Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hxna- --------CHHHCCCCCCCEEEECCCCCEEEEECCEEEECCCC-----CCCCEEHHHCCCCCCCCCCEEEEEC---CEEEEEECCEEEEEECCCCCEECCCCCEEHHHHHCCCCCCCCCCCEEECCC----CCCEEEEEECCEEEEEEHHHHHHCCCE---EECCCC-------CCCEEEEECCCCCCCCCCCCCCEEEEEECCEEEEECHHHHHCC-----CCCCEEHHH-HCCCCC----- >P1;d1itva- --------CCHHHCC-CCCEEEEEC-CEEEEEECCEEEEECCCCCCCCE-EEEEHHHHCCCCCCCCCEEEECCC-CCCEEEEECCEEEEEEC---CEEE--EEEEHHHH--CCCCCCCCCCEEEECC-----CCEEEEEECCEEEEEECCCC---EECHHHCEEHHHHCCCCCCCCCEEEEEC------------CEEEEEECCEEEEEECCCCCCEEE-----EEEECCCCCCCCC----CC >P1;d1qhua1 --------CHHHCCCCCCCEEEECCCCCEEEEECCEEEECC-----CCE--EEEHHHHCCCCCCCCCEEEEEC--CCEEEEEECCEEEEEC----------CCEEHHHHCCCCC---CCCCEEEEECCCCCCCCEEEEEECCEEEEEECCCC---EEE---EECCC----CC-CCCCEEEEEC------------CEEEEEECCEEEEECCC--CCCCCC---CCCEEHHHHCCCCCCCCCCC >P1;d1rtga- CCCCCCCCCCCCCCCCCCCEEEEEC-CEEEEEECCEEEEECC-CCCCCE-EEEEHHHHCCCCCCCCCEEEEECC-CCEEEEEECCEEEEECC---CCCCCCCCEEHHHH--CCCCCCCCCCEEEECC----CCCCEEEEECCEEEEEECCCC---EECCCCCEEHHHHCCCCCCCCCEEEECC----------CCCEEEEEECCEEEEEECC--CCCEE-----EEEEHHHHCCCC------- >P1;d1su3a2 ----CCCCCCCCCCCCCCCEEEEEC-CEEEEEECCEEEECCC-CCCCCE--EEEHHHCCCCCCCCCCEEEEEHH-HCEEEEEECCEEEEEEC---CEEC-CCCEEHHHHH-CCC-CCCCCCEEEECC----CCCEEEEEECCEEEEEECCCC---EECCCCCEEHHHHCCCCCCCCCEEEEE------------CCEEEEEECCEEEEEECC--CCEEE-----EEEECCC-CCC-------- >P1;d3c7xa- --------CCHHH--CCCCEEEEEC-CEEEEEECCEEEEEE--CCEECCCCCEEHHHHCCCCCCCCCEEEECCC--CCEEEEECCEEEEEEC---CEECCCCCEEHHHCCCCCCC--CCCCEEEECC----CCCCEEEEECCEEEEEECCCC---EECCCCCEEHH-HCCCCCCCCCEEEECC----------CCCEEEEEECCEEEEEECC--CCEECC---CCCEEHHHHCCCCC----CC >P1;d6o5ea- --------CCCCC-CCCCCEECCCCCCEEEEEECCEEEEEECCCCCCCC--EEEHHHHH-CCCCCCCEEEECCCCCCCEEEEECCEEEEEEC---CEECCCCCEEHHHHCCCCC---CCCCEEEECC------CEEEEEECCEEEEEEC--------C---CEEHHHHCCCCCCCCCEEEECC------------CEEEEEECCEEEEEECC--CCEECCCCCCCCEEHHHHCCCCCC----- PSA >P1;d1hxna- --------961248a060300010479000001645003023a-----c362450743058009503000116---42000016340000306ba0813ca13370571014086919502000013----d32500001755002030747390905---517007-------502000016720589332ba6200000446200102a802839-----a43485016-1050a7----- >P1;d1itva- --------a501816-401000319-c3010035240020468964505-024508850640387030011029-4641000177400004c---a835--14370660--206a80740100042a-----97401000553006031a64---506691426076405a016603000204------------931000454301104878a92514-----5434013410405----7d >P1;d1qhua1 --------961059c14030000037631000267300336-----606--525046407808250200001c--6610100373501127----------8563068304803---46050000046b30754000003866000013966---534---42a08----50-3705000158------------25000034150120703--508139---b1332012300607d35599 >P1;d1rtga- b98a95a506017590601000005-7200002240003074-366508-034506720440485000001136-76200000564001055---5813a813350440--8037917602000005----356200001653003011767---5108a03540773069033703000018----------a942010048870210408--43733-----573413630011------- >P1;d1su3a2 ----a6a508044680303000205-b500002530001528-958501--25506410560285030001037-45000003645000041---7603-c044403810-804-907501000027----a40201001744012000576---6119b0443038304807750200013------------983010037260120128--54824-----5455013-30a-------- >P1;d3c7xa- --------57036--0803000205-421000266300206--84823ba031405640870324020002145--3200003844000056---6822891435075009700a--6300000213----351201003664013021685---402a9034608-4068026204000038----------846202003925002010a--745029---a0334025210207----af >P1;d6o5ea- --------47121-66403000033a820200084300411a83b7505--34403630-81605030000145b7001000365501203a---59318a024706610aa02---4804000012------2500003865003272--------b---3660572068041705000018------------90010037540130318--33512a2a470414027310808f----- Translating the sequences --------C***CCCCCCCEEEE*C*C*EEEEECCEEEE*CC*-----****EEHHH*CCCCCCCCCEEEE*C---C*EEEEECCEEEEEEC***CEEC*CCCEEHHHH**CCC***CCCCEEE*CC----CCCEEEEEECCEEEEEE**********---*E****-------CCCEEEE*C************CEEEEEECCEEEEE******C*-----****EEHHH-*CCCC*----- --------CC***CC-CCCEEEE*C-CEEEEEECCEEEE*CC*CC*CC*-*EEEHHHHCCCCCCCCCEEEE*C*-*C*EEEEECCEEEEEEC---CEE*--**EEHHHH--CCC***CCCCEEEECC-----CCEEEEEECCEEEEEECCCC---EEC***CEEHH*HCCCCCCCCCEEEE*C------------CEEEEEECCEEEEEECC**CC*E*-----**EE****CCCCC----** --------C***CCCCCCCEEEE*C*C*EEEEECCEEEE*C-----CC*--EEEHHHHCCCCCCCCCEEEE*C--*C*EEEEECCEEEEE*----------CCEEHHHH**CCC---CCCCEEEE*C****CCCEEEEEECCEEEEEECCCC---EE*---*E***----CC-CCCCEEEE*C------------CEEEEEECCEEEEE*CC--CC****---***EEHHH*CCCCC****** ********CC**CCCCCCCEEEE*C-CEEEEEECCEEEE*CC-CC*CC*-*EEEHHHHCCCCCCCCCEEEE*C*-*C*EEEEECCEEEEE*C---C**C*CCCEEHHHH--CCC***CCCCEEEECC----CCC*EEEEECCEEEEEECCCC---EEC***CEEHH*HCCCCCCCCCEEEE*C----------**CEEEEEECCEEEEEECC--CC*E*-----**EEHHH*CCCC------- ----****CC**CCCCCCCEEEE*C-CEEEEEECCEEEE*CC-CC*CC*--EEEHHH*CCCCCCCCCEEEE***-*C*EEEEECCEEEEEEC---CEEC-CCCEEHHHH*-CCC-**CCCCEEEECC----CCCEEEEEECCEEEEEECCCC---EEC***CEEHH*HCCCCCCCCCEEEE*------------*CEEEEEECCEEEEEECC--CC*E*-----**EE***-CCC-------- --------CC***--CCCCEEEE*C-CEEEEEECCEEEE**--CC**C****EEHHHHCCCCCCCCCEEEE*C*--C*EEEEECCEEEEEEC---CEEC*CCCEEHHH***CCC*--CCCCEEEECC----CCC*EEEEECCEEEEEECCCC---EEC***CEEHH-HCCCCCCCCCEEEE*C----------**CEEEEEECCEEEEEECC--CC*E**---***EEHHH*CCCCC----** --------CC**C-CCCCCEE***C*CEEEEEECCEEEE**C*CC*CC*--EEEHHHH*-CCCCCCCEEEE*C***C*EEEEECCEEEEEEC---CEEC*CCCEEHHHH**CCC---CCCCEEEECC------CEEEEEECCEEEEEEC--------C---CEEHH*HCCCCCCCCCEEEE*C------------CEEEEEECCEEEEEECC--CC*E********EEHHH*CCCCC*----- 50923.tem _________________________________ --------CC**CCCCCCCEEEE*C*CEEEEEECCEEEE*CC*CC*CC*-*EEEHHHHCCCCCCCCCEEEE*C*-*C*EEEEECCEEEEEEC---CEEC*CCCEEHHHH**CCC***CCCCEEEECC----CCCEEEEEECCEEEEEECCCC---EEC***CEEHH*HCCCCCCCCCEEEE*C----------**CEEEEEECCEEEEEECC--CC*E**---***EEHHH*CCCCC*---** Structural block scores 0 7 - 4.4 M 75.0 75.0 75.0 8.6 41.5 75.0 75.0 8 9 C 4.6 H 7.5 7.8 7.5 3.0 4.0 6.0 5.5 10 11 * 1.0 P 1.5 0.5 0.5 0.5 2.0 1.5 1.5 12 18 C 4.7 H 4.5 13.6 4.9 4.0 3.4 23.9 13.6 19 22 E 4.8 H 0.2 0.8 0.0 0.0 0.5 0.5 0.0 27 32 E 4.9 H 0.2 1.2 1.0 0.7 1.2 0.8 0.7 33 34 C 5.0 H 5.0 3.5 6.5 3.0 4.0 6.0 6.0 35 38 E 5.0 H 2.0 1.5 1.5 0.8 0.2 1.2 1.8 40 41 C 4.3 M 2.5 5.0 40.5 5.5 5.0 40.5 5.8 43 44 C 4.4 M 75.0 7.5 75.0 4.5 7.0 6.0 7.2 46 47 C 4.4 M 75.0 2.5 3.0 2.5 2.5 2.5 2.5 51 53 E 4.7 H 3.7 3.7 4.0 4.0 4.0 2.7 3.7 54 57 H 4.8 H 3.5 5.2 3.5 3.8 2.8 3.8 3.0 58 66 C 4.9 H 3.3 3.4 3.6 2.8 3.2 2.9 10.9 67 70 E 5.0 H 0.2 0.5 0.0 0.2 0.2 0.5 0.0 78 82 E 5.0 H 0.2 0.4 0.8 0.0 0.6 0.6 0.8 83 84 C 5.0 H 4.5 7.0 5.0 5.5 5.0 6.0 5.5 85 90 E 4.9 H 1.2 1.3 2.7 1.7 1.5 1.5 1.8 92 94 - 4.6 H 9.3 75.0 75.0 75.0 75.0 75.0 75.0 96 97 E 4.3 M 4.5 5.5 75.0 4.5 3.0 5.0 6.0 100 102 C 4.5 M 4.8 26.7 29.3 4.0 5.5 4.7 4.2 103 104 E 5.0 H 5.0 5.0 4.5 4.0 4.0 4.0 5.5 105 108 H 4.9 H 3.2 3.0 4.2 2.0 3.0 3.0 3.2 109 110 * 2.8 P 0.5 75.0 2.0 75.0 37.5 4.5 5.2 111 113 C 5.0 H 4.0 2.7 3.7 3.7 4.0 2.3 4.2 114 116 * 3.1 M 5.3 6.2 75.0 5.7 28.0 53.5 75.0 117 120 C 5.0 H 4.0 3.0 3.8 3.8 3.2 2.2 4.0 121 124 E 4.9 H 0.0 1.0 0.0 0.0 0.0 0.5 0.0 125 126 C 4.8 H 2.0 6.2 2.0 2.5 4.5 2.0 1.5 127 130 - 4.6 H 75.0 75.0 5.1 75.0 75.0 75.0 75.0 131 133 C 4.7 H 6.2 30.3 5.3 4.7 4.8 3.0 50.7 134 139 E 4.9 H 1.0 0.8 0.5 0.5 0.7 1.0 1.3 140 141 C 5.0 H 6.0 5.0 7.0 5.5 5.5 6.0 7.0 142 147 E 5.0 H 1.7 2.0 1.2 1.2 1.2 1.7 2.8 148 151 C 4.4 M 4.5 5.4 6.0 5.2 4.5 5.0 56.8 152 154 - 4.6 H 4.0 75.0 75.0 75.0 75.0 75.0 75.0 155 156 E 4.3 M 4.5 2.5 4.0 3.0 3.5 2.0 75.0 158 160 * 3.1 M 75.0 5.3 75.0 6.2 6.8 6.5 75.0 162 163 E 4.6 H 4.0 4.0 6.2 4.5 3.5 5.0 6.0 164 165 H 4.2 M 0.0 3.5 4.0 3.5 1.5 4.0 2.5 168 176 C 4.7 H 50.8 3.5 27.2 3.4 3.7 3.1 3.4 177 180 E 5.0 H 0.0 0.5 0.2 0.0 0.2 0.0 0.0 183 192 - 4.6 H 5.0 75.0 75.0 75.0 75.0 75.0 75.0 193 194 * 3.4 M 8.2 75.0 75.0 9.8 42.0 6.0 75.0 196 201 E 5.0 H 0.7 1.3 1.3 1.2 1.2 1.2 0.7 202 203 C 5.0 H 5.0 4.5 2.5 8.0 4.5 5.5 6.0 204 209 E 4.9 H 0.8 1.5 2.5 2.3 1.7 1.3 1.8 210 211 C 4.6 H 9.2 7.5 1.5 4.0 5.0 5.2 4.5 212 213 - 4.2 M 1.0 9.2 75.0 75.0 75.0 75.0 75.0 214 215 C 4.8 H 5.5 5.5 2.5 3.5 4.5 5.5 3.0 218 219 * 2.8 P 75.0 39.5 6.0 39.0 39.5 5.5 6.2 220 222 - 4.5 M 53.5 75.0 75.0 75.0 75.0 75.0 5.5 223 225 * 1.7 P 3.7 28.0 5.2 29.0 28.0 4.5 3.7 226 227 E 5.0 H 6.5 3.5 2.5 3.5 5.0 3.5 2.5 228 230 H 4.2 M 2.3 1.3 1.0 3.3 1.3 2.3 3.0 232 236 C 4.7 H 3.3 2.0 2.6 15.4 32.7 2.0 3.4 238 240 - 4.6 H 75.0 75.0 4.3 75.0 75.0 75.0 75.0 241 242 * 3.7 M 75.0 10.2 9.0 75.0 75.0 16.5 75.0 >>>>>>