Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1dd9a- CHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHCCEEECCCCCHHHHHHCCCHHHHHHHHHCCCEEECCEEECCCCEEEEEEECCCCCEEEEEEEECCCCCCCEEECCCCCCCCCCCCCCCHHHHHHCCCCCCCEEEECCHHHHHHHHHCCC--CCEEECCC------CCCHHHHHHHHHHCCEEEEEEECCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHC >P1;d1nuia1 CCC------CCCCHHH-----CCCCCCCCHHHCCCHHHHHHHCEEEEEEC--------------------------------CEEEEEEEEECCCCCEEEEEEECC-----CCCCEEEE--CCCCCCCCCHHHC----CCCCCCEEECCHHHHHHHHHHHCCCCCEECCCCCCCCHHHHHHHCHHHHCC-CCCEEEECCCCHHHHHHHHHHHHHCCC----C-CEEECCCCC-CCHHHHHCCCCHHHHHHHHC----------------------------------------------------------------- PSA >P1;d1dd9a- 61381075005104800768507703620974a05a91172000000147732027520c55834630270200349802020140000001167030000001015b68554120451a10316530000100375598092000094021000002460--41000106------90445004100600820000160678145402700440033055c2500001048c150130046264a50183048025014000730365072957a247602720351055030882445015300730a4a625715 >P1;d1nuia1 e97------b2174a8-----17043530aa4505660045010000449--------------------------------a43130000247856230010017-----97753404--6074410002121----b0861000018010000002107065100000472a204700430581036-07200000114a80370083035200a----b-313307031-520040146b3383036305----------------------------------------------------------------- Translating the sequences CHH******HHHHHHH*****HHHHHHHHHH*CCCHHHHHHHC*EEE**C********************************C**EEEEEEECCCCCEEEEEEEEC*****CEEE******CCCCCCCCCHHHH****CCCCCEEEECCHHHHHHHHH**C--CCEEECCC------***HHHHHHHHH*CCEEEEEEECCHHHHHHHHHHHHHHHH****C*EEEEEEECC*CCHHHHHHHHHHHHHHHHHC***************************************************************** C**------****HHH-----********HHHCCCHHHHHHHCEEEEEEC--------------------------------CEEEEEEEEECCCCCEEEEEEE*C-----C***EEEE--CCCCCCCCCHHH*----CCCCC*EEECCHHHHHHHHHHHC**CCEE*CCC******HHHHH*HHHH**-CC*EEEE**CCHHHHHHHHHHHHH***----C-*EEE***CC-CCHHHHH****HHHHHHHHC----------------------------------------------------------------- 56731.tem _________________________________ CHH------HHHHHHH-----HHHHHHHHHHHCCCHHHHHHHCEEEEEEC--------------------------------CEEEEEEEEECCCCCEEEEEEEEC-----CEEEEEEE--CCCCCCCCCHHHH----CCCCCEEEECCHHHHHHHHHHHC--CCEEECCC------HHHHHHHHHHHH-CCEEEEEEECCHHHHHHHHHHHHHHHH----C-EEEEEEECC-CCHHHHHHHHHHHHHHHHHC----------------------------------------------------------------- Structural block scores 1 2 H 3.0 P 2.0 8.0 3 8 - 3.0 P 3.5 75.0 9 15 H 3.9 M 2.6 6.3 16 20 - 3.0 P 5.2 75.0 21 31 H 3.4 M 4.1 4.4 32 34 C 5.0 H 5.2 3.3 35 41 H 5.0 H 4.4 3.0 43 48 E 4.0 M 0.8 1.3 50 81 - 3.0 P 3.5 75.0 83 91 E 4.6 H 0.7 1.4 92 96 C 5.0 H 3.4 6.0 97 104 E 4.8 H 0.1 0.9 106 110 - 3.0 P 7.1 75.0 112 118 E 3.0 P 2.4 4.3 119 120 - 3.0 P 5.8 75.0 121 129 C 5.0 H 2.0 2.4 130 133 H 4.5 M 0.2 1.5 134 137 - 3.0 P 5.0 75.0 138 142 C 5.0 H 5.6 5.3 143 146 E 4.5 M 0.0 0.0 147 148 C 5.0 H 6.5 4.5 149 159 H 4.6 H 1.4 0.4 161 162 - 3.0 P 75.0 3.0 163 164 C 5.0 H 2.5 3.0 165 167 E 4.3 M 0.0 0.0 168 170 C 5.0 H 2.3 1.3 171 176 - 3.0 P 75.0 4.2 177 188 H 4.0 M 2.8 3.1 190 191 C 5.0 H 4.0 3.5 192 198 E 4.1 M 1.3 0.4 199 200 C 5.0 H 3.0 2.5 201 216 H 4.6 H 3.1 3.8 217 220 - 3.0 P 3.2 75.0 223 229 E 3.9 M 0.9 2.4 230 231 C 5.0 H 6.0 2.0 233 234 C 5.0 H 3.0 3.5 235 251 H 4.5 M 3.1 3.3 253 317 - 3.0 P 3.7 75.0 >>>>>>