Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3bofa2 CCCHHHHCCCCCCCEECCCCCHHHHHHHCCCC---CHHHHHHHCHHHHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHC---CEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHCC-----CCEEEEECCCCCCEEEC----------CEEE--CCCCHHHHHCCHHHHHHCCCCEECCCCCCCHHHHHHHHHHHC---CCCCCCCCCCC------------------------------------------------------------------------ >P1;d4m3pa- CCCHHHHHH-CCCCEECCCCHHHHHHHCCCCCCCCCCCCHHHHCHHHHHHHHHHHHHHCCCEEECCCCCC-------------CHHHHHHHHHHHHHHHCCCCCEEEEEEECCC--------CCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHCC--CCCEEEEECCCCC-CCCCCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCHHHCCCCCCCCHHHCCCHHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHCHHHHCCCCHHHHHCCHHHHHHCCCCCHHHHCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC PSA >P1;d3bofa2 54329603307730000000154006639483---2201003504700160042017050100000040004020544a12941540024006003600b---5000000010b3406764908395025003200400261400000002031340030004000611770000000105672507140302500430182601000001300074036005400410-----5220000000242575b----------a753--142828500510630262000000013102170053027407---82705291676------------------------------------------------------------------------ >P1;d4m3pa- 365037007-584000000103000243930809524030045537102700320140200001000348-------------6760123006003600646600000104207--------67496026106700800462a0200002201305102100300470--a120000000027-003691503500130161503000000000172006005402430683a3a02000000005041064300530331176063120331300700240282502000021102230010000101630966061067149134a469494571463055722584a597b57a76a529188ac5aa93567697787686866747897a Translating the sequences CCCHHHH***CCCCEECCCC*HHHHHHHCCCC---CHHHHHHHCHHHHHHHHHHHH**CCCEEECCCCCC*************HHHHHHHHHHHHHHHHC---CEEEEEE*CCC********CCHHHHHHHHHHHHHHHHH*CCCEEEEEEECCHHHHHHHHHHHHHH**CCCEEEEECCCCC*CCCCCCCHHHHHHHHH*CCCCEEEEECCCCHHHHHHHHHHHHH**-----CCEEEEECCCCCCEEEC----------CEEE--*CCCHHHHH**HHHHHHCC**EECCCCCCCHHHHHHHHHHH*---CCCC*****CC------------------------------------------------------------------------ CCCHHHHHH-CCCCEECCCCHHHHHHH*CCCC***C***HHHHCHHHHHHHHHHHHHHCCCEEECCCCCC-------------*HHHHHHHHHHHHHHHC***CEEEEEEECCC--------CCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHH**--CCCEEEEECCCCC-CCCCCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHH*****CCEEEEECCCCCC***C**********C*****HCCCHHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHH*H***CCCCHHHHHCC************************************************************************ 82282.tem _________________________________ CCCHHHHHH-CCCCEECCCCHHHHHHHHCCCC---CHHHHHHHCHHHHHHHHHHHHHHCCCEEECCCCCC-------------HHHHHHHHHHHHHHHHC---CEEEEEEECCC--------CCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHH--CCCEEEEECCCCC-CCCCCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHH-----CCEEEEECCCCCCEEEC----------CEEE--HCCCHHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHH---CCCCHHHHHCC------------------------------------------------------------------------ Structural block scores 0 2 C 5.0 H 4.0 4.7 3 8 H 4.3 M 3.8 2.8 10 13 C 5.0 H 4.2 4.2 14 15 E 5.0 H 0.0 0.0 16 19 C 5.0 H 0.0 0.2 20 27 H 4.5 M 3.1 1.5 28 31 C 5.0 H 6.0 5.0 32 34 - 3.0 P 75.0 4.7 36 42 H 4.1 M 1.6 2.3 44 57 H 4.7 H 2.3 2.1 58 60 C 5.0 H 2.0 0.7 61 63 E 5.0 H 0.0 0.3 64 69 C 5.0 H 0.7 2.5 70 82 - 3.0 P 3.5 75.0 83 98 H 4.9 H 1.9 2.5 100 102 - 3.0 P 75.0 5.3 104 110 E 4.7 H 0.0 0.7 111 113 C 5.0 H 4.2 3.0 114 121 - 3.0 P 4.9 75.0 122 123 C 5.0 H 4.0 6.5 124 141 H 4.9 H 2.3 3.4 142 144 C 5.0 H 1.3 4.2 145 151 E 5.0 H 0.3 0.6 152 153 C 5.0 H 2.0 2.0 154 167 H 4.7 H 1.5 1.6 168 169 - 3.0 P 4.0 75.0 170 172 C 5.0 H 2.3 4.5 173 177 E 5.0 H 0.0 0.0 178 182 C 5.0 H 3.8 1.8 184 190 C 5.0 H 2.9 3.4 191 200 H 4.8 H 2.3 1.9 201 204 C 5.0 H 2.2 2.2 205 209 E 5.0 H 0.0 0.0 210 213 C 5.0 H 1.0 0.0 214 228 H 4.7 H 2.3 2.3 229 233 - 3.0 P 75.0 6.1 234 235 C 5.0 H 3.5 5.2 236 240 E 5.0 H 0.4 0.4 241 246 C 5.0 H 1.3 0.8 247 249 E 3.0 P 5.7 1.7 251 260 - 3.0 P 75.0 2.2 262 264 E 3.0 P 5.0 4.3 265 266 - 3.0 P 75.0 4.5 268 270 C 5.0 H 4.7 1.7 271 283 H 4.7 H 2.9 2.3 284 285 C 5.0 H 1.0 3.5 286 289 E 4.0 M 0.0 0.5 290 296 C 5.0 H 1.0 0.9 297 308 H 4.7 H 3.0 0.7 309 311 - 3.0 P 75.0 3.0 312 315 C 5.0 H 4.2 5.2 316 320 H 3.0 P 4.6 4.0 321 322 C 5.0 H 6.5 2.5 323 394 - 3.0 P 75.0 6.5 >>>>>>