Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bvsa2 --------------------------------------------------------------------------------------------------CHHHHHHHHHHHCCC----CCCHHHHHHHHHHC--CHHHHC-CCC------CCCCCC-CC------------CCC-CHHHHHHHH--CCHHHCC--C-- >P1;d1cuka2 --------------------------------------------------------------------------------------------------CHHHHHHHHHHHHCC----CCCHHHHHHHHHHC--CHHHHHHHHHCC----CHHHHHCCC------------CCC-CCCC-CHHH--HHCCCCCCCC-- >P1;d1dgsa1 CCCCCCCCCCCCCEEECCEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHCCHHHHCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHCCCC----CCCHHHHHHHHHCCC-CHHHHCCC--------CHHHHHCCCCCCHHHHHHHHHHHHCHHHHHHHHH--HHHCCCCCCCC- >P1;d1kfta- ------------------------------------------------------------------------------------------------------CCCCC-------CCCCCCCCHHHHHHHHHC-CHHHHHHCC--------HHHHCCCC------------CCCHHHHHHHHHH--HCC--------- >P1;d1x2ia1 -------------------------------------------------------------------------------------------------CCCHHHHHHHHHCCCC----CCCHHHHHHHHHHHC-CHHHHHHC--------CHHHHCCCC------------CCCHHHHHHHHHH--HH---CCC-CC- >P1;d2a1ja1 --------------------------------------------------------------------------------------------------------CCHHHHCCC----CCCHHHHHHHHHHCC-CHHHHHCC--------CHHHHHHHHC-------------CHHHHHHHHHH--HH---CCCCCCC >P1;d2a1jb1 -----------------------------------------------------------------------------------------CHHHHHHHHHHHHHHHHHHHCCCC----CCCHHHHHHHHHHHC-CHHHHHCC--------CHHHHHCCC------------CCCCHHHHHHHHH--HH---CCCCCC- >P1;d2csba1 -------------------------------------------------------------------------------------------------------CHHHHHHHHH----CCCHHHHHHHHHHHC-CHHHHHCCC--------HHHHHCCCC----------CCCCHHHHHHHHHHC------------- >P1;d2csba2 -----------------------------------------------------------------------------------------------------CHHHHHHHHHHH----CCCHHHHHHHHHHCC-CCCCCCCCC--------HHHHHHHCC-----------CCCHHHHHHHC---------------- >P1;d2csba3 ---------------------------------------------------------------------------------------------------------CHHHHCCC----CCCHHHHHHHHHHHC-CHHHHHHHHHCC----CHHHHHCCCCCC----------------HHHHHH--HC---------- >P1;d2csba4 -------------------------------------------------------------------------------------------------------CCHHHHHCCC----CCCHHHHHHHHHHHC-CHHHHHCC--------CHHHHHHC-CCC----------------HHHHHH--HHCCC------- >P1;d2duya1 --------------------------------------------------------------------------------------------------------CCHHHC--CEECCCCCCCCCC-CCCCCHHHHHHHHHCC----CCCCHHHHHHCC------------CCCHHHHHHHHHHEEC----------- >P1;d2edua1 --------------------------------------------------------------------------------------CCCCCCHHHCCCHHHHHHHHHHHHHH---HHHCCHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHCC------------CCCHHHHHHHHHH--HHHHHHC---CC >P1;d3bzca1 -----------------------------------------------------------------------------------CHHHCC----HHHHHHHHHHHHHHHHHHHCEECCCCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHCC------------CCCHHHHHHHHHHEECCCC-------- >P1;d3bzca2 ---------------------------------------------------------------------------------------------------------CCHHHHCCCCHHH--HHHHHHHHHHHCCCHHHHCCC---------HHHHHHCCHHHCCCC-----CCCHHHHHHHHHH--HHCCCCCCCC-C PSA >P1;d1bvsa2 --------------------------------------------------------------------------------------------------87636622650470a----b076a307401752--718706-209------65a705-07------------b0a-850861194--13853a5--8-- >P1;d1cuka2 --------------------------------------------------------------------------------------------------88456303530260c----8076a208401671--706500400475----53b403817------------b06-7406-0097--0490e27b10-- >P1;d1dgsa1 