Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1k8ea2 --CC------CCEECCC----CCCCCCHHHHHHHHHCC-CCCEEEEECCCCCCCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCEEEEEHH-HHCHHHHHCHHHHHHHC-CCC-HHHHCHHHC--CCCCCCEEEEECC------------CHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEECCEEEEEEEEHHHHCCCCCCHHHCCCCCHHHHHHHHHHHHCCCC--HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHC--CHHHHHHHHHHHCCCHHHHHHHHCCC-- >P1;d2elca2 CCCC----CCCEEEEEECCCCCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHC-CCCCCCCHHHHHHHHHHHCEEEEEHH-HHCHHHHHCHHHHHHHC-CCC-HHHHHCCCC--CCCCCCEEEEECC------------CHHHHHHHHHHHHHCCC-EEEEEEEC-CCCCCCC-CCEEEEECC---CEEEEECHHHHCCCCCCHHHHCCCCHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHC------------- >P1;d4eada2 -CCHHHCCCCCCEEEEECCC---CCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHCEEEECCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCC-EEEEEEEECC------------------------------------CCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCHHHHHHHHCC PSA >P1;d1k8ea2 --15------7000005----a4600100000000001-21100003532a8a43200000520-00605056941750066040000016-5137837837a739857-773-732238304--0118012000006------------35a2056006404847041000010343030000333020100169426835030560619403275040b41650022002002942--950120000000000200630961450163056006--60291055004501548607801774-- >P1;d2elca2 1807----4440000010791a4b0050200000000018000000352399552200000450-30509064930150036110000115-20278376356739968-733-632148005--0109030000002------------328408400630675a0-50000005-5012000-160501119---585240106509094171830403739601620450030526-6411200001000002004408517500620581045150150055017206a------------- >P1;d4eada2 -6097290c21000030130---3000000000000000801000018427d61611040041049040509994125005501000002599225a14963760585a626327310811052024070600000002393040565850440174039602a5a0-6040211506------------------------------------74004337515005100200426521730271003000200300920866930484046006674017103400210701940175286207 Translating the sequences --CC------CCEE***----CCCCCCHHHHHHHHH**-CCCEEEEECCCCCCCCCHHHHHHH*-CCCCCCCHHHHHHHHHHHCEEEEEHH-HHCHHHHHCHHHHHHHC-CCC-HHHH*HHHC--CCCCCCEEEEECC------------CHHHHHHHHHHH**CCC*EEEEEEECCCCCCCCC*C*EEEEE******EEEEE*HHHHCCCCCCHHHCCCCCHHHHHHHHHHHHCCCC--HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH*--*HHHHHHHHHHHCCC***HHHHH***-- *CCC----CCC*EEEEECCC*CCCCCC*HHHHHHHHHHCCC*EEEEECCCCCCCCCHHHHHHHC-CCCCCCCHHHHHHHHHHHCEEEEEHH-HHCHHHHHCHHHHHHHC-CCC-HHHHH***C--CCCCCCEEEEECC------------CHHHHHHHHHHHHHCCC-EEEEEEEC-CCCCCCC-C*EEEEE**---*EEEEE*HHHHCCCCCCHHH*CCCCHHHHHHHHHHHHCCCCC-*HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH*CHHHHHHHHHHHH**C------------- -CC*****CCCCEEEEECCC---CCCCHHHHHHHHHHHCCCCEEEE*CCCCCCCCCHHHHH**C*CCCCCCCHHHHHHHHHHHCEEEE******CHHHHH*HHHH***C*CCC*HHHHHHHH****CCCCCEEEEE***************HHHHHHHHHHHHHCCC-EEEEEEE*CC------------------------------------***CCCCC*HHHHHHHHHHHCCCCC*HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH*CHHHHHHHHHHHHCCC***HHHHH***** 52418.tem _________________________________ -CCC----CCCCEEEEECCC-CCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHC-CCCCCCCHHHHHHHHHHHCEEEEEHH-HHCHHHHHCHHHHHHHC-CCC-HHHHHHHHC--CCCCCCEEEEECC------------CHHHHHHHHHHHHHCCC-EEEEEEECCCCCCCCC-C*EEEEE**---*EEEEE*HHHHCCCCCCHHHCCCCCHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH*CHHHHHHHHHHHHCCC***HHHHH***-- Structural block scores 1 3 C 4.3 M 27.0 5.0 5.0 4 7 - 4.0 M 75.0 75.0 4.5 8 11 C 4.2 M 39.2 3.0 3.9 12 16 E 4.4 M 1.0 0.2 0.6 17 19 C 4.0 M 75.0 5.3 1.3 21 26 C 4.7 H 3.6 5.2 25.5 27 37 H 4.7 H 0.1 0.2 0.0 38 41 C 4.5 M 19.8 2.2 2.2 42 46 E 4.8 H 0.6 0.6 0.2 47 55 C 5.0 H 5.3 4.7 5.4 56 62 H 4.7 H 1.0 1.3 1.4 65 71 C 5.0 H 2.3 3.3 3.9 72 82 H 5.0 H 4.0 2.9 3.6 84 88 E 4.8 H 0.0 0.2 0.0 89 90 H 4.0 M 3.5 3.0 3.5 92 93 H 4.0 M 3.0 1.0 5.5 95 99 H 5.0 H 6.6 6.2 5.9 101 107 H 4.6 H 7.1 6.4 4.9 110 112 C 5.0 H 5.7 4.3 3.7 114 121 H 4.5 M 3.5 3.0 2.6 123 124 - 4.0 M 75.0 75.0 1.0 125 130 C 4.8 H 1.8 2.2 3.2 131 135 E 5.0 H 0.4 0.0 0.0 136 137 C 4.0 M 3.0 1.0 0.0 138 149 - 4.0 M 75.0 75.0 4.2 151 163 H 4.8 H 3.9 3.7 3.9 164 166 C 5.0 H 3.7 5.2 5.2 168 174 E 5.0 H 0.3 0.7 2.0 175 183 C 4.1 M 1.4 9.8 51.2 187 191 E 4.0 M 0.6 1.4 75.0 192 193 * 2.7 P 0.5 5.0 75.0 194 196 - 4.0 M 6.3 75.0 75.0 198 202 E 4.0 M 4.4 3.8 75.0 204 207 H 4.0 M 2.8 2.8 75.0 208 213 C 4.0 M 3.8 5.0 75.0 214 216 H 4.0 M 4.7 4.0 3.7 217 221 C 4.8 H 3.9 2.8 3.4 222 233 H 4.9 H 1.5 3.0 1.6 234 238 C 4.8 H 18.4 3.2 3.8 240 256 H 4.9 H 1.1 1.0 1.6 257 262 C 5.0 H 4.0 3.5 4.2 263 275 H 4.9 H 2.8 3.0 3.8 278 289 H 4.9 H 3.1 2.6 1.9 290 292 C 4.3 M 2.0 5.5 2.3 293 295 * 2.7 P 6.0 75.0 4.7 296 300 H 4.0 M 3.2 75.0 3.0 301 303 * 2.7 P 6.0 75.0 5.3 304 305 - 4.0 M 75.0 75.0 3.5 >>>>>>