Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1d5ya3 --------------------CCCCCCEEEEEECCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEE-HHHH-----HHHCCCCEEEEECCEEEEEEEEEEE--HHHHHHHHHHHHHCHHHHCC-CEECCCCEEEEECHHHCCCCCEEEEEEEEEEEC- >P1;d1jyha- ------------------------CCCEEEEECCEEEEEEEEEC--CHH---HHHHHHHHHHHHHHHHC-CCCCCEEEEEECCCCCCCCHHH--CEEEEEEEECCCC---CCCCCCCCCEEEEECCEEEEEEEEEEC--CCCCHHHHHHHHH-HHCCCCCEEECCCCEEEEECCCHHHHC-CEEEEEEEEEEEC >P1;d1r8ea2 -----------------------CCCCEEEEECCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHC----CCCCCEEEEECCCCCCCHHH--CCCCEEEEECCCC---CCCCCCCCCCEEEEECCEEEEEEEEECC--HHHHHHHHHHHHH-HHHHCC-CCEEEEEEEEEEECCCCCCCCCEEEEEEEEEC-- >P1;d2gova1 CCCCCCCCCCCCEEE--EEEECCCCEEEEEECCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCC---CCCCCCEEEEEECCCHHHHCCCCCCCCCCEEEEECCCCEEEEEEECCCCCHHHHHHHHHHHHH-HCCCC-CCCCCCCCEEEEECCCCCCCCCCCEEEEEECC--- >P1;d3r8ja- -----CCCCCCEECCCCCCCCCC--CCEEEEECCEEEEEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCC--CCCC-CEEEEEEEECCHHHHCCCCCCCCCCEEEEEECCEEEEEEEECCCCCHHHHHHHHHHHHH-HHHHC-CCCCCCCCEEEEECCCCCCCCCCCEEEEEECC--C PSA >P1;d1d5ya3 --------------------b5a228382261a63501032651a056752194067015601560296058506201001446629877865532000002-6a30-----7b30790481606174001021745--3950380042049401562b-0523a300002011452ca66714000000075- >P1;d1jyha- ------------------------2c181571a61100014051--419---71286015405800872-a091623000121639726597--0400000002691---932aa0bb0335507253000062507--aa63560175048-20772a72522823200014360774a-3320200000554 >P1;d1r8ea2 -----------------------53606147285340000708722077179830540272035009----95051200004157184285--050520001153a---7a18b24970643203645000030344--8a50460034017-20755a-2724220101341347589a753303000306-- >P1;d2gova1 caa875556265935--67807b90611114001030000416a450550165025207402726065624660a4230100305b---837065202010100482009106243b40404657b120000412a5054541170065048-107b3-92725931010052586a76659410000035--- >P1;d3r8ja- -----b3430a3962a667a34c--4041040673300004271560560077017303300614046837092000000214479--4993-523010001007922a8006041b605137096110002409a6044730651184017-20583-a26034712000002104803c4400000235--b Translating the sequences --------------------*CCCCC*EEEEECCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHH***CCCCCCCEEEEEE***CCCCCCC***EEEEEEE-*HHH-----***CCCCEEEEECCEEEEEEEEE**--HHHHHHHHHHHHH*HHHHCC-C*ECCCCEEEEEC***CCCCC*EEEEEEEEE**- ------------------------CCCEEEEECCEEEEEEEEEC--CHH---HHHHHHHHHHHHHH**C-CCCCC*EEEEE*CCCCCCC***--CEEEEEEE*C***---CCCCCCCCCEEEEECCEEEEEEEEE*C--****HHHHHHHHH-HH**CCC**ECCCCEEEEECCC****C-CEEEEEEEEE*** -----------------------CCCCEEEEECCEEEEEEE**CCCC****HHHHHHHHHHHHHHHC----CCCCCEEEEE*CCCCCC***--CC**EEEEECC**---CCCCCCCCCCEEEEECCEEEEEEEEECC--HHHHHHHHHHHHH-HHHHCC-CCE****EEEEE*CCCCCCCCCEEEEEEEEE*-- ***************--****CCCC**EEEE*CC*EEEEEEEECCC*HHHHHHHHHHHHHHHH***C*CCCCCCCC*EEEEECCCC---CCC*CCEEEEEE*CCHHH**CCCCCCCCC*EEEE*CC*EEEEEEE*CC**HHHHHHHHHHHHH-H***C-CCC*CCCCEEEEECCCCCCCCCC*EEEEEE**--- -----****************CC--CCEEEEECCEEEEEEEEE*CC*HHHHHHHHHHHHHHH****C*CCCCCCCC*EEEEE*CCC--CCCC-C*EEEEEEECCHHH**CCCCCCCCC*EEEEECCEEEEEEEE*CC**HHHHHHHHHHHHH-HHHHC-CCC*CCCCEEEEECCCCCCCCCC*EEEEEE**--* 55136.tem _________________________________ --------------------*CCCCCCEEEEECCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHC*CCCCCCCCEEEEEECCCCCCCCCC-CCEEEEEEECCHHH--CCCCCCCCCCEEEEECCEEEEEEEEECC--HHHHHHHHHHHHH-HHHHCCCCCECCCCEEEEECCCCCCCCCCEEEEEEEEE*-- Structural block scores 0 19 - 4.0 M 75.0 75.0 75.0 13.5 23.4 21 26 C 4.2 M 5.1 40.1 27.3 5.8 28.4 27 31 E 4.9 H 3.8 4.4 4.0 1.4 1.8 32 33 C 5.0 H 8.2 8.2 6.5 0.5 6.5 34 42 E 4.8 H 2.8 1.3 2.4 1.6 2.1 43 46 C 4.3 M 4.1 38.8 2.8 4.9 3.0 47 65 H 4.6 H 3.7 14.8 3.7 3.1 2.8 68 75 C 4.7 H 4.0 13.2 30.6 4.8 3.6 76 81 E 4.6 H 1.0 1.0 1.0 1.0 0.5 82 91 C 4.2 M 6.3 5.5 11.6 26.2 19.9 93 94 C 3.9 M 4.0 37.5 2.5 5.5 3.5 95 101 E 4.8 H 0.6 0.6 1.1 0.9 0.7 102 103 C 4.3 M 40.5 1.0 3.0 0.0 0.0 104 106 H 3.9 M 4.5 5.3 29.5 4.7 6.0 107 108 - 3.8 M 75.0 75.0 75.0 0.0 6.2 109 118 C 4.5 M 26.2 13.3 6.0 4.0 3.6 119 123 E 4.9 H 3.8 3.2 3.0 3.8 3.2 124 125 C 5.0 H 3.5 4.5 4.5 9.2 7.5 126 134 E 4.8 H 2.4 2.3 1.7 1.1 1.9 135 136 C 4.2 M 4.5 3.5 4.0 7.8 8.2 137 138 - 3.8 M 75.0 75.0 75.0 2.5 2.0 139 151 H 4.8 H 3.6 5.1 3.7 3.5 3.6 153 156 H 4.3 M 3.0 4.0 3.5 4.9 3.8 157 161 C 4.3 M 18.7 5.3 19.9 19.2 19.3 163 166 C 4.5 M 4.1 3.8 2.0 4.5 3.8 167 171 E 5.0 H 0.4 0.6 1.8 1.2 0.4 172 181 C 4.5 M 5.5 11.9 6.0 6.5 3.5 182 190 E 4.6 H 0.6 0.8 1.3 1.4 1.6 192 193 - 3.8 M 40.0 4.5 75.0 75.0 43.2 >>>>>>