Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1agqa- ----------------------------------------------------------------------------------------------------------------------------------------------------CCCCEEEEEEEE---HHHHC--CCCCCC--CEEEEEEEECCC---CCCCC-------HHHHHHHHHHHHC----------CCCCEEEEEEECC-CEEEECC----CC--CEEEECCCCEEEEEEE---------------------- >P1;d1aoca- CCCCCCCCCCCCCCCCC---------CCCCCC--HHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCHHHHHHCCCCCCCCCHHHHCHHHCCCCCCCCCCCCEEEECCC-CCEEECCC---------------------------------CCEEEEC-CCC-------------CCCCC-CCCCEEEECC---------------------CCCCCCC-------------CCEECCEEEEEEEEEEECC------CCEEEEEEEEEEEECCEECC-------------------- >P1;d1bnda- C-------------------------------------------------------------------------------------------CCCCCCEEEEEEEHHHHCEEECCC---------------------------------CCEEEECCEEE-C-----------CCCEEECEEEEEEECC----------------------CCHHHCCCCCCCCCCE---EEEEEEEEEEEEEEEECC-------CCCEEEEEEEEEEEEEEEEEEC------------------ >P1;d1hcna- ------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCEEEECCCCCCCC---------CCCEEEECCCCCEEEE----CCHHHHC---------------CCCCCCCEEEECCEEEEEEEEEEECCC--------------CCEEEEEEEEEEECCC------------------- >P1;d1hcnb- -------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCEEEEEEEEECC--------CCCCCCE-EEEEEEEECCCCCC----CCCCCCC---------------C------CCCCCEEEEEEEEEEEEEECCCCC--CC---CCCEEEEEEEEEEEEEECCCCCCCCCCCCCCCCCC--- >P1;d1m4ua1 ----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHCCCCCEECCCCCCCCCCCHHHHHHHHHHHCCCCC---------------------CCCHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECC-----------CCEECCEEEEEECCC-------------------------------CCCCCCCC---CCEEEEEEEEEEEEEEEEECCHHHCCEEEEEEEEEEEEEEEEEC--------------------- >P1;d2aska- ----------------------------------------------------------------------------------------------------------------------------------------------------CCCCEEEEEEEE---HHHHC--CCCCCC--CEEEEEEEECCC---HHHCC-------HHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEE--EEEEECC----CC--CEEEEEEEEEEEEEEE---------------------C >P1;d2x1wa- ----------------------------------------------------------------------------------------------------------------------------------------CHHHHHHHHHHHHHCCEEEEEEEE---CCCCCCCCCCCEEECCEEEEEEEECCCCCC-------------------------------------CCEEEEEEEEEEEEEEEEECCCCCCCCEEEEEEEEEEEEEEEEC--------------------- >P1;d4ay9b- -------------------------------------------------------------------------------------------------------------------------------------------------C----CEEEEEEEEEEEE--------HHHCEEE-EEEEEEEEECCCCC----CCCCCCC---------------C------CCCCCCEEEEEEEEEEEEEECCCC--CC---CCEEEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCC >P1;d5e4ga- ------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCCCCCCEEECCEEE---CCCCC--C-CCEEECCEEECCEEECCC---CCCC---CC-CCCHHHHHHHHC---CC-------CCCCCEEEEEEEEEEEEEEECC----CCCEEEEEEEEEEEEEEEEE---------------------- >P1;d5vz3a- ---------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCCCEEEEEEEE---CCCCC--CCCCEEECCEEEEEEEECCC---CCCC---CC-CCHHHHHHHHHHHHCCC-------CCCCCEEEEEEEEEEEEEEECC-----CCEEEEEEEEEEEEEEEEE---------------------- >P1;d6z3ja- ------------------------------------------------------------------------------------------------------------------------------------------C----------CCCEEECCEEE---CCCCC--HHHCEEECCEEECCEEECCC---CCCCCHHHC-CCHHHHHHHHHHHHCCC-------CCCCCCEEEEEEEEEEEEEECC----CCCEEEEEEEEEEEEEEEEC---------------------- >P1;d6zflv- ----------------------------------------------------------------------------------------------------------------------------------------CCCC-CHHHHHHHHCCEEEEEEEE---HHHHCHHHCCCEEECCEEEEEEEECCCCCC-------------------------------------CEEEEEEEEEEEEEEEEEECCC--CCEEEEEEEEEEEEEEEEEEC-------------------- >P1;d7l0ja- ----------------------------------------------------------------------------------------------------------------------------------------------------CCCCEEECCEEE---CCCC-----CCEEECCEEECCEEECCC---CCCCCCCCCCCCHHHHHHHHHHHCCCC-------CCCCCEEEEEEEEEEEEEEEEC-----CEEEEEEEEEEEEEEEEEE---------------------- PSA >P1;d1agqa- ----------------------------------------------------------------------------------------------------------------------------------------------------1a9062445626---0351a--4b380a--451533406560---97157-------7725638857957----------aa8160613232a-5250416----79--6725177200560507---------------------- >P1;d1aoca- 7ba85540042199a28---------839826--9824740272045028709954991420353620560053306707345020341676771a72050225303-03213047---------------------------------8553100-005-------------91502-0003002057---------------------a56914b-------------a04041332405000054a------86506012030000000577-------------------- >P1;d1bnda- d-------------------------------------------------------------------------------------------a66502352671203717515158---------------------------------99605025516-4-----------ba76651505023134----------------------80906a403b159873---60604244533501031a-------8765552304023405143785------------------ >P1;d1hcna- ------------------------------------------------------------------------------------------------------------------------------------------------------aa688043352583059c---------7403406120855638----0479347---------------72a766a5265345040653684522c--------------b691422440443529------------------- >P1;d1hcnb- -------------------------------------------------------------------------------------------------------------------------------------------------8686160333a3520064--------b705513-50802204060638----93b78b4---------------8------994553512357256443704905--9b---37152512104304046178854a17696ba5373--- >P1;d1m4ua1 ----------b9977799887bb06595693775753307985375a7057506d6146a20249166799d78975585066405909b---------------------9148917a4716616a835a6533764368303621113200113613406-----------500004202306003-------------------------------83100599---933041372650100215046a6067070563712003507148--------------------- >P1;d2aska- ----------------------------------------------------------------------------------------------------------------------------------------------------6a6053228532---0461c--2c2937--551433505230---69416-------9816712851a79549849aa73712050614725--2040409----87--6754486200350414---------------------e >P1;d2x1wa- ----------------------------------------------------------------------------------------------------------------------------------------788777474776656042364714---0394a827b50705663160510628096b-------------------------------------d4803326156463605223587888545263502215507247--------------------- >P1;d4ay9b- -------------------------------------------------------------------------------------------------------------------------------------------------b----7074492410030--------8507302-72913206490737----93a9648---------------9------56457550114626654370504a--a5---a5665403106503127267a53934888886551429 >P1;d5e4ga- ------------------------------------------------------------------------------------------------------------------------------------------9036076a2b275002146423---05758--4-950353441610405370---7652---20-567703742879---4a-------c4a6080532534316042529----7b643646375211440005---------------------- >P1;d5vz3a- ---------------------------------------------------------------------------------------------------------------------------------------------5805615560043335613---0872a--33960443860712405470---3680---31-0797056237438655a-------727407032244451504145a-----a954655477210560204---------------------