Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3b8ma1 CEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHCC---CHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCEEEEEEEC-CHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHHHCCCCCC---CCCCCEEEECCCCC---- >P1;d3b8oa1 CEEEEEEEECCCC-CCCHHHHHHHHHHCCC---CCCCCHHHHHHC-CCCCHHHHHHHHHCCHHHHCCCCCHHHHHHHHHC-CCCEEEECCCCC------CCCCCEEEEEEC-CHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHHC-CCCCCC------------------------------HHHHHHHHHCCC--CCHHHHHHH-CCHHHHHCCCCCC---CCCCCEEEECCCCCCCCC >P1;d4e29a- -CEEEEEEECCCC-CCHHHHHCCCCCC------CCCCCCCCCHHHHHHHHHHHHCCCC----------------------CCCCCEEEECC-----------CEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHCCHHHHCCCC----CCCCHHHHHHHHHHHHHHHHH-------HCCCCCCCC--CCCCCCCCCCCCHHHHHCCC------------CCCCCCCCCCCCCCCCCCCCCCCCCCEEC--CCCCC--C PSA >P1;d3b8ma1 8550302001056920760570066058171817144670063008105479202710371840375b---a75687046207406073328969c784964023010206-739103600450082017201--74006704651871266177407633863487156516513601740585826844893586361450075066517625809601673890682472154078280791---a0400434550461---- >P1;d3b8oa1 6200303024067-b086038123403838---987034008202-1045570154003609116738a7a953763157-06304166076a------876212030206-515301600460072006200--74018706860672187-565077237705563685-772779------------------------------96377278752a--288607625-7186159318516---806006246307519864 >P1;d4e29a- -520414025076-b06823705615a------9053881070284038205812708----------------------a573070761a-----------4230106392a043066006502770195028068327857766942839----715717742632420275069-------591674528--b3b28394333006605729------------a9482a2699162499b209910601444--1762b--7 Translating the sequences CEEEEEEEECCC****HHHHHHHHHHH*CC***CCC**HHHHHHHHHHCCHHHHHHHHHCCHHHH*CC---*HHHHHHH***CCEEEEECCCC******CCCCEEEEEEEC-CHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHH***HHHHHHHHHHHHHHHHHHHHHHH*******HCCCCCCCC**CCCCCCCC****HHHHHHHH**CC***CCHHHHHHH***HHHHHCCCCCC---CCCCCEEEECCCCC---- CEEEEEEEECCCC-CC*HHHHHHHHHH*CC---CCCCCHHHHHH*-**CCHHHHHHHHHCCHHHH*CC****HHHHHHH*-CCCEEEE*CCCC------CCCC*EEEEEEC-CHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHC-*HHHHHHHHHHHHHHHH*-******------------------------------HHHHHHH**CC*--CCHHHHHHH-CCHHHHHCCCCCC---CCCCCEEEECCCCCC**C -*EEEEEEECCCC-CCHHHHH******------CCCCC****HHHHHH**HHHH****----------------------*CCC*EEEECC-----------CEEEEEE*C*C***HHHHHHHHHHHHHHHH***HHHHHHH**HHHH***C----****HHHHHHHHHHHHHHHHH-------HCCCCCCCC--CCCCCCCC****HHHHH***------------*****CC*****CCCCCC***CCCCCEE*--CCCCC--C 160355.tem _________________________________ CEEEEEEEECCCC-CCHHHHHHHHHHH*CC---CCCCCHHHHHHHHHHCCHHHHHHHHHCCHHHH*CC---*HHHHHHH**CCCEEEEECCCC------CCCCEEEEEEEC-CHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHC-*HHHHHHHHHHHHHHHHHHHHHHH*------HCCCCCCCC--CCCCCCCC****HHHHHHHH**CC*--CCHHHHHHH*CCHHHHHCCCCCC---CCCCCEEEECCCCCC--C Structural block scores 1 8 E 4.9 H 1.9 1.2 2.2 9 12 C 4.8 H 3.0 4.2 4.5 14 15 C 4.0 M 1.0 5.8 5.8 16 26 H 4.4 M 3.8 3.5 4.9 28 29 C 4.0 M 4.0 5.5 75.0 30 32 - 4.0 M 3.3 75.0 75.0 33 37 C 4.6 H 4.4 5.4 5.0 38 47 H 4.2 M 2.5 9.2 3.3 48 49 C 4.0 M 4.5 4.5 5.0 50 58 H 4.4 M 3.4 2.8 11.8 59 60 C 4.0 M 4.0 3.0 75.0 61 64 H 4.0 M 3.8 4.2 75.0 66 67 C 4.0 M 8.2 5.5 75.0 68 70 - 4.0 M 75.0 9.3 75.0 72 78 H 4.0 M 5.3 4.3 75.0 79 80 * 2.7 P 4.0 41.0 42.8 81 83 C 4.7 H 3.7 3.0 5.0 84 88 E 4.6 H 3.2 3.4 4.0 89 92 C 4.5 M 5.5 5.9 40.4 93 98 - 4.0 M 7.8 75.0 75.0 99 102 C 4.2 M 4.8 5.8 57.2 103 109 E 4.7 H 1.1 1.1 2.1 113 132 H 4.8 H 2.6 2.1 3.1 133 134 - 4.0 M 75.0 75.0 4.0 135 150 H 4.7 H 4.0 4.4 5.7 154 176 H 4.4 M 4.6 8.1 10.3 178 183 - 4.0 M 4.2 75.0 75.0 185 192 C 4.0 M 6.1 75.0 5.2 193 194 - 4.0 M 4.0 75.0 75.0 195 202 C 4.0 M 4.1 75.0 6.5 203 206 * 2.7 P 3.0 75.0 2.2 207 214 H 4.5 M 4.8 14.5 4.4 215 216 * 2.7 P 4.0 7.5 75.0 217 218 C 4.0 M 7.5 3.5 75.0 220 221 - 4.0 M 3.5 75.0 75.0 222 223 C 4.0 M 5.0 5.0 75.0 224 230 H 4.0 M 5.3 4.9 36.6 232 233 C 4.0 M 1.5 4.0 6.2 234 238 H 4.0 M 4.8 5.8 6.2 239 244 C 5.0 H 4.5 4.0 6.2 245 247 - 4.0 M 75.0 75.0 6.0 248 252 C 5.0 H 2.9 2.8 1.6 253 256 E 4.5 M 4.0 4.5 21.8 257 262 C 4.7 H 15.2 4.2 17.1 263 264 - 4.0 M 75.0 7.0 75.0 >>>>>>