Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1n62c1 CCEEEEEEECCCC-CCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHC-------- >P1;d1rm6b1 CCEEEEEEECCCCCCCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECC--CHHHCCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHC--------- >P1;d1t3qc1 --CEEEEEECCCC-CCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHC------ >P1;d2w3sa4 -CCEEEEEECCCCCCCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCC >P1;d3nvvb2 CEEEEEEECCCCCCCCCCCCEEEEEEEECCCCCCEEEEEEEEECCCCCCEECHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC------- >P1;d4zohb2 CCEEEEEEECCCC-CCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC----CCHHHHHHHHHHHHHHHHHHHHC---------- PSA >P1;d1n62c1 e505052333589-b18000004060418-b-b6065050504401b7826046006304536068710570174017408076-5914649402520030036008403840-------- >P1;d1rm6b1 a37545122276a783a210004010238-c-86041050403502b674607--0970397506b911640052049207066-83a252a50281014004500560078--------- >P1;d1t3qc1 --4535334067a-b3b000403000508-c-65036050103304a9634067007305646068910240062005c08095-596266850271036002600360073049------ >P1;d2w3sa4 -b26350530776ab25200403040728-c-76055060505603d7744084007406954165710480163058109185-483173a501800260023004226b5a12768788 >P1;d3nvvb2 352616270a6655ba30304030202047a44304503040210498723088007803666068701820275049106178a08062285055103510560054039419------- >P1;d4zohb2 a348051323889-b3b130005050325-d-53053040504301b864407000710575737a81156005202620a096----85484146202400460046018---------- Translating the sequences CCEEEEEEECCCC-CCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHH**-------- CCEEEEEEECCCC*CCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEEC*--*HHHCCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHH*--------- --*EEEEEECCCC-CCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECHHHHHHHCCCCCCHHHHHHHHHHHH**CCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHH****------ -C*EEEEEECCCC*CCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECHHHHH**CCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHH************* C*EEEEEE*CCCC*CCCCC*EEEEEEEE**C*C*EEEEEEEEECCCCCCEECHHHHH**CCCCCCHHHHHHHHHHHHHHCCCCC*CCCCCHHHHHHHHHHHHHHHHHHHHH***------- CCEEEEEEECCCC-CCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC----CCHHHHHHHHHHHHHHHHHHHH*---------- 55447.tem _________________________________ CCEEEEEEECCCC*CCCCCEEEEEEEEEE-C-CEEEEEEEEEECCCCCCEECHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHH***------- Structural block scores 0 1 C 4.2 M 9.8 6.8 75.0 43.2 4.0 6.8 2 8 E 4.8 H 2.6 3.7 3.9 3.4 3.4 3.3 9 12 C 5.0 H 6.2 6.4 5.9 5.0 6.9 7.0 14 18 C 5.0 H 4.1 4.9 5.2 4.1 5.6 6.0 19 28 E 4.9 H 2.3 1.8 2.0 2.8 1.5 2.0 33 42 E 5.0 H 3.1 2.3 2.3 3.2 2.1 2.4 43 48 C 5.0 H 5.2 5.2 5.4 6.1 4.8 4.9 49 50 E 5.0 H 4.0 5.0 3.5 4.0 2.5 4.0 52 58 H 4.5 M 2.7 24.7 3.3 3.3 4.4 2.1 59 64 C 5.0 H 4.0 5.0 4.5 5.2 4.5 5.7 65 78 H 4.9 H 3.7 3.9 3.5 3.5 3.9 3.5 79 83 C 5.0 H 4.2 3.8 4.4 4.6 4.4 5.1 85 89 C 4.7 H 5.0 5.7 5.6 4.6 3.2 47.6 90 110 H 4.9 H 2.9 2.9 3.0 3.1 3.2 3.0 111 113 * 2.7 P 26.3 52.7 2.3 5.5 4.7 75.0 114 120 - 4.4 M 75.0 75.0 65.6 6.6 75.0 75.0 >>>>>>