Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2gm5a- --CEEEEEEECC-C----HHHHHHHHHHHHHCCCCHHH-----EEEEE------CC-CHHHHHHCCCCC----CC-EEEECCHHHCCCCC-CCCHHHH-HHHHCCCEEEECCC---CEECC-----CCCC-CCHHHHHHHHHHHHHHHHHHHHC----- >P1;d3bvpa1 -CEEEEEEEECCCCHHHCCCCHHHHHHHHHHHHH-HCCCEEEEEEEEECCCCCCCC-CHHHHHHHHHHHHCC--CCEEEECCHHHHCCCHHHHHHHHHHCCHHHCCEEEECCC---CEECC-----CHHHHHHHHHHHHHHHHHHC------------- >P1;d3guva- CCEEEEEEECCC-CHHHHHHHHHHHHHHHHHHHC--CCCEEEEEEEECCCCCCCCC-CHHHHHHHHHHHCCCCCCCEEEECCHHHCCCHH-HHHHHHH-HHHHCCCEEEECCC---CEEHH-----H--C-CHHHHHHHHCC-HHHHHHHHHHHHHCCC >P1;d3pkza- --CEEEEEEECCC---------CCCHHHHHHHHH-HCC--CCEEEEEE-CCCCCCCCCHHHHHHHHHCCCC----CEEEECCHHHHCCCHHHHHHHHH-HHHHCCCEEEECCCHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHC--------------- PSA >P1;d2gm5a- --4300000099-7----69407602820473806693-----01305------24-491057027088----a0-40101549200577-5216015-40384601040244---53205-----5950-541884276267656867778a8----- >P1;d3bvpa1 -35000000056784a81d311950364037306-849171162030314605818-060044028308696--050000142310053562015004500684903000153---91305-----68816541763276178749------------- >P1;d3guva- 653000000055-249720940781375047309--671522440200067c6815-2830760061046962a0410001227200814-4017005-50384a02000044---94203-----8--3-81376148507-36667667777a8789 >P1;d3pkza- --43000000457---------a47275026405-738--07501305-450922a70740570075087a----13000130110034393017006-404937040100634502874889851753255104720650586--------------- Translating the sequences --*EEEEEEECC-C----***HHHHHHHHHH****H**-----EEEEE------CC-CHHHHHH*****----*C-EEEECCHHH*CCC*-***HHHH-HHHHCCCEEEECCC---CEECC-----****-**HHHHHHHHHHHH*********----- -**EEEEEEECC*C*******HHHHHHHHHHHH*-HCC****EEEEEE*CCCCCCC-CHHHHHHHHH***C*--CCEEEECCHHH*CCCH*HHHHHHH***HH*CCEEEECCC---CEECC-----******HHHHHHHHHHHHH*------------- ***EEEEEE*CC-C*******HHHHHHHHHHHH*--CC****EEEEE**CCCCCCC-CHHHHHHHHH***C***CCEEEECCHHH*CC*H-HHHHHHH-HHHHCCCEEEECCC---CEE**-----*--*-*HHHHHHHH**-HH************** --*EEEEEEECC*---------***HHHHHHHH*-HCC--**EEEEEE-CCCCCCC*CHHHHHHHHH***C----CEEEECCHHH*CCCH*HHHHHHH-HHHHCCCEEEECCC******CC***********HHHHHHHHHHH*--------------- 53041.tem _________________________________ -**EEEEEEECC*C*******HHHHHHHHHHHH*-HCC****EEEEEE*CCCCCCC-CHHHHHHHHH***C*-*CCEEEECCHHH*CCCH*HHHHHHH-HHHHCCCEEEECCC---CEECC-----******HHHHHHHHHHHHH*********----- Structural block scores 1 2 * 2.2 P 39.5 4.0 4.0 39.5 3 9 E 4.9 H 0.4 0.0 0.0 0.4 10 11 C 5.0 H 9.0 5.5 5.0 4.5 14 20 * 3.0 P 45.6 5.9 5.0 75.0 21 32 H 4.6 H 3.9 3.4 3.8 10.2 36 37 C 4.3 M 6.0 6.5 6.5 5.5 38 41 * 2.9 P 75.0 2.5 2.5 39.2 42 47 E 4.8 H 14.0 2.3 1.7 2.3 49 55 C 4.5 M 54.4 4.6 6.5 4.6 58 66 H 4.8 H 3.4 3.0 3.4 3.9 67 69 * 1.4 P 30.3 4.7 3.3 5.0 74 75 C 4.3 M 37.5 2.5 2.0 38.0 76 79 E 5.0 H 1.2 0.0 0.2 0.8 80 81 C 5.0 H 3.0 2.5 1.5 2.0 82 84 H 5.0 H 5.0 2.0 3.7 0.7 86 88 C 4.8 H 4.0 2.7 3.0 2.3 91 97 H 4.7 H 2.9 1.7 2.4 2.4 99 102 H 4.7 H 3.8 3.5 4.0 4.2 103 105 C 4.8 H 3.3 4.3 4.8 3.3 106 109 E 5.0 H 1.2 0.8 0.5 1.2 110 112 C 5.0 H 3.3 3.0 2.7 3.0 113 115 - 4.3 M 75.0 75.0 75.0 3.0 117 118 E 4.3 M 2.5 2.0 3.0 7.5 119 120 C 4.3 M 2.5 2.5 1.5 6.0 121 125 - 4.3 M 75.0 75.0 75.0 6.2 126 131 * 1.8 P 16.5 5.7 40.7 4.5 132 144 H 4.7 H 5.1 4.8 9.7 9.2 145 153 * 3.4 M 7.5 67.7 6.6 75.0 154 158 - 4.3 M 75.0 75.0 8.5 75.0 >>>>>>