Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ej8a- ---CEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEEC-CEEEEEEEEE---EECC---CEEEEEEEECCCCCC-----------CHHHHCCCEEEECC----------------CCEEECEEEECCCCEEEEEEEEEEC------CCHHHCC---CCEEEEEEE-CC---------CHHHCCCC------------EEEEEEECC------------ >P1;d1pzsa- ---CEEEEEEEC-----CC----CCEEEEEEEEEEC--CEEEEEEEECCCCCCCC----EEECEEEECCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCC------CCCCCCCCCEEECC-------CCCCEEEEEECCCC-----HHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEEECCC----------C >P1;d1xtma- --CCEEEEEEEE-----CC----CCEEEEEEEEECC-CCCEEEEEEEC---CCCC---CCEECEEEECCCCCCCC----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCC-------CCCEEEEEEECCCCCCCCCCCCCCCCCCEEEEEECCCCCCC-------------------CCCCCCCCCEEEEEEEC-----------C >P1;d2aqma- ---CEEEEEEEEEE---CCEE--EEEEEEEEEECCC--CCEEEEEEEC---CCCC----EEECEEEECCCCCCC-EEECC--EEECCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC-------CCCEEEEEEECCCC----CHHHHC---CEEEEEECCCCCCCCC-----------------CCHHHHCCCEEEEEEEC------------ >P1;d2jlpa- CCCEEEEEEEEECC---CCCCCCCCCEEEEEEEECCCCCCEEEEEEEE---CCCCCCCEEEEEEEEECCCCCC-----------CHHHHHCCCCCCCCCCCC------CCCCEEEEEEEE--------CCCEEEEEEEECCCCCC--CCCCC---CCEEEEECCCCCCCCCC-------------CCCHHHHCCCCCEEEEEECEECCCHHHHHHHC >P1;d3f7la- --CCEEEEEECC---------CCC-CEEEEEEEEECC--EEEEEEEEE---CCC----CEEEEEEEECCCCCC-----------CCCHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEECC-------CCCEEEEEEECCCCCCC--CCCCC---CCEEEEECCCCCCCCCC-------------CCCHHHHCCCCCEEEEEECEECC--------- PSA >P1;d1ej8a- ---65020603034a073062885440150504247a-7504030406---0001---234050101361629-----------7126203842350a----------------73060593348c4601206260407------1008305---620000218-06---------64771729------------500001408------------ >P1;d1pzsa- ---730403032-----38----8750040504159--c4030403026783085----86000000410515481534a79945403100700318c7aa------27010105107069-------60107152528407-----492037b7300000047604509336a7652b7765025870455040a913000301a----------b >P1;d1xtma- --a374506022-----47----1650330202509-98201020204---4065---80500000054031756----------408531501216a4400371770400000410808a-------61506451405401087c3830014b500000004540536-------------------55840705522000206-----------a >P1;d2aqma- ---64350604203---6905--254033040412a--9104060504---6085----960000004534152-6768a--853202404800138838504008590040002305079-------81506330302408----607403---6300000663052349-----------------7675010c711000208------------ >P1;d2jlpa- cb141010706108---406ba12604520002066593702000207---604698a443100000460538-----------810520560031783503------601000320507--------80506632760602038--84203---7200000366034074b-------------68404650409620000408828544177258 >P1;d3f7la- --5440305074---------b18-0634060435cb--400043502---708----385000000450479-----------8a07205900325935000282950000000007099-------81406083507304068--92202---7200000565023064b-------------6a50563040792200340873a--------- Translating the sequences ---CEEEEEEE******CC****CCEEEEEEEEE***-C*EEEEEEE*---**CC---*EEE*EEEECCCCCC-----------C**HH*CC****CC----------------CCEEEC***********EEEEEEEC------*****CC---CCEEEEE**-CC---------********------------*EEEEEECC------------ ---CEEEEEEE*-----CC----CCEEEEEEEEE*C--C*EEEEEEE****CCCC----EEE*EEEECCCCCC***********CCCHHHCCCCCCCCCCC------CCCCC**CCEEECC-------CCC*EEEEEECCCC-----********CCEEEEECCCCCCCCC*******************HHCCCCCEEEEEECC*----------* --*CEEEEEEE*-----CC----CCEEEEEEEEE*C-*C*EEEEEEE*---CCCC---**EE*EEEECCCCCC**----------CC***CCCCCCCCCCCC*****CCCCC**CCEE*CC-------CCCEEEEEEECCCC********CC***C*EEEEECCCCCCC-------------------****CCCCCEEEEEE*C-----------* ---CEEEEEEE***---CC**--**EEEEEEEE**C--C*EEEEEEE*---CCCC----EEE*EEEECCCCCC*-*****--***CCHHHCCCCCCCCCCCC*****CCCCC**CCEEECC-------CCCEEEEEEECCCC----*****C---C*EEEEECCCCCCCCC-----------------**HH**CCCEEEEEE*C------------ ****EEEEEEE***---CC****CC*EEEEEEEE*C**C*EEEEEEE*---CCCC****EEE*EEEECCCCCC-----------C**HHHCCCCCCCCCCCC------CCCC****EEE*--------CCCEEEEEEE*CCC***--***CC---CCEEEEECCCCCCCCC*-------------*****HHCCCCCEEEEEEC************* --*CEEEEEE**---------**C-*EEEEEEEE*C*--*EEEEEEE*---CCC----*EEE*EEEECCCCCC-----------CCCHHHCCCCCCCCCCCC*****CCCCC****EEECC-------CCCEEEEEEECCCC***--***CC---CCEEEEECCCCCCCCC*-------------*****HHCCCCCEEEEEEC****--------- 49329.tem _________________________________ --*CEEEEEEE***---CC****CCEEEEEEEEE*C*-C*EEEEEEE*---CCCC---*EEE*EEEECCCCCC*----------CCCHHHCCCCCCCCCCCC*****CCCCC**CCEEECC-------CCCEEEEEEECCCC***-****CC---CCEEEEECCCCCCCCC*-------------*****HHCCCCCEEEEEECC*----------* Structural block scores 0 1 - 4.5 M 75.0 75.0 75.0 75.0 12.0 75.0 4 10 E 4.9 H 2.3 1.9 3.4 3.1 2.1 2.7 11 13 * 2.6 P 2.3 50.7 50.7 1.7 3.0 51.3 14 16 - 4.5 M 5.8 75.0 75.0 75.0 75.0 75.0 17 18 C 4.5 M 1.5 5.5 5.5 7.5 2.0 75.0 19 22 * 3.4 M 6.0 75.0 75.0 38.8 7.2 40.6 23 24 C 4.3 M 4.5 7.5 3.5 3.5 4.0 41.5 25 33 E 4.8 H 2.3 2.1 2.2 2.1 1.4 2.9 40 46 E 5.0 H 1.6 1.4 0.7 2.1 0.6 1.7 48 50 - 4.5 M 75.0 7.0 75.0 75.0 75.0 75.0 51 54 C 4.6 H 0.2 4.0 3.8 4.8 4.0 22.5 55 57 - 4.5 M 75.0 75.0 75.0 75.0 9.2 75.0 59 61 E 4.8 H 2.3 4.7 1.7 5.0 2.7 4.3 63 66 E 5.0 H 0.5 0.0 0.0 0.0 0.0 0.0 67 72 C 5.0 H 4.5 2.7 3.3 3.7 4.3 4.8 74 83 - 4.2 M 75.0 6.0 68.1 27.6 75.0 75.0 84 86 C 4.1 M 3.3 3.0 26.3 1.7 3.0 6.2 87 89 H 4.4 M 2.7 1.3 5.3 2.0 2.3 3.0 90 101 C 4.6 H 28.0 11.2 2.9 4.0 3.4 3.4 102 106 * 3.4 M 75.0 75.0 5.0 3.4 75.0 4.2 107 111 C 4.5 M 75.0 2.0 0.8 2.6 16.4 1.0 112 113 * 1.9 P 75.0 0.5 0.0 0.0 0.0 0.0 114 115 C 4.1 M 5.0 3.0 2.5 2.5 2.5 0.0 116 118 E 4.8 H 2.0 2.3 2.7 1.7 1.7 2.3 119 120 C 4.3 M 7.0 7.5 9.2 8.0 41.0 9.0 121 127 - 4.5 M 5.8 75.0 75.0 75.0 75.0 75.0 128 130 C 4.5 M 1.0 2.3 4.0 4.7 4.3 4.3 131 137 E 4.9 H 2.6 3.1 2.9 2.1 4.3 3.1 138 141 C 4.5 M 58.0 4.8 2.5 3.5 2.0 3.5 142 144 * 3.4 M 75.0 75.0 5.0 75.0 3.7 4.7 146 149 * 1.6 P 2.8 22.5 3.5 4.2 22.2 22.0 150 151 C 4.3 M 2.5 1.5 0.5 1.5 1.5 1.0 152 154 - 4.1 M 75.0 8.5 6.8 75.0 75.0 75.0 155 156 C 4.5 M 4.0 1.5 0.0 4.5 4.5 4.5 157 161 E 5.0 H 0.4 0.0 0.0 0.0 0.0 0.0 162 170 C 4.6 H 43.3 4.2 19.7 4.2 3.7 3.4 172 184 - 4.3 M 32.2 5.8 75.0 75.0 75.0 75.0 185 189 * 2.8 P 75.0 4.8 47.0 47.6 4.4 5.3 190 191 H 4.2 M 75.0 5.0 6.0 6.0 5.5 4.5 192 196 C 4.4 M 61.0 4.7 3.4 4.1 3.8 4.0 197 202 E 5.0 H 0.8 1.2 1.0 0.7 1.0 1.8 203 204 C 4.1 M 4.0 0.5 3.0 4.0 4.0 4.0 206 215 - 4.4 M 75.0 75.0 75.0 75.0 4.5 61.4 >>>>>>