Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1kf6b1 -------------------------------------------------------------C-HHHHHHHHHCCCCCCCC-CCCHHHCCCCCCHHHHHCCHHHHCCCCCCHHHHHCHHHHHCC-CCCCHHHHHHHHHHHCCCCCCC-CHHHHHHHHC-----CCCHHHCCCCCHHHHHCCC-----CCCHHHHHHHHHHHHHHHHHHHH---------CCCC >P1;d2bs2b1 -------------------------------------------------------------CHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHCCHHHHHCC-CCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHCC-----CCCHHHCCCCCHHHHHCCC-----CCCHHHHHHHHHHHHCCCC----------------- >P1;d2h88b2 -------------------------------------------------------------C-HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCHHHCHHHHHHCCCCCHHHHHHHHHHHHCCCCCCC-C-CCCHHHCC-----CCCCCCCCCCCHHHHHCCC-----CCCHHHHHHHHHHHHHHCC----------------- >P1;d6lumb2 -------------------------------------------------------------C-HHHHHHHCCCCCCCCCC--CCCCCCCCCCCCCCHHHHCCCCCCCCCCCCHHHCHHHHCC-CCCCCHHHHHHHHHHHCCCCCCC-HHHHHHHCCC-----CCCHHHCCCCCHHHHHCCC-----CCCHHHHHHHHHHHHHCC------------------ >P1;d7m32a1 CCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC--HHHHHHHHHHCCCCC----------------------------------CCHHHHCCCCCCCHHHHHHHHHC--------CCHHHHHHHHHHHCCCHHHHHHHCCHHHCCHHHCHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCC PSA >P1;d1kf6b1 -------------------------------------------------------------6-83067017404163282-b36a969a3905995476076039155305108014229837-7000000001001102043060-48400a4034-----9400411654260283134-----90400400451172066387866---------768a >P1;d2bs2b1 -------------------------------------------------------------7bb30870274040532399b56a87996927783676175053163305118217017569-700000000100100204505063750381006-----9500231464441374143-----902056204303720771b----------------- >P1;d2h88b2 -------------------------------------------------------------5-a706712960416222685877b69a4a17a9347505714315230510521201573275010000000011101043042-4-60065055-----7310431674441293144-----a15007006303730783a----------------- >P1;d6lumb2 -------------------------------------------------------------5-87036325404062417--9a6498939159845660450331523051062131266a-89010000001002101043060-4a50283045-----9200420664640293144-----805016006402530576------------------ >P1;d7m32a1 a69a75899568747a69b9a8a5a688866776767739893975a9aa8a9895a3a541a--581028106315229----------------------------------90312541656030430042018--------661530074036417702620373729921254150993a65103010000100432784a47a7467935688839 Translating the sequences -------------------------------------------------------------C-HHHHHHHHHCCCCCCCC-CCC***CCCCCCHHHHH******CCCCCC**HHHCHHHHHCC-CCC*HHHHHHHHHHHCCCCCCC-*HHHHHHH*C-----CCCHHHCCCCCHHHHHCCC-----CCCHHHHHHHHHHHHHH******---------**** -------------------------------------------------------------C*HHHHHHHHHCCCCCCCC*CCCCCCCCCCCCHHHHH******CCCCCC**HH*CHHHHHCC-CCCHHHHHHHHHHHHCCCCCCC*HHHHHHHHCC-----CCCHHHCCCCCHHHHHCCC-----CCCHHHHHHHHHHHH**C*----------------- -------------------------------------------------------------C-HHHHHHHHHCCCCCCCC*CCCCCCCCCCCCHHHHH******CCCCCC**HHHCHHHHH*CCCCCHHHHHHHHHHHHCCCCCCC-*-***HHHCC-----CCC***CCCCCHHHHHCCC-----CCCHHHHHHHHHHHHHHC*----------------- -------------------------------------------------------------C-HHHHHHH**CCCCCCCC--CCCCCCCCCCC***HH******CCCCCC**HHHCHHHH*C-CCCC*HHHHHHHHHHHCCCCCCC-HHHHHHH*CC-----CCCHHHCCCCCHHHHHCCC-----CCCHHHHHHHHHHHHH*C------------------ *************************************************************C*--HHHHHHH***CCCCC----------------------------------*CHHHH*CCCCCCHHHHHHHHH*--------C*HHHHHHHH**********HHHCC*****HHHC*******CCC*HHHHHHHHHHHHH******************* 46548.tem _________________________________ -------------------------------------------------------------C-HHHHHHHHHCCCCCCCC-CCCCCCCCCCCCHHHHH******CCCCCC**HHHCHHHHHCCCCCCHHHHHHHHHHHHCCCCCCC-HHHHHHHHCC-----CCCHHHCCCCCHHHHHCCC-----CCCHHHHHHHHHHHHHHC*----------------- Structural block scores 0 60 - 4.5 M 75.0 75.0 75.0 75.0 7.6 63 71 H 4.8 H 4.0 4.7 5.4 4.2 19.4 72 79 C 4.8 H 3.2 3.2 2.9 3.0 3.5 81 92 C 4.4 M 6.9 7.5 7.2 12.4 75.0 93 97 H 4.3 M 6.8 6.2 6.7 6.4 75.0 98 103 * 2.1 P 3.7 4.0 3.7 3.0 75.0 104 109 C 4.5 M 3.8 2.7 2.3 2.3 75.0 110 111 * 2.1 P 3.0 3.0 3.0 3.0 75.0 112 114 H 4.3 M 2.7 3.7 2.3 2.7 53.0 116 120 H 4.8 H 5.0 4.0 3.0 3.6 3.0 121 126 C 4.7 H 15.3 16.2 3.0 17.2 3.5 127 138 H 4.8 H 0.2 0.2 0.2 0.3 14.3 139 145 C 4.6 H 2.1 2.3 2.0 2.0 65.1 147 154 H 4.5 M 3.8 3.4 12.0 4.1 2.5 155 156 C 4.2 M 3.5 3.0 5.0 4.5 4.5 157 161 - 4.5 M 75.0 75.0 75.0 75.0 3.8 162 164 C 4.5 M 4.3 4.7 3.7 3.7 3.3 165 167 H 4.5 M 1.7 1.7 2.3 2.0 3.3 168 172 C 4.7 H 3.6 3.8 4.4 4.4 6.0 173 177 H 4.8 H 3.8 3.8 3.8 3.6 2.8 178 180 C 4.7 H 2.7 2.7 3.0 3.0 2.0 181 185 - 4.5 M 75.0 75.0 75.0 75.0 7.5 186 188 C 5.0 H 4.3 3.7 5.5 4.3 2.0 189 202 H 4.8 H 2.6 3.3 3.1 2.8 1.5 205 221 - 4.2 M 43.1 75.0 75.0 75.0 6.8 >>>>>>