Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d4rz9a- --------CCC--CCCCCCCCCC-CCCHHHHCCHHHHHHHHCCHHHHHHCCCCCHHHHHHHHCC-CCCEECEECCCCEECHHHHHHHHHHHHCCCHHHHHHHHH--CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCEEEEECCCCCEEEEEHHHHHHHHHHCCEECCEECCCCCCHHHHHHCCCCCC----------------------- >P1;d5f5ta- CCHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCCHHHHHHHHHCHHHHHHCCCCCHHHHHHHHHHHCCCCCCEECCCCEECHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCEEEEECCC-CEEEEEHHHHHHHHHHCCEECCEECCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCC PSA >P1;d4rz9a- --------593--704a907614-a34005106770172015282065308b072960352037-081000025c91500300000000010108571026005--29843101000000000028131006102403a17460311549274562402600540063a51020701a0673740275a51a6----------------------- >P1;d5f5ta- b5856742760278139807504074101600478015301619106530310849302720562062020118b95700200000000012408792076005810753310000000000000305400530161171937044278b-b263040350052006695101060290572740285930964a2486698636778677888a9 Translating the sequences --------***--CCCCCCCCCC-CCCHHHHCCHHHHHHHH*CHHHHHHCCCCCHHHHHHHH**-CCCEECEECCCCEECHHHHHHHHHHHHCCCHHHHHHHHH--***CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCEEEEECCC*CEEEEEHHHHHHHHHHCCEECCEECCCCCCHHHHHHCCCCCC----------------------- ********HHH**CCCCCCCCCC*CCCHHH*CCHHHHHHHHHCHHHHHHCCCCCHHHHHHHHHH*CCC**CEECCCCEECHHHHHHHHHHHHCCCHHHHHHHHH**HHHCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCEEEEECCC-CEEEEEHHHHHHHHHHCCEECCEECCCCCCHHHHHHCCCCCC*********************** 345917.tem _________________________________ --------HHH--CCCCCCCCCC-CCCHHHHCCHHHHHHHHHCHHHHHHCCCCCHHHHHHHHHH-CCCEECEECCCCEECHHHHHHHHHHHHCCCHHHHHHHHH--HHHCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCEEEEECCC-CEEEEEHHHHHHHHHHCCEECCEECCCCCCHHHHHHCCCCCC----------------------- Structural block scores 0 7 - 3.0 P 75.0 6.1 8 10 H 3.0 P 5.7 4.3 11 12 - 3.0 P 75.0 4.5 13 22 C 5.0 H 4.8 4.5 24 26 C 5.0 H 5.8 4.0 27 30 H 4.5 M 1.5 1.8 31 32 C 5.0 H 3.0 2.0 33 41 H 4.8 H 3.3 3.4 43 48 H 5.0 H 4.0 4.0 49 53 C 5.0 H 5.3 2.4 54 63 H 4.6 H 3.7 3.8 65 67 C 5.0 H 3.0 2.7 68 69 E 3.0 P 0.0 1.0 71 72 E 5.0 H 1.0 1.0 73 76 C 5.0 H 6.9 8.4 77 78 E 5.0 H 2.5 3.5 80 91 H 5.0 H 0.3 0.4 92 94 C 5.0 H 3.0 4.0 95 103 H 5.0 H 2.9 4.0 104 105 - 3.0 P 75.0 4.5 106 108 H 3.0 P 6.3 4.0 110 123 H 5.0 H 0.4 0.3 124 125 C 5.0 H 5.0 1.5 126 138 H 5.0 H 2.4 2.5 139 141 C 5.0 H 4.0 4.3 142 146 E 5.0 H 2.2 3.4 147 149 C 5.0 H 6.0 8.8 152 156 E 5.0 H 4.2 3.0 157 166 H 5.0 H 2.3 2.1 167 168 C 5.0 H 6.8 7.5 169 170 E 5.0 H 3.0 3.0 171 172 C 5.0 H 1.0 0.5 173 174 E 5.0 H 3.5 3.0 175 180 C 5.0 H 4.1 3.8 181 186 H 5.0 H 3.8 3.8 187 192 C 5.0 H 6.3 5.3 193 215 - 3.0 P 75.0 6.9 >>>>>>