Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ewqa3 --CCCHHHCCC-CCCCEEEEEEC-CCEEEEEECCCCCCEEEEEECCHHHHHHHHHHHCCCEEEECHHHHHCHHHHHHHHHHCCCCCCCC---CCC--CC-----------------CCCHHHHHHHHHHHHHHHHHHCCCCC-CCCCEECCHHHCCCCHHHHHHCCCCCCC >P1;d1wb9a3 CCCCCHHHCCCCCCCCEEEEEECCCCEEEEEECCCCCCEEEECCCCHHHHHHHHHHHCCCEEEEECCC----CCHHHCCC-CCCEEEECHHHHCHHHHHHHHHHHHCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEECCHHHCCCC------------- PSA >P1;d1ewqa3 --547a9514a-94210000034-94200000012604010010664810030002120540000440287990185059307213804---083--57-----------------a634003100100131046649890a-2781651703675541930476446486 >P1;d1wb9a3 01448a9628aa76310000124981000010103504030120674930311095060100000450----8335006b-2532452447105383026101710a3a507b2803a052000000000210373278a074075051447968959------------- Translating the sequences --CCCHHHCCC-CCCCEEEEEEC-CCEEEEEECCCCCCEEEEEECCHHHHHHHHHHHCCCEEEE*HHH****HHHHHHHH*CCC****C---*C*--**-----------------CCCHHHHHHHHHHHHHHHHHHCCCCC-CCCCEECCHHHCCCC************* **CCCHHHCCC*CCCCEEEEEEC*CCEEEEEECCCCCCEEEE**CCHHHHHHHHHHHCCCEEEEE***----**HHH***-CCCEEEEC***HCH**HH*****************CCCHHHHHHHHHHHHHHHHHHCCCCC*CCCCEECCHHHCCCC------------- 53150.tem _________________________________ --CCCHHHCCC-CCCCEEEEEEC-CCEEEEEECCCCCCEEEEEECCHHHHHHHHHHHCCCEEEEEHHH----HHHHHHHH-CCCEEEEC---HCH--HH-----------------CCCHHHHHHHHHHHHHHHHHHCCCCC-CCCCEECCHHHCCCC------------- Structural block scores 0 1 - 3.0 P 75.0 0.5 2 4 C 5.0 H 5.3 5.3 5 7 H 5.0 H 8.2 8.5 8 10 C 5.0 H 5.2 6.8 12 15 C 5.0 H 4.0 4.2 16 21 E 5.0 H 0.5 0.5 24 25 C 5.0 H 6.5 4.5 26 31 E 5.0 H 0.3 0.2 32 37 C 5.0 H 2.2 2.2 38 43 E 4.3 M 0.3 1.0 44 45 C 5.0 H 6.0 6.5 46 56 H 5.0 H 1.7 3.2 57 59 C 5.0 H 2.3 2.3 60 64 E 4.6 H 0.8 0.0 65 67 H 3.0 P 2.7 3.0 68 71 - 3.0 P 6.5 75.0 72 79 H 3.8 M 4.6 4.6 81 83 C 5.0 H 3.0 3.3 84 87 E 3.0 P 3.0 3.2 89 91 - 3.0 P 75.0 4.0 95 96 - 3.0 P 75.0 5.5 97 98 H 3.0 P 6.0 1.0 99 115 - 3.0 P 75.0 4.3 116 118 C 5.0 H 6.5 4.5 119 136 H 5.0 H 1.9 1.4 137 141 C 5.0 H 7.3 6.5 143 146 C 5.0 H 4.5 3.0 147 148 E 5.0 H 5.5 3.0 149 150 C 5.0 H 4.0 4.0 151 153 H 5.0 H 3.0 7.3 154 157 C 5.0 H 5.2 7.8 158 170 - 3.0 P 4.8 75.0 >>>>>>