Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1jr2a- CEEEEEECCCCCCCCCCHHHHHHHCCCCEEEEEECEEEEECCHHHHHHHHCCHHH-CCEEEECCHHHHHHHHHHHHHCCCHHHHHHHCHHHHHHCEEEECCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCEEEEECCHHHCCHHHHHHCCCCCEEEEECEEEEECC-CHHHHHHHHHHHHCCCCEEEECC---HHHHHHHHHHHHHHHHHHHHHCEEEECCHHHHHHHHHCCCCCCEECCCCCHHHHHHHHHHHCC---- >P1;d1wcwa1 -CEEECCCCC-----HHHHHHHHHHCCCCEEECCCEEEEECCHHHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHCCCC------CHHHHHHCEEEECCHHHHHHHHHCCCCCCEECCCCHHHHHHHCC---CCCEEEEEECCCCCCHHHHHHHHHCCEEEEEECCEEEEECHHHHHHHHHHHHH--CCCCEEEECCHHHHHHHHHHCCCHHHHHHHHHHCCEEEEECHHHHHHHHHCCCCCCEEECCCCHHHHHHHHHHHHHHHHC PSA >P1;d1jr2a- 6300000577675a860113310663b1804002013462350630062015056-0000000123003006300563b2694077503850182502016a7006204613083b52a18626700840176b35b5200000166970400830586a050411200353427-60794076007748203000013---4500730083058209a62980400012670172067591813120a6641720054047208---- >P1;d1wcwa1 -600000344-----3a6055305829160331100525616367057304400850500000206005102600761a18------07710590400012670160067290404330742172047304---74a61000001027165048006826081140300424436800360060036--6407000004210020005507648303700364030000654004006838080221063570320065057347667b Translating the sequences *EEEEEECCC*******HHHHHHH*CCCEEEEEECEEEEECCHHHHHHHH**HHH-CCEEEECCHHHHHHHHHHHHHCCCH******CHHHHHHCEEEECCHHHHHHHHHCCCCCC**CCCCHHHHHHHHH***CCC**EEEEECCHHH**HHHHHH*CC**EEEEECEEEEEC*-*HHHHHHHHHH**CCCCEEEECC---HHHHHHHHHHHHHHHHHHHHHCEEEE*CHHHHHHHHHCCCCCCEE*CCCCHHHHHHHHHHH**---- -*EEE**CCC-----HHHHHHHHHHCCC*EEE**CEEEEECCHHHHHHHHHHHH**CCEEEECCHHHHHHHHHHHHHCCC*------CHHHHHHCEEEECCHHHHHHHHHCCCCCCEECCCCHHHHHHH**---CCCEEEEEE*CC***HHHHHHHHHCCEEEEEE*CEEEEECH*HHHHHHHHHHH--CCCCEEEECC***HHHHHHH***HHHHHHHHHH*CEEEEECHHHHHHHHHCCCCCCEEECCCCHHHHHHHHHHHHH**** 69618.tem _________________________________ -EEEEEECCC-----HHHHHHHHHHCCCEEEEEECEEEEECCHHHHHHHHHHHHH-CCEEEECCHHHHHHHHHHHHHCCCH------CHHHHHHCEEEECCHHHHHHHHHCCCCCCEECCCCHHHHHHHHH---CCCEEEEEEECCHHHHHHHHHHHHCCEEEEEEECEEEEECH-HHHHHHHHHHH--CCCCEEEECC---HHHHHHHHHHHHHHHHHHHHHCEEEEECHHHHHHHHHCCCCCCEEECCCCHHHHHHHHHHHHH---- Structural block scores 1 6 E 4.0 M 0.5 1.0 7 9 C 5.0 H 6.3 3.7 10 14 - 3.0 P 7.3 75.0 15 24 H 4.4 M 2.7 4.5 25 27 C 5.0 H 5.2 4.0 28 33 E 4.0 M 2.3 2.3 35 39 E 5.0 H 3.2 3.6 40 41 C 5.0 H 4.0 3.5 42 54 H 4.5 M 2.6 3.6 56 57 C 5.0 H 0.0 2.5 58 61 E 5.0 H 0.0 0.0 62 63 C 5.0 H 0.5 1.0 64 76 H 5.0 H 2.2 2.5 77 79 C 5.0 H 5.5 4.2 81 86 - 3.0 P 5.3 75.0 88 93 H 5.0 H 4.2 4.8 95 98 E 5.0 H 1.8 1.0 99 100 C 5.0 H 3.5 1.5 101 109 H 5.0 H 3.9 3.7 110 115 C 5.0 H 4.4 3.2 116 117 E 3.0 P 3.5 3.0 118 121 C 5.0 H 6.4 3.2 122 130 H 4.6 H 3.1 3.1 131 133 - 3.0 P 8.2 75.0 134 136 C 5.0 H 6.5 7.2 137 143 E 4.1 M 1.0 1.0 144 145 C 5.0 H 3.5 0.5 146 157 H 4.0 M 4.2 3.9 158 159 C 5.0 H 8.2 4.0 160 166 E 4.1 M 1.9 2.4 168 172 E 5.0 H 3.0 2.8 176 186 H 4.8 H 4.2 2.2 187 188 - 3.0 P 5.5 75.0 189 192 C 5.0 H 3.2 4.2 193 196 E 5.0 H 0.0 0.0 197 198 C 5.0 H 2.0 2.0 199 201 - 3.0 P 75.0 1.0 202 222 H 4.6 H 4.3 3.0 224 228 E 4.6 H 1.0 0.6 230 238 H 5.0 H 4.0 3.0 239 244 C 5.0 H 4.5 3.5 245 247 E 4.3 M 1.0 1.0 248 251 C 5.0 H 6.6 5.2 252 264 H 4.7 H 3.1 3.2 265 268 - 3.0 P 75.0 7.6 >>>>>>