONT><BR><FONT face="courier">----NNTTAATCCN</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>PHO2(MacIsaac)/Yeast</H4>
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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>0.65</TD</TR>
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320 <TR><TD>Offset:</TD><TD>5</TD</TR>
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321 <TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
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322 <TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC</FONT><BR><FONT face="courier">-----CTTAAT-</FONT></TD></TR></TABLE>
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323 </TD><TD>
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324 <svg width="305" height="50">
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455 </TD></TR></TABLE>
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456 </TD></TR>
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457 <TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
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458 <H4>oc/dmmpmm(Noyes)/fly</H4>
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459 <TABLE><TR><TD>
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460 <TABLE>
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iuc
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461 <TR><TD>Match Rank:</TD><TD>3</TD></TR>
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iuc
parents:
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462 <TR><TD>Score:</TD><TD>0.65</TD</TR>
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463 <TR><TD>Offset:</TD><TD>6</TD</TR>
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iuc
parents:
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464 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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iuc
parents:
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465 <TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC-</FONT><BR><FONT face="courier">------TTAATCC</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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466 </TD><TD>
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467 <svg width="330" height="50">
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608 </TD></TR></TABLE>
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609 </TD></TR>
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610 <TR><TD>
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iuc
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diff changeset
611 <H4>Gsc/dmmpmm(Noyes_hd)/fly</H4>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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612 <TABLE><TR><TD>
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613 <TABLE>
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diff changeset
614 <TR><TD>Match Rank:</TD><TD>4</TD></TR>
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615 <TR><TD>Score:</TD><TD>0.64</TD</TR>
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616 <TR><TD>Offset:</TD><TD>4</TD</TR>
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617 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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618 <TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC--</FONT><BR><FONT face="courier">----NNTTAATCCN</FONT></TD></TR></TABLE>
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619 </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>bcd/dmmpmm(Noyes_hd)/fly</H4>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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775 <TABLE><TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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776 <TABLE>
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diff changeset
777 <TR><TD>Match Rank:</TD><TD>5</TD></TR>
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parents:
diff changeset
778 <TR><TD>Score:</TD><TD>0.64</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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779 <TR><TD>Offset:</TD><TD>4</TD</TR>
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diff changeset
780 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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781 <TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC--</FONT><BR><FONT face="courier">----GGTTAATCCN</FONT></TD></TR></TABLE>
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782 </TD><TD>
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934 </TD></TR></TABLE>
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iuc
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diff changeset
937 <H4>OTX2/MA0712.1/Jaspar</H4>
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938 <TABLE><TR><TD>
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939 <TABLE>
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diff changeset
940 <TR><TD>Match Rank:</TD><TD>6</TD></TR>
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diff changeset
941 <TR><TD>Score:</TD><TD>0.64</TD</TR>
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942 <TR><TD>Offset:</TD><TD>6</TD</TR>
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943 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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944 <TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC--</FONT><BR><FONT face="courier">------TTAATCCT</FONT></TD></TR></TABLE>
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1095 </svg>
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1097 </TD></TR></TABLE>
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1098 </TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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1099 <TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1100 <H4>OTX1/MA0711.1/Jaspar</H4>
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iuc
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1101 <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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1102 <TABLE>
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iuc
parents:
diff changeset
1103 <TR><TD>Match Rank:</TD><TD>7</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1104 <TR><TD>Score:</TD><TD>0.63</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
1105 <TR><TD>Offset:</TD><TD>6</TD</TR>
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iuc
parents:
diff changeset
1106 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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iuc
parents:
diff changeset
1107 <TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC--</FONT><BR><FONT face="courier">------TTAATCCG</FONT></TD></TR></TABLE>
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1108 </TD><TD>
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1109 <svg width="355" height="50">
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1264 <TABLE><TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1265 <TABLE>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1266 <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
parents:
diff changeset
1267 <TR><TD>Score:</TD><TD>0.63</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1268 <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
parents:
diff changeset
1269 <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
1270 <TR><TD>Alignment:</TD><TD><FONT face="courier">-ATGAGCTTAATC</FONT><BR><FONT face="courier">NATGACCTTGA--</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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1271 </TD><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1272 <svg width="330" height="50">
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iuc
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1273 <g font-family="Arial" font-weight="bold" font-size="66.5">
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1409
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1411 </svg>
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1412
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1413 </TD></TR></TABLE>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1414 </TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1415 <TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1416 <H4>GSC2/MA0891.1/Jaspar</H4>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1417 <TABLE><TR><TD>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1418 <TABLE>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1419 <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
1420 <TR><TD>Score:</TD><TD>0.63</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1421 <TR><TD>Offset:</TD><TD>5</TD</TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1422 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1423 <TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC---</FONT><BR><FONT face="courier">-----CCTAATCCGC</FONT></TD></TR></TABLE>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
parents:
diff changeset
1424 </TD><TD>
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iuc
parents:
diff changeset
1425 <svg width="380" height="50">
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diff changeset
1426 <g font-family="Arial" font-weight="bold" font-size="66.5">
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1586 </TD></TR></TABLE>
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1587 </TD></TR>
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1588 <TR><TD>
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iuc
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1589 <H4>Pitx1/MA0682.1/Jaspar</H4>
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1590 <TABLE><TR><TD>
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iuc
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1591 <TABLE>
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diff changeset
1592 <TR><TD>Match Rank:</TD><TD>10</TD></TR>
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iuc
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diff changeset
1593 <TR><TD>Score:</TD><TD>0.63</TD</TR>
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1594 <TR><TD>Offset:</TD><TD>6</TD</TR>
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1595 <TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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1596 <TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC--</FONT><BR><FONT face="courier">------TTAATCCC</FONT></TD></TR></TABLE>
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1597 </TD><TD>
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