Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1tsja- ---CCCCCEECCCCCCHHHHHHHHHHHCCCCEEEEEECC-------CCCCEEEEEEEECCEEECCC--------------------CCEEEECC----CCHHHHHHHC--EEECCCCC-----CCCCEEEEEECCCCEEEEECC >P1;d1u6la1 -----CCCCCCEECCCHHHHHHHHHHHHC-CEEEE-CCCCCCCCCCC-CCC-EEEEEECCEEEEEECCCC----CCCCCCC----CCCCCCCC-CCC-CHHHHHHHHC-CCCCCCCEEEC---CEEEE-CCCCCCCCCCCEECC >P1;d1u7ia1 ---CCCCCCEEEECCCCCCC-CHHHHHCCCEEEEEEEECCC-CCCCCCCCEEEEEEEECCEEEEEEEECC----CCCCCCCC---CCCEEEECCCHHHHHHHHHHHHC-CCEECCCCCCC---CCCEEEEEECCCCCEEEEEEC >P1;d2q48a- CCCCCCCCCCEECCCCHHHHHHHHHHHCC-CEEC---------------CCCEEEEEECCEEEEEEE-HHHCCCCC--CCCCCCCCCEEEEECC---CHHHHHHHHHHCCCEECCCC--HHHHHCCEEEEEECCCCCEEEEEC- PSA >P1;d1tsja- ---aa34613212a66067107632665a907434644e-------77820550201154722047--------------------70311329----7685059237--15337379-----883530403168650100045 >P1;d1u6la1 -----9a2450506240760061047219-36343-52148196853-540-503023c99000101648----7927417----b9417283-769-0660161018-82746815739---40304-10305080400107b >P1;d1u7ia1 ---b8593241022540460-6102701b705237274078-73605670033000205b5101030246----64b77265---99114180855920550193029-a1733626559---616410302040400010109 >P1;d2q48a- b998a795603045840a60081046007-0838---------------a452130319b9201020-05219b69--5082ba1b4516264a---60a62076048280854927--872477524110404140201024- Translating the sequences ---CCCCC*****CCCHHHHHHHHHHHCC*CEEEE***C-------C*CC**EEEEEECCEEE***--------------------CCEEEECC----**HHHHHHHC--*EECCCC*-----CCC*EEEEE*CCCCEEEEECC -----CCCC**E*CCCHHHHHHHHHHH*C-CEEEE-**C*******C-CC*-EEEEEECCEEEEEE****----CC**CCC----CCC****C-***-*HHHHHHHHC-CC**CCC****---C**EE-***CCCCC***EECC ---CCCCCC**E*CCC****-*HHHHHCC**EEEE***C**-****C*CC**EEEEEECCEEEEEE****----CC**CCC*---CCCEEEECC*****HHHHHHHHC-CCEECCCC***---CCCEEEEEECCCCCEEEEE*C ***CCCCCC**E*CCCHHHHHHHHHHHCC-CEE*---------------C**EEEEEECCEEEEEE*-******CC--CCC****CC*EEEECC---**HHHHHHHH**CCEECCCC--*****CCEEEEEECCCCCEEEEEC- 54593-3.tem _________________________________ ---CCCCCC**E*CCCHHHHHHHHHHHCC*CEEEE***C**-****C*CC**EEEEEECCEEEEEE****----CC**CCC*---CCCEEEECC*****HHHHHHHHC-CCEECCCC***---CCCEEEEEECCCCCEEEEECC Structural block scores 0 2 - 4.3 M 75.0 75.0 75.0 9.8 3 8 C 4.7 H 5.8 29.2 6.4 7.6 9 10 * 1.0 P 2.5 2.5 2.5 1.5 13 15 C 5.0 H 7.5 4.0 3.7 5.7 16 26 H 4.6 H 4.0 3.0 9.2 3.2 27 28 C 4.7 H 7.8 5.0 6.2 3.5 31 34 E 4.7 H 4.5 4.0 4.2 23.5 35 37 * 2.7 P 4.7 27.3 4.3 75.0 39 40 * 3.5 M 75.0 6.0 7.5 75.0 42 45 * 3.5 M 75.0 7.0 4.0 75.0 48 49 C 4.7 H 5.0 4.5 3.5 42.8 50 51 * 1.6 P 2.5 37.5 1.5 4.5 52 57 E 5.0 H 1.5 2.2 0.8 1.7 58 59 C 5.0 H 4.5 10.8 8.2 10.2 60 65 E 4.7 H 3.7 1.7 1.7 2.3 66 69 * 2.6 P 75.0 4.8 3.0 20.0 70 73 - 4.3 M 75.0 75.0 75.0 5.9 74 75 C 4.3 M 75.0 8.0 5.0 7.5 76 77 * 3.5 M 75.0 4.5 9.2 75.0 78 80 C 4.3 M 75.0 4.0 5.0 4.3 82 84 - 4.3 M 75.0 75.0 75.0 7.7 85 87 C 4.5 M 27.3 8.2 6.3 6.8 88 91 E 4.3 M 2.0 4.5 3.5 3.8 92 93 C 4.7 H 5.5 39.0 4.0 7.2 94 98 * 3.0 P 61.4 19.4 4.2 46.2 99 106 H 4.9 H 4.8 2.6 3.1 4.4 109 110 C 4.3 M 38.0 5.0 5.8 4.0 111 112 E 4.3 M 4.0 5.5 5.0 6.5 113 116 C 4.8 H 5.0 5.0 4.2 5.5 117 119 * 2.7 P 53.0 6.3 6.3 52.7 120 122 - 4.3 M 75.0 75.0 75.0 4.3 123 125 C 4.3 M 6.3 2.3 4.3 6.3 126 131 E 4.4 M 2.5 13.8 1.7 2.0 132 136 C 4.9 H 5.2 2.6 1.6 1.8 137 141 E 4.6 H 0.2 1.0 0.4 1.0 142 143 C 4.3 M 4.5 9.2 4.5 39.5 >>>>>>