Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1n67a2 --CCCEEECCEEEEECCCEEECCCCEEEEEEEECCCCCCEEEEEEEEEECC--------CCCCCEECCCCCCEEEEEEECCH-HH-CCCCCCC-CHHHEEECHHHC--EEEEE----ECCEEEEECCCCCCEEC---CCEEEEEEEEECCCC--------------C--CCEEEEEEEEEECCC------CCCEEEEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCCCCCCC------ >P1;d1zk5a- -------------------CCCC-CCC-CEEEECCCCEEEECCCCCEEC---CCCCCEEE-EEEEEEECCCEEEEEEEECCCE--EEEEC-----------------CEEEEECCCCEEEEEEEECCCHHHCEECCCCCCEEEEEEEECCC---------------CEEEEEEEEEEEEEECCCCCEEEECC-EEEEEEEEEEE-CCCCCC-----------CCCCEEEEEE-CCEEEEC >P1;d4x5pa- ----------CEEEECCCCEECC-CCEEEEEEECCC-CCCCCCCCEEEE---HHHCEEEE-CCCCCCC-CEEEEEEEEEEC-------------------------------HHHHHHEEEEEEECC-----EEEEECCCCCCCCEEECCC-----------------CCEECCEEEEEEECCCCCEEEECCCCEEEEEEEEEEECCCCCC------------EEEEEEEEECCCEEECC >P1;d4z3ga1 CCEEEEEEEECCEEEEEEEEEECCCCCEEEECCCC--EEEE-EEEEEECCCC----EECCCCCEEEEE-EEEEEEECEEECCCCCEEE--EEEEECCCCEEECCCCC------------------------------CEEEEEEEEEEEEEECCCEECCCCCCCEEEECCCCCCEEEEEECCCCCCCEEEEEEEEEEEEEEEEEECCC---CCCCCCCHHHHCCCCCCEEEEEEEEEEEC >P1;d5ihwa2 --CCCEEECCEEEEEEEEEEECCCCEEEEEEEECCCCCCEEEEEEEEECEEECCCCCEEEEEEECCCCC-CCEEEEEECC-C-CCCCCCCCCCCCHHHCEECHHHHCCCEEEE-----CCEEEEEEE----EEC---CCEEEEEEEECCCCC--------------CCCCEEEEEEEEEEECCC------CCEEEEEEEEEEECC----------------------------------- PSA >P1;d1n67a2 --6a31435100000203824197330400010001037044000010210--------9380004049a206050240473-92-06b9170-669327512a60--72513----28300203051987304---1001010604034a2--------------a--240000000001289------8501000000135158b8c9bb4344425083096636125605------ >P1;d1zk5a- -------------------9071-406-47050056826171ac63420---18680024-3560002660000000206063--4673a-----------------a1000004a50000010022619704305758246029034089---------------78330000000300114b84515095-38001030214-8b271a-----------b244304020-1202045 >P1;d4x5pa- ----------0205042a67077-308416040a05-75066a870504---03810202-0341751-201010360204-------------------------------910673062504047-----6435040882075140855-----------------94440201020404a9029400749430010102030646b35------------2503020204440403a >P1;d4z3ga1 612000000032733381a9051964050402053--3603-0112719049----606283101201-1000000251509682204--04138358051247c1c------------------------------80100033226265049836011757453508261530202010188037580403040000001000247---60524053a40280533030303040513 >P1;d5ihwa2 --4913327300000200623697520100000004138055020400004046607358b50604047-8050400307-a-a2904a803076196065038707a32819-----b41030506----808---10100102050733b--------------793040000010202278------784340012173559----------------------------------- Translating the sequences --***EEE***EEEE***EEECCCC*EEEEEEECCCCCCEE*EEEEEE***--------**CC*EECCCCC*EEEEEEECC*-**-***C***-*****EE*****--*EEEE----***EEEEECC*****E*---CCEEEEEEEEECCC*--------------C--C*EEEEEEEEEECCC------CC*EEEEEEEEE***CCCCCC***********CCCC*******C------ -------------------**CC-CC*-*EEEECCCC**EE*****EEC---***C*EEE-**EEE**CCCEEEEEEEECCC*--****C-----------------**EEEE*******EEEEECC*****E****CC*EEEEEEEECCC---------------C***EEEEEEEEEEECCCCC*EEECC-EEEEEEEEEEE-CCCCCC-----------CCCC**EEEE-C*EEE*C ----------*EEEE****EECC-CCEEEEEEECCC-CC******EEE*---***C*EEE-CC***CC-C*EEEEEEEE*C-------------------------------********EEEEECC-----E****CC******EEECCC-----------------CCEE**EEEEEEECCCCC*EEECC**EEEEEEEEEE*CCCCCC------------*****EEEE*C*EEE*C *****EEE****EEE***EEE*CCCC*EEEE**CC--**EE-EEEEEEC***----*E***CCEEE**-**EEEEE*EE*CC******--*********EE******------------------------------C*EEEEEEEEE********************CC****EEEEEE*CCCCC*EEE***EEEEEEEEEEE*CCC---***********CCCC**EEEE***EEE*C --***EEE***EEEE***EEECCCC*EEEEEEECCCCCCEE*EEEEEEC******C*EEE***E**CCC-C*EEEEEE*C-C-******C*********EE********EEEE-----**EEEEE**----*E*---CCEEEEEEEE*CCC*--------------C*CCEEEEEEEEEEECCC------CC*EEEEEEEEEE**----------------------------------- 49401-2.tem _________________________________ --***EEE***EEEE***EEECCCCCEEEEEEECCCCCCEE*EEEEEEC**-***C*EEE*CCEEECCCCCEEEEEEEECCC-******C***-*****EE*****--*EEEE----***EEEEECC----*E*---CCEEEEEEEEECCC*--------------C*CCEEEEEEEEEEECCCCC*EEECC*EEEEEEEEEEE*CCCCCC-----------CCCC**EEEE*C*EEE*C Structural block scores 0 1 - 4.5 M 75.0 75.0 75.0 3.5 75.0 2 4 * 3.0 P 6.5 75.0 75.0 0.7 4.7 5 7 E 4.2 M 2.7 75.0 75.0 0.0 2.7 8 10 * 2.7 P 2.0 75.0 50.0 1.0 3.3 11 14 E 4.4 M 0.0 75.0 1.8 3.8 0.0 15 17 * 2.1 P 1.7 75.0 5.5 4.0 0.7 18 20 E 4.4 M 4.7 28.0 4.3 6.5 3.7 21 25 C 4.5 M 4.6 17.4 18.4 5.0 5.8 26 32 E 4.5 M 0.7 13.9 3.3 1.6 0.1 33 38 C 4.4 M 1.8 4.5 17.1 27.8 2.7 39 40 E 4.5 M 2.0 4.0 3.0 1.5 2.5 42 47 E 4.3 M 0.2 6.3 5.1 2.0 1.0 49 50 * 3.0 P 0.5 75.0 75.0 2.0 2.0 52 54 * 3.0 P 75.0 5.0 3.7 75.0 5.3 57 59 E 4.1 M 53.0 2.0 1.3 2.7 5.3 61 62 C 3.8 M 4.0 4.0 1.5 2.0 2.5 63 65 E 3.8 M 1.3 2.0 4.0 1.0 3.3 66 70 C 3.9 M 5.1 2.8 16.6 15.4 18.8 71 78 E 4.7 H 2.1 0.2 1.6 1.0 1.5 79 81 C 4.1 M 4.7 4.0 26.3 4.7 30.8 83 88 * 2.7 P 17.2 28.3 75.0 15.2 6.0 90 92 * 3.0 P 2.7 75.0 75.0 1.7 1.0 94 98 * 3.0 P 5.2 75.0 75.0 4.8 4.4 99 100 E 4.2 M 6.0 75.0 75.0 3.0 5.5 101 105 * 3.0 P 3.9 75.0 75.0 5.3 3.6 106 107 - 3.8 M 75.0 42.8 75.0 43.8 8.8 109 112 E 4.2 M 2.8 0.0 58.5 75.0 5.0 113 116 - 3.8 M 75.0 4.9 3.5 75.0 75.0 117 119 * 2.4 P 4.3 0.0 3.0 75.0 30.2 120 124 E 4.5 M 1.0 0.2 2.2 75.0 1.8 125 126 C 4.1 M 2.5 2.0 5.5 75.0 3.0 127 130 - 3.8 M 6.2 5.8 75.0 75.0 75.0 134 136 - 3.8 M 75.0 4.0 2.7 75.0 75.0 137 138 C 4.8 H 0.5 6.5 2.0 4.0 0.5 139 147 E 4.5 M 1.3 3.3 3.9 1.9 1.0 148 150 C 4.5 M 5.8 5.7 6.0 4.3 4.3 152 165 - 4.5 M 75.0 75.0 75.0 4.5 75.0 168 169 C 4.3 M 38.5 3.0 6.5 5.0 1.5 170 180 E 4.6 H 0.5 0.4 1.5 1.8 0.8 181 185 C 4.7 H 33.8 5.7 5.1 4.0 33.4 187 189 E 4.2 M 75.0 2.0 1.3 4.3 75.0 190 191 C 4.5 M 6.5 7.0 5.5 2.0 7.5 193 203 E 4.8 H 1.0 2.0 1.3 0.5 2.8 205 210 C 4.3 M 10.1 6.7 5.9 39.7 75.0 211 221 - 3.8 M 4.4 75.0 75.0 3.6 75.0 222 225 C 4.1 M 5.2 5.4 20.5 3.8 75.0 226 227 * 2.1 P 4.5 1.5 1.5 3.0 75.0 228 231 E 4.1 M 3.5 1.5 1.0 1.5 75.0 235 237 E 4.2 M 75.0 0.7 1.3 3.0 75.0 >>>>>>