Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1p4ua- -----CCCCCCCCC--HHHCCCCCCCCEEEEEE----CCEEEEEEECCCCCCCCCCEEEEEEEEEECCC-CCCEEEEEEEECC----CCCEEEECCCCCCCCCCCCCCCCCCEEEEEEEEECCC----------CCCCCEEEEEEEEEC-----------CEEEEEEEEECCCCCHHHCCCC >P1;d1qtsa1 -----CCCCCCCCCCCCCHHHHCCCCCEEEEEC----CCEEEEEEEEEE-----CCEEEEEEEEEECCC-CCCEEEEEEEECCHHHHHHEEEEECCC-CCCCCCC------CEEEEEEEEEECC----------CCCCCCEEEEEEEEC-----------CEEEEEEEECCCCCCC------ >P1;d1r4xa1 CHHHHHHHHHHCCHHHCCCCCCCEECCCCEECCCCCCCEEEEEEEEECC------CEEEEEEEEEECCCCEEEEEEEEEEEE-CC---CCEECC-CCEE-EECCC------CCEEEEEEEECCCCCCCCC------CEEEEEEEEEEEEECCCCCCCCCCCCEEEEEECCCEEEC----CCC >P1;d2a7ba- -----------------------CCCCEEEEEE----CCEEEEEEE--EECCCCCCEEEEEEEEEECCC-CCCEEEEEEEECC----CCCEEEECCCCCCCCCHHH----CCCEEEEEEEECCC----------CCCCCEEEEEEEEEC-----------CEEEEEEEEECCCCHHHCC--- >P1;d2g30a1 C---------------------CCCCCCEEEECHHHCCCEEEEEEEECC-------CEEEEEEEEECC-CCCCCCCEEEECCCCC---CCEECCCCCCCCCCCCC------CEEEEEEEEEC-----CCCCCCCCCCCEEEEEEECCCC-------------EEEEEEECCCCC-------- PSA >P1;d1p4ua- -----3608a0615--5a60680a493140054----a50402040044109b2820000102040428-7305705060703----a403131072575507334797834403000000027----------75604070504003d-----------b7825265405800518602a0 >P1;d1qtsa1 -----d59b938b13233297039545740244----a10302040719-----96605020203031a-5404706050609b9079204072990-8530608------5524020604246----------709700401040429-----------5663514030002571------ >P1;d1r4xa1 94486148506716607b0980730167445008aa3404050010108------820000040103466110360203072-65---507133-2107-50346------7552010100208866934------802060205020161539698369a06955380650606----991 >P1;d2a7ba- -----------------------a053130055----630403040--731b95831010204020628-5404706060703----a306162493665402175----68303020303046----------646040503030407-----------b683433250570055016--- >P1;d2g30a1 d---------------------98458374103197062020201034a-------923020302052-a650270508055005---0040369080983043a------54370502044-----9156581955310501040314-------------407140513660-------- Translating the sequences -----******CC*--******CCCCCEEEEE*----CCEEEEEEE*CC*****CCEEEEEEEEEECCC-CCCEEEEEEEECC----*CCEEEECCCCCCCCCCC******CEEEEEEEEECCC----------CCCCCEEEEEEEEEC-----------CEEEEEEEE*CCCCC******* -----******CC*********CCCCCEEEEEC----CCEEEEEEEE**-----CCEEEEEEEEEECCC-CCCEEEEEEEECC*******EEEECCC-CCCCCCC------CEEEEEEEEE*CC----------CCCCC*EEEEEEEEC-----------CEEEEEEEECCCCCC*------ ***********CC*********C**CC**EE*C****C*EEEEEEEECC------CEEEEEEEEEECCC****EEEEEEEE*-**---CCEE**-CC**-**CCC------C*EEEEEEEECCC******------C**EEEEEEEEE************C*EEEEEE*CC***C----*** -----------------------CCCCEEEEE*----CCEEEEEEE--******CCEEEEEEEEEECCC-CCCEEEEEEEECC----*CCEEEECCCCCCCCC***----*C*EEEEEEEECCC----------CCCCCEEEEEEEEEC-----------CEEEEEEEE*CCCC*****--- *---------------------CCCCC*EEEEC****CCEEEEEEEECC-------*EEEEEEEEECC-*CCC***EEEE*CC**---CCEE**CCCCCCCCCCC------CEEEEEEEEEC-----*******CCCC*EEEEEE***C-------------EEEEEEECCCCC-------- 49348.tem _________________________________ -----******CC*--******CCCCCEEEEEC----CCEEEEEEEECC-----CCEEEEEEEEEECCC-CCCEEEEEEEECC**--*CCEEEECCCCCCCCCCC------CEEEEEEEEECCC----------CCCCCEEEEEEEEEC-----------CEEEEEEEECCCCCC*------ Structural block scores 0 4 - 4.4 M 75.0 75.0 6.2 75.0 62.7 5 10 * 3.0 P 4.6 8.5 4.0 75.0 75.0 11 12 C 4.2 M 3.5 9.8 4.0 75.0 75.0 14 15 - 3.8 M 75.0 2.5 3.0 75.0 75.0 16 21 * 3.0 P 5.9 4.0 5.9 75.0 75.0 22 26 C 4.7 H 5.3 5.2 3.4 18.7 6.8 27 31 E 4.6 H 2.0 3.4 4.0 1.8 3.0 33 36 - 3.8 M 75.0 75.0 8.0 75.0 4.2 37 38 C 4.8 H 7.8 5.8 2.0 4.5 4.0 39 46 E 4.9 H 1.2 2.0 1.4 10.8 1.0 47 48 C 3.9 M 4.0 5.0 4.0 41.0 7.2 49 53 - 3.8 M 4.7 75.0 75.0 5.9 75.0 54 55 C 4.3 M 5.0 7.5 41.5 5.5 75.0 56 65 E 5.0 H 0.7 1.8 0.7 1.0 2.1 66 68 C 4.8 H 4.7 4.8 4.3 5.3 27.3 70 72 C 4.5 M 3.3 3.0 0.7 3.0 3.7 73 80 E 4.8 H 3.8 3.5 2.6 3.8 3.4 81 82 C 4.5 M 1.5 4.5 38.5 1.5 2.5 83 84 * 3.0 P 75.0 10.2 5.5 75.0 2.5 85 86 - 4.5 M 75.0 3.5 75.0 75.0 75.0 88 89 C 4.5 M 2.0 1.0 2.5 1.5 0.0 90 93 E 4.4 M 2.0 3.2 3.5 3.8 3.2 94 104 C 4.6 H 4.0 11.2 16.2 4.3 5.0 105 110 - 4.3 M 6.3 75.0 75.0 51.8 75.0 112 120 E 4.9 H 0.8 2.6 1.6 1.6 2.8 121 123 C 4.5 M 3.0 4.0 3.3 3.3 51.3 124 133 - 4.3 M 75.0 75.0 33.6 75.0 26.0 134 138 C 4.5 M 4.4 4.6 32.0 4.0 4.6 139 147 E 4.8 H 2.1 1.7 1.7 1.7 1.6 149 159 - 4.5 M 75.0 75.0 5.9 75.0 75.0 161 168 E 4.8 H 4.9 3.5 4.5 4.2 12.0 169 174 C 4.4 M 3.0 2.3 3.8 2.8 15.2 176 181 - 3.8 M 4.4 75.0 40.7 38.7 75.0 >>>>>>