Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ecma- -----------------------------------------------------------------------------------------------------------------------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-----------------CCCCCHHHHHHHHHHHHHHHHHC-------CCCHHHHHHHHHHHHHHHHHHHHHHHHCC------------------------------------------------------------------------------------ >P1;d1ybza1 --------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC-------------------------CCCCCHHHHHHH------------------HHHHHHHHHHCCCC-------------------------------------------------------------------------------------------- >P1;d2d8da1 -----------------------------------------------------------------------------------------------------------------------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----------------CCCCCHHHHHHHHHHHHHHCC-C-------CCCHHHHHHHHHHHHHHCC---------------------------------------------------------------------------------------------- >P1;d2fp1a- -------------------------------------------------------------------------------------------------------------------------------------------------C-CCCCHHHHHHHHHHHHCHHHHHHHHHHHC-----------------CCCCCHHHHHHHHHHHHHHHHHC-------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCCCH-HHHHHHHHHHHHHHHHHHHCHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCC >P1;d2gtvx1 -----------------------------------------------------------------------------------------------------------------------------------------------------CCHHHHHHHHHHHHHHHHHHCCCCC-------------------CCCCCCHHHHHHHHHHHHHHHHC-------CCC---CC--CHHHHHHHHHHHHHHHHHCC----------CCCH-HHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------------- >P1;d3reta- CCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--------------CHHHCCCHHHHHHHHHHHHHHHHHC---------------------------------------------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHC------------------------------------------------------------------------------------ >P1;d4ppua- CCCCCC----CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCC--CCCCCCCCHHH--HHHHHHHHHHHCCCHHHCCCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHCCCHHHHHHHHHHCCHHHHCC-CCCCC-CHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCHHHHHHHHHHHHHCCCC--------------------------------------------------------------------------------- >P1;d5csma- CCCCCHH--HHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCCCHHH--HHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCC--CCCHHHHHHHHHHCHHHHHHHHHHHHHHCCCCC-------------------------------------------------------------------------------- >P1;d5ts9a- -------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC-----------------CCCCC--CCHHHHHHHHHHC-CC-------CCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHC-CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHC-CCCCCHHHHHHHHHHCCCCCC----- >P1;d6cnza- ----------------------------------------------------------------------------------------------------------------------------------------------------CHHHHHHHHHHHHHHCHHHHHHHHHHHC-----------------CCCCCHHHHHHHHHHHC-CCCCC-------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCC---- PSA >P1;d1ecma- -----------------------------------------------------------------------------------------------------------------------------------------796777688786668868875763687036605713858-----------------78056587178118723650787-------95857503653672073117205722876------------------------------------------------------------------------------------ >P1;d1ybza1 --------------------------------------------------------------------------------------------------------------------------------------------a8786787865985788475336606850628669-------------------------866a01860996------------------48733711750923-------------------------------------------------------------------------------------------- >P1;d2d8da1 -----------------------------------------------------------------------------------------------------------------------------------------89787887775667756886464276737562662786a-----------------575655852661065228708-4-------9675731266347305824---------------------------------------------------------------------------------------------- >P1;d2fp1a- -------------------------------------------------------------------------------------------------------------------------------------------------d-90802600300040031044100301449-----------------56065aa4178508701730584-------90528004500400050126005422760787695046a08727-a07842680185005106423a1043770883174025203772a079104800620053022a479c >P1;d2gtvx1 -----------------------------------------------------------------------------------------------------------------------------------------------------9486157127603710441047977-------------------90861594056104500600962-------a57---26--4382167016105730763d----------146a-712730770072025104921874-------------------------------------------- >P1;d3reta- 45688707a7914681684565668653972188244417719--------------63a40458a7288023511550677---------------------------------------------------------------------------------------------------------------------------------------------b5717613853582085025202633684------------------------------------------------------------------------------------ >P1;d4ppua- 451878----7112951893248102500510150041320740155914--a19b2a20203--52027304730451206130101025a4138164792622910181099131096025001710035009-99536-5284005101500320030000000100441586284039107745594048404679648723840261046217568a241506300500053014101300030004138--------------------------------------------------------------------------------- >P1;d5csma- 