Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1s12a- CEEEEECC------CEEEEECCCC-----CHHHHHHHHHHHHHHHHHHHH--CCCEEEEEEC---CEEEEEEC-CCC----HHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCC >P1;d2idla1 CEEEEEEECCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEC--- >P1;d4peoa- -CEEEEEECCCCCEEEEEEECC-------------HHHHHHHHHHHHHHHHCCCCCEEEEE--CCCEEEEECC----CCCCHHHHHHHHHHHHHHHHHCCCEEE----------- PSA >P1;d1s12a- 3040212b------7202137607-----479017605930470083058--491071557a---33010404-a17----8606630550164055238736910405358a9e >P1;d2idla1 604030422a76303003043118508895270174048305800710485071806275698a7030304029a05a8139402830570274037118936740406276--- >P1;d4peoa- -47020344a88202103055b-------------80483048119304970906072756--a443010505----628197018205700740584300657----------- Translating the sequences CEEEEE**------*EEEEECCCC-----*HHHHHHHHHHHHHHHHHHHH--CCC*EEEEEC---CEEEEE*C-CCC----HHHHHHHHHHHHHHHHHHHHCCCCEEEEE*C*** CEEEEEEECCCCCEEEEEEECCCC******HHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC*CCCEEEEECC*CCC****HHHHHHHHHHHHHHHHHHHHCCCCEEEEE*C--- -*EEEEEECCCCCEEEEEEECC-------------HHHHHHHHHHHHHHHHCCCCCEEEEE--CCCEEEEECC----****HHHHHHHHHHHHHHHHH******----------- 118010.tem _________________________________ CEEEEEEECCCCCEEEEEEECCCC-----*HHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC-CCCEEEEECC-CCC****HHHHHHHHHHHHHHHHHHHHCCCCEEEEE*C--- Structural block scores 1 7 E 4.6 H 2.9 1.9 2.9 8 12 C 4.0 M 75.0 5.7 6.5 13 19 E 4.7 H 12.9 1.4 1.6 20 23 C 4.5 M 5.0 3.2 41.6 24 28 - 4.0 M 75.0 6.0 75.0 30 50 H 4.7 H 7.5 3.5 21.1 51 55 C 4.6 H 17.8 3.2 3.0 56 60 E 5.0 H 5.0 5.2 5.4 63 65 C 4.3 M 51.0 5.8 6.2 66 70 E 5.0 H 1.6 2.0 1.8 71 72 C 4.5 M 2.0 1.0 2.5 74 76 C 4.0 M 6.2 5.2 75.0 77 80 * 2.7 P 75.0 5.6 4.2 81 100 H 4.8 H 4.0 4.0 3.5 101 104 C 4.0 M 4.8 5.0 23.2 105 109 E 4.0 M 2.4 2.4 75.0 112 114 - 4.0 M 11.3 75.0 75.0 >>>>>>