a658507718360656a97351211203533464053005740020850a68007401748207100200506739202716088a606702510550172001300100402----807560042007407-40740180--------5282047076097a50540181051820350073--05708050727- >P1;d1kfta- ------------------------------------------------------------------------------------------------------c7649-------90650a550363026627-649604802--------37601603------------c067720320240--02b--------- >P1;d1x2ia1 -------------------------------------------------------------------------------------------------b378546335502903----408650043018416-32850270--------638603709------------9095930650276--15---268-88- >P1;d2a1ja1 --------------------------------------------------------------------------------------------------------959604903----405960175047607-73820761--------64a6039109-------------57920660245--14---77987ac >P1;d2a1jb1 -----------------------------------------------------------------------------------------699667866667257017703708----a05781034007418-53860470--------658503707------------c058630530254--24---67aa9b- >P1;d2csba1 -------------------------------------------------------------------------------------------------------a156203862----a06691073038319-438505727--------575045365----------860547006003811------------- >P1;d2csba2 -----------------------------------------------------------------------------------------------------4a9017404762----a04780044006229-061a03917--------395048407-----------80569107403---------------- >P1;d2csba3 ---------------------------------------------------------------------------------------------------------29402649----10a781054029319-627404400758----45a50371970b----------------970182--01---------- >P1;d2csba4 -------------------------------------------------------------------------------------------------------b14a50480a----a07772066017518-53970470--------a4850481-607----------------681055--02777------- >P1;d2duya1 --------------------------------------------------------------------------------------------------------05aa41--500038075a404-04a0787205304642----809714304509------------7087930570464054----------- >P1;d2edua1 --------------------------------------------------------------------------------------aa8896148b0589438602850062---0370627504719506673053007216a64709506106609------------7073960550020--2047238---ca >P1;d3bzca1 -----------------------------------------------------------------------------------987765----69827876666468711782020270739502402507971062026317779507746404708------------80ab9127501940305b1-------- >P1;d3bzca2 ---------------------------------------------------------------------------------------------------------b420780706660--260085018409372650264---------68108717275024a-----7254730470181--0162575779-b Translating the sequences --------------------------------------------------------------------------------------------------********HHH***C----CCCHHHHHHHHHH*--CHHHH*-C**------C*****-CC------------CCC-*HHHHHHHH--*******--*-- --------------------------------------------------------------------------------------------------********HHH***C----CCCHHHHHHHHHH*--CHHHHH******----CHHHHH*CC------------CCC-****-*HHH--**********-- **********************************************************************************************************HHH***C----CCCHHHHHHHHH***-CHHHH**C--------CHHHHH*CC****************HHHHHHHHH--***********- ------------------------------------------------------------------------------------------------------*****-------***CCC**HHHHHHHH**-CHHHHH*C*--------HHHH**CC------------CCC*HHHHHHHHH--***--------- -------------------------------------------------------------------------------------------------*********HHH***C----CCCHHHHHHHHHH**-CHHHHH*C--------CHHHH**CC------------CCC*HHHHHHHHH--**---***-**- --------------------------------------------------------------------------------------------------------**HHH***C