Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1n1ca1 --CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHHHHCC-CCCCCHHHHCC-------HHHCCCHHHHHC-----CCCCCC-----CHHHCCCCCCC--CHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHHHHHHHHHCCC------------- >P1;d1s9ua1 CCCCCCCHHHHHHHHHHHHHHCCC----C----CCCCHHHHHHHHHCCCHHHCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHCCCCC--CCCHHHHHHHHCC-CCCCC----------CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHCHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC---------- >P1;d2o9xa1 ----------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCC >P1;d2xola1 ----CHHHHHHHHHHHHHHHHHHH----CCCCCCHHHHHHHHCCC-----------------CCCCCCC-----HHHHH-----------CCCHHH-HCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH-HHHHHHHHCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCC------------------ PSA >P1;d1n1ca1 --a7776766747715722616307793175026a9239405720669a55b8057427405708----7883188317713a520a-95135685676-------898687997747-----732778-----88877276475--76168629556116314750254078418726662c--47717506811770673177155428889------------- >P1;d1s9ua1 8a8967642060042001003340----7----2a604640640356b249902089a406601705682926137015400518aa1201020000018825--4519206504809-62a1a----------705010020023005004482681031000410000074004100760-9020040003004300740487083923b37334---------- >P1;d2o9xa1 ----------------------------------------------------------------------------------------------------------------------------------------6711370461af7a5dca57a7348517820b505011044a4760160540959c27401001222243272394934105199637130 >P1;d2xola1 ----62990150030006003201----475a047804620365a-----------------9050807-----29504-----------601004-128b15a952a7127505700952a1a04705000000003000600540460694959a4157024-001600330032006104825005201720470073067315c8------------------ Translating the sequences --**C**HHHHHHHHHHHHHH************C***HHHHH**********************C----*****HHHHH********-**CCCHHH**C-------**H***HHHH**-----C*****-----****C******--*HHHH*CCHHHHHHHHHHHC***HHH*HHHHHH*CC--*HHHHHHHHHHHHHHHHHHH*H****CCC------------- ****C**HHHHHHHHHHHHHH***----*----C***HHHHH**********************C*********HHHHH***********CCCHHH**C****--***H***HHHH**-****C----------****C*********HHHHCCCHHHHHHHHHHHC***HHH*HHHHHH*C-CC*HHHHHHHHHHHHHHHHHHH******CCC***---------- ----------------------------------------------------------------------------------------------------------------------------------------**C*************CCC***HHHHHHHHC**************CCCC*********************H****CCC************* ----C**HHHHHHHHHHHHHH***----*****C***HHHHH***-----------------**C****-----HHHHH-----------CCCHHH-*C*********H***HHHH*******C************************HHHHCCCHHHHHHHHH-H****HHH*HHHHHH*CCCC*HHHHHHHHHHHHHHHHHHH*H**------------------ 89155.tem _________________________________ --**C**HHHHHHHHHHHHHH***----*****C***HHHHH**********************C*********HHHHH********-**CCCHHH**C****--***H***HHHH**-****C*****-----****C*********HHHHCCCHHHHHHHHHHHC***HHH*HHHHHH*CCCC*HHHHHHHHHHHHHHHHHHH*H****CCC***---------- Structural block scores 0 1 - 4.3 M 75.0 9.2 75.0 75.0 2 3 * 3.5 M 8.8 8.5 75.0 75.0 5 6 * 2.3 P 6.5 6.5 75.0 5.5 7 20 H 4.3 M 4.9 1.6 75.0 1.9 21 23 * 2.3 P 3.0 2.3 75.0 1.0 24 27 - 4.3 M 6.5 75.0 75.0 75.0 28 32 * 3.3 M 3.0 61.4 75.0 5.3 34 36 * 2.3 P 7.2 5.5 75.0 5.0 37 41 H 4.3 M 4.2 4.0 75.0 3.0 42 63 * 3.2 M 5.0 4.5 75.0 59.3 65 73 * 3.5 M 36.3 4.3 75.0 43.3 74 78 H 4.3 M 5.4 3.2 75.0 4.0 79 86 * 3.5 M 4.9 4.9 75.0 75.0 88 89 * 3.5 M 7.0 1.0 75.0 75.0 90 92 C 4.3 M 3.0 1.0 75.0 2.3 93 95 H 4.3 M 6.3 0.0 75.0 1.3 96 97 * 2.9 P 6.5 0.0 75.0 38.0 99 102 * 3.5 M 75.0 5.8 75.0 6.4 103 104 - 4.3 M 75.0 75.0 75.0 9.8 105 107 * 2.7 P 30.7 3.3 75.0 5.8 109 111 * 2.3 P 7.0 2.7 75.0 3.3 112 115 H 4.3 M 8.0 4.2 75.0 4.2 116 117 * 2.3 P 5.5 4.5 75.0 0.0 119 122 * 3.5 M 75.0 4.9 75.0 4.6 124 128 * 3.5 M 5.4 75.0 75.0 3.2 129 133 - 4.3 M 75.0 75.0 75.0 0.0 134 137 * 1.6 P 7.8 3.0 40.8 0.8 139 147 * 1.3 P 20.9 0.8 6.1 2.1 148 151 H 4.3 M 5.2 2.2 9.0 5.2 152 154 C 4.8 H 5.7 4.7 9.3 6.0 155 165 H 4.7 H 4.0 2.2 5.7 10.7 167 169 * 1.0 P 3.7 0.0 5.5 2.3 170 172 H 4.3 M 5.0 3.7 2.0 2.0 174 179 H 4.3 M 5.0 2.0 4.9 1.8 181 184 C 4.5 M 41.1 21.0 1.8 3.5 186 204 H 4.3 M 4.6 2.3 3.5 2.8 207 210 * 1.6 P 4.8 4.2 5.2 42.6 211 213 C 4.3 M 8.3 7.2 5.3 75.0 214 216 * 3.5 M 75.0 3.3 1.7 75.0 217 226 - 4.3 M 75.0 75.0 4.4 75.0 >>>>>>