Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1k4za- CCCEEEEE-CCEEEEECCCCCCCCEEE-ECCCCCEEEEEEEEEEEEEEECCCCEEEEEEEEEEEEEECCCCCCEEEEEEECEEEEECCCCCEEEEECCEEEEEECCCCCCCCEEEEECCEEEEEEECCCHHHCCEEEECCCCEEEEEECCEEEEEECCC-- >P1;d1k8fa- -CCEEEEE-CCEEEEECCCCCCC-EEECCCCCCCEEEEECCCCCEEEEEEEECEEEEECCEEEEEEEEEECCEEEEECCEEEEEEECCCCCEEEEECCEEEEEECCCCCCCCEEEEECCEEEEEEEEE-CCCEEEEEECCCEEEEEECCCCEEEEEECCCC >P1;d2b0ra- CCCCCCCCCCCCEECCCCCCCCCCEEECCCCCCCEEEE-EEECCEEEECCCCCEEEEEEEEEEEEEECCCCCEEEEECCEEEEEEECCCCCEEEEECC-EEEEECC-CC-CCEEEEECCC-CEEEEECCCCCCEEEEECCCCEECCCCCC--CCEEC---- PSA >P1;d1k4za- 78533536-c55130111693a93130-8077702030040360403057504302015063040202105600604504803050453054040450630504036703a061627905802002043a9774455625486646659886557649a-- >P1;d1k8fa- -b522626-c6312014067379-13077066603030350460403047505201015055020203304730402405504020545043020440400402015704807162780280210314-a9c7265621237443664786644543939f >P1;d2b0ra- 490a38b63582040500372a9423057166926030-20060502054303204042001040304004630502502804030625043030350-6020102-71-d060717705-0310345a9b96275571458564979b6--65864---- Translating the sequences CCCEEEEE-CCEEEEECCCCCCCCEEE-*CCCCCEEEEEEEE**EEEEECCCCEEEEEEEEEEEEEECCCCC*EEEE**E*EEEEECCCCCEEEEECCEEEEEECCCCCCCCEEEEECCEEEEEEE*CC***C*EEEECCCCEEEEE*CC*EEEEECCC-- -CCEEEEE-CCEEEEECCCCCCC-EEECCCCCCCEEEEE***CCEEEEE***CEEEEE**EEEEEEE***CCEEEEECCEEEEEEECCCCCEEEEECCEEEEEECCCCCCCCEEEEECCEEEEEEEE*-CCC*EEEEECCC*EEEEECCC*EEEEE*CC** CCC******CC*EE**CCCCCCCCEEECCCCCCCEEEE-EEECCEEEE*CCCCEEEEEEEEEEEEEECCCCCEEEEECCEEEEEEECCCCCEEEEECC-EEEEECC-CC-CCEEEEECC*-*EEEEECCCCCCEEEEECCCCEE***CCC--**EEC---- 69340.tem _________________________________ CCCEEEEE-CCEEEEECCCCCCCCEEECCCCCCCEEEEEEEECCEEEEECCCCEEEEEEEEEEEEEECCCCCEEEEECCEEEEEEECCCCCEEEEECCEEEEEECCCCCCCCEEEEECCEEEEEEEECCCCCCEEEEECCCCEEEEECCC*EEEEECCC-- Structural block scores 0 2 C 4.7 H 6.7 30.5 4.3 3 7 E 4.0 M 4.0 3.6 7.8 9 10 C 5.0 H 8.8 9.2 6.5 11 15 E 4.4 M 2.0 1.4 2.2 16 23 C 4.9 H 5.3 13.9 4.4 24 26 E 5.0 H 1.3 1.3 1.7 27 33 C 4.7 H 14.9 4.6 5.1 34 41 E 4.5 M 1.5 2.2 10.8 42 43 C 4.0 M 3.0 3.0 3.0 44 48 E 4.8 H 2.4 2.2 2.4 49 52 C 4.2 M 4.0 4.2 2.5 53 66 E 4.9 H 1.9 1.6 1.4 67 71 C 4.4 M 2.8 3.4 2.8 72 76 E 4.8 H 2.0 1.8 2.0 77 78 C 4.0 M 2.5 2.0 2.5 79 85 E 4.9 H 2.9 2.3 2.4 86 90 C 5.0 H 3.4 3.6 3.4 91 95 E 5.0 H 2.4 1.8 1.8 96 97 C 5.0 H 2.5 2.0 2.5 98 103 E 4.8 H 3.0 1.7 14.0 104 111 C 4.8 H 3.7 3.1 21.7 112 116 E 5.0 H 4.4 4.6 4.2 117 118 C 5.0 H 4.5 4.0 3.5 119 126 E 4.5 M 2.1 2.1 11.4 127 132 C 4.0 M 6.8 19.7 8.5 133 137 E 4.8 H 4.8 4.2 5.2 138 141 C 4.8 H 4.8 3.2 4.5 142 146 E 4.4 M 5.6 4.6 6.2 147 149 C 4.7 H 7.3 6.3 8.8 151 155 E 4.4 M 5.8 4.6 20.0 156 158 C 4.0 M 7.8 5.0 51.3 159 160 - 4.0 M 75.0 15.8 75.0 >>>>>>