Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vmha- ----CEEEE-CCCCCEEEECHHHHHHHHHHHCCCCEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHCCCC--CCCC---CCCCHHHHHHHHHHCCEEEEEEECCEECCCCCEEEEEEECCCCCCEEEEEEEE-- >P1;d1vmja- CCEEEEEEECCCCCCEEEECHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEECC-CHHHHHHHHHHHHHHCCCCHHHCHHHCCCCCCHHHHHHHHHHCCEEEEEEECCEECCCCCCEEEEEECCCCCCEEEEEEEEC- >P1;d2cu5a- CCCCEEEEEEEC-CCEEEECHHHHHHCCC--CC-CEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCC---CCCCHHHHHHHHHHCCEEEEEEECCEECCCCCCEEEEEECCCCEEEEEEEEEC-- >P1;d2p6ha- -CEEEEEEEECCCCCEEEECHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEECC-CHHHHHHHHHHHHHHHCCCC-CCHHHH-CCCCHHHHHHHHHHCCEEEEEEECCEECCCCCCEEEEEECCCCCEEEEEEEEEEE PSA >P1;d1vmha- ----35181-077822024028306600683a3764303050228000011532348841652146257734b7--b284---a6812204400941573360604847051997400000002065b03040707-- >P1;d1vmja- 631551151608711413200650660064061653603000337000001544-5893276146503640428593165069a64100025017406441504058480516894300000010546040204054- >P1;d2cu5a- 3bb253160605-732024018601710a--62-6740403012800002152255763377319715870559578294---96723004500841736141705817051986540000002064603030536-- >P1;d2p6ha- -55734160706730202201a50581086190554502040428000040641-37832872157046405083-83a449-7581000340176275435040784904087845000000106570302020659 Translating the sequences ----*EEEE-CCCCCEEEECHHHHHHHHH**CCCCEEEEEECCCCCEEEEEE*C*CHHHHHHHHHHHHHHCCCC--CC**---CCCCHHHHHHHHHHCCEEEEEEECCEECCCCC*EEEEEECCCCC*EEEEEEEE-- *C**EEEEE*CCCCCEEEECHHHHHHHHH**CCCCEEEEEE*CCCCEEEEEECC-CHHHHHHHHHHHHHHCCCC***C*****CCCCHHHHHHHHHHCCEEEEEEECCEECCCCCCEEEEEECCCCC*EEEEEEEE*- *C**EEEEE**C-CCEEEECHHHHHH***--CC-CEEEEEECCCCCEEEEEECC*CHHHHHHHHHHHHHHCCCC**CC**---CCCCHHHHHHHHHHCCEEEEEEECCEECCCCCCEEEEEECCCC**EEEEEEE*-- -C**EEEEE*CCCCCEEEECHHHHHHHHH**CCC*EEEEEECCCCCEEEEEECC-CHHHHHHHHHHHHHH*CCC*-CC****-CCCCHHHHHHHHHHCCEEEEEEECCEECCCCCCEEEEEECCCCC*EEEEEEEE** 111038.tem _________________________________ *C**EEEEE*CCCCCEEEECHHHHHHHHH**CCCCEEEEEECCCCCEEEEEECC*CHHHHHHHHHHHHHHCCCC**CC****-CCCCHHHHHHHHHHCCEEEEEEECCEECCCCCCEEEEEECCCCC*EEEEEEEE*- Structural block scores 2 3 * 2.3 P 75.0 3.0 6.8 6.0 4 8 E 4.9 H 3.6 2.6 3.0 2.8 10 14 C 4.7 H 4.8 3.4 18.0 3.2 15 18 E 5.0 H 2.0 2.5 2.0 1.5 20 28 H 4.8 H 3.4 3.2 3.8 4.3 29 30 * 2.3 P 5.5 2.0 75.0 3.5 31 34 C 4.7 H 6.6 4.5 22.2 4.8 35 40 E 5.0 H 2.5 2.0 3.0 2.5 41 45 C 4.9 H 2.4 2.6 2.2 2.8 46 51 E 5.0 H 1.2 1.0 1.3 1.7 52 53 C 4.7 H 2.5 4.0 2.0 2.5 56 69 H 5.0 H 4.7 4.6 5.3 4.6 70 73 C 4.8 H 6.4 3.5 4.8 3.2 74 75 * 2.9 P 75.0 7.0 6.0 39.0 76 77 C 4.7 H 6.8 2.0 5.0 5.5 78 81 * 2.2 P 40.5 4.2 40.8 6.9 83 86 C 5.0 H 6.4 5.4 6.0 5.2 87 96 H 5.0 H 2.6 1.9 2.5 2.3 97 98 C 5.0 H 6.0 5.0 5.0 6.0 99 105 E 5.0 H 3.1 2.7 3.4 3.3 106 107 C 5.0 H 6.0 6.0 4.5 6.0 108 109 E 5.0 H 3.5 4.0 3.5 4.5 110 115 C 4.9 H 5.8 5.5 5.7 5.2 116 121 E 5.0 H 0.0 0.5 0.7 0.8 122 126 C 4.9 H 2.6 2.0 2.4 2.4 128 135 E 4.9 H 2.6 1.9 2.5 1.6 >>>>>>