----CCCHHHHHHHHHH**-CHHHHH*C--------CHHHHH****-------------C*HHHHHHHHH--**---******* -----------------------------------------------------------------------------------------*****************HHH***C----CCCHHHHHHHHHH**-CHHHHH*C--------CHHHHH*CC------------CCC*HHHHHHHHH--**---******- -------------------------------------------------------------------------------------------------------***HHH****----CCCHHHHHHHHHH**-CHHHHH*C*--------HHHHH*CC*----------*CCC*HHHHHHHHH*------------- -----------------------------------------------------------------------------------------------------*****HHH****----CCCHHHHHHHHHH**-C******C*--------HHHHH**C*-----------CCC*HHHHHH*---------------- ---------------------------------------------------------------------------------------------------------*HHH***C----CCCHHHHHHHHHH**-CHHHHH******----CHHHHH*CC***----------------HHHHHH--**---------- -------------------------------------------------------------------------------------------------------***HHH***C----CCCHHHHHHHHHH**-CHHHHH*C--------CHHHHH*C-***----------------HHHHHH--*****------- --------------------------------------------------------------------------------------------------------**HHH*--C****CCC*****-********HHHHH*C*----***CHHHHH*CC------------CCC*HHHHHHHHH***----------- --------------------------------------------------------------------------------------********************HHH***---***CCHHHHH*********HHHHH**********CHHHHH*CC------------CCC*HHHHHHHHH--*******---** -----------------------------------------------------------------------------------******----*************HHH***C****CCCHHHHH*********HHHHH**********CHHHHH*CC------------CCC*HHHHHHHHH******-------- ---------------------------------------------------------------------------------------------------------**HH***C*****--HHHHHHHHHH***CHHHH**C---------HHHHH*CC*******-----CCC*HHHHHHHHH--**********-* 47781.tem _________________________________ -------------------------------------------------------------------------------------------------*********HHH***C--**CCCHHHHHHHHHH**-CHHHHH*C**------CHHHHH*CC*-----------CCC*HHHHHHHHH--***********- Structural block scores 0 96 - 4.7 H 75.0 75.0 3.8 75.0 75.0 75.0 69.4 75.0 75.0 75.0 75.0 75.0 67.3 68.0 75.0 97 105 * 2.9 P 12.8 12.4 1.6 44.9 5.6 59.9 4.4 51.8 36.1 66.9 51.8 58.9 5.0 6.2 67.9 106 108 H 4.7 H 3.7 2.7 0.3 53.0 3.3 5.0 4.7 2.7 3.7 4.3 5.2 8.3 4.3 5.3 2.0 109 111 * 1.6 P 3.7 2.7 1.3 75.0 3.7 4.3 3.3 5.7 5.7 4.0 4.0 50.3 2.7 5.3 5.0 113 114 - 4.3 M 75.0 75.0 75.0 42.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 0.0 75.0 1.0 3.0 115 116 * 4.0 M 75.0 75.0 75.0 3.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 1.5 1.5 1.0 6.0 117 119 C 4.7 H 6.2 5.0 5.0 5.2 4.0 3.0 5.2 5.5 4.8 3.8 5.8 5.0 4.3 4.7 50.0 120 129 H 4.6 H 4.3 4.5 2.8 3.6 3.1 4.5 3.4 4.0 3.1 3.9 4.1 11.3 4.0 3.0 3.4 130 131 * 1.4 P 38.5 38.0 3.5 4.5 3.5 3.5 4.5 5.0 5.5 5.0 4.5 7.5 6.0 8.0 4.5 134 138 H 4.7 H 4.4 2.2 2.4 4.6 3.4 4.0 4.2 4.2 4.1 3.4 4.6 2.4 1.6 2.0 3.0 141 142 * 3.5 M 4.5 2.0 75.0 38.5 75.0 75.0 75.0 41.0 41.0 3.5 75.0 38.5 3.5 4.0 75.0 143 148 - 4.4 M 75.0 52.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 52.2 75.0 40.3 6.1 5.8 75.0 150 154 H 4.7 H 5.5 4.3 3.2 3.4 4.0 4.7 4.2 4.2 4.2 4.7 4.2 2.4 2.6 3.6 4.6 156 157 C 4.7 H 3.5 4.0 3.5 1.5 4.5 0.5 3.5 4.5 2.0 5.0 38.0 4.5 4.5 4.0 4.0 159 169 - 4.6 H 75.0 75.0 4.5 75.0 75.0 75.0 75.0 68.9 75.0 62.4 62.0 75.0 75.0 75.0 36.7 170 172 C 4.4 M 7.3 5.8 2.0 6.2 6.0 51.7 5.8 3.7 4.3 75.0 75.0 5.0 4.7 6.2 4.7 174 182 H 4.7 H 4.7 12.0 3.1 2.2 4.2 3.8 3.1 2.8 19.3 28.0 27.8 4.2 3.0 4.2 3.4 183 184 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 75.0 38.0 75.0 75.0 75.0 2.5 75.0 1.5 75.0 185 195 * 3.3 M 24.4 11.3 3.7 55.8 30.7 25.3 26.0 75.0 75.0 61.5 43.0 68.5 24.0 49.3 11.3 >>>>>>