Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d4wwxb3 ------CCHHHHHHHHHHHHHHHHHHHHCCCCCCCC--CCHHHHHHHHHHHHHHHHHHCCCCCCC-------------CCCHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHCHHHHHCHHHHHHHHHHHHHCCCCCCCCC----------------------------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHHHHHCCCHHHC------------------------------------------------------------------------------------------------------------ >P1;d4wwxx- CEEEEEEC------CCHHHCCCCC-EE-EEECCEEEEECCCCCCCC-------CCCCCEEEEEEECCEEEEEECEECC---------------------------------------------------------------CCCCCCCCCCCEEEECCCEEEECEECCCCCEECCEEEEEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEECCEEECCCCCCCHHHCCCEEECCCCEEEEECCCCEEEEECCCCCCCCCCCCEEEEECCEEEEECCCCCC----------CCCCCCCEEEEECCCCCCCCEEEECCCCCCCEEEEEECCEEEEECCCCCCCCCCCCCEEEECCCCCCEEECCCCCCCCHHHHCCCCCEEEECCCCCEEEEECCCCCCCCEEEEECC PSA >P1;d4wwxb3 ------140560224004101400110011235688--748545672375026105651b07368-------------a063710750054700600251053960270045005002402300307507861493376086017405710774061207c----------------------------------------------------------------------------------------------------------------------------84292054014504810974a000471------------------------------------------------------------------------------------------------------------ >P1;d4wwxx- b0640604------833a201410-10-050aa310000076516a-------906000000338a54050250701a---------------------------------------------------------------70550200230021524210000011165801450010231565b7502040524909144043002010210517292300000000025a972489757425007130000407914051370850891002000004721010000113b----------6761254012040536570a07437340030220517a5420000024567600440120606759052662841a0587058175010140390000100309965833001075 Translating the sequences ------*C******HHHHHHHHHH*******CC***--CCHHHHHH*******HHHHH*******-------------***************************************************************HHHHHHHHHHH****CCC**----------------------------------------------------------------------------------------------------------------------------***HHHHHH**********HCCCHHH*------------------------------------------------------------------------------------------------------------ ******EC------**HHH*****-EE-EEECCEEE**CC******-------*****EEEEEEE*************---------------------------------------------------------------***********EEEECCCEE****************************************************************************************************************************EEE******----------*CCC***E************************************************************************************************************ 418749.tem _________________________________ ------EC------HHHHHHHHHH-EE-EEECCEEE--CCHHHHHH-------HHHHHEEEEEEE----------------------------------------------------------------------------HHHHHHHHHHHEEEECCCEE----------------------------------------------------------------------------------------------------------------------------EEEHHHHHH----------HCCCHHHE------------------------------------------------------------------------------------------------------------ Structural block scores 0 5 - 3.0 P 75.0 4.6 8 13 - 3.0 P 2.5 75.0 14 23 H 3.6 M 1.4 3.2 25 26 E 3.0 P 0.5 0.5 28 30 E 3.0 P 1.3 1.7 31 32 C 5.0 H 4.0 10.5 33 35 E 3.0 P 7.3 1.3 36 37 - 3.0 P 75.0 0.0 38 39 C 5.0 H 5.5 0.0 40 45 H 3.0 P 5.8 5.9 46 52 - 3.0 P 3.6 75.0 53 57 H 3.0 P 3.4 3.0 58 64 E 3.0 P 5.2 2.0 65 140 - 3.0 P 15.5 62.8 141 151 H 3.0 P 3.5 2.2 152 155 E 3.0 P 4.2 2.0 156 158 C 5.0 H 1.0 2.7 159 160 E 3.0 P 9.8 0.5 161 284 - 3.0 P 75.0 2.8 285 287 E 3.0 P 4.7 0.3 288 293 H 3.0 P 3.3 2.8 294 303 - 3.0 P 3.9 75.0 305 307 C 5.0 H 3.5 4.7 308 310 H 3.0 P 3.7 3.7 312 419 - 3.0 P 75.0 3.3 >>>>>>