Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vz6a- ----------------------CCCCEEEEEECCCCCC---------CCCCEEEEEEC-----CCCEEEEEECCCCCCCHHHHHHHHHCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCCCC---CCCHHHEEEEEEEE---CCCCCCCCCCCCCCCC----CCCCCCHHH-HCCCCCC--------CEEECCC-----CCCEEEEEECCCCC--CCCCC----------------------------CCEEEEEEEECCCHHHHHHHHHHHHHHCHHHCCCCCCCCCCCEEEEEEEEEEECC-----------------HHHHC-CHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEECCEEEECCCCCHHHHHCCCCEEEEEEECCCCCCEEEEEECCCHHHHHHC >P1;d3ndva- CCCHHHHCCCCCCCCCCCCCHHHCCCCEEEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCHHHHHH---HCEEECCEEEEE-HHHH--HHHHHHHHHHHCCCCCCCCHHHHCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCHHHCCCEECCEECEEEEEEEEEEECCEEEEEEEEEEECCCCCCCCEECCEECCCCCCCCCCEECCEECCCCCCCCCCEEEEEEECCCCCHHHHHHHHH-CHHHHHHHCCCCCCCCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCEEECCCC-HHHHHHHHHHHCC----------------------------------------------------------------------------------------- PSA >P1;d1vz6a- ----------------------9070000201406057---------93300000004-----260200000052981010061046017854010000001100050b7604500550050130---c0667200000028---343030605209032b----a33405006-0011608--------3052418-----b0201000000040--10504----------------------------0000000000705564046004600640000000146301000000000141507-----------------39702-105700350034005200405000103051045570034001200106600410494534463034009519a094059860303029151145a8751572059850200040315250200000308428764 >P1;d3ndva- a430361904075721a3100010a702011121479748276680010000000001229233000002132344250210a2058---512012000000-4301--b40370033007b5059913810670000004057000180a1065930370059075570700120000001002000000000021605b561100000001027083050171500730890111598523337548681000000030003350042005-2047007302082aa91000000000310122c685625760839477106001600100000000000020931400752302102-4910450097447----------------------------------------------------------------------------------------- Translating the sequences ----------------------*CCCEEEEEE****CC---------****EEEEEEC-----C**EEEEEE**CCCCCHHHHHHHH****C***EEEEEEE*******HHHHHHHHHH*CCCCC---***HHHEEEEEEEE---CCCCCCCCC*******----CCCCCCHHH-H**CCC*--------*EEE***-----***EEEEEE*CCCC--CC**C----------------------------C*EEEEEEEECCCHHHHHHHHH*HHHH*HHHCCCCCCCCCC*EEEEEEEEEEECC-----------------HHHH*-*HHHHHHHHHHHHHH*CCC**CEEEEEEECCC*HHHHHHHHHHHHC***************************************************************************************** **********************HCCC*EEEEEEEEECC*********EEEEEEEEE*C*****CEEEEEEEEEECCCCC**HHHHHH---HCEEE**EEEEE-HHHH--HHHHHHHHHHHCCCCC***HHHH***EEEEE*****CCCCCCCCCHHHHHHH****CCCCCC****HHHCCCE********EEEEEEE*****EEEEEEEEEECCCC**CCEEC****************************CEEEEEEE**CCCHHHHHHHHH-*HHHHHHHCCCCCCCCCCEEEEEEEEEEEECC*****************HHHHH*HHHHHHHHHHHHHHHHCCCEEC***EEE*CCC-HHHHHHHHHHH*C----------------------------------------------------------------------------------------- 56266.tem _________________________________ ----------------------HCCCEEEEEEEEEECC---------EEEEEEEEEEC-----CEEEEEEEEEECCCCCHHHHHHHH---HCEEEEEEEEEE-HHHH--HHHHHHHHHHHCCCCC---HHHHHHEEEEEEEE---CCCCCCCCCHHHHHHH----CCCCCCHHH-HHHCCCE--------EEEEEEE-----EEEEEEEEEECCCC--CCEEC----------------------------CEEEEEEEEECCCHHHHHHHHH-HHHHHHHHCCCCCCCCCCEEEEEEEEEEEECC-----------------HHHHH-HHHHHHHHHHHHHHHHCCCEECEEEEEEECCC-HHHHHHHHHHHHC----------------------------------------------------------------------------------------- Structural block scores 0 21 - 3.0 P 75.0 3.5 23 25 C 5.0 H 2.3 5.8 26 35 E 4.0 M 1.3 1.9 36 37 C 5.0 H 6.0 8.0 38 46 - 3.0 P 75.0 4.6 47 56 E 4.0 M 1.5 0.1 58 62 - 3.0 P 75.0 3.6 64 73 E 4.2 M 1.3 1.1 74 78 C 5.0 H 4.0 3.0 79 86 H 4.5 M 2.2 3.6 87 89 - 3.0 P 2.7 75.0 92 101 E 4.0 M 0.6 0.5 103 106 H 3.0 P 1.2 2.0 107 108 - 3.0 P 5.8 75.0 109 119 H 4.8 H 2.9 2.9 120 124 C 5.0 H 1.8 5.7 125 127 - 3.0 P 75.0 6.3 128 133 H 3.3 M 5.6 4.2 134 141 E 4.2 M 1.2 0.5 142 144 - 3.0 P 75.0 4.0 145 153 C 5.0 H 2.7 2.9 154 160 H 3.0 P 3.9 3.9 161 164 - 3.0 P 75.0 3.5 165 170 C 5.0 H 4.2 5.2 171 173 H 3.0 P 2.0 0.3 175 177 H 3.7 M 0.3 0.0 178 180 C 5.0 H 2.3 0.0 182 189 - 3.0 P 75.0 0.2 190 196 E 3.9 M 3.3 0.4 197 201 - 3.0 P 75.0 5.5 202 211 E 4.2 M 1.4 0.8 212 215 C 5.0 H 1.0 2.5 216 217 - 3.0 P 75.0 4.0 218 219 C 5.0 H 0.5 1.5 220 221 E 3.0 P 2.5 2.5 223 250 - 3.0 P 75.0 4.2 252 260 E 4.3 M 0.0 0.3 261 263 C 5.0 H 4.0 1.0 264 272 H 5.0 H 3.2 2.1 274 281 H 4.5 M 1.2 2.9 282 291 C 5.0 H 1.5 4.3 292 303 E 4.8 H 0.9 0.4 304 305 C 5.0 H 3.5 2.0 306 322 - 3.0 P 75.0 5.7 323 327 H 4.6 H 4.2 1.4 329 344 H 4.8 H 2.2 0.2 345 347 C 5.0 H 1.3 4.0 348 349 E 3.0 P 2.5 2.5 351 357 E 3.9 M 1.3 2.7 358 360 C 5.0 H 1.7 1.0 362 373 H 4.8 H 1.8 3.9 375 463 - 3.0 P 3.5 75.0 >>>>>>