Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2gu0a2 CCCCCHHHCCCCCEEEECCCEEEEEEECCCCCCCCCC---CEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCEEEEEEHHHHHHHHHHHHHHHHCC-------CCCCCCCCCCCHHHHHHHHHHHHCCCHHHHCCHHHHCCCCHHHHHHHHHHHHHHHCC >P1;d2r7ja1 CCCCCHHHCCCCEEEEECCCEEEEECCHHHCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHC-CC-CCCCCHHHHHHHHHC-- PSA >P1;d2gu0a2 c9121266042b6442448200003051295aa9568---550100002655b0599313700020433097100003173101003595046103701783769-------9171370400230045008404a9381870351074372788138318635646787 >P1;d2r7ja1 a833129605426422516100014022374ba924988a24110001266691677404500210435088001001070001003493047005600771672796a6b1a06113740034002300210388474840263076-91-981990667356858-- Translating the sequences CCCCCHHHCCCC*EEEECCCEEEEEEE***CCCCCCC---CEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEE*CCCCEEEEEEHHHHHHHHHHHHHHHH**-------CCCCCCCCCCCHHHHHHHHHHHHCCCHHHH**HHHH*CC*HHHHHHHHHHHHHHH** CCCCCHHHCCCCEEEEECCCEEEEE**HHHCCCCCCC***C*EEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEECCCC*EEEEEHHHHHHHHHHHHHHHHHH*******CCCCCCCCCCCHHHHHHHHHHH*CCCHHHHHHHHH*-CC-*****HHHHHHHHH*-- 75347.tem _________________________________ CCCCCHHHCCCCEEEEECCCEEEEEEEHHHCCCCCCC---CEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCEEEEEEHHHHHHHHHHHHHHHHHH-------CCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHH-CC-HHHHHHHHHHHHHHH-- Structural block scores 0 4 C 5.0 H 5.1 5.1 5 7 H 5.0 H 4.7 5.7 8 11 C 5.0 H 4.4 2.8 12 16 E 4.6 H 4.0 3.8 17 19 C 5.0 H 4.7 2.7 20 26 E 4.4 M 1.1 1.0 27 29 H 3.0 P 4.0 4.0 30 36 C 5.0 H 7.7 7.1 37 39 - 3.0 P 75.0 8.8 41 47 E 4.7 H 0.9 1.0 48 54 C 5.0 H 4.9 5.1 55 68 H 5.0 H 3.1 3.0 69 71 C 5.0 H 5.3 5.3 72 76 E 4.6 H 0.2 0.2 77 80 C 5.0 H 3.5 2.0 81 86 E 4.7 H 0.8 0.7 87 104 H 4.8 H 4.5 3.8 105 111 - 3.0 P 75.0 7.3 112 122 C 5.0 H 3.1 3.2 123 134 H 4.8 H 3.2 1.9 135 137 C 5.0 H 6.7 6.3 138 147 H 4.4 M 3.6 4.0 149 150 C 5.0 H 4.5 5.0 152 166 H 4.2 M 5.1 6.0 167 168 - 3.0 P 7.5 75.0 >>>>>>