- >P1;d6z3ja- ------------------------------------------------------------------------------------------------------------------------------------------a----------85063585423---06848--53930453351312306250---55704b704-16b8066205524766a-------427508043062331303143b----79763756376210430003---------------------- >P1;d6zflv- ----------------------------------------------------------------------------------------------------------------------------------------8a75-8875648744032665705---037136a3862605664030310555045a-------------------------------------934032254584428013144a--8b6854704041147060576-------------------- >P1;d7l0ja- ----------------------------------------------------------------------------------------------------------------------------------------------------774043385644---0685-----a40471641612606070---738091a1660ab80272035367a4a-------1b55060312445036031479-----a865556267110340206---------------------- Translating the sequences ----------------------------------------------------------------------------------------------------------------------------------------------------**CCEEE**EEE---*****--***C**--CEEEEEEEECCC---*****-------*************----------**CCEEEEEEE**-*EEEE**----**--*EEEE****EEEEEEE---------------------- *****************---------******--*************************************************************************-********---------------------------------*C*EEE*-***-------------C****-****EEEECC---------------------*******-------------CCEE**EEEEEEEEEEE**------***EEEEEEEEEEE**EE**-------------------- *-------------------------------------------------------------------------------------------************************---------------------------------*C*EEE**EEE-*-----------C******EEEEEEECC----------------------********C*******---**EEEEEEEEEEEEEE**-------***EEEEEEEEEEEEEEE****------------------ ------------------------------------------------------------------------------------------------------------------------------------------------------CC*****EEE********---------*C*EEEE***CC****----*******---------------C**********CCEEEEEEEEEEE***--------------**EEEEEEEEEEE***------------------- -------------------------------------------------------------------------------------------------------------------------------------------------*****CCEEE**EEE***--------**C****-EEEEEEEECCC***----*******---------------C------****C*EEEEEEEEEEEEE*****--**---***EEEEEEEEEEEEE*******************--- ----------********************************************************************************---------------------***************************************CC**E**EEE**-----------C****CEEEEEE**C-------------------------------C*******---CCEEEEEEEEEEEEEEE***********EEEEEEEEEEEEEEE*--------------------- ----------------------------------------------------------------------------------------------------------------------------------------------------**CCEEE**EEE---*****--***C**--CEEEEEEEECCC---*****-------**************C**********CCEEEEEEEE--EEEEE**----**--*EEEEEEEEEEEEEEE---------------------* ----------------------------------------------------------------------------------------------------------------------------------------**************CCEEE**EEE---**********C****CEEEEEEEECCC***-------------------------------------CCEEEEEEEEEEEEEEE***********EEEEEEEEEEEEEEE*--------------------- -------------------------------------------------------------------------------------------------------------------------------------------------*----C*EEE**EEE***--------*******-EEEEEEEE*CC***----*******---------------C------****CCEEEEEEEEEEEEEE****--**---**EEEEEEEEEEEEEE********************** ------------------------------------------------------------------------------------------------------------------