Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2ed6a1 CHHHHHHHHHHHHHHC---CEEEEEEEEEECCCCCCEEECCEEEEECCCEEEEECCCCCHHHHCCCCCCEEEEECCCCCCCCCHHHCCEEECCEEEEECCCCCEEEEEEEEEECCCCCCCCCCCCEEEEECCEEECC--CCEEEECEEEEECCCCCCHHHCCEEEEEEEEECCCC------- >P1;d2edma1 --------------CEEECCEEEEEEEEEEE-CCEEEECCEEEEEEC-CEEEEEECCCCCCHHHHCCCCEEEEECCCCCCCCCCCC-CEEEEEEEEEECCCCCEEEEEEEEECEEECCEEECCCCCEEEECCCEECCCCCCCEEEEEEEECCCCC-----CEEEEEEEEEEECCCEEECCCC PSA >P1;d2ed6a1 6978676667768339---363706050405452010408454371b206501024c37695058290400001357342a07496232000001000428250104308041561988663638281837423055--56135030005055606698321401030401063d------- >P1;d2edma1 --------------58574451406020207-7440302c5443916-153000531244860393a04000003871a35bb167-310101000004093403066040632649975308190a0622856041588500506010605737-----2230001030203647485a9b Translating the sequences **************H*---CEEEEEEEEEE**CC**EEEC*EEEEEC*CEEEEE*CCCCHHHH**CCCCEEEEECCCCCCCCCHHH*CEEE**EEEEECCCCCEEEEEEEEEE***CC***CCCCEEEEECCEEECC--CCEEEE*EEEEECCCC*****C*EEEEEEEEE*CCC------- --------------*E***CEEEEEEEEEEE-CCEEEE*CEEEEEEC-CEEEEEECCCC**HHHHCCCCEEEEECCCCCCCCC***-CEEEEEEEEEECCCCCEEEEEEEEE*EEECCEEECCCC*EEEECC*EECC**CC*EEEEEEEE*CCCC-----CEEEEEEEEEEECCC******* 158974.tem _________________________________ --------------HE---CEEEEEEEEEEE-CCEEEEECEEEEEEC-CEEEEEECCCCHHHHHHCCCCEEEEECCCCCCCCCHHH-CEEEEEEEEEECCCCCEEEEEEEEEEEEECCEEECCCCEEEEECCEEECC--CCEEEEEEEEEECCCC-----CEEEEEEEEEEECCC------- Structural block scores 0 13 - 3.0 P 6.6 75.0 16 18 - 3.0 P 75.0 5.3 20 30 E 4.8 H 3.3 2.5 32 33 C 5.0 H 3.5 5.5 34 38 E 3.8 M 1.0 1.8 40 45 E 4.7 H 4.0 4.3 49 54 E 4.7 H 2.3 2.2 55 58 C 5.0 H 6.6 2.5 59 64 H 3.7 M 5.5 5.0 65 68 C 5.0 H 3.8 4.4 69 73 E 5.0 H 0.2 0.0 74 82 C 5.0 H 4.6 6.7 83 85 H 3.0 P 6.3 4.7 88 97 E 4.6 H 0.3 0.3 98 102 C 5.0 H 4.2 4.0 103 115 E 4.4 M 2.5 3.1 116 117 C 5.0 H 8.5 9.0 118 120 E 3.0 P 6.7 5.0 121 124 C 5.0 H 5.0 4.5 125 129 E 4.6 H 4.4 3.7 130 131 C 5.0 H 5.5 5.0 132 134 E 4.3 M 1.7 3.7 135 136 C 5.0 H 5.0 2.5 137 138 - 3.0 P 75.0 6.5 139 140 C 5.0 H 5.5 6.5 141 150 E 4.4 M 1.7 1.8 151 154 C 5.0 H 4.0 5.5 155 159 - 3.0 P 6.4 75.0 161 171 E 4.6 H 1.3 1.0 172 174 C 5.0 H 7.5 4.3 175 181 - 3.0 P 75.0 7.9 >>>>>>