Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1agqa- ------------CCCCEEEEEEEE---HHHHC-----CCCCCC--C--------EEEEEEEECCC---CCCCC-------HHHHHHHHHHHHC----------CCCCEEEEEEECC-CEEEEC----CCC--CEEEECCCCEEEEEEE---------------------- >P1;d1bnda- ----------CCCCCCCEEEEEEE---HHHHCEEECCCC-CEEEECCEEECCCCEEECEEEEEEECCCCHHH----------------------CCCCCCCCCCEEEEEEE-EEEEEEEEEECC----CC--CEEEEEEEEEEEEEEEEEEC------------------ >P1;d1hcna- --------------CCCCCCEEEECCCCCCCC------------CC--------CEEEECCCCCEEEE----CCHHHHC---------------CCCCCCCEEEECCEEEEEEEEEEECCC--------------CCEEEEEEEEEEECCC------------------- >P1;d1hcnb- ---------CCCCCCCEEEEEEEEECC-----------CCCCCCE---------EEEEEEEECCCCCC----CCCCCCC---------------C------CCCCCEEEEEEEEEEEEEECCCCCC-----CCCCEEEEEEEEEEEEEECCCCCCCCCCCCCCCCCC--- >P1;d2aska- ------------CCCCEEEEEEEE---HHHHC-----CCCCCC--C--------EEEEEEEECCC---HHHCC-------HHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEE--EEEEEC----CCC--CEEEEEEEEEEEEEEE---------------------C >P1;d2x1wa- CHHHHHHHHHHHHHCCEEEEEEEE---CCCCC---CCCCCCEEECC--------EEEEEEEECCCCCC-------------------------------------CCEEEEEEEEEEEEEEEEECCCCCCCCEEEEEEEEEEEEEEEEC--------------------- >P1;d4ay9b- ---------C----CEEEEEEEEEEEE-----------HHHCEEE---------EEEEEEEEECCCCC----CCCCCCC---------------C------CCCCCCEEEEEEEEEEEEEECCCCC-----CCCEEEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCC >P1;d5e4ga- --CCCCCCCCCCCCCCEEECCEEE---CCCCC-----C-CCEEECC--------EEECCEEECCC---CCCC---CC-CCCHHHHHHHHC---CC-------CCCCCEEEEEEEEEEEEEEEC----CCCCEEEEEEEEEEEEEEEEE---------------------- >P1;d5vz3a- -----CCCCCCCCCCCEEEEEEEE---CCCCC-----CCCCEEECC--------EEEEEEEECCC---CCCC---CC-CCHHHHHHHHHHHHCCC-------CCCCCEEEEEEEEEEEEEEEC----C-CCEEEEEEEEEEEEEEEEE---------------------- >P1;d6z3ja- --C----------CCCEEECCEEE---CCCCC-----HHHCEEECC--------EEECCEEECCC---CCCCCHHHC-CCHHHHHHHHHHHHCCC-------CCCCCCEEEEEEEEEEEEEEC----CCCCEEEEEEEEEEEEEEEEC---------------------- >P1;d6zflv- CCCC-CHHHHHHHHCCEEEEEEEE---HHHHC---HHHCCCEEECC--------EEEEEEEECCCCCC-------------------------------------CEEEEEEEEEEEEEEEEEECCC--CCEEEEEEEEEEEEEEEEEEC-------------------- >P1;d7l0ja- ------------CCCCEEECCEEE---CCCC--------CCEEECC--------EEECCEEECCC---CCCCCCCCCCCCHHHHHHHHHHHCCCC-------CCCCCEEEEEEEEEEEEEEEE----C-CEEEEEEEEEEEEEEEEEE---------------------- PSA >P1;d1agqa- ------------1a9062445626---0351a-----4b380a--4--------51533406560---97157-------7725638857957----------aa8160613232a-525041----679--6725177200560507---------------------- >P1;d1bnda- ----------da665023526712---037175151589-96050255164ba7665150502313480906----------------------a403b159873606042-44533501031a----87--65552304023405143785------------------ >P1;d1hcna- --------------aa688043352583059c------------74--------03406120855638----0479347---------------72a766a5265345040653684522c--------------b691422440443529------------------- >P1;d1hcnb- ---------8686160333a3520064-----------b705513---------50802204060638----93b78b4---------------8------9945535123572564437049059-----b37152512104304046178854a17696ba5373--- >P1;d2aska- ------------6a6053228532---0461c-----2c2937--5--------51433505230---69416-------9816712851a79549849aa73712050614725--204040----987--6754486200350414---------------------e >P1;d2x1wa- 788777474776656042364714---0394a---827b5070566--------3160510628096b-------------------------------------d4803326156463605223587888545263502215507247--------------------- >P1;d4ay9b- ---------b----7074492410030-----------8507302---------72913206490737----93a9648---------------9------56457550114626654370504aa-----5a5665403106503127267a53934888886551429 >P1;d5e4ga- --9036076a2b275002146423---05758-----4-9503534--------41610405370---7652---20-567703742879---4a-------c4a608053253431604252----97b643646375211440005---------------------- >P1;d5vz3a- -----5805615560043335613---0872a-----339604438--------60712405470---3680---31-0797056237438655a-------727407032244451504145----a-a954655477210560204---------------------- >P1;d6z3ja- --a----------85063585423---06848-----539304533--------51312306250---55704b704-16b8066205524766a-------427508043062331303143----b79763756376210430003---------------------- >P1;d6zflv- 8a75-8875648744032665705---03713---6a386260566--------4030310555045a-------------------------------------934032254584428013144a--8b6854704041147060576-------------------- >P1;d7l0ja- ------------774043385644---0685--------a404716--------41612606070---738091a1660ab80272035367a4a-------1b5506031244503603147----9-a865556267110340206---------------------- Translating the sequences ------------**CCEEE*EEEE---****C-----***C**--C--------EEE*EEEECCC---*****-------*************----------C*CCEEEEEEE**-*EEEE*----**C--*EEEE****EEEEEEE---------------------- ----------****CC*EE*EEEE---****C*******-C****C********EEE*EEEE**********----------------------C********C***EEEE-EEEEEEEEEE**----*C--*EEEEEEEEEEEEEEE****------------------ --------------CC****EEEE*******C------------*C--------*EE*E***CC****----*******---------------C**********CCEEEEEEEEEEE***--------------**EEEEEEEEEEE***------------------- ---------*****CCEEE*EEEE***-----------**C****---------EEE*EEEECCC***----*******---------------C------**C*C*EEEEEEEEEEEEE******-----****EEEEEEEEEEEEE*******************--- ------------**CCEEE*EEEE---****C-----***C**--C--------EEE*EEEECCC---*****-------**************C********C*CCEEEEEEEE--EEEEE*----**C--*EEEEEEEEEEEEEEE---------------------* **************CCEEE*EEEE---****C---*****C****C--------EEE*EEEECCC***-------------------------------------CCEEEEEEEEEEEEEEE*******C***EEEEEEEEEEEEEEE*--------------------- ---------*----C*EEE*EEEE***-----------*******---------EEE*EEEE*CC***----*******---------------C------**C*CCEEEEEEEEEEEEEE*****-----***EEEEEEEEEEEEEE********************** --************CCEEE**EEE---****C-----*-*C****C--------EEE**EEECCC---****---**-************---*C-------*C*CCEEEEEEEEEEEEEEE*----**C***EEEEEEEEEEEEEEE---------------------- -----*********CCEEE*EEEE---****C-----***C****C--------EEE*EEEECCC---****---**-****************C-------*C*CCEEEEEEEEEEEEEEE*----*-C***EEEEEEEEEEEEEEE---------------------- --*----------*CCEEE**EEE---****C-----***C****C--------EEE**EEECCC---*********-****************C-------*C*CC*EEEEEEEEEEEEEE*----**C***EEEEEEEEEEEEEE*---------------------- ****-*********CCEEE*EEEE---****C---*****C****C--------EEE*EEEECCC***-------------------------------------C*EEEEEEEEEEEEEEE*****--C***EEEEEEEEEEEEEEE**-------------------- ------------**CCEEE**EEE---****--------*C****C--------EEE**EEECCC---**************************C-------*C*CCEEEEEEEEEEEEEEE*----*-C***EEEEEEEEEEEEEEE---------------------- 57501-1.tem _________________________________ --*--*********CCEEE*EEEE---****C-----***C****C--------EEE*EEEECCC*****************************C------**C*CCEEEEEEEEEEEEEEE****-**C***EEEEEEEEEEEEEEE***------------------- Structural block scores 0 1 - 4.6 H 75.0 75.0 75.0 75.0 75.0 7.5 75.0 75.0 75.0 75.0 9.2 75.0 3 4 - 4.4 M 75.0 75.0 75.0 75.0 75.0 7.0 75.0 1.5 75.0 75.0 40.0 75.0 5 13 * 3.4 M 59.6 45.7 75.0 36.6 60.2 5.9 67.9 5.8 4.6 67.6 6.3 59.9 14 15 C 4.9 H 4.5 2.5 10.5 3.0 3.0 3.0 3.5 2.5 0.0 2.5 2.0 2.0 16 18 E 4.7 H 4.0 3.3 7.3 3.0 3.3 3.0 5.0 1.0 3.3 4.7 3.7 3.3 20 23 E 4.8 H 4.8 4.0 3.8 2.5 4.5 4.0 1.8 3.8 3.8 3.5 4.2 4.8 24 26 - 4.3 M 75.0 75.0 5.0 3.3 75.0 75.0 1.0 75.0 75.0 75.0 75.0 75.0 27 30 * 1.9 P 2.2 2.8 4.2 75.0 2.8 4.0 75.0 4.2 4.2 4.5 2.8 4.8 32 36 - 4.6 H 75.0 3.4 75.0 75.0 75.0 47.0 75.0 75.0 75.0 75.0 48.3 75.0 37 39 * 2.3 P 6.2 30.7 75.0 31.2 5.5 7.8 29.3 29.3 5.0 5.7 5.7 53.5 41 44 * 1.8 P 40.1 2.8 58.0 3.5 40.0 4.5 3.0 2.8 2.8 3.0 4.2 3.0 46 53 - 4.8 H 75.0 6.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 54 56 E 4.9 H 3.7 5.7 2.3 4.3 3.3 3.3 6.0 3.7 4.3 3.0 2.3 3.7 58 61 E 4.7 H 3.2 2.5 2.2 2.0 3.2 3.0 2.8 2.2 2.8 2.8 2.2 3.5 62 64 C 4.7 H 3.7 2.0 6.0 2.0 1.7 3.3 4.3 3.3 3.7 2.3 3.3 2.3 65 93 * 3.4 M 32.2 57.9 50.9 51.6 29.5 68.2 51.4 29.0 21.5 14.4 67.9 12.3 95 100 - 4.3 M 75.0 4.1 7.0 75.0 8.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 101 102 * 3.0 P 75.0 8.5 3.5 9.0 5.0 75.0 5.5 43.8 41.0 39.5 75.0 38.0 105 106 C 4.5 M 4.5 3.0 3.5 4.0 1.0 8.8 6.0 3.0 2.0 2.5 6.0 2.5 107 121 E 4.8 H 8.3 7.7 9.2 3.9 12.7 3.9 3.7 3.4 3.1 2.7 3.5 2.8 122 125 * 3.3 M 56.5 40.4 75.0 5.8 56.2 3.0 6.2 56.8 57.5 57.0 3.0 58.0 127 128 * 3.2 M 6.5 41.5 75.0 75.0 8.5 7.5 75.0 8.0 42.8 9.2 75.0 42.0 130 132 * 2.5 P 52.0 52.0 75.0 29.8 52.0 5.7 30.2 4.3 6.0 5.3 8.5 6.3 133 147 E 4.8 H 3.6 2.9 13.6 2.6 3.5 3.3 3.1 3.2 3.6 3.1 3.2 3.2 148 150 * 3.7 M 75.0 6.0 5.3 4.7 75.0 52.3 5.0 75.0 75.0 75.0 29.3 75.0 151 169 - 4.6 H 75.0 71.3 75.0 17.3 71.8 75.0 6.0 75.0 75.0 75.0 75.0 75.0 >>>>>>