Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1aa6a1 ----------------------------------CCCCCCCCCCEEEEECCCCCCCCCCCCHHHCHHHHCC--CC------CCCEEEEEHHHHHHHCCCCCCEEEEEE--CCEEEEEEEEEECCCC--------CCEEEECCCCCCCC----------------------------------------------------CCEEEEEEECC---CHHHHHHHHHHHHHHHHHHHHHHHCC--- >P1;d1cr5a1 ------------------------------------------C-EEEEEEECCC-----------HHHHCC------------CEEEECCCCC-----CCCCEEEECC-----CEEEEEEECC--------CCCCCEEEEC-HHHHHHHCCC---CCCEEEEEECCC-----------CCC-------------------------------------------------------------- >P1;d1cz4a1 -------------------------------CC-------CCCEEEEEEECCCC------------CCCCC------------CEEEECHHHHHCCCCCCCCEEEEE--CCC-EEEEEEEECC------CCCCCCCEEECC-HHHHHHHCCC---CCCEEEEEEEC----------------------------------------------------------------------------- >P1;d1eu1a1 ---------------------------CCCCCCC------CCCCEEEECCCCCCCCCC-CCCC--CHHHHH--CCCC----CCCEEEECHHHHHCCCCCCCCEEEEEC--CCCEEEEEEEECCCCC--------CCEEECCCCC-C--CCCCCCCCCCCCCCCCCHHHCCCCCCCCCC----------------CCCCCCCCCEEEEEECCCCCCCCCCCCCCCC-----------------C >P1;d1g8ja1 -------------------------------CCHHHHHHHHHCCEEEEEECCCCCCCCCCCHHHCHHHHHH--CC-------CCEEEECHHHHHHHCCCCCEEEEEEC--CCCEEEEEEEECCCCC--------CCEEEEECCCC-----------------CCCHHHHCCCCCCC------------------CCCCCCCCCEEEEEEEEEC---------------HHHHHHCCCCCCCCC >P1;d1kqfa1 CCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCC-----CCCCCEEEEEECCCCCCC--CCHHHCHHHHHH--CC-------CCEEEECHHHHHHHCCCCCCEEEEEC--CCCEEEEEEEECCCCCCEEECCEEECEEEEECCCCC----------CCCCCCCCCHHHCCCCCCCCC-----------------CCCCCCCCEEEEEEEC--------------------------------- >P1;d1ppya- ----------------------------------------CEEEEEEEEEEEEECC--CCCC------------------CCCCCEEEEHHHHHHHCCCCCCEEEEEECCCC-CEEEEEEEEC----------CCCCCEECCCCCCC-CC-----CCCEEEEEEE-----EEEEHHHHHCCCEEEEEECCCEEECC----------------------------------------------- >P1;d1q16a1 ---------------------------------CCCCCCCCCEEEEEECCCCCCCCCC-CCCC-CHHHHHH--CC------CCCEEEEEHHHHHHHCCCCCCEEEEEE--CCEEEEEEEEEECCCC--------CCEEECCCCCCCCCCCCCCCCCC---CCCCCHHHCCCCCC-CHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCEECCCC-------CC---------CCCEECCC >P1;d1qcsa1 ------------------------------------------CCCCCCEEECCC-----------HHHHHC------------CCEEECCCCC-----CCCCEEEEEEE-CCEEEEEEEEECC--------CCCCCCEEEC-HHHHHHHCCC---CCCCCEEEEECC---------------------------------------------------------------------------- >P1;d1ti6a1 -----------------------------------------CCCEEEECCCCCCCCCC-CCCCCCCHHHHCCCCEEEECCEEEEEEEEEHHHHHHCCCCCCCEEEEEE--CCEEEEEEEEEECCCC--------CCEEECCCCCCC--CCCCCC-CCCCCCCCCCHHHCCCCCCCCCC----------------CCCCCCCCEEEEEEECCCC-CCCCC------------------------ >P1;d1wlfa2 ------------------------------------------CCEEEEEEEECC------------CC---------------CCEEECHHHHHHCCCCCCCCEEEE-C-CCCCEEECEEECC----------CCCEEEEE-HHHHHHCCCC---CCCEEEEEECC--------------C-------------------------------------------------------------- >P1;d3iam34 ----------------------------------------CCCCCCEEEEECCCCHHHCC---------------CCCCCCCCEEEEECHHHHHCCCCCCCCEEEEEE--CCEEEEEEEEECCCCCC--------CCEEEEECCCCCCCEECCEECC-------------------------------------------------------------------------------------- >P1;d3ml1a2 --------------------------------CC-----CC-CCEEEEEECCCCCCCCCCCHHHCHHHHHH--CC-------CCEEEECHHHHHHCCCCCCCEEEEEC--CCCEEEEEEECCCCCCCCC------CEEEEECCCC-----------------CCCHHHCCCCCCCCC-----------------CCCCCCCCEEEEEEEC--------------------------------- >P1;d3ouga- -----------------------------------------CEEEEEEEEEEEECC--EEEC------------------CCC-CEEEECCC-CCCCCCCCCEEEEEECCCCCEEEEEEEEEC----------CCCCCEEEEHHHHHHCC-----CCCEEEEEEE-----EEECCCCCCCCCEEEECC------------------------------------------------------- >P1;d3qq8a1 -------------------------------CCCCCCCCCCCCCCEEEEEECCC--------------CCC------------CEEEECHHHHHHCCCCCCCEEEEE-CHHHCEEEEEEEECC--------CCCCCEEEEC-HHHHHHHCCC---CCCEEEEEECC----------------------------------------------------------------------------- PSA >P1;d1aa6a1 ----------------------------------5a4834a62301213466a208281490396a94476--27------210302013600752909553002022--9a65600104139908--------36002117014858----------------------------------------------------7330040430a---8396046516454673666468786a--- >P1;d1cr5a1 ------------------------------------------6-4605044168-----------872183------------8000003810-----5583501036-----713030431a--------a065620002-6b01960909---594704046177-----------a87-------------------------------------------------------------- >P1;d1cz4a1 -------------------------------a8-------938026050117e7------------b2724------------440200560283270786150103--147-6091404708------378607520302-6602940707---6337030313a----------------------------------------------------------------------------- >P1;d1eu1a1 ---------------------------374a2bc------272403030370920755-7601--5a4287--2125----800101014710872b07652302020--6333000006238717--------6300202220-4--50245697bb0000002062013b61479a----------------777a2554000304519789181520777ab-----------------9 >P1;d1g8ja1 -------------------------------3282047047615020301609407460582486991562--02-------00000014700951808100103030--5265040000207517--------75301002404-----------------40606501093249------------------8873375001030535644---------------9604700619624bf >P1;d1kqfa1 22100104313956b5326681526991486007-----3771312020351a4064--482056794075--25-------40101005700872909864402030--405504020311862718945b46113000020007----------70507813405400080060a-----------------7373346300020654--------------------------------- >P1;d1ppya- ----------------------------------------7556320020250403--7098------------------71940000034006405085729030204579-6361402219----------5724200032725b-08-----6612010003-----350528606933520307ba0425a7----------------------------------------------- >P1;d1q16a1 ---------------------------------9a65191513602020250830753-7505-5983176--14------600102004700750a08462100012--a260000100129605--------58201022113463400001139---73003062017974-6763554b798247699626368754a260300104505244-------c7---------b835428a >P1;d1qcsa1 ------------------------------------------3b1456037014-----------b90394------------8200006800-----93843030314-7a54230405137--------6084610000-6601760a08---453805033396---------------------------------------------------------------------------- >P1;d1ti6a1 -----------------------------------------81506040370730745-71016a294064a400352a82200001004710962a09653100020--8400000003228919--------353010221013--431126-7a50003002043001b966688----------------6588327907020451766-51363------------------------ >P1;d1wlfa2 ------------------------------------------e016040403b3------------a3---------------740201960184090899250102-2-b5a3260614519----------91550201-5720591807---66460305129--------------a-------------------------------------------------------------- >P1;d3iam34 ----------------------------------------8a342304035184459538---------------ba2675030201013720877906784512040--45955504022487055--------861200004922425062724a-------------------------------------------------------------------------------------- >P1;d3ml1a2 --------------------------------15-----b8-14140201509206360772275793484--14-------50200035500863a08461201030--5357050601173438075------6201003007-----------------71605600596258a-----------------6882455511050553--------------------------------- >P1;d3ouga- -----------------------------------------566333020120505--5262------------------93a-10100330-760708572702010454936161502619----------49483010039107507-----6713020105-----2725498ab493460626------------------------------------------------------- >P1;d3qq8a1 -------------------------------418757b93ab343304027055--------------767------------610000661075190965450103-04784525040221a--------7056630100-8501750408---47340104548----------------------------------------------------------------------------- Translating the sequences ----------------------------------********C*EEEEE**CCC*****************--**------**CEEEE*HHHHH**CCCCCCEEEEE*--CC*EEEEEEEE*C***--------CCEEEE********----------------------------------------------------***********---**************************--- ------------------------------------------C-EEEEEE*CCC-----------******------------CEEEE*****-----CCCCEEEE**-----*EEEEEEE*C--------***CCEEEE*-**********---CC**********-----------***-------------------------------------------------------------- -------------------------------**-------**C*EEEEEE*CCC------------*****------------CEEEE*HHHHH**CCCCCCEEEEE--*CC-EEEEEEEE*C------*****CCEEE**-**********---CC*********----------------------------------------------------------------------