Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1c0aa2 ----CCCCEEECHHHHCCCCCHHHHHHHHCCCEEEEEEEECCHHHCC---------HHHHHHHHHHHHHCCCCCCCEEEECCHHHHHHH-EECCCHHHCCHHHHHHHHHHC-CCCCCCEEEEEEEE-HHHHHHHHHHHHHHHHHHCCCC------ >P1;d1l0wa2 ----CCCCCEECHHHHCCCCCCHHHHC-----CEEEEEEECC--CCC---------HHHHHHHHHHHHHCCCCCCEEEEEEC------CEEECCCHHHH-HHHHHHHHHHH-CCCCCCEEEEEEEC-HHHHHHHHHHHHHHHHHHCCCC------ >P1;d1zq1c2 CCCCCCCCCEECCCCCCCCCCHHHHHHCC--CCEEEECEECCCCCCCCCEEECCEE--HHHHHHHHHCCC-CCCCEE-----HHHCCC--------CCCCHHHHHHHHHHC-CCCCCCEEEEEEEC-HHHHHHHHHHHHHHHHHHHHCC------ >P1;d2p8ta2 --CCCCCEEEEEC------------------CEEEEEEEECCCC---------CCC---HHHHHHHHHHCCCCEEEEEEEEC------CEEECCCCCCCHHHCCHHHHHHCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHCCHHHHCCC PSA >P1;d1c0aa2 ----0609126026105a0a297029106589020000203800907---------684066037105737177020020552956490-070402740669104500640-70757000001026-6810550051026300742924------ >P1;d1l0wa2 ----3a18233016307a542840171-----9001001044--507---------7a207303710475a07303102069------73055311830-65238402840-80858100000027-594047005103630182092a------ >P1;d1zq1c2 19460756135026107a09095057229--a130000301503940275469934--203203540763-086010-----013037--------560479107602840-b07a7100000016-366023003200610330278b------ >P1;d2p8ta2 --420a3470707------------------9330100003b05---------917---37703540474704201002069------850013a554205752590185086285900000010657940470062004300696158875999 Translating the sequences ----CCCC*EEC****CCCCC*HHHH*****C*EEEEEEECC***CC---------**HHHHHHHHHHHCCCCCC*EEEE*C*******-EECCC***C*HHHHHHHHHHC-CCCCCCEEEEEEE*-HHHHHHHHHHHHHHHHHH*CCC------ ----CCCC*EEC****CCCCC*HHHH*-----*EEEEEEECC--*CC---------**HHHHHHHHHHHCCCCCCEEEEE*C------**EECCC****-HHHHHHHHHH*-CCCCCCEEEEEEEC-HHHHHHHHHHHHHHHHHH*CCC------ ****CCCC*EEC****CCCCC*HHHH***--C*EEEE*EECC***CC*********--HHHHHHHHH**C-CCCCEE-----******--------**C*HHHHHHHHHHC-CCCCCCEEEEEEEC-HHHHHHHHHHHHHHHHHH**CC------ --**CCC**EE**------------------C*EEEEEEECC**---------***---HHHHHHHHHHCCCC**EEEEE*C------**EECCC***C*HH**HHHHHHC*CCCCCCEEEEEE*C*HHHHHHHHHHHHHHHHHH*CC******* 55261.tem _________________________________ --**CCCC*EEC****CCCCC*HHHH***--C*EEEEEEECC***CC------*****HHHHHHHHHHHCCCCCCEEEEE*C********EECCC***C*HHHHHHHHHHC-CCCCCCEEEEEEEC-HHHHHHHHHHHHHHHHHH*CCC------ Structural block scores 0 1 - 4.3 M 75.0 75.0 5.0 75.0 2 3 * 3.5 M 75.0 75.0 5.0 3.0 4 7 C 4.8 H 3.8 5.6 4.5 4.4 9 10 E 5.0 H 4.0 3.0 4.0 3.5 12 15 * 2.0 P 2.2 2.5 2.2 58.0 16 20 C 4.3 M 5.6 5.7 5.3 75.0 22 25 H 4.3 M 4.5 3.0 4.2 75.0 26 28 * 3.1 M 2.3 50.3 4.3 75.0 29 30 - 4.3 M 6.5 75.0 75.0 75.0 33 39 E 4.9 H 0.6 0.3 0.9 0.6 40 41 C 5.0 H 5.5 4.0 3.0 7.2 42 44 * 2.3 P 3.0 51.7 4.0 26.7 45 46 C 4.3 M 3.5 3.5 2.0 75.0 47 52 - 4.3 M 75.0 75.0 5.5 75.0 53 57 * 3.5 M 47.8 48.5 33.2 33.4 58 68 H 4.8 H 3.5 3.1 2.9 10.5 69 74 C 4.7 H 4.2 4.2 15.3 2.8 75 79 E 4.4 M 0.8 1.2 45.2 0.6 82 89 * 3.4 M 13.8 57.5 20.5 57.9 90 91 E 4.3 M 3.5 2.5 75.0 0.0 92 94 C 4.3 M 1.3 3.0 75.0 4.8 95 97 * 1.4 P 4.3 4.0 28.7 4.7 100 109 H 4.9 H 3.5 4.2 4.4 4.7 112 117 C 5.0 H 4.3 5.0 6.2 5.0 118 124 E 4.9 H 0.4 0.3 0.1 0.1 127 144 H 5.0 H 2.9 3.2 2.1 3.4 146 148 C 4.5 M 5.0 7.2 8.8 4.7 149 154 - 4.3 M 75.0 75.0 75.0 7.8 >>>>>>