Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vpqa1 CEEEEECCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEECCCCCCCCCC-CHHHH-CCCCCCEEEEECCHHHHH--CHHHHC-CCCCHHHHHC-CCHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCEEEECCCHHHCC----HHHHHHHHHCCCEEEEEECCCCC-CCCCCCCCCCCC-EEEEEECCCCC--CC--CCCHHHCCCCCCC-CCC-CCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHC---------- >P1;d1ztva1 CEEEEEECCC--CCHHHHC----CCHHHHCC--CCCEEEECHHHHCCCCHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHCCCCHHHHHHHHHHHCHHHHHC-CEEEEEEECCCCCCCC-CHHHHHHHHHHCCCCEEEECCCHHHHCCCCHHHHC-CC-CCCCEECEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCHHHCCCCCCCCCHHHHHHHCCCCCCCCCEEEEECCCCCCCHHHHHHHHC-CCCCCCCCCCCCCC PSA >P1;d1vpqa1 61000013013850431047a37b0082023515040000511b837163-60493-002960100020393004--51055a-670a407912-50440276910200000014505168125004301720645000000063025----76006104838000000000529-200324342015-20000000239--03--929c353143407-b20-9034062116200000100260200400250273177---------- >P1;d1ztva1 7100001426--6095018----17035000--303000033017600559405802501a502000000100043573657284376006302700210282-10000002056a1218-248106501800c2300000114300587407800-10-9180000000105076510423350016a00000000324b6276b2a82834252407981057002012a604000002014472003003303-51b2ba2186597b Translating the sequences CEEEEE*CCC**CC****C****CCHHHHHH**CCCEEEEC****CCCC*-*HHHH-CCCCCCEEEEECCHHHHH--CHHHHC-C***HHHHH*-*CHHHHHC*CEEEEEEECCCCCCCC*CHHHHHHHHHHCCCCEEEECCCHHH*C----HHHH*HH*HCCCEEEEEECCCCC-CCCCCCCCCCCC-EEEEEECCCCC--CC--C**HHHCCCCCCC-***-**CCCCCCCCEEEEEECCCHHHHHHHHHHHHH*HHHC---------- CEEEEEECCC--CCHHHHC----CCHHHH**--CCCEEEECHHHHCCCCH*HHHHH*CCCCCCEEEEECC*******CHHH*C*CHHHHHHHHH*HCHHHHHC-CEEEEEEECCCCCCCC-CHHHHHHHHHHCCCCEEEECCCHHHHC****HHH*-**-*CCCEE*EEECCCCC*CCCCCCCCCCCC**EEEEECCCCC**CC**CHHH**CCCCCCC*HHH*HHCCCCCCCC*EEEEECCC****HHHHHHHH*-***C********** 117396.tem _________________________________ CEEEEEECCC--CCHHHHC----CCHHHHHH--CCCEEEECHHHHCCCCH-HHHHH-CCCCCCEEEEECCHHHHH--CHHHHC-CHHHHHHHHH-HCHHHHHC-CEEEEEEECCCCCCCC-CHHHHHHHHHHCCCCEEEECCCHHHHC----HHHH-HH-HCCCEEEEEECCCCC-CCCCCCCCCCCC-EEEEEECCCCC--CC--CHHHHHCCCCCCC-HHH-HHCCCCCCCCEEEEEECCCHHHHHHHHHHHHH-HHHC---------- Structural block scores 1 6 E 4.7 H 0.3 0.3 7 9 C 5.0 H 1.3 4.0 10 11 - 3.0 P 5.5 75.0 12 13 C 5.0 H 2.5 3.0 14 17 H 3.0 P 2.0 3.8 19 22 - 3.0 P 6.9 75.0 23 24 C 5.0 H 5.8 4.0 25 30 H 4.3 M 2.5 1.3 31 32 - 3.0 P 3.0 75.0 33 35 C 5.0 H 3.0 2.0 36 39 E 5.0 H 0.0 0.0 41 44 H 3.0 P 5.4 2.8 45 48 C 5.0 H 4.2 2.8 51 55 H 4.6 H 4.4 3.4 57 62 C 5.0 H 2.8 3.6 63 67 E 5.0 H 0.6 0.4 68 69 C 5.0 H 1.5 0.0 70 74 H 3.0 P 3.2 1.0 75 76 - 3.0 P 75.0 4.0 78 81 H 4.5 M 2.8 5.2 85 93 H 4.1 M 4.5 3.0 97 101 H 5.0 H 3.4 2.6 105 111 E 5.0 H 0.3 0.3 112 119 C 5.0 H 2.8 4.2 122 131 H 5.0 H 2.4 3.3 132 135 C 5.0 H 3.8 4.4 136 139 E 5.0 H 0.0 0.0 140 142 C 5.0 H 0.0 0.7 143 146 H 4.5 M 2.8 1.8 148 151 - 3.0 P 75.0 4.8 152 155 H 4.5 M 3.2 3.8 157 158 H 3.0 P 0.5 0.5 161 163 C 5.0 H 3.7 3.0 164 169 E 4.7 H 0.0 0.0 170 174 C 5.0 H 3.2 2.6 176 187 C 5.0 H 2.2 2.5 189 194 E 4.7 H 0.3 0.0 195 199 C 5.0 H 2.8 1.8 200 201 - 3.0 P 75.0 8.8 202 203 C 5.0 H 1.5 4.5 204 205 - 3.0 P 75.0 8.8 207 211 H 3.4 M 6.3 6.3 212 218 C 5.0 H 3.1 3.4 220 222 H 3.0 P 4.5 3.0 224 225 H 3.0 P 4.5 3.5 226 233 C 5.0 H 2.9 2.7 234 239 E 4.7 H 0.3 0.7 240 242 C 5.0 H 0.3 1.0 243 255 H 4.2 M 1.8 2.2 257 259 H 3.0 P 3.7 5.8 261 270 - 3.0 P 75.0 7.2 >>>>>>