<?xml version="1.0" encoding="ISO-8859-1"?>
<!--
/*      This program is free software; you can redistribute it and/or modify  */
/*       it under the terms of the GNU General Public License as published by */
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/*       (at your option) any later version.                                  */

/*       This program is distributed in the hope that it will be useful, but  */
/*       WITHOUT ANY WARRANTY; without even the implied warranty of           */
/*       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU    */
/*       General Public License for more details.                             */

/*       You should have received a copy of the GNU General Public License    */
/*       along with this program; if not, write to the Free Software          */
/*       Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 */
/*       USA                                                                  */

/*       Marine Dumousseau                                                    */
/*       EMBL-EBI, neurobiology computational group,                          */
/*       Cambridge, UK. e-mail: marine@ebi.ac.uk                   */
-->

<hybridization type="dnadna">
	<dangling_end type="single">
    	<origine article="Bommarito_2000">
    	<!--/******************************************************************************/
    	/* contains the parameters for DNA/DNA single dangling ends of ;
	REF: Bommarito et al. (2000). Nuc Acids Res 28: 1929-1934 
    	/******************************************************************************/-->
			<dangling sequence="AA/T" sens="5">
               	<enthalpy>200.0</enthalpy>
                <entropy>2.3</entropy>
	    	</dangling>
	    	<dangling sequence="TA/T" sens="5">
               	<enthalpy>-6900.0</enthalpy>
                <entropy>-20.0</entropy>
	    	</dangling>
	    	<dangling sequence="GA/T" sens="5">
               	<enthalpy>-1100.0</enthalpy>
                <entropy>-1.6</entropy>
	    	</dangling>
	    	<dangling sequence="CA/T" sens="5">
               <enthalpy>600.0</enthalpy>
               <entropy>3.3</entropy>
			</dangling>
			<dangling sequence="AC/G" sens="5">
	        	<enthalpy>-6300.0</enthalpy>
               	<entropy>-17.1</entropy>
	    	</dangling>
	    	<dangling sequence="TC/G" sens="5">
	        	<enthalpy>-4000.0</enthalpy>
                <entropy>-10.9</entropy>
	    	</dangling>
	    	<dangling sequence="GC/G" sens="5">
	        	<enthalpy>-5100.0</enthalpy>
                <entropy>-14.0</entropy>
	    	</dangling>
	    	<dangling sequence="CC/G" sens="5">
	        	<enthalpy>-4400.0</enthalpy>
                <entropy>-12.6</entropy>
			</dangling>				
			<dangling sequence="AG/C" sens="5">
	        	<enthalpy>-3700.0</enthalpy>
                <entropy>-10</entropy>
	    	</dangling>
	    	<dangling sequence="TG/C" sens="5">
	        	<enthalpy>-4900.0</enthalpy>
                <entropy>-13.8</entropy>
	    	</dangling>
	    	<dangling sequence="GG/C" sens="5">
	        	<enthalpy>-3900.0</enthalpy>
                <entropy>-10.9</entropy>
	    	</dangling>
	    	<dangling sequence="CG/C" sens="5">
	        	<enthalpy>-4000.0</enthalpy>
                <entropy>-11.9</entropy>
			</dangling>				
			<dangling sequence="AT/A" sens="5">
	        	<enthalpy>-2900.0</enthalpy>
                <entropy>-7.6</entropy>
	    	</dangling>
	    	<dangling sequence="TT/A" sens="5">
	        	<enthalpy>-200.0</enthalpy>
                <entropy>-0.5</entropy>
	    	</dangling>
	    	<dangling sequence="GT/A" sens="5">
	        	<enthalpy>-4200.0</enthalpy>
                <entropy>-15.0</entropy>
	    	</dangling>
	    	<dangling sequence="CT/A" sens="5">
	        	<enthalpy>-4100.0</enthalpy>
                <entropy>-13.0</entropy>
			</dangling>		
			<dangling sequence="AA/T" sens="3">
               	<enthalpy>-500.0</enthalpy>
                <entropy>-1.1</entropy>
	    	</dangling>
	    	<dangling sequence="AC/T" sens="3">
	        	<enthalpy>4700.0</enthalpy>
                <entropy>14.2</entropy>
	    	</dangling>
	    	<dangling sequence="AG/T" sens="3">
	        	<enthalpy>-4100.0</enthalpy>
                <entropy>-13.1</entropy>
	    	</dangling>
	    	<dangling sequence="AT/T" sens="3">
	        	<enthalpy>-3800.0</enthalpy>
                <entropy>-12.6</entropy>
			</dangling>				
			<dangling sequence="TA/A" sens="3">
               	<enthalpy>-700.0</enthalpy>
                <entropy>-0.8</entropy>
	    	</dangling>
	    	<dangling sequence="TC/A" sens="3">
	        	<enthalpy>4400.0</enthalpy>
                <entropy>14.9</entropy>
	    	</dangling>
	    	<dangling sequence="TG/A" sens="3">
	        	<enthalpy>-1600.0</enthalpy>
                <entropy>-3.6</entropy>
	    	</dangling>
	    	<dangling sequence="TT/A" sens="3">
	        	<enthalpy>2900.0</enthalpy>
                <entropy>10.4</entropy>
			</dangling>				
			<dangling sequence="GA/C" sens="3">
               	<enthalpy>4700.0</enthalpy>
                <entropy>12.9</entropy>
	    	</dangling>
	    	<dangling sequence="GC/C" sens="3">
	        	<enthalpy>-200.0</enthalpy>
                <entropy>-0.1</entropy>
	    	</dangling>
	    	<dangling sequence="GG/C" sens="3">
	        	<enthalpy>-3900.0</enthalpy>
                <entropy>-11.2</entropy>
	    	</dangling>
	    	<dangling sequence="GT/C" sens="3">
	        	<enthalpy>-4400.0</enthalpy>
                <entropy>-13.1</entropy>
			</dangling>				
			<dangling sequence="CA/G" sens="3">
               	<enthalpy>-5900.0</enthalpy>
                <entropy>-16.5</entropy>
	    	</dangling>
	    	<dangling sequence="CC/G" sens="3">
	        	<enthalpy>-2600.0</enthalpy>
                <entropy>-7.4</entropy>
	    	</dangling>
	    	<dangling sequence="CG/G" sens="3">
	        	<enthalpy>-3200.0</enthalpy>
                <entropy>-10.4</entropy>
	    	</dangling>
	    	<dangling sequence="CT/G" sens="3">
	        	<enthalpy>-5200.0</enthalpy>
                <entropy>-15.0</entropy>
			</dangling>
		</origine>
	</dangling_end>
	
