Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1aisa1 CCCCCCCCCCCCCEEEEEECCCC----CCHHHHCCCCC-C-CCCCCCCCCCEEEECC----CCCCEEEECCCCEEEEEEEC------------CHHHHHHHHHHHHHHHHHCCC------------------------------ >P1;d1mpga2 --------CE----EEECCCCCCHHH--HHHHHHHHCCCCCEEE-CC--CCEEEEEEECCEEEEEEEEEECCCEEEEEEC-----------HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCC------------------- >P1;d1pcza2 -CCCCCCCCCCCCEEEEEECCCC----CCHHHHHHHCC-C-EEEECCCEEEEEEEEC----CCCEEEEECCCCEEEEEEEC------------CHHHHHHHHHHHHHHHHHCCCC----------------------------- >P1;d2xhia1 CCCCCCCCCCHHH-CEEEE--CCCCCCCHHHHCCCCCC-CCCEEEEC--CEEEEEEC----CEEEEEEECC-CEEEEEEECCCCCCCCCCC-------HHHHHHHHHHCCCCCCHHHHHHHHHHHCHHHHHHHHHCCCCCCCCC >P1;d3eika1 -----CCCCCCCCEEEEEECCCC----CCHHHHHHHCC-C-EECCCCCCCCEEEEEC----CCCEEEEECCCCEEEEEEEC------------CHHHHHHHHHHHHHHHHHCCCC-----------------------CCCCCC >P1;d3eika2 ---------CCCCEEEEEECCCE----ECHHHHHHHCC-CCEECCCCCCCCEEEEEC----CCCEEEEECCCCEEEEEEEC------------CHHHHHHHHHHHHHHHHHCEE------------------------------ PSA >P1;d1aisa1 a8768949986752538231839----06087038108-b-04164a846003051a----60902020267060303706------------5772163027403740564a3------------------------------ >P1;d1mpga2 --------43----4360546170a7--1084147617aa4160-4b--830136142d956460205066a43040505-----------9704421940243036305093506855a85994------------------- >P1;d1pcza2 -a999978976a43528640748----08165018304-5-05173a8560010407----82902010365050303506------------5684073016303710653a12----------------------------- >P1;d2xhia1 88a5133a62682-02307--04351010520035420-96084429--71002307----a350000067-74010002159a6a36506-------8a21530371030955068418641565883685188640408075 >P1;d3eika1 -----da9875852516020448----0708401840a-8-05175a8580010609----96901010374060303606------------478306600640273067181a-----------------------073582 >P1;d3eika2 ---------87763546440824----06056008437-9406165a7280040806----91804030346060202706------------778306602840552047273------------------------------ Translating the sequences *****CCCCCCCCEEEEEECCCC----CCHHHH***CC-C-****CCC*CCEEEE*C----CCC*EEEECCCCEEEEEEEC------------CHHHHHHHHHHHHHHHHHCCC------------------------------ --------C*----EEE**CCCC***--*HHHHHHHCC*C*EE*-CC--CCEEEEE********EEEEE*CCCEEEEEE*-----------***HHHHHHHHHHHHHHH**CCC***********------------------- -****CCCCCCCCEEEEEECCCC----CCHHHHHHHCC-C-EE**CCC***EEEEEC----CCCEEEEECCCCEEEEEEEC------------CHHHHHHHHHHHHHHHHHCCC*----------------------------- *****CCCCC***-*EEEE--CC****C*HHH****CC-C**E***C--C*EEEEEC----C**EEEEECC-CEEEEEEEC**********-------HHHHHHHHHH***CCC****************************** -----CCCCCCCCEEEEEECCCC----CCHHHHHHHCC-C-EE**CCC*CCEEEEEC----CCCEEEEECCCCEEEEEEEC------------CHHHHHHHHHHHHHHHHHCCC*-----------------------****** ---------CCCCEEEEEECCC*----*CHHHHHHHCC-C*EE**CCC*CCEEEEEC----CCCEEEEECCCCEEEEEEEC------------CHHHHHHHHHHHHHHHHHC**------------------------------ 55945.tem _________________________________ -****CCCCCCCCEEEEEECCCC----CCHHHHHHHCC-C*EE**CCC*CCEEEEEC----CCCEEEEECCCCEEEEEEEC------------CHHHHHHHHHHHHHHHHHCCC*----------------------------- Structural block scores 1 4 * 3.4 M 7.2 75.0 9.4 6.1 75.0 75.0 5 12 C 4.3 M 7.1 57.1 7.6 5.1 8.2 41.0 13 18 E 4.6 H 3.8 15.5 4.7 14.5 2.7 4.3 19 22 C 4.6 H 5.2 4.5 4.8 38.5 4.0 3.5 23 26 - 4.2 M 75.0 23.1 75.0 2.2 75.0 75.0 27 28 C 4.2 M 3.0 38.0 4.0 0.5 3.5 3.0 29 35 H 4.5 M 3.9 4.3 3.4 2.7 3.6 3.3 36 37 C 5.0 H 4.0 4.0 2.0 1.0 5.2 5.0 41 42 E 4.3 M 2.0 3.5 2.5 4.0 2.5 3.0 43 44 * 1.4 P 3.5 37.5 4.0 4.0 4.0 3.5 45 47 C 4.6 H 7.5 30.2 7.2 28.7 7.8 7.5 49 50 C 4.3 M 3.0 5.5 3.0 4.0 4.0 4.0 51 55 E 4.9 H 1.8 2.2 1.0 1.0 1.4 2.4 57 60 - 4.5 M 75.0 7.4 75.0 75.0 75.0 75.0 61 63 C 4.2 M 5.0 5.3 6.3 6.2 8.0 6.0 64 68 E 4.9 H 0.8 1.4 0.6 0.0 0.4 1.4 69 72 C 4.8 H 3.8 6.6 3.5 23.8 3.5 3.2 73 79 E 4.9 H 2.7 2.4 2.3 1.0 2.6 2.4 81 92 - 4.5 M 75.0 63.8 75.0 17.6 75.0 75.0 94 110 H 4.7 H 3.8 2.9 3.5 20.2 3.8 3.9 111 113 C 4.7 H 5.8 5.7 4.8 6.3 3.3 4.0 115 143 - 4.3 M 75.0 51.5 75.0 4.9 60.3 75.0 >>>>>>