Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1q7fa- CCC-EEECEEEEECCCCCCCCCCCCEEEEEECCCCCEEEEEHHHCEEEEECCCCCEEEEECCCCCCCCCCCCEEEEEECCCCCCEEEEECHHHCEEEEECCCCCEEEEECC-----CCCCCEEEEEECCCCCEEEEECCCCEEEEECCCCCEEEEEECC---CCCCCEEEEEECCCCEEEEEEHHHCEEEEEECCCCEEEEECCCC---CCCCEEEEEECCCCCEEEEECCCCCEEEEECCCCCEEEEEEECC----CCCCEEEEEEECCCEEEEEEC-CCEEEEEECCCCCCCCC >P1;d1rwia1 CEEECCCC-----------CCCCCCEEEEEECCCCCEEEEECCCCEEEEEC---CEEECCCC------CCCCCCCEEECC-CCCEEEEEC--CCEEEEECCCCCCCEECCCC-----CCCCEEEEEECCCCCEEEEEHHHCEEEEECCCCCCEECCCC-----CCCCCCCEEECCCCCEEEEEHHHCEEEEECCCCCEEECCCC------CCCCCCEEECCCCCEEEEEC--C-EEEEECCCCCCCEECCCC-----CCCCEEEEEECCCCCEEEEEHHHCEEEEECCCC------ >P1;d6xg7a- CCCCCCCCCCEEEECCCCCCCCCCCCCCEEEEHHHEEEEEEHHHCEEEEECCCCCCC-CCCEECCCCCEEC-CCCEEEC--CCCEEEEEH-HHCEEEEECCCCCEEEEECCCCCCCCCCCCEEEEEECCCCCEEEEEHHHCEEEEECCCCCEEEEECEECCCCEECCEEEEEECCCCEEEEEEHHHCEEEEEECC--CCEEECCCCCCCCCCCCCCEEECCCCCEEEEEHHHC-EEEEECCCCCEEEEECEECCCCCEECCEEEEEECCCCCEEEEEHHHCEEEEC---------- PSA >P1;d1q7fa- 3a1-9607252410572786310120100101370100000051100000258071333107548875102301101006a422000003362210000357071333105-----a306203001007632000001761100003470723451707---84064020010067510000015310010020707233400389---30260100021985200000139300000032718344002075----804701001005500000006-3330000205a657bc8 >P1;d1rwia1 d1650707-----------c1a20300001018762000001880400214---a0731409------b04201201029-832000001--542000066c48a1752609-----9055013010179400000032352003066c4b1651408-----c0530310101775200000253520020345771451406------a0750101005530000005--5-4003076c3970750709-----b065041010169400000024452003163bb------ >P1;d6xg7a- a33078080534108667953101301001106b22000001312000105480736-3108639872302-0000100--811000002-5111000023808133211663774340230000101983300000131100000545052464107556a440230000000786400000040110000642--336312666785240602001019731000001722-1000033816222210771586330220000100871200000241100000---------- Translating the sequences CCC-***C**EEE*CCCCCCCCCCCEEEEEECCCCCEEEEEHHHCEEEEECCCCCEEE**CC*CCCCCCCCC***EEECC*CCCEEEEEC*HHCEEEEECCCCCEEEEECC-----CCCCCEEEEEECCCCCEEEEE***CEEEEECCCCCEEEEE*C*---CCCCCEEEEEECCCCEEEEEEHHHCEEEEEECCCCEEEEECCCC---CCCC***EEECCCCCEEEEEC**C*EEEEECCCCCEEEEE*ECC----CCCCEEEEEE*CCC*EEEEE*-*CEEEEE*CCC****** C***CCCC-----------CCCCCCEEEEEECCCCCEEEEE***CEEEEEC---CEEECCCC------CCCCCCCEEECC-CCCEEEEEC--*CEEEEECCCCC**EE*CCC-----CCCCEEEEEECCCCCEEEEEHHHCEEEEECCCCC*EE**CC-----CCCC***EEECCCC*EEEEEHHHCEEEEE*CCCCEEE**CC------CCCCCCEEECCCCCEEEEEC--C-EEEEECCCCC**EE*C*C-----CCCCEEEEEECCCCCEEEEEHHHCEEEEE*CCC------ CCC*CCCC**EEE*CCCCCCCCCCC***EEE*****EEEEEHHHCEEEEECCCCC**-CCC**CCCCC**C-CCCEEEC--CCCEEEEE*-HHCEEEEECCCCCEEEEECCC****CCCCCEEEEEECCCCCEEEEEHHHCEEEEECCCCCEEEEEC*****C**CCEEEEEECCCCEEEEEEHHHCEEEEEECC--**EEECCCC***CCCCCCCEEECCCCCEEEEE***C-EEEEECCCCCEEEEECE*C******CCEEEEEECCCCCEEEEEHHHCEEEE*---------- 101898.tem _________________________________ CCC*CCCC**EEE*CCCCCCCCCCCEEEEEECCCCCEEEEEHHHCEEEEECCCCCEEECCCC*CCCCCCCCCCCCEEECC-CCCEEEEEC-HHCEEEEECCCCCEEEEECCC----CCCCCEEEEEECCCCCEEEEEHHHCEEEEECCCCCEEEEECC*---CCCCCEEEEEECCCCEEEEEEHHHCEEEEEECCCCEEEEECCCC---CCCCCCCEEECCCCCEEEEEC**C-EEEEECCCCCEEEEECECC----CCCCEEEEEECCCCCEEEEEHHHCEEEEE*CCC------ Structural block scores 0 2 C 4.3 M 4.8 6.8 5.5 4 7 C 4.2 M 5.5 3.5 5.8 8 9 * 2.7 P 3.5 75.0 2.5 10 12 E 4.0 M 2.3 75.0 2.7 14 24 C 4.5 M 3.8 36.7 4.5 25 30 E 4.5 M 0.3 0.2 0.5 31 35 C 4.0 M 2.4 4.8 4.3 36 40 E 5.0 H 0.0 0.0 0.0 41 43 H 4.0 M 2.0 5.7 1.7 45 49 E 5.0 H 0.0 1.4 0.2 50 54 C 4.4 M 4.4 47.9 4.8 55 57 E 4.0 M 2.3 3.3 28.0 58 61 C 4.2 M 2.8 3.5 3.0 63 74 C 4.1 M 3.3 33.0 9.1 75 77 E 5.0 H 0.3 0.3 0.3 78 79 C 4.5 M 3.0 5.5 37.5 81 83 C 5.0 H 2.7 4.3 3.3 84 88 E 5.0 H 0.0 0.0 0.0 91 92 H 4.0 M 4.0 40.0 3.0 94 98 E 5.0 H 0.2 0.4 0.2 99 103 C 5.0 H 4.4 7.3 4.2 104 108 E 4.4 M 2.2 5.1 2.0 109 111 C 4.7 H 26.7 5.0 4.3 112 115 - 4.0 M 75.0 75.0 5.2 116 120 C 4.8 H 4.3 18.8 2.4 121 126 E 5.0 H 0.7 0.8 0.2 127 131 C 5.0 H 3.6 4.2 4.8 132 136 E 5.0 H 0.0 0.0 0.0 137 139 H 4.0 M 4.7 2.7 1.7 141 145 E 5.0 H 0.2 1.0 0.0 146 150 C 5.0 H 4.2 8.0 3.8 151 155 E 4.4 M 3.0 3.4 3.4 156 157 C 4.0 M 3.5 4.0 3.5 159 161 - 4.0 M 75.0 75.0 7.2 162 166 C 4.4 M 4.4 19.1 2.6 167 172 E 4.5 M 0.5 0.8 0.0 173 176 C 5.0 H 4.5 5.0 5.2 177 182 E 4.8 H 0.2 0.3 0.7 183 185 H 5.0 H 3.0 3.3 1.3 187 192 E 4.8 H 0.5 1.2 1.2 193 196 C 4.5 M 3.5 5.8 39.0 197 201 E 4.2 M 2.4 3.0 3.2 202 205 C 4.5 M 5.0 39.0 5.0 206 208 - 4.0 M 75.0 75.0 6.7 209 215 C 4.4 M 1.7 14.1 2.0 216 218 E 5.0 H 0.7 0.3 0.3 219 223 C 5.0 H 5.0 2.6 4.2 224 228 E 5.0 H 0.0 0.0 0.0 230 231 * 2.7 P 6.0 75.0 4.5 234 238 E 5.0 H 0.0 1.4 0.2 239 243 C 5.0 H 4.2 7.5 4.2 244 248 E 4.4 M 2.2 3.8 1.8 251 252 C 4.0 M 6.0 42.0 4.0 253 256 - 4.0 M 75.0 75.0 5.5 257 260 C 4.5 M 4.8 5.6 1.8 261 266 E 5.0 H 0.3 1.0 0.2 267 271 C 4.6 H 2.0 4.0 3.6 272 276 E 5.0 H 0.0 0.0 0.0 277 279 H 4.0 M 28.0 3.3 2.3 281 285 E 4.8 H 0.6 1.2 0.0 287 289 C 4.0 M 5.2 8.7 75.0 290 295 - 4.0 M 8.3 75.0 75.0 >>>>>>