	<dangling_end type="long">
    	<origine article="Sugimoto_2002">
    	<!--/******************************************************************************/
    	/* contains the parameters for DNA/DNA long dangling ends of ;
	REF: Sugimoto et al. (2002). J. Am. Chem. Soc. 124: 10367-10372 
    	/******************************************************************************/-->
			<dangling sequence="CA/G" sens="3">
				<enthalpy>-1500.0</enthalpy>
				<entropy>-3.5</entropy>
			</dangling>
			<dangling sequence="CAA/G" sens="3">
				<enthalpy>-2150.0</enthalpy>
				<entropy>-5.5</entropy>
			</dangling>
			<dangling sequence="CAAA/G" sens="3">
				<enthalpy>-3300.0</enthalpy>
				<entropy>-8.5</entropy>
			</dangling>
			<dangling sequence="CAAAA/G" sens="3">
				<enthalpy>-4850.0</enthalpy>
				<entropy>-13.5</entropy>
			</dangling>			
			<dangling sequence="AG/C" sens="5">
				<enthalpy>-150.0</enthalpy>
				<entropy>0.5</entropy>
			</dangling>
			<dangling sequence="AAG/C" sens="5">
				<enthalpy>-250.0</enthalpy>
				<entropy>0.5</entropy>
			</dangling>
			<dangling sequence="AAAG/C" sens="5">
				<enthalpy>-150.0</enthalpy>
				<entropy>1.5</entropy>
			</dangling>
			<dangling sequence="AAAAG/C" sens="5">
				<enthalpy>-750.0</enthalpy>
				<entropy>-0.5</entropy>
			</dangling>			
			<dangling sequence="TA/A" sens="3">
				<enthalpy>-550.0</enthalpy>
				<entropy>0.0</entropy>
			</dangling>
			<dangling sequence="TAA/A" sens="3">
				<enthalpy>-1000.0</enthalpy>
				<entropy>-1.0</entropy>
			</dangling>
			<dangling sequence="TAAA/A" sens="3">
				<enthalpy>-1950.0</enthalpy>
				<entropy>-4.5</entropy>
			</dangling>
			<dangling sequence="TAAAA/A" sens="3">
				<enthalpy>-2350.0</enthalpy>
				<entropy>-6.0</entropy>
			</dangling>			
			<dangling sequence="AA/T" sens="5">
				<enthalpy>-1300.0</enthalpy>
				<entropy>-2.0</entropy>
			</dangling>
			<dangling sequence="AAA/T" sens="5">
				<enthalpy>-1500.0</enthalpy>
				<entropy>-2.5</entropy>
			</dangling>
			<dangling sequence="AAAA/T" sens="5">
				<enthalpy>-1750.0</enthalpy>
				<entropy>-3.5</entropy>
			</dangling>
			<dangling sequence="AAAAA/T" sens="5">
				<enthalpy>-3950.0</enthalpy>
				<entropy>-10.5</entropy>
			</dangling>
		</origine>
	</dangling_end>
</hybridization>

