Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1wpxb1 CHHHCCHHHHHHHHHHHCCHHHHCCCCCCCCCCEEEEEEEECCEEE-CCCCCCCHHHHC---------CCCEEEEEEECCCCCCCCCCCCC-CEEEEEEECCCCCCCCCCCCCEEEEEEEEEEECCCCEEEEEEECC----CCEEEE------CCCCCCCCCCCCCEEEEEEEEECCCCCCHHHCCCCCCCCHHHCCCCCCCHHHHHHCC-CC-EEEEEEEEEECCC------------ >P1;d3n08a1 ---------------------------------CEEECC------CCCCCEECCHHH-CCCC----CCCCCCEEEE---------CCCCCCCEEEEEEEECCCC-CCCCCCCCEEEEEEEEECCCCCEEC----CCCCC--CCEECCCCCCCCCCCCCCCC--CCCEEEEEEEEEECC-----CCCCCC----------CCCHHHHHHHHCCCEEEEEEEEEEECC------------- >P1;d4bega1 -----------------CCCCCCCCCCCCCCCCCEEECC------CCCCCCCCCHHHCCCCCCCCCCCCCCCEEEE---------CCCCCCCEEEEEEEECCCC-CC----CCEEEEEEEEEECCCCEECCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCEEEEEEEEEEECCC----CCCCCC----------CCCHHHHHHHHHHHEEEEEEEEEEEECC------------ >P1;d6ensa- -------CCCHHHCCCCCCHH-HCCC----CCCEECEEEEC-CEEECCCCEECCCHHHC---------CCCCEEECC--------CCCCCC-EEEEEEEECCCCCCCCCCCCCEEEEEEEEEECC---------CHH----HCEEEE------CCCCCCCCCCCCCEEEEEEEEECC---CCCCCCCCCCCCCCCCCCCCCCHHHHHHHC-CCCCCCEEEEEEECCCCCHHHHHHHHCC >P1;d6igga1 C--CCCCCCHHHHC----CHHHHCCC--CCCCCCCEEEEEC-CEEC-CCCEECCHHHCC---------CCCEEEECCCCC---------CC-EEEEEEEECCCCCCCCCCCCCEEEEEEEEEECC--------CCHH----HCEEEE------CCCCCCCCC--CCEEEEEEEEECC---CCCCCCCCCCCC-------CCCHHHHHHHC-CCCCCCEEEEEEECCC------------ PSA >P1;d1wpxb1 aa97867265115206833005500557907000304040697040-620470438408---------84070402045802c50816b61-30000000000128a637500200000010505786623060278----a07331------8031070479255000000001037a35086059076230002b7553002600940-90-4100000020249------------ >P1;d3n08a1 ---------------------------------080709------108536504740-0254----7030010306---------9126806000000002301-7963a64321000001051a26708----41290--80230301477510220405--565040102010044-----61886a----------314187047509a33325140101053------------- >P1;d4bega1 -----------------9ba286116a538167060708------0085466067400043490b06020010607---------b22b706000000201215-4a----9032000000023a122054410426a059b0210404174320000104694640100000000548----80a057----------9060850461065402010213012339------------ >P1;d6ensa- -------80727704491305-4005----40742060109-b2205700250606403---------b30650309--------b247a5-200000000014139728620200000020604---------608----205200------200000037c28300000000407---861a09257163654870161403900651-a092010000010542910570583088 >P1;d6igga1 a--94898150282----60052004--30b460603010c-9540-713360514506---------c50605040728---------81-20000000001422a926420200000010205--------3109----606311------704506066--7501000000406---767505228726-------60604600772-80c6010010030664------------ Translating the sequences **********HHH****CCHH*HCCC**CCCCC*EEEEEE**CEE*-CCC**CCHHH*C---------CCC*EEEE*********CCCCCC-*EEEEEEECCCCCCCCCCCCCEEEEEEEEEE*CCC*E******CC----CCEEEE------CCCCCCCCCCCCCEEEEEEEEECCC**C***CCCCCCCC*******CCCHHHHHH*C-CC-EEEEEEEEEECCC------------ ---------------------------------CEEE**------CCCCCEECCHHH-C***----**CCCCEEEE---------CCCCCC*EEEEEEEECCCC-CCCCCCCCEEEEEEEEE*CCCC*E*----CCC**--CCEE********CCCCCCCC--CCCEEEEEEEEE*CC-----CCCCCC----------CCCHHHHHHH**CC*EEEEEEEEEECC------------- -----------------CC****CCC**CCCCCCEEE**------CCCCC**CCHHH*C*********CCCCEEEE---------CCCCCC*EEEEEEEECCCC-CC----CCEEEEEEEEEECCCC*E*****CCC****CCEE********CCCCCCCCCCCC*EEEEEEEEE*CC*----CCCCCC----------CCCHHHHHHH*****EEEEEEEEEE*CC------------ -------***HHH****CCHH-HCCC----CCC*E*EEEE*-CEE*CCCCEECC*HH*C---------CCCCEEE**--------CCCCCC-EEEEEEEECCCCCCCCCCCCCEEEEEEEEEECC---------C**----*CEEEE------CCCCCCCCCCCCCEEEEEEEEECC---C**CCCCCCCCC*******CCCHHHHHHHC-CC****EEEEEEECCC************ *--*******HHH*----CHH*HCCC--CCCCCC*EEEEE*-CEEC-CCCEECCHHH*C---------CCC*EEE*****---------CC-EEEEEEEECCCCCCCCCCCCCEEEEEEEEEECC--------*C**----*CEEEE------CCCCCCCCC--CCEEEEEEEEECC---C**CCCCCCCCC-------CCCHHHHHHHC-CC****EEEEEEECCC------------ 49777.tem _________________________________ -------***HHH*---CCHH*HCCC--CCCCCCEEEEEE*-CEECCCCCEECCHHH*C---------CCCCEEEE*--------CCCCCC-EEEEEEEECCCCCCCCCCCCCEEEEEEEEEECCCC*E*---*CCC----CCEEEE------CCCCCCCCCCCCCEEEEEEEEECCC--C**CCCCCCCCC-------CCCHHHHHHHC-CC*EEEEEEEEEECCC------------ Structural block scores 0 6 - 4.0 M 8.3 75.0 75.0 75.0 27.2 7 9 * 3.0 P 4.3 75.0 75.0 5.0 4.7 10 12 H 4.2 M 2.3 75.0 75.0 5.3 3.3 14 16 - 3.8 M 4.7 75.0 75.0 5.7 75.0 17 18 C 4.3 M 3.0 75.0 10.2 2.0 40.5 19 20 H 4.1 M 0.0 75.0 6.2 2.5 0.0 23 25 C 4.5 M 1.7 75.0 2.7 1.7 1.3 26 27 - 3.8 M 6.0 75.0 7.8 75.0 75.0 28 33 C 4.3 M 2.7 62.5 4.2 27.5 4.1 34 39 E 4.3 M 1.8 16.5 16.0 1.5 1.7 43 44 E 4.2 M 2.0 75.0 75.0 2.0 4.5 45 49 C 4.6 H 16.6 3.4 3.4 2.4 17.2 50 51 E 3.8 M 5.5 5.5 6.0 3.5 4.5 52 53 C 5.0 H 2.0 2.0 3.0 3.0 2.5 54 56 H 4.8 H 5.0 3.7 3.7 3.3 3.3 59 67 - 4.1 M 75.0 35.3 4.2 75.0 75.0 68 71 C 4.7 H 4.8 1.0 0.8 5.1 5.9 72 75 E 4.7 H 1.5 2.2 3.2 2.0 2.2 77 84 - 4.2 M 4.6 75.0 75.0 75.0 49.0 85 90 C 4.7 H 5.6 4.3 5.7 6.7 51.5 92 99 E 4.9 H 0.4 0.0 0.2 0.2 0.2 100 112 C 4.8 H 3.3 10.0 31.3 3.3 3.3 113 122 E 5.0 H 0.8 0.9 0.7 1.0 0.5 123 126 C 4.5 M 5.0 4.9 4.1 38.5 38.8 130 132 - 3.8 M 3.0 75.0 3.0 75.0 75.0 134 136 C 4.0 M 5.7 2.3 4.0 4.7 3.3 137 140 - 4.2 M 75.0 39.8 6.1 75.0 75.0 141 142 C 4.4 M 5.2 4.0 5.8 1.0 3.0 143 146 E 4.4 M 3.5 2.0 1.8 1.8 2.8 147 152 - 3.8 M 75.0 4.0 3.2 75.0 75.0 153 165 C 4.8 H 3.9 13.8 2.8 2.9 15.1 166 174 E 5.0 H 0.1 0.9 0.1 0.4 0.6 175 177 C 4.3 M 3.3 2.7 3.0 27.3 27.0 178 179 - 4.2 M 6.8 75.0 41.5 75.0 75.0 181 182 * 3.0 P 4.0 75.0 75.0 3.5 6.5 183 191 C 4.7 H 4.2 29.4 28.4 4.8 4.1 192 198 - 3.8 M 3.6 75.0 75.0 4.4 75.0 199 201 C 5.0 H 2.7 2.7 5.0 3.7 4.0 202 208 H 4.9 H 3.0 4.6 3.4 3.3 3.4 211 212 C 4.5 M 4.5 6.8 4.5 5.2 4.0 214 223 E 4.6 H 0.7 1.7 1.2 0.4 1.1 224 226 C 4.7 H 5.0 27.7 5.0 3.7 5.3 227 238 - 4.5 M 75.0 75.0 75.0 4.5 75.0 >>>>>>