Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1g4ia- ---------------CHHHHHHHHHHHCC--------------------------CCCHHHHCCCCCCCCCCCCC------CCCCCHHHHHHHHHHHHHHHHHHCHHHHHCCCCHHHCCCCEEEECCEEEECC-------CCCHHHHHHH-----HHHHHHHHHHHCC--CCC-----------HHHCCCCHHHC----------------- >P1;d1lwba- CCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHCCCCH-----------------------------------HHHHHHHH-----HHHHHHHHHHCCC-------------------------------------------- >P1;d1poca- -------------------------------------------------------------CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC-----------------CEECCCCEECCEECCCCCCEECHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCEEEEECCEEECCCCCCCCCCCCEECCCCCCEEEEECCCCC >P1;d2g58a- ---------------CHHHHHHHHHHHHC---------------------------CCHHHHCCCCCCCCCCCCC------CCCCCHHHHHHHHHHHHHHCCC--------CCCCCCCCCCEEEECCEEEECC--------CCHHHHHHH-----HHHHHHHHHHHHHHHHCC-----------HHHCCCCHHHCC-----------CCCCC >P1;d5owca- ---------------CHHHHHHHHHHHCC---------------------------CCHH-HHCCCCCCCCCCCC------CCCCCHHHHHHHHHHHHHHHHHHC------CCCCCCCCCCEEEECCEEEECC-------CCCHHHHHHH-----HHHHHHHHHHHCC--CCC-----------HHHCCCCHHHCCC----------CCCCC PSA >P1;d1g4ia- ---------------26701150040125--------------------------9060683065000104bc08------59121500500371362076057394078591607709071739a670713b-------a067025300-----6003600240171--733-----------88237174852----------------- >P1;d1lwba- 33b626810470044658009602503674a738718051724408813a2568060850000020023005759------52a8207200400230033308a2ac-----------------------------------a6392057-----005601532397f-------------------------------------------- >P1;d1poca- -------------------------------------------------------------91372010056a45096795328275004002713408-----------------3307384733c16081a2410217105701640490728a00661044101638040035123357284548a12261514786946222020441 >P1;d2g58a- ---------------17a21360054108---------------------------3728510330000059495------090222006001704132a807--------a0818838080536c9704049--------678324500-----600270053058228603-----------871291588409-----------a95a7 >P1;d5owca- ---------------06802570031115---------------------------2627-10660000049b13------060127005000804001550575------a0605837061735b8606129-------1868215200-----6003700640180--a14-----------8713714895069----------a32a7 Translating the sequences ---------------CHHHHHHHHHHH*C--------------------------*CCHHHHCCCCCCCCCCCCC------CCCCCHHHHHHHHHHHHHHHH**C******CCC***CCCCEEEECCEEEECC-------*CCHHHHHHH-----HHHHHHHHHHHCC--CCC-----------HHHCCCCHHHC----------------- ***************CHHHHHHHHHHH*****************************C*HHHH************C------C****HHHHHHHHHHHHHHHH**C**-----------------------------------*HHHHHHH-----HHHHHHHHHH*CC-------------------------------------------- -------------------------------------------------------------*CCCCCCCCCCCCC******CCCC*HHHHHHHHHH***-----------------C**CC**EECCEE**CC**********HHHHHHH*****HHHHHHHHHHH*C**CC***************CCCC****************CCCCC ---------------CHHHHHHHHHHH*C---------------------------CCHHHHCCCCCCCCCCCCC------CCCCCHHHHHHHHHHHHHH***--------CCC**CCCCCEEEECCEEEECC--------CCHHHHHHH-----HHHHHHHHHHH*****CC-----------HHHCCCCHHHC*-----------CCCCC ---------------CHHHHHHHHHHH*C---------------------------CCHH-H*CCCCCCCCCCCC------CCCCCHHHHHHHHHHHHHHHH**C------CCC**CCCCCEEEECCEEEECC-------*CCHHHHHHH-----HHHHHHHHHHHCC--CCC-----------HHHCCCCHHHC**----------CCCCC 48619.tem _________________________________ ---------------CHHHHHHHHHHH*C---------------------------CCHHHHCCCCCCCCCCCCC------CCCCCHHHHHHHHHHHHHHHH**C------CCC**CCCCCEEEECCEEEECC-------*CCHHHHHHH-----HHHHHHHHHHHCC--CCC-----------HHHCCCCHHHC*-----------CCCCC Structural block scores 0 14 - 4.5 M 75.0 4.0 75.0 75.0 75.0 16 26 H 4.5 M 2.3 3.5 75.0 3.6 3.0 29 55 - 4.5 M 72.6 4.8 75.0 75.0 75.0 56 57 C 4.3 M 3.0 4.0 75.0 5.0 4.0 58 61 H 4.4 M 4.2 1.2 58.5 4.0 21.2 62 74 C 4.5 M 3.7 2.5 3.4 2.9 3.1 75 80 - 4.5 M 75.0 75.0 6.0 75.0 75.0 81 85 C 4.5 M 3.6 5.5 4.4 2.6 1.8 86 101 H 4.8 H 2.8 1.7 16.2 2.8 2.2 102 103 * 2.5 P 6.0 9.2 75.0 41.0 6.0 105 110 - 4.3 M 5.5 53.8 75.0 75.0 75.0 111 113 C 4.2 M 5.3 75.0 75.0 6.2 5.5 114 115 * 3.0 P 3.5 75.0 75.0 4.5 2.5 116 120 C 4.3 M 4.6 75.0 3.2 5.4 4.8 121 124 E 4.3 M 5.0 75.0 5.5 3.5 4.0 125 126 C 4.5 M 8.2 75.0 7.8 10.8 9.8 127 130 E 4.3 M 3.8 75.0 3.8 2.8 3.2 131 132 C 4.5 M 7.2 75.0 5.8 6.5 5.5 133 139 - 4.5 M 75.0 75.0 2.4 75.0 75.0 141 142 C 3.9 M 3.0 42.8 2.5 6.5 7.0 143 149 H 5.0 H 2.4 4.6 3.1 3.1 2.6 150 154 - 4.5 M 75.0 75.0 5.2 75.0 75.0 155 165 H 5.0 H 2.0 3.1 3.0 2.5 2.5 166 167 C 4.2 M 4.0 14.8 3.5 5.0 4.0 168 169 - 3.8 M 75.0 75.0 5.5 5.0 75.0 170 172 C 4.2 M 4.3 75.0 1.3 3.0 5.2 173 183 - 4.5 M 75.0 75.0 3.5 75.0 75.0 184 186 H 4.1 M 6.0 75.0 4.3 5.3 5.3 187 190 C 4.5 M 4.5 75.0 5.4 4.2 3.8 191 193 H 4.1 M 5.7 75.0 3.0 6.7 7.3 196 206 - 4.4 M 75.0 75.0 4.5 75.0 69.0 207 211 C 4.2 M 75.0 75.0 2.2 8.4 6.6 >>>>>>