Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2gu0a1 CCHHHCEEEECCCCCCEEEECCHHHHHHHHHCCCCHHHCCCCEECCCCCEECCHHHHHHCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHCCCHHHCCHHHHHCCCCHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHCCCC >P1;d2r7ja2 CCHHHCEEEEECCCCEEEEECCHHHHHHHCCCCCCHHHCCCCEECCCCCEECCHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCH-HHHHHCCCCHHHHHHHHHHHCCCCCHHHHCHHHHHHHHHHHCCCC PSA >P1;d2gu0a1 01000001133969503053065400630182917896466127088494000050484044b85-9215063a40650051008004633242870857204260528405900641858a270395495227201600515 >P1;d2r7ja2 210100021546ba515032073400540181a19a83456337086483000041393024c9299018045820530050004003437079861-970074506395048007424459270473694037202500324 Translating the sequences CCHHHCEEEE*CCCC*EEEECCHHHHHHHHHCCCCHHHCCCCEECCCCCEECCHHHHHHCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHCCCHHH**HHHHHCCCCHHHHHHHHHHHHCCCCHHH*CHHHHHHHHHHHCCCC CCHHHCEEEEECCCCEEEEECCHHHHHHH**CCCCHHHCCCCEECCCCCEECCHHHHHHCCCCCC*CCCCCCCHHHHHHHHHHHHHHH**CCC***H-HHHHHCCCCHHHHHHHHHHH*CCCCHHHHCHHHHHHHHHHHCCCC 75574.tem _________________________________ CCHHHCEEEEECCCCEEEEECCHHHHHHHHHCCCCHHHCCCCEECCCCCEECCHHHHHHCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHCCCHHHH-HHHHHCCCCHHHHHHHHHHHHCCCCHHHHCHHHHHHHHHHHCCCC Structural block scores 0 1 C 5.0 H 0.5 1.5 2 4 H 5.0 H 0.0 0.3 6 10 E 4.6 H 1.6 2.4 11 14 C 5.0 H 7.2 8.2 15 19 E 4.6 H 2.2 2.2 20 21 C 5.0 H 3.0 3.5 22 30 H 4.6 H 3.0 2.8 31 34 C 5.0 H 4.8 5.4 35 37 H 5.0 H 7.7 7.2 38 41 C 5.0 H 4.2 4.5 42 43 E 5.0 H 4.5 5.0 44 48 C 5.0 H 5.8 5.2 49 50 E 5.0 H 2.0 1.5 51 52 C 5.0 H 0.0 0.0 53 58 H 5.0 H 3.5 3.3 59 64 C 5.0 H 5.4 4.9 66 72 C 5.0 H 3.7 3.9 73 89 H 4.8 H 3.1 2.2 90 92 C 5.0 H 3.0 4.7 93 96 H 3.0 P 4.2 6.0 98 102 H 5.0 H 3.6 4.6 103 106 C 5.0 H 3.2 3.8 107 118 H 4.8 H 3.9 3.8 119 122 C 5.0 H 6.4 5.0 123 126 H 4.5 M 4.8 4.5 128 138 H 5.0 H 3.5 3.5 139 142 C 5.0 H 2.8 2.2 >>>>>>