Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1iqra1 ------------CCCCCCCHHHHHHHHHHHHH--HCHHHH-HHHCCCCCCC-CCCCCHHHHHCCCCCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHHHHHHCHHHHCCCCCHHHCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCHHHCCCCCCCCHHHHHHHCCCCCHHHHHHCCCCC------CCCCC-------------------CCCCCHHHHHHHHHHHHHC------------- >P1;d1np7a1 --------CCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHH-HHHCCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHC------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCHHHHHHHHCCCCHHHHHHCHHHCCCCCHHHHCHHHCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCC--------------- >P1;d1owla1 --------------CCCCCHHHHHHHHHHHHH--CHHHHH-HHHCCCCCCC-CCCCCHHHHHCCCCCHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCCCCCHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCC-CCCCCHHHHHHHHCCCCHHHHHHCHHHCCCCHHHHHHCC-CCHHHHC--------CCCCCCCCHHHHHHHHHHHHHHHHHHC-------- >P1;d1u3da1 CCHHHHHHHCCHHHHCCCCHHHHHHHHHHHHC--CHHHHC-CCCCCCCCCC-CCCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHCHHHCCCCHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC------ >P1;d2wq7a2 -----------CCCCCCCCHHHHHHHHHHHHCCHHHHHHCCHHHCCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHCC-----CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCHHHHCCCCCHHHHHHCHHHCCCCHHHHCCHHHCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC PSA >P1;d1iqra1 ------------48648887a10486078005--740460-1442330225-141503110088306594037306636-----------a800940142173164045029546302740126804a05164569205102506020000000021036401006102100000000-0000205400520172030025021016003000010592427501503600671069470077105607------60625-------------------9221626406620263069------------- >P1;d1np7a1 --------3b3102b08a77a2047004500172330350-37513603823021004000088204284056103400863------444700530162166245067118738950464000195935077498515302105000000000020044020005102400000000-001000320062047104022513100600220600-677a9263140150045204807001400530680588300201507a8229729060764025113618710461483a--------------- >P1;d1owla1 --------------209897a30353077006--840470-263323015b-121204001376305285059204711790---85aa04600520074064354246029656703900359106604035569015201705001000000021035532008102200000000-00001043016103640400350610180030020015369-270050460076106805002520550730848301229-0669325--------c02442071770264046217716874-------- >P1;d1u3da1 57a966a8488397625877640371066006--630440-0724650148-121304100278206295067405732651596849604700720273176264037039557704473147507403117489225103503000000000020073421007202300000000-0000204200710452030114341018004000005703804303201620540058070025207204705483001026059820880708165501612072b8047405701540686499------ >P1;d2wq7a2 -----------669304a77a10451057208735400404258120054912110040002672061930263065029528-----721746300201043254058208708402428b0720240705937a3250014040000000000200350100031021000000000000020220161057104020503100400200000-1155166023027103740660600240063048052c1002026075841671a0302640271116166226503830470167166688877 Translating the sequences ------------CCCCCCCHHHHHHHHHHHH*--**HHHH-HHHCCCCCCC-CCCCCHHHHHCCCCCHHHHHHHHHHH*-----------CHHHHHHHHHHHHHHHHHHHHHHCHHHHCCCCC***CCCCCCCCHHHHHHHH*CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC***CCCCCCCCHHHHHHH*CCCCHHHHHHC***C------*CCCC-------------------CCCCCHHHHHHHHHHHHH*------------- --------****CCCCCCCHHHHHHHHHHHHC**C*HHHH-HHHCCCCCCC*CCCCCHHHHHCCCCCHHHHHHHHHHHHHHC------**CHHHHHHHHHHHHHHHHHHHHHH*HHHH*CCCCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCHHHHHHHHCCCCHHHHHHCHHHCCCC*HHH*C***CCHHHHHH*CCCCCCCCCCCCCCHHHHHHHHH***--------------- --------------CCCCCHHHHHHHHHHHH*--CHHHHH-HHHCCCCCCC-CCCCCHHHHHCCCCCHHHHHHHHHHHHHHC---******HHHHHHHHHHHHHHHHHHHHHHCHHHH*CCCCC****CCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCC*HHHHHHHH**CCCCCHHHHHHHHHH*CCCC*CCCC-CCCCCHHHHHHHHCCCCHHHHHHCHHHCCCCHHHH**CC-CCHHHH*--------CCCCCCCCHHHHHHHHHHHHHHHHHH*-------- ***************CCCCHHHHHHHHHHHHC--CHHHH*-***CCCCCCC-CCCCCHHHHHCCCCCHHHHHHHHHHHHHH**********HHHHHHHHHHHHHHHHHHHHH*C****CCCCCCCCCCCCCCCCHHHHHHHH*CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHH*CCC*CCCCCCCCCCHHHHHHHHCCCCHHHHHHCHHHCCCCHHHHCCCC*CCHHHHHH*CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH***------ -----------*CCCCCCCHHHHHHHHHHHHC***HHHH**HHHCCCCCCC*CCCCCHHHHHCCCCCHHHHHHHHHHHHHHC*-----**C*****HHHHHHHHHHHHHHHH*C****CCCCCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHH***CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCC***HHHH*CCCCHHHHHHCHHHCCCCHHHHCC***CCHHHHHH*CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH********* 48173.tem _________________________________ -----------*CCCCCCCHHHHHHHHHHHHC--CHHHHH-HHHCCCCCCC-CCCCCHHHHHCCCCCHHHHHHHHHHHHHHC------**CHHHHHHHHHHHHHHHHHHHHHHCHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC*CCCCCCCCCCHHHHHHHHCCCCHHHHHHCHHHCCCCHHHHCCCC*CCHHHHHH*CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH*-------- Structural block scores 0 10 - 4.3 M 75.0 56.1 75.0 7.5 75.0 12 18 C 4.7 H 6.6 5.6 25.4 6.3 5.6 19 30 H 5.0 H 4.3 3.3 3.8 3.3 3.5 32 33 - 3.8 M 75.0 4.5 75.0 75.0 5.0 35 39 H 4.5 M 2.8 2.2 3.0 2.2 1.6 41 43 H 4.5 M 3.0 5.0 3.7 3.0 5.0 44 50 C 5.0 H 2.4 3.3 3.6 4.0 3.0 52 56 C 5.0 H 2.2 0.6 1.2 1.4 0.8 57 61 H 5.0 H 1.0 0.8 1.6 1.4 1.2 62 66 C 5.0 H 5.0 4.4 4.2 4.6 4.2 67 80 H 4.9 H 14.4 3.4 4.3 4.4 3.6 82 87 - 4.0 M 75.0 75.0 41.4 6.8 63.8 88 89 * 2.1 P 75.0 4.0 5.2 3.0 4.5 91 112 H 4.8 H 3.4 3.5 3.4 3.7 3.2 114 117 H 3.8 M 2.8 5.5 4.0 4.5 3.5 118 133 C 4.7 H 4.0 4.0 3.5 3.6 4.0 134 141 H 5.0 H 3.1 4.1 3.0 3.8 3.6 142 147 C 4.8 H 2.2 1.0 2.2 1.3 1.3 148 160 H 5.0 H 1.2 0.8 1.2 1.2 0.8 161 164 C 5.0 H 0.2 0.5 1.2 0.8 0.2 165 177 H 4.9 H 0.8 0.9 1.0 1.1 0.5 179 183 C 5.0 H 0.4 0.2 0.2 0.4 0.4 184 194 H 4.9 H 2.4 2.3 2.5 2.3 2.3 195 199 C 5.0 H 1.0 1.6 1.4 1.0 1.2 200 210 H 5.0 H 1.6 1.8 2.2 2.3 1.4 211 214 C 4.9 H 0.2 1.5 0.5 0.0 0.0 216 225 C 4.8 H 4.0 5.5 11.2 3.0 3.0 226 233 H 4.7 H 2.9 2.1 3.0 2.2 3.0 234 237 C 5.0 H 4.8 3.0 3.5 3.2 3.0 238 243 H 5.0 H 3.7 2.0 2.3 2.7 2.0 245 247 H 4.5 M 3.7 2.7 3.3 3.0 3.0 248 251 C 4.6 H 58.0 4.8 4.5 4.0 4.2 252 255 H 4.4 M 57.8 4.8 3.8 3.8 3.9 256 259 C 4.0 M 3.2 0.8 3.5 0.8 1.0 261 262 C 4.5 M 75.0 3.5 3.0 2.5 3.5 263 268 H 4.4 M 75.0 6.4 16.7 5.8 5.2 270 283 C 4.5 M 49.6 3.6 34.4 3.5 3.1 284 301 H 4.7 H 19.6 28.0 4.2 4.4 3.7 303 310 - 4.3 M 75.0 75.0 75.0 58.5 7.0 >>>>>>