Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bgva2 ------CHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHCCHHHHH-CCHHHHHC--CCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEECC----CCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECC--CCCCCCHHHHHHHHHHHHHHHHH--HCCCCCEEEECCCCCCHHHHHHHHHHHHHHHC---CCCHHHCCC---------- >P1;d1c1da2 ----------------------------------------------------CHHHHH-CCCCCEEEEEEEC-------CCCEEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCHHHCCHHHHHHHHHHHHHHHHH----CCCCEEEEECCCCCHHHHHHHHHHCC------------CCCCCCHHHCCCCC >P1;d1gtma2 ------CCHHHHHHHHHHHHHHH------C------------------CCCHHHHHHHC--CCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCEECCEEECC----CCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC--CHHHCCHHHHHHHHHHHHHHHHH--HCCCCCEECCCCCCCCHHHHHHHHHHHH-HHHCCCCCHHHHCCCCCCCC----- >P1;d1hwxa3 CCCCCCCCHHHHHHHHHHHHHHH------HHHHHHHCCCCCCCCCHHHHHHHHHHHHHC--CCCEEEEEEEEEECCCCCEEEEEEEEEECCCCCCCEEEEEEECC----CCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECC--CHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCHHHHCCCHHHHCCCCCHHHCCC-- >P1;d3vpxa1 ---------------------------------------------------CCHHHHHHHCCCCEEEEEEEC-------CCCEEEEEEEEECCCCCEECCEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC--CCCCCCC---HHHHHHHHHHHHC----CCCCEECCCCCCCCHHHHHHHCCCCC------------CC------------ PSA >P1;d1bgva2 ------0a008501760487179164018005710583176067476358-75303620--605521418040514a6763523000000318523110002015----8063010031004113605849772100000030--41ac2566103200330063025--20129600022374098401930282068229---67669006a---------- >P1;d1c1da2 ----------------------------------------------------84a815-a1a0551243518-------705030000021294440010020341993150053008204612861495a5720000000102443940799206300400030048----16270202326508281024017307------------1051237948292b >P1;d1gtma2 ------68405502761575166------5------------------a278a514721--60332252605061588756603000000148542011001023----8063220213006213604868472000000030--20870565022300220062039--1030830002234506550011004003-63078826068005713a93----- >P1;d1hwxa3 a19a7645318403852579279------51664176283a529671265055517842--50461251604051496663604010000126641010001036----9054420201004102617879463000000030--4197068600440034004100677101195000223750674002100610063506949706600580178491b-- >P1;d3vpxa1 ---------------------------------------------------283a82198390340350539-------a08060000013184530300020660967350051005103811770495a592000000022--4297725---6800520074059----18240204428206880062065109------------20------------ Translating the sequences ------C*HHHHHHHHHHHH******************************-*CHHHHHC--CCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEECC----CCCHHHHHHHHHHHHHHHHHCCCCC*EEEEEE*C--C***CCHHHHHHHHHHHHHHHHH--*CCCCCEEEECCCCCCHHHHHHHHHHHH**H*---CC*HHHCCC---------- ----------------------------------------------------CHHHHH-**CCCEEEEEEE*-------***EEEEEEEEECCCCCEEEEEEE*C*******HHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC**CHHHCCHHHHHHHHHHHHHHHHH----CCCCEEEE*CCCCCHHHHHHHHHH**------------*CCCCC******** ------C*HHHHHHHHHHHH***------*------------------*****HHHHHC--CCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCEE**EEECC----CCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC--CHHHCCHHHHHHHHHHHHHHHHH--*CCCCCEE**CCCCCCHHHHHHHHHHHH-*H****CC*HHHCCCCC***----- ******C*HHHHHHHHHHHH***------************************HHHHHC--CCCEEEEEEEEEECCCCCEEEEEEEEEE**CCCCCEEEEEEECC----CCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEE*C--CHHHCCHHHHHHHHHHHHHHHHH***CCCCCEEEECCCCCCHHHHHHHHHHHH**H****CC*HHHCCCCC******-- ---------------------------------------------------*CHHHHH***CCCEEEEEEE*-------***EEEEEEEEECCCCCEE**EEE*C*******HHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC--C***CC*---HHHHHHHHHHHH*----CCCCEE**CCCCCCHHHHHHH*****------------*C------------ 53223-3.tem _________________________________ ------C*HHHHHHHHHHHH***------*------------------**-*CHHHHHC--CCCEEEEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEECC----CCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC--CHHHCCHHHHHHHHHHHHHHHHH--*CCCCCEEEECCCCCCHHHHHHHHHHHH-*H*---CC*HHHCCCCC***----- Structural block scores 0 5 - 4.5 M 75.0 75.0 75.0 7.3 75.0 8 19 H 4.2 M 3.8 75.0 3.9 4.6 75.0 20 22 * 3.0 P 5.7 75.0 4.3 6.0 75.0 23 28 - 4.5 M 3.3 75.0 75.0 75.0 75.0 30 47 - 3.8 M 4.2 75.0 75.0 4.8 75.0 48 49 * 3.0 P 6.5 75.0 6.2 5.5 75.0 53 57 H 5.0 H 2.8 5.7 3.8 5.0 4.9 59 60 - 3.8 M 75.0 5.8 75.0 75.0 5.5 61 63 C 5.0 H 3.7 5.2 3.0 3.0 4.0 64 73 E 4.7 H 3.0 17.9 3.1 3.0 17.9 74 78 C 4.2 M 5.7 75.0 5.8 5.2 75.0 79 90 E 4.6 H 1.8 1.5 1.8 1.8 2.4 91 95 C 5.0 H 3.8 4.6 4.6 3.8 4.2 96 102 E 4.7 H 0.6 0.4 0.4 0.3 0.7 103 104 C 4.4 M 3.0 3.5 2.5 4.5 6.0 105 108 - 3.8 M 75.0 5.5 75.0 75.0 5.5 109 111 C 3.8 M 4.7 2.0 4.7 4.7 2.7 112 128 H 5.0 H 2.1 3.5 2.5 2.5 3.1 129 133 C 5.0 H 5.8 5.9 5.4 5.8 6.3 134 141 E 4.8 H 0.5 0.1 0.4 0.4 0.2 143 144 - 4.5 M 75.0 3.0 75.0 75.0 75.0 146 148 H 3.8 M 8.0 5.3 5.0 5.7 6.0 149 150 C 5.0 H 3.5 3.5 2.5 3.0 4.5 151 167 H 4.9 H 2.4 2.8 2.5 2.4 16.2 168 169 - 4.5 M 75.0 75.0 75.0 7.0 75.0 171 175 C 4.8 H 3.6 18.2 2.8 3.2 18.0 176 179 E 4.4 M 0.5 1.0 0.5 0.5 1.5 180 185 C 4.9 H 4.2 4.0 3.3 3.8 3.7 186 197 H 4.7 H 3.6 2.9 1.6 1.8 3.8 202 204 - 3.8 M 75.0 75.0 7.7 6.3 75.0 205 206 C 4.2 M 6.5 75.0 4.0 8.0 75.0 208 210 H 4.1 M 5.0 50.3 4.7 4.0 50.7 211 215 C 4.5 M 33.3 2.2 3.2 2.8 60.0 216 218 * 3.0 P 75.0 6.7 7.5 6.3 75.0 219 223 - 4.1 M 75.0 6.5 75.0 34.3 75.0 >>>>>>