Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1faqa- -------------------------------------------------CCCCCCEEECCC---CCEECCCCCCEEC-----CEEECCCCCCCCCCCCCCCCC---CCCCCC----------------- >P1;d1kbea1 -------------------------------------------------CCCCCEEEECCC----CCCCCCCCC-----CCCCEEEECCCCEEECCCCCCCCCCCC----------------------- >P1;d1r79a1 -------CCCCCCCCCCCCCCC-------------------------CCCCCCCEEECCCC---CCCCCCCCCCCCCCCCCCCCEEECCCCCEECHHHHHHCC---CCC-------------------- >P1;d1v5na1 ----------------------CCCCCHHHHHHHHHHCCCCCCEECCCCCCCCCEEEECCC----CCCCCCCCCCCC----CCEEECCCCCCCCCHHHHHC-----------CCCCC------------ >P1;d1z60a1 ---------------------------------------------------CCCCCEEECCCCCCCCCCCCCCCCCCCC---EEECCCCCCCCCCHHHHHHCCCCCCCCHHHC---------------- >P1;d2e73a1 ----------------------------------------------------CCCEECCCC---CCEECCCCCCEECC-CCCCEEECCCCCCEEEHHHHHHCC---CCCCCCCCCCCCCCCCCCCCCCC >P1;d2yuua1 CCCCEEC------------------------------------------HHHCCEEEECCC---CCCCCCCCCCCCCC-CCCCEEEECCCCCEECCCHHHCCC---CCCCCCC---------CCCCC-C >P1;d4fkda1 ----------------------------------------------------CCEEEECCC---CCCCCCCCCCCCCC-CCCCEEEECCCCCEECHHHHHHCC---CCC-------------------- PSA >P1;d1faqa- -------------------------------------------------7b8064464519---a7170a32b8406-----73520822523028805c807---85094c----------------- >P1;d1kbea1 -------------------------------------------------8c918347546a----955061287-----b43420503626450077379606a1b----------------------- >P1;d1r79a1 -------cca8aa5999c559a-------------------------b5747161470704---b90604237780119a85603207347220369118709---860-------------------- >P1;d1v5na1 ----------------------b2a84794477177707a23951506615734050533a----519082497415----310030a6381301060049-----------75a7b------------ >P1;d1z60a1 ---------------------------------------------------2a8636053a61d692502148680428---301001a04310045077317a934920029---------------- >P1;d2e73a1 ----------------------------------------------------060445a1a---95150533957065-b9640130822710015604770a---7a0434a97995b395da6999d >P1;d2yuua1 9c27317------------------------------------------447010203808---85370633569076-7c750130642830004700861a---b70a71a---------7d79b-b >P1;d4fkda1 ----------------------------------------------------070754608---87260533874092-a3700030433501005704a609---7a2-------------------- Translating the sequences -------------------------------------------------***CC*EEECCC---CC**CCCCCC**C-----CEEE*CCCCC**C******CC---CCC***----------------- -------------------------------------------------***CC*EEECCC----CCCCCCCCC-----**CCEEE*CCCC***C******CC***----------------------- -------***************-------------------------*****CC*EE*CCC---CCCCCCCCCC**C****CC*EE*CCCCC**C**HHH*CC---CCC-------------------- ----------------------******************************CC*EEECCC----CCCCCCCCC**C----CCEEE*CCCCC**C**HHH*-----------*****------------ ---------------------------------------------------*CC**EE*CC***CCCCCCCCCC**C**---*EE**CCCCC**C**HHH*CC***CCC****---------------- ----------------------------------------------------CC*EE*CCC---CC**CCCCCC**C*-**CCEEE*CCCCC*****HHH*CC---CCC******************** *******------------------------------------------***CC*EEECCC---CCCCCCCCCC**C*-**CCEEE*CCCCC**C**HHH*CC---CCC****---------*****-* ----------------------------------------------------CC*EEECCC---CCCCCCCCCC**C*-**CCEEE*CCCCC**C**HHH*CC---CCC-------------------- 57889.tem _________________________________ -------------------------------------------------***CC*EEECCC---CCCCCCCCCC**C*-**CCEEE*CCCCC**C**HHH*CC---CCC****---------------- Structural block scores 0 48 - 4.7 H 75.0 75.0 52.1 36.7 75.0 75.0 65.1 75.0 49 51 * 2.7 P 8.8 9.8 6.0 4.3 50.7 75.0 5.0 75.0 52 53 C 5.0 H 3.0 4.5 3.5 3.5 9.2 3.0 0.5 3.5 55 57 E 4.7 H 4.7 5.3 3.7 3.3 3.0 4.3 1.7 5.3 58 60 C 4.9 H 5.0 6.8 3.7 5.5 6.2 7.3 5.3 4.7 61 63 - 4.7 H 75.0 75.0 75.0 75.0 6.8 75.0 75.0 75.0 64 73 C 4.8 H 6.0 11.8 5.0 12.0 4.3 4.5 4.6 4.9 74 75 * 1.7 P 2.0 75.0 4.0 2.5 4.0 3.5 4.5 2.0 79 80 * 2.9 P 75.0 7.8 9.2 75.0 75.0 10.2 9.8 6.8 81 82 C 4.6 H 41.0 3.5 5.5 2.0 39.0 5.0 6.0 3.5 83 85 E 4.8 H 3.3 2.3 1.7 1.0 0.3 1.3 1.3 1.0 87 91 C 4.9 H 3.8 4.2 4.6 5.7 3.7 4.0 4.6 3.0 92 93 * 1.0 P 1.5 2.5 1.0 1.5 0.5 0.0 0.0 0.5 95 96 * 1.0 P 8.0 7.0 7.5 3.0 4.5 5.5 5.5 6.0 97 99 H 4.3 M 5.8 6.3 3.3 1.3 4.7 3.7 2.7 4.8 101 102 C 4.7 H 3.5 3.0 4.5 75.0 4.0 5.2 5.8 4.5 103 105 - 4.3 M 75.0 7.7 75.0 75.0 7.5 75.0 75.0 75.0 106 108 C 4.5 M 4.3 75.0 4.7 75.0 5.0 5.8 6.2 6.5 109 112 * 3.4 M 25.1 75.0 75.0 58.0 2.8 5.4 7.2 75.0 113 128 - 4.4 M 75.0 75.0 75.0 58.4 75.0 8.6 50.6 75.0 >>>>>>