Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vjfa- ---CCHHHHHHHHHHHCC--CCCEECC----CCCCHHHHHHHHHC--CCEEEEEEEEECC--CCEEEEEEECCCCCC--CCHHHHCC-CCEECCCC--CCCCC-CCCCCCCHHHHHHCCCCCEEEEECHHHHCCCCEEECCCCCCEEEEECHHHHHHHHHHCCCCCCCCCCCCCC >P1;d1wdva- ------CHHHHHHHHHCC-CCEEEC-CC---CCCCHHHHHHHHCCCHHH-CEEEEEEEEC-CCCEEEEEEECCCCCCCCC-CCCCCC-CEEECCHHHHHHHHC-CCHHHCCCCCCCC----CCEEEEEHHHCCCCCEEEECCCCCCEEEECHHHHHHHH---CC-EEECCCC--- >P1;d2dxaa- ------CHHHHHHHHCCC-CCEEEECCCCCCCCCCCCHHHHHHCCCCCC-EEEEEEEEECCEEEEEEEEEECCCEECHHHHHHHHCC-CCEECCC-CHHHHHC-CCCCCCCCCCCCC----CCCEEEEHHHHHCCCEEEEEEECCEEEEECHHHHHHHH---CC-EEECCEEC-- >P1;d2z0xa- CCCHHHHHHHHHHHHCCCCCCCEEECCC---CCCCHHHHHHHHCCCHHH-EEEEEEEEEC-C-CEEEEEEECCCCCCHHHHHHHHCC-CEEECCHHHHHHHHC-CCCCCCCCCCCCC----CCCEEEEHHHHHCCCEEEECCCCCEEEEECHHHHHHHH---CC-EEECCCCC-- >P1;d3op6a- -----CCCHHHHHHHCCC-CCCCEECC--CCCC---CCCCCC------CCCEEEEEEEC---CCC-EEEEECCCCCC-CCHHHHHCCCCCEECCHHHCHHHCCCCCCC-CCCCHHHH----CCCCEEEHHHHCCCEECCCCCCCCEE-CEEHHHHCCC----CC-EEECC----- PSA >P1;d1vjfa- ---483950272077490--9215618----43969643781586--7312030110409--8400000036a290a--204930a0-70870579--69103-065a0200000010785506000045007263000300634010405070054008109192302095754 >P1;d1wdva- ------760671198492-a06125-98---529737400762926431-0030200107-5b60100000053903472-574095-504507691157309-1367000002039----7050000560294a500020074502010207502922---a0-5117006--- >P1;d2dxaa- ------150173068491-a163261a2579761825101743a15442-002040010356a6000000101150249500911a0-8505097-3048106-0941000002076----8160000250482a300020062010020408201611---a0-61370266-- >P1;d2z0xa- a159405400720585923606042286---306418400901a08401-0030300207-9-901000000418025a30493076-605805683068302-0462000003056----80600004202a18401020015400050408202600---a0-6415025f-- >P1;d3op6a- -----2350592077591-a1754717--9a48---a6183a------c4202221026---872-10000392807-6505a12926707707683126629b1556-01002312----a140100450274a501012125450-2050940410----90-73080----- Translating the sequences ---****HHHHHHHH*CC--CC*EECC----CCCCHHHHHHHH*C--*C*EEEEEEEE*C--CCEEEEEEECCCCCC--C*HHHHCC-CCEECC**--****C-CCCCCCC**********C**EEE*HHHHCCCCEEE*CCCCCEEEEECHHHHHHHH***CC****CCCCC** ------CHHHHHHHH*CC-CC*EE*-CC---CCCCHHHHHHHHCCC***-*EEEEEEEEC-*CCEEEEEEECCCCCC**C-****CC-C*EECCHHHHHHHHC-CC***CCCCCCCC----CC*EEEEHHH*CCCCEEEECCCCC*EEEECHHHHHHHH---CC-EEECCCC--- ------CHHHHHHHHCCC-CC*EEECCC***CCCC**HHHHHHCCC**C-EEEEEEEEEC****EEEEEEECCC**C***HHHHHCC-CCEECC*-*HHHHHC-CCCCCCCCCCCCC----CCCEEEEHHHH*CCCEEEE***CCEEEEECHHHHHHHH---CC-EEECC**C-- *******HHHHHHHHCCC*CCCEEECCC---CCCCHHHHHHHHCCC***-EEEEEEEEEC-*-CEEEEEEECCCCCC***HHHHHCC-C*EECCHHHHHHHHC-CCCCCCCCCCCCC----CCCEEEEHHHH*CCCEEEECCCCCEEEEECHHHHHHHH---CC-EEECCCCC-- -----*C*HHHHHHHCCC-CCC*EECC--**CC---******------C**EEEEEEE*---CC*-EEEEECCCCCC-*CHHHHHCC*CCEECCHHH*HHH*C*CCCC-CCCC****----CCC*EEEHHHHCCC*E***CCCCCEE-*E*HHHH***----CC-EEECC----- 55826.tem _________________________________ -----*CHHHHHHHHCCC-CCCEEECCC---CCCCHHHHHHHHCCC**C-EEEEEEEEEC-*CCEEEEEEECCCCCC**CHHHHHCC-CCEECCHHHHHHHHC-CCCCCCCCCCCCC----CCCEEEEHHHHCCCCEEEECCCCCEEEEECHHHHHHHH---CC-EEECCCCC-- Structural block scores 0 4 - 4.2 M 47.4 75.0 75.0 5.9 75.0 7 14 H 4.9 H 3.8 4.8 3.8 3.2 4.4 15 17 C 4.6 H 4.3 5.0 4.7 5.3 5.0 19 21 C 4.4 M 28.7 5.5 5.8 4.0 6.2 22 24 E 4.4 M 4.0 2.7 3.7 2.0 5.3 25 27 C 4.6 H 28.0 30.7 4.5 5.3 27.7 28 30 - 4.0 M 75.0 75.0 7.0 75.0 31.5 31 34 C 4.8 H 5.5 5.8 5.5 3.2 40.5 35 42 H 4.4 M 5.4 3.6 2.9 2.9 23.6 43 45 C 4.3 M 29.7 5.7 5.5 6.2 75.0 46 47 * 2.5 P 41.0 3.5 4.0 2.0 75.0 50 58 E 4.7 H 1.2 0.7 0.8 0.9 1.9 62 63 C 4.3 M 6.0 8.8 8.2 42.0 7.5 64 70 E 4.9 H 0.4 0.1 0.1 0.1 11.1 71 76 C 4.8 H 6.3 3.3 1.5 2.5 4.8 77 78 * 2.5 P 75.0 5.5 6.5 7.8 40.5 80 84 H 4.4 M 3.2 18.2 2.2 3.2 3.7 85 86 C 5.0 H 5.2 7.0 5.2 6.5 5.5 88 89 C 4.4 M 3.5 2.5 6.5 3.0 3.5 90 91 E 5.0 H 7.5 4.5 2.5 6.5 7.0 92 93 C 5.0 H 2.5 3.5 4.5 2.5 3.5 94 101 H 4.2 M 22.8 4.0 12.2 4.2 4.2 104 116 C 4.4 M 1.9 2.4 2.2 2.0 7.8 117 120 - 4.5 M 5.0 75.0 75.0 75.0 75.0 121 123 C 4.4 M 3.7 4.0 5.0 4.7 5.2 124 127 E 4.8 H 0.0 0.0 0.0 0.0 0.2 128 131 H 4.9 H 2.2 3.2 2.8 2.0 2.8 132 135 C 4.6 H 4.5 7.1 5.9 5.9 6.6 136 139 E 4.5 M 0.8 0.5 0.5 0.8 0.5 140 144 C 4.7 H 2.6 3.2 1.6 2.0 2.8 145 149 E 4.7 H 1.0 0.6 0.6 1.0 16.4 151 158 H 4.8 H 2.0 3.4 2.4 2.2 11.6 159 161 - 4.5 M 3.0 75.0 75.0 75.0 75.0 162 163 C 5.0 H 5.0 5.2 5.2 5.2 4.5 165 167 E 4.5 M 1.7 2.3 3.3 3.7 3.3 168 172 C 4.5 M 4.6 17.6 4.2 6.9 46.6 173 174 - 4.5 M 4.5 75.0 75.0 75.0 75.0 >>>>>>