Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d5a0ya2 CCCCCCCHHHCCHHHHHHHCCHHHCCCCCHHHHHHHHHHHHHHHHHIIIIIIICCCC----CCCHHHHHCCC--CCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHC------------------HHHHHHCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCHHHHCC--CCCCCCCCHHHCCCCCHHHCCCCC-CHHHHHHHHHHHHHHHC----CCCCCCHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHCCC >P1;d7b1sb2 CC----HHHCCCHHHHHHHCCC----------CHHHHHHHHHHHH-HHHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC-------------------CCHHHHHHHHHHHHHHCCCEEEEEECCCCCEEEEECC---HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHCC---CCCCCCHHHHHHHHHHHHCC--CH-HHHCHHHHHHHHHHH-------HHHHC-- PSA >P1;d5a0ya2 aa39ab30192100300020001452694004000000010022002500063453b----b1367302201--46900260043016204942612706565900530034004200510577------------------8a249517810000000000000000000502000000020032048329-6004b0360505a2052--97d92045014010a043035200-00000000000011058----3940334921863259a35252250261274587962957b779a859b >P1;d7b1sb2 33----9306230030010044----------6220000100210-25007517418aa6760071024000224950064037703b-------------------4916500700181038381054665399744413153---6220000000000000104017662075006001500250385040400147302800730353052868073102000437004503000000000000217---84397007420783086607--68-732302843887658-------67978-- Translating the sequences CC*****HHHCCHHHHHHHCCH**********HHHHHHHHHHHHH********CCCC----***HHHHH***--***HHHHHHHHHHH*******************HHHHHHHHHHHHHHHHC------------------HH***H******HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHC-CC*********HHHH**--CCCCCCCCHHHCCCCCHHHCCCCC-CHHHHHHHHHHHH***C----C*****HHHHHH*CC**C*****CHHHHHHHHH**********HHHC** CC----HHH*CCHHHHHHHCC*----------*HHHHHHHHHHHH-HHHHHHCCCCC****HHHHHHHHHHH**HHHHHHHHHHHH**-------------------**HHHHHHHHHHHHHHC********************---HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHC*CCHHHHHHHHHHHHHHH**CCCCCCCCHHHCCCCC***CCCCC*CHHHHHHHHHH**---C****CHHHHHHHHHHHHCC--CH-HHHCHHHHHHHHHHH-------HHHHC-- 48081.tem _________________________________ CC----HHHHCCHHHHHHHCCH----------HHHHHHHHHHHHH-HHHHHHCCCCC----HHHHHHHHHHH--HHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHHHC------------------HH---HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHH--CCCCCCCCHHHCCCCCHHHCCCCC-CHHHHHHHHHHHH---C----CHHHHHHHHHHHHCC--CH-HHHCHHHHHHHHHHH-------HHHHC-- Structural block scores 0 1 C 5.0 H 10.5 3.0 2 5 - 3.0 P 8.5 75.0 6 9 H 4.0 M 3.2 4.5 10 11 C 5.0 H 1.5 2.5 12 18 H 5.0 H 0.7 0.6 19 20 C 5.0 H 0.0 2.0 22 31 - 3.0 P 3.5 75.0 32 44 H 4.8 H 0.4 1.1 46 51 H 3.0 P 2.2 3.2 52 56 C 4.6 H 5.3 4.2 57 60 - 3.0 P 75.0 8.5 61 71 H 3.9 M 3.3 1.8 72 73 - 3.0 P 75.0 2.0 74 87 H 4.3 M 2.9 4.2 88 106 - 3.0 P 3.8 75.0 107 122 H 4.8 H 2.1 3.3 124 141 - 3.0 P 75.0 4.4 142 143 H 3.0 P 9.2 4.0 144 146 - 3.0 P 5.0 75.0 147 169 H 4.5 M 1.0 1.3 170 171 C 5.0 H 2.5 4.0 172 190 H 5.0 H 1.4 2.5 193 194 C 5.0 H 3.0 2.0 195 209 H 3.5 M 3.6 2.9 210 211 - 3.0 P 75.0 1.5 212 219 C 5.0 H 6.2 4.9 220 222 H 5.0 H 1.7 1.0 223 227 C 5.0 H 2.3 1.4 228 230 H 3.0 P 2.3 2.3 231 235 C 5.0 H 2.0 2.4 238 249 H 4.7 H 0.1 0.8 250 252 - 3.0 P 2.0 75.0 254 257 - 3.0 P 75.0 5.8 259 270 H 4.0 M 4.3 4.2 271 272 C 5.0 H 3.5 3.5 273 274 - 3.0 P 9.8 75.0 278 280 H 3.0 P 3.0 4.0 282 292 H 4.6 H 4.6 5.4 293 299 - 3.0 P 6.8 75.0 300 303 H 4.5 M 8.6 7.2 305 306 - 3.0 P 10.2 75.0 >>>>>>