0414548--30265730671246003400620050131010500066427b1528b2920202--4200530363045330322120102585249074854a239000701760220a4025202650042006697136a317300730050011002000000010003048557402810787449304840388953672173048106626588a--4043840240065001401140014002214a7-------------------------------------------------------------------------------- >P1;d5ts9a- -------------------------------------------------------------------------------------------------------------------------------------------------ea57300500400060040041100212469-----------------76069--4288526602950-92-------909-62055003001401150064106506778805a593574685075537-115500620570572073a70882078007500-54a079304700530044006----- >P1;d6cnza- ----------------------------------------------------------------------------------------------------------------------------------------------------a307600320070031051000213548-----------------67054775277218604-40883-------a06480044005101501350064116706778-12b890450785024517900540051027036248396038507711662377274784037006300550058---- Translating the sequences -----------------------------------------------------------------------------------------------------------------------------------------**************HHHHHHHHHHHH*HHHHHHHHHH*C-----------------**CCC*HHHHHHHHHHHHH***C-------CCCHHHHHHHHHHHHHHHHHHHHHHHH**------------------------------------------------------------------------------------ --------------------------------------------------------------------------------------------------------------------------------------------***********HHHHHHHHHHHH*HHHH*******-------------------------*****HHHHHHH------------------HHHHHHHHHH****-------------------------------------------------------------------------------------------- -----------------------------------------------------------------------------------------------------------------------------------------**************HHHHHHHHHHHH*HHHHHHHHHH*C-----------------**CCC*HHHHHHHHHHHHH**-C-------CCCHHHHHHHHHHHHHH**---------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------------------*-****HHHHHHHHHHHH*HHHHHHHHHH*C-----------------**CCC*HHHHHHHHHHHHH***C-------CCCHHHHHHHHHHHHHHHHHHHHHHHHH****************-******************************************************************** -----------------------------------------------------------------------------------------------------------------------------------------------------**HHHHHHHHHHHH*HHHHH*****-------------------**CCC*HHHHHHHHHHHHH***C-------CCC---**--*HHHHHHHHHHHHHHHHH**----------****-************************-------------------------------------------- *******************************************--------------*************************---------------------------------------------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHHHHHHHHHHHHH*------------------------------------------------------------------------------------ ******----****************************************--***********--**********************************************************************-*****-*********HHHHHHHHHHHH*HHHHHHHHHH*C*******************CCC*HHHHHHHHHHHHH***********CCCHHHHHHHHHHH*HHHHHHHHHHHHH****--------------------------------------------------------------------------------- *******--******************************************************--**************************************************************************************HHHHHHHHHHHH*HHHHHHHHHH*C*******************CCC*HHHHHHHHHHHHH***C*****--CCCHHHHHHHHHH*HHHHHHHHHHHHHH*****-------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------------------******HHHHHHHHHHHH*HHHHHHHHHH*C-----------------**CCC--**HHHHHHHHHH*-*C-------CCC-**HHHHHHHHHHHHHHHHHHHHHH************************-*********************************-*********************----- ----------------------------------------------------------------------------------------------------------------------------------------------------***HHHHHHHHHHHH*HHHHHHHHHH*C-----------------**CCC*HHHHHHHHHH*-****C-------CCCHHHHHHHHHHHHHHHHHHHHHHHHH*****-***************************************************************************---- 48600.tem _________________________________ -----------------------------------------------------------------------------------------------------------------------------------------**************HHHHHHHHHHHH*HHHHHHHHHH*C-----------------**CCC*HHHHHHHHHHHHH***C-------CCCHHHHHHHHHHHHHHHHHHHHHHHHH*****-------****-*******-****************-------------------------------------------- Structural block scores 0 136 - 4.3 M 75.0 75.0 75.0 75.0 75.0 40.3 8.1 5.2 75.0 75.0 137 150 * 3.0 P 7.0 21.8 7.1 50.4 65.2 75.0 8.8 3.7 45.7 59.9 151 162 H 4.7 H 6.7 6.1 5.8 1.5 4.4 75.0 1.2 0.8 1.6 2.3 164 173 H 4.5 M 3.9 4.7 5.2 1.7 4.3 75.0 1.5 0.8 1.5 1.7 176 192 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 4.2 4.3 75.0 75.0 193 194 * 2.1 P 7.5 75.0 6.0 5.5 4.5 75.0 6.0 6.0 6.5 6.5 195 197 C 4.6 H 3.7 75.0 5.3 3.7 5.0 75.0 3.3 3.7 5.0 3.0 199 211 H 4.5 M 4.9 11.1 4.5 4.7 3.1 75.0 4.6 4.3 10.2 9.8 212 214 * 2.4 P 5.0 75.0 27.7 4.3 5.0 75.0 3.3 4.0 28.0 5.3 216 222 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 5.6 26.8 75.0 75.0 223 225 C 4.7 H 7.3 75.0 7.3 4.7 7.5 7.8 3.3 2.7 6.0 5.5 226 250 H 4.6 H 4.0 35.4 29.6 2.5 18.0 4.0 1.4 2.0 5.2 2.6 251 255 * 3.1 M 61.2 75.0 75.0 5.6 48.3 60.8 18.2 4.9 5.6 5.6 256 262 - 4.2 M 75.0 75.0 75.0 4.9 75.0 75.0 75.0 75.0 5.8 15.2 263 266 * 3.8 M 75.0 75.0 75.0 6.0 5.4 75.0 75.0 75.0 5.5 4.0 268 274 * 3.8 M 75.0 75.0 75.0 5.4 3.9 75.0 75.0 75.0 4.6 3.4 276 291 * 3.8 M 75.0 75.0 75.0 2.9 3.2 75.0 75.0 75.0 2.9 2.4 292 335 - 4.2 M 75.0 75.0 75.0 4.1 75.0 75.0 75.0 75.0 13.5 10.5 >>>>>>