<hybridization type="rnarna">
		<dangling_end type="single">
			<origine article="Serra_2006_2008">
    	<!--/******************************************************************************/
    	/* contains the parameters for RNA/RNA dangling ends of ;
	REF: Martin J Serra et al. (2006). Nucleic Acids research 34: 3338-3344
	REF: Martin J Serra et al. (2008). Nucleic Acids research 36: 5652-5659 
    	/******************************************************************************/-->
			<dangling sequence="UA/A" sens="3">
				<enthalpy>-5200.0</enthalpy>
				<entropy>-14.3</entropy>
			</dangling>
			<dangling sequence="UC/A" sens="3">
				<enthalpy>-3000.0</enthalpy>
				<entropy>-8.7</entropy>
			</dangling>
			<dangling sequence="UG/A" sens="3">
				<enthalpy>-6600.0</enthalpy>
				<entropy>-18.8</entropy>
			</dangling>
			<dangling sequence="UU/A" sens="3">
				<enthalpy>-3100.0</enthalpy>
				<entropy>-8.9</entropy>
			</dangling>
			<dangling sequence="UA/G" sens="3">
				<enthalpy>-2900.0</enthalpy>
				<entropy>-6.5</entropy>
			</dangling>
			<dangling sequence="UC/G" sens="3">
				<enthalpy>-2800.0</enthalpy>
				<entropy>-6.7</entropy>
			</dangling>
			<dangling sequence="UG/G" sens="3">
				<enthalpy>-6400.0</enthalpy>
				<entropy>-17.5</entropy>
			</dangling>
			<dangling sequence="UU/G" sens="3">
				<enthalpy>-1500.0</enthalpy>
				<entropy>-3.1</entropy>
			</dangling>			
			<dangling sequence="GA/U" sens="3">
				<enthalpy>-2600.0</enthalpy>
				<entropy>-6.8</entropy>
			</dangling>
			<dangling sequence="GC/U" sens="3">
				<enthalpy>-4000.0</enthalpy>
				<entropy>-10.2</entropy>
			</dangling>
			<dangling sequence="GG/U" sens="3">
				<enthalpy>-1700.0</enthalpy>
				<entropy>-4.4</entropy>
			</dangling>
			<dangling sequence="GU/U" sens="3">
				<enthalpy>-2200.0</enthalpy>
				<entropy>-5.4</entropy>
			</dangling>			
			<dangling sequence="AU/G" sens="5">
				<enthalpy>-2800.0</enthalpy>
				<entropy>-9.7</entropy>
			</dangling>
			<dangling sequence="CU/G" sens="5">
				<enthalpy>-400.0</enthalpy>
				<entropy>-4.6</entropy>
			</dangling>
			<dangling sequence="GU/G" sens="5">
				<enthalpy>-1400.0</enthalpy>
				<entropy>-5.3</entropy>
			</dangling>
			<dangling sequence="UU/G" sens="5">
				<enthalpy>-4300.0</enthalpy>
				<entropy>-14.0</entropy>
			</dangling>			
			<dangling sequence="AG/U" sens="5">
				<enthalpy>-1600.0</enthalpy>
				<entropy>-5.3</entropy>
			</dangling>
			<dangling sequence="CG/U" sens="5">
				<enthalpy>-500.0</enthalpy>
				<entropy>-1.6</entropy>
			</dangling>
			<dangling sequence="GG/U" sens="5">
				<enthalpy>600.0</enthalpy>
				<entropy>1.7</entropy>
			</dangling>
			<dangling sequence="UG/U" sens="5">
				<enthalpy>-2200.0</enthalpy>
				<entropy>-6.8</entropy>
			</dangling>
		</origine>
	</dangling_end>
	
	<dangling_end type="double">
		<origine article="Serra_2005">
    	<!--/******************************************************************************/
    	/* contains the parameters for RNA/RNA dangling ends of ;
	REF: Martin J Serra et al. (2005). RNA 11: 512-516 
    	/******************************************************************************/-->
			<dangling sequence="x-pyr-x/x-x" sens="3">
				<enthalpy>0.0</enthalpy>
				<entropy>0.0</entropy>
			</dangling>
			<dangling sequence="x-pur-pyr/x" sens="3">
				<enthalpy>-6200.0</enthalpy>
				<entropy>-18.2</entropy>
			</dangling>
			<dangling sequence="x-pur-pur/x" sens="3">
				<enthalpy>-4300.0</enthalpy>
				<entropy>-12.4</entropy>
			</dangling>
		</origine>
		
