Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hlra7 ---------------------------------CCHHHHHHCCCCCCCEEEEEECCCCCEEEEEEECHHHHCCCCEEEEECHHHCC---CCCEECCCCCCCCCCCCCCCEECCCCCEECCCCCEEEEEEECCHHHHHHHHCCCEEEEEECCCC >P1;d1n62b1 CCCCCHHHHHHHHCCCCCCCCCCCHHHHCCCCCCCHHHC--CC-CCCCEEEEEECCCCCEEEEEEECHHHHHCCCEEEEEEHHHHHHHCCCEEECC---------CCCEEECCCCCEECCCCCEEEEEEECCHHHHHHHHHHCEEEEEECCCC >P1;d1rm6a1 ----------CC---CCCCCCCCCHHHHHCCCCCCHHHC--CC-CCCCEEEEEECCCCCEEEEEEECHHHHHCCCEEEEEEHHHCC-----CCCCCCC-------CCCCCCCCCCCEECCCCCEEEEEEECCHHHHHHHHHHCEEEEEECCCC >P1;d2w3sb1 --------------CCCCCCCCCCHHHHHCCCCCCHHHC--CCCCCCCEEEEEECCCCCEEEEEEECHHHHCCCCEEEEEEHHHCCC---CCCCCCCC---------CCCCCCCCCEECCCCCEEEEEEECCHHHHHHHHCCCEEEEEEC--- >P1;d3nvvc1 -------------CCCCCCCCCCCHHHHHCCCCCCHHHC--CCCCCCCEEEEEECCCCCEEEEEEECCCHHHCCCEEEEECHHHCCC---CCEECCCC---------C-EECCCCCEECCCCCEEEEEEECCHHHHHHHHHCCEEEEEECCC- PSA >P1;d1hlra7 ---------------------------------4a9a4649658bb2335050306352040681628504827406303138519---a61243989289a6a982497050028305762210020006469306600840817166283a >P1;d1n62b1 6aa2789557997589b3a59564485376a7087a754--87-9c4330420407332050371517505838205404108515669614583b---------9a855130028306567020030205549206701830606146195b >P1;d1rm6a1 ----------da---bb6a698a7585484a7368aa56--95-8a642744250434205146251760583a105604108625-----9253a68-------964a52410393055741100303055881055008407051552738 >P1;d2w3sb1 --------------7bb69676a3583483972589a65--667bb43451405083750308525062056085054043195279---a1360859---------87624005a3066631200200055782054007407181655--- >P1;d3nvvc1 -------------a5ab69577934a5385a7157ab66--869aa4424450407453040471526405717404413308519a---62843998---------8-6341057405666240000105447204600740606066294- Translating the sequences ---------------------------------CCHHH***CCCCCCCEEEEEECCCCCEEEEEEECHHHH*CCCEEEEE*HHHCC---*CCEECCCC*******CCCCEECCCCCEECCCCCEEEEEEECCHHHHHHHH*CCEEEEEECCCC **************CCCCCCCCCCHHHH*CCCCCCHHHC--CC-CCCCEEEEEECCCCCEEEEEEECHHHHHCCCEEEEEEHHH******C*EECC---------CCC*EECCCCCEECCCCCEEEEEEECCHHHHHHHHH*CEEEEEECCCC ----------**---CCCCCCCCCHHHHHCCCCCCHHHC--CC-CCCCEEEEEECCCCCEEEEEEECHHHHHCCCEEEEEEHHHCC-----C**CCCC-------CCCC**CCCCCEECCCCCEEEEEEECCHHHHHHHHH*CEEEEEECCCC --------------CCCCCCCCCCHHHHHCCCCCCHHHC--CCCCCCCEEEEEECCCCCEEEEEEECHHHH*CCCEEEEEEHHHCC*---CC**CCCC---------CC**CCCCCEECCCCCEEEEEEECCHHHHHHHH*CCEEEEEEC--- -------------*CCCCCCCCCCHHHHHCCCCCCHHHC--CCCCCCCEEEEEECCCCCEEEEEEEC**HHHCCCEEEEE*HHHCC*---CCEECCCC---------C-EECCCCCEECCCCCEEEEEEECCHHHHHHHHHCCEEEEEECCC- 54665.tem _________________________________ --------------CCCCCCCCCCHHHHHCCCCCCHHHC--CCCCCCCEEEEEECCCCCEEEEEEECHHHHHCCCEEEEEEHHHCC*---CCEECCCC-------CCCCEECCCCCEECCCCCEEEEEEECCHHHHHHHHHCCEEEEEECCCC Structural block scores 0 13 - 4.3 M 75.0 7.1 66.0 75.0 70.4 14 23 C 4.5 M 75.0 7.1 15.5 7.8 7.3 24 28 H 4.4 M 75.0 5.4 6.0 5.6 6.1 29 34 C 4.7 H 52.4 6.4 6.4 5.7 5.9 35 37 H 5.0 H 7.8 7.5 8.7 8.5 9.3 39 40 - 4.5 M 6.5 75.0 75.0 75.0 75.0 41 47 C 4.9 H 6.7 16.9 16.8 7.0 7.4 48 53 E 5.0 H 2.7 2.2 4.0 3.2 3.2 54 58 C 5.0 H 3.2 3.0 2.6 4.6 3.8 59 65 E 5.0 H 3.6 3.0 3.3 3.3 3.0 67 71 H 4.6 H 5.0 5.0 5.2 3.8 4.4 72 74 C 5.0 H 4.3 4.3 4.8 4.3 4.0 75 80 E 4.8 H 2.2 2.3 2.7 2.7 2.5 81 83 H 5.0 H 5.3 4.3 4.7 5.0 4.3 84 85 C 4.5 M 5.0 3.0 3.5 4.5 5.0 87 89 - 4.3 M 53.5 7.0 75.0 75.0 75.0 90 91 C 4.5 M 3.5 2.5 42.0 5.8 4.0 92 93 E 3.8 M 3.0 6.5 3.5 4.5 6.0 94 97 C 4.8 H 7.2 41.1 6.9 5.5 7.2 98 104 - 4.5 M 7.9 75.0 75.0 75.0 75.0 105 108 C 4.4 M 5.8 8.1 7.4 41.2 58.2 109 110 E 3.8 M 3.5 3.0 3.5 4.0 4.5 111 115 C 5.0 H 3.0 2.6 3.4 3.9 3.4 116 117 E 5.0 H 1.5 1.5 1.5 1.5 2.0 118 122 C 5.0 H 4.4 4.8 4.4 4.4 5.0 123 129 E 5.0 H 0.4 1.0 1.0 0.6 0.7 130 131 C 5.0 H 5.0 5.0 5.0 5.0 4.5 132 140 H 4.9 H 4.2 4.1 3.9 3.7 3.3 141 142 C 4.4 M 2.0 1.5 2.0 2.0 2.0 143 148 E 5.0 H 4.8 3.8 3.8 4.7 4.0 149 152 C 4.5 M 5.9 6.6 5.0 57.5 22.5 >>>>>>