------------------------************CCEEE**EEE---*****--*-*C****CEEE**EEECCC---****---**-************---*C-------***CCEEEEEEEEEEEEEEE**----*****EEEEEEEEEEEEEEE---------------------- ---------------------------------------------------------------------------------------------------------------------------------------------*********CCEEE**EEE---*****--***C****CEEEEEEEECCC---****---**-****************C-------***CCEEEEEEEEEEEEEEE**-----****EEEEEEEEEEEEEEE---------------------- ------------------------------------------------------------------------------------------------------------------------------------------*----------*CCEEE**EEE---*****--***C****CEEE**EEECCC---*********-****************C-------***CC*EEEEEEEEEEEEEE**----*****EEEEEEEEEEEEEE*---------------------- ----------------------------------------------------------------------------------------------------------------------------------------****-*********CCEEE**EEE---**********C****CEEEEEEEECCC***-------------------------------------C*EEEEEEEEEEEEEEE*****--****EEEEEEEEEEEEEEE**-------------------- ----------------------------------------------------------------------------------------------------------------------------------------------------**CCEEE**EEE---****-----*C****CEEE**EEECCC---**************************C-------***CCEEEEEEEEEEEEEEE**-----****EEEEEEEEEEEEEEE---------------------- 57501.tem _________________________________ ------------------------------------------------------------------------------------------------------------------------------------------*--*********CCEEE**EEE-*-*****--***C****CEEEEEEEECCC************-*-**************C------****CCEEEEEEEEEEEEEEE***---*****EEEEEEEEEEEEEEE**-------------------- Structural block scores 0 137 - 4.7 H 75.0 21.6 62.2 75.0 75.0 21.5 75.0 74.0 75.0 75.0 75.0 75.0 74.0 75.0 139 140 - 4.3 M 75.0 75.0 75.0 75.0 75.0 7.0 75.0 7.0 75.0 1.5 75.0 75.0 40.0 75.0 141 149 * 3.4 M 59.6 67.6 67.7 75.0 36.6 2.2 60.2 5.9 67.9 5.8 4.6 67.6 6.3 59.9 150 151 C 4.7 H 4.5 5.0 7.5 10.5 3.0 1.0 3.0 3.0 3.5 2.5 0.0 2.5 2.0 2.0 152 154 E 4.7 H 4.0 1.3 1.7 7.3 3.0 0.7 3.3 3.0 5.0 1.0 3.3 4.7 3.7 3.3 155 156 * 1.2 P 4.5 37.5 3.5 2.0 6.8 4.5 5.0 5.0 5.5 5.0 4.0 6.5 5.5 6.5 157 159 E 4.8 H 4.7 1.7 4.0 3.7 2.3 2.7 3.3 4.0 1.7 3.0 3.3 3.0 4.0 4.7 163 167 * 2.9 P 3.9 75.0 75.0 5.9 75.0 75.0 4.7 5.3 75.0 5.0 5.5 5.2 2.8 18.8 168 169 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 5.0 75.0 75.0 75.0 75.0 8.2 75.0 170 172 * 3.0 P 6.2 75.0 75.0 75.0 31.2 75.0 5.5 7.8 29.3 29.3 5.0 5.7 5.7 53.5 174 177 * 1.7 P 40.1 2.0 7.4 58.0 3.5 0.0 40.0 4.5 3.0 2.8 2.8 3.0 4.2 3.0 179 186 E 4.6 H 3.4 0.6 2.1 2.0 2.6 1.6 3.2 2.8 3.8 2.6 3.1 2.6 2.0 3.2 187 189 C 4.7 H 3.7 29.0 27.3 6.0 2.0 51.0 1.7 3.3 4.3 3.3 3.7 2.3 3.3 2.3 190 201 * 3.7 M 46.2 75.0 75.0 28.3 29.6 75.0 45.9 58.5 29.5 39.3 39.2 22.4 57.9 22.5 205 218 * 3.5 M 11.0 40.9 34.8 75.0 75.0 75.0 5.7 75.0 75.0 20.2 5.0 4.9 75.0 4.9 220 225 - 4.2 M 75.0 75.0 6.9 7.0 75.0 3.0 8.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 226 229 * 3.1 M 42.8 75.0 57.0 4.5 6.8 58.5 4.5 75.0 5.0 25.5 22.8 22.0 75.0 23.1 230 231 C 4.6 H 4.5 5.2 3.0 3.5 4.0 6.0 1.0 8.8 6.0 3.0 2.0 2.5 6.0 2.5 232 246 E 4.8 H 8.3 2.1 2.7 9.2 3.9 2.3 12.7 3.9 3.7 3.4 3.1 2.7 3.5 2.8 247 249 * 2.4 P 27.3 29.8 53.5 75.0 4.7 3.0 28.0 2.3 4.8 28.7 30.2 29.8 2.7 30.3 250 252 - 4.3 M 75.0 75.0 75.0 75.0 53.0 7.5 75.0 6.7 53.5 75.0 75.0 75.0 29.8 75.0 253 257 * 2.6 P 34.4 33.8 34.2 75.0 47.9 4.0 34.2 6.6 48.1 6.3 20.7 6.4 21.7 20.9 258 272 E 4.8 H 3.6 1.1 2.9 13.6 2.6 2.9 3.5 3.3 3.1 3.2 3.6 3.1 3.2 3.2 273 274 * 3.4 M 75.0 7.0 5.0 3.5 3.5 41.5 75.0 41.0 4.5 75.0 75.0 75.0 6.5 75.0 275 294 - 4.6 H 75.0 75.0 68.2 71.7 16.8 75.0 72.0 75.0 6.0 75.0 75.0 75.0 75.0 75.0 >>>>>>