		<origine article="Serra_2006">
    	<!--/******************************************************************************/
    	/* contains the parameters for RNA/RNA dangling ends of ;
	REF: Martin J Serra et al. (2006). Nucleic Acids research 34: 3338-3344 
    	/******************************************************************************/-->
			<dangling sequence="pur-pyr-x/pyr" sens="3">
				<enthalpy>0.0</enthalpy>
				<entropy>0.0</entropy>
			</dangling>
			<dangling sequence="pur-pur-pur/pyr" sens="3">
				<enthalpy>0.0</enthalpy>
				<entropy>0.0</entropy>
			</dangling>
			<dangling sequence="pur-pur-pyr/pyr" sens="3">
				<enthalpy>-2500.0</enthalpy>
				<entropy>-6.7</entropy>				
			</dangling>
			
			<dangling sequence="pyr-pyr-x/pur" sens="3">
				<enthalpy>0.0</enthalpy>
				<entropy>0.0</entropy>
			</dangling>
			<dangling sequence="pyr-pur-x/pyr" sens="3">
				<enthalpy>-2500.0</enthalpy>
				<entropy>-6.7</entropy>			
			</dangling>
		</origine>
	</dangling_end>
	
	<dangling_end type="long">
    	<origine article="Sugimoto_2002">
    	<!--/******************************************************************************/
    	/* contains the parameters for RNA/RNA long dangling ends of ;
	REF: Sugimoto et al. (2002). J. Am. Chem. Soc. 124: 10367-10372 
    	/******************************************************************************/-->
			<dangling sequence="CA/G" sens="3">
				<enthalpy>-1050.0</enthalpy>
				<entropy>1.0</entropy>
			</dangling>
			<dangling sequence="CAA/G" sens="3">
				<enthalpy>-6750.0</enthalpy>
				<entropy>-16.0</entropy>
			</dangling>
			<dangling sequence="AAA" sens="3">
				<enthalpy>-10450.0</enthalpy>
				<entropy>-26.5</entropy>
			</dangling>
			<dangling sequence="AAAA" sens="3">
				<enthalpy>-11950.0</enthalpy>
				<entropy>-31</entropy>
			</dangling>			
			<dangling sequence="AG/C" sens="5">
				<enthalpy>-400.0</enthalpy>
				<entropy>-0.5</entropy>
			</dangling>
			<dangling sequence="AAG/C" sens="5">
				<enthalpy>-5200.0</enthalpy>
				<entropy>-20.5</entropy>
			</dangling>
			<dangling sequence="AAAG/C" sens="5">
				<enthalpy>-8250.0</enthalpy>
				<entropy>-24.5</entropy>
			</dangling>
			<dangling sequence="AAAAG/C" sens="5">
				<enthalpy>-13100.0</enthalpy>
				<entropy>-39.5</entropy>
			</dangling>			
			<dangling sequence="TA/A" sens="3">
				<enthalpy>-950.0</enthalpy>
				<entropy>-1.0</entropy>
			</dangling>
			<dangling sequence="TAA/A" sens="3">
				<enthalpy>-3200.0</enthalpy>
				<entropy>-7.0</entropy>
			</dangling>
			<dangling sequence="TAAA/A" sens="3">
				<enthalpy>-4200.0</enthalpy>
				<entropy>-9.5</entropy>
			</dangling>
			<dangling sequence="TAAAA/A" sens="3">
				<enthalpy>-5250.0</enthalpy>
				<entropy>-13.0</entropy>
			</dangling>			
			<dangling sequence="AA/T" sens="5">
				<enthalpy>-1100.0</enthalpy>
				<entropy>-2.5</entropy>
			</dangling>
			<dangling sequence="AAA/T" sens="5">
				<enthalpy>-3350.0</enthalpy>
				<entropy>-9.0</entropy>
			</dangling>
			<dangling sequence="AAAA/T" sens="5">
				<enthalpy>-3800.0</enthalpy>
				<entropy>-10.0</entropy>
			</dangling>
			<dangling sequence="AAAAA/T" sens="5">
				<enthalpy>-3850.0</enthalpy>
				<entropy>-9.0</entropy>
			</dangling>
		</origine>
	</dangling_end>
</hybridization>

		    
        