------- ---------------------------*******------**C*EEEE***CCC****-****--******--****----**CEEEE*HHHHH**CCCCCCEEEEE*--CC*EEEEEEEE*C***--------CCEEE*****-*--*******CC*********************----------------*******************************-----------------* -------------------------------***********C*EEEEEE*CCC*****************--**-------*CEEEE*HHHHH**CCCCC*EEEEE*--CC*EEEEEEEE*C***--------CCEEEE*****-----------------**************------------------*******************---------------*************** **********************************-----***C*EEEEEE*CCC***--************--**-------*CEEEE*HHHHH**CCCCCCEEEEE*--CC*EEEEEEEE*C************CEEEE******----------C********************-----------------****************--------------------------------- ----------------------------------------****EEEEEE******--****------------------***C*EEE*HHHHH**CCCCCCEEEEE***CC-*EEEEEEE*C----------*CC**EE*******-**-----CC********-----**************************----------------------------------------------- ---------------------------------***********EEEE***CCC****-****-*******--**------**CEEEE*HHHHH**CCCCCCEEEEE*--CC*EEEEEEEE*C***--------CCEEE****************CC---**************-******************************************-------**---------******** ------------------------------------------C*****EE*CCC-----------******------------C*EEE*****-----CCCCEEEEE**-CC*EEEEEEEE*C--------***CC*EEE*-**********---CC**********---------------------------------------------------------------------------- -----------------------------------------*C*EEEE***CCC****-*************************EEEE*HHHHH**CCCCCCEEEEE*--CC*EEEEEEEE*C***--------CCEEE*******--******-CC*********************----------------*******************-*****------------------------ ------------------------------------------C*EEEEEE**CC------------**---------------C*EEE*HHHHH**CCCCCC*EEEE-*-CC**EEE*EEE*C----------*CCEEEE*-**********---CC*********--------------*-------------------------------------------------------------- ----------------------------------------**C***EEEE*CCC******---------------*********EEEE*HHHHH**CCCCCCEEEEE*--CC*EEEEEEEE*C****--------C*EEE***************CC-------------------------------------------------------------------------------------- --------------------------------**-----**-C*EEEEEE*CCC*****************--**-------*CEEEE*HHHHH**CCCCCCEEEEE*--CC*EEEEEEE**C******------CEEEE*****-----------------***************-----------------****************--------------------------------- -----------------------------------------***EEEEEE******--****------------------***-*EEE****-***CCCCCCEEEEE***CC*EEEEEEEE*C----------*CC**EE**********-----CC********-----******************------------------------------------------------------- -------------------------------***********C**EEEEE*CCC--------------***------------CEEEE*HHHHH**CCCCCCEEEEE-*****EEEEEEEE*C--------***CCEEEE*-**********---CC*********----------------------------------------------------------------------------- 50692.tem _________________________________ -------------------------------***-----***C*EEEEEE*CCC*****************--**------**CEEEE*HHHHH**CCCCCCEEEEE**-CC*EEEEEEEE*C***-----***CCEEEE************---CC*********************--*-------------*****************-------------------------------- Structural block scores 0 30 - 4.8 H 75.0 75.0 75.0 66.1 75.0 4.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 31 33 * 3.9 M 75.0 75.0 31.2 8.7 4.3 2.3 75.0 53.0 75.0 75.0 75.0 75.0 27.0 75.0 4.3 34 38 - 4.2 M 6.1 75.0 75.0 75.0 2.6 75.0 75.0 6.3 75.0 75.0 75.0 75.0 75.0 75.0 7.9 39 41 * 3.0 P 6.8 75.0 29.0 28.0 5.7 5.7 29.0 2.3 75.0 52.7 75.0 31.2 31.5 51.7 8.3 44 49 E 4.6 H 1.8 3.2 2.3 1.5 1.0 1.3 1.2 1.0 3.2 2.2 2.5 2.0 1.3 1.8 2.0 51 53 C 4.6 H 6.2 5.0 9.5 3.7 4.3 5.2 3.0 3.7 1.7 3.3 5.8 4.3 3.7 2.3 3.3 54 70 * 3.0 P 5.3 50.2 54.5 17.2 4.8 12.8 50.1 13.0 50.7 8.3 67.0 50.5 4.7 49.7 62.9 71 72 - 4.8 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.2 75.0 75.0 75.0 75.0 75.0 73 74 * 3.5 M 4.5 75.0 75.0 1.5 1.0 3.5 75.0 2.5 75.0 0.0 75.0 75.0 2.5 75.0 75.0 75 80 - 4.5 M 75.0 75.0 75.0 51.2 75.0 75.0 63.7 75.0 75.0 5.1 75.0 7.0 75.0 64.0 75.0 81 82 * 3.1 M 1.5 75.0 75.0 4.0 37.5 39.5 5.0 3.0 75.0 1.0 75.0 1.5 40.0 6.8 75.0 84 87 E 4.8 H 1.2 0.0 1.5 0.5 0.0 0.5 0.0 0.8 0.5 0.2 1.5 0.8 0.5 0.5 0.2 89 93 H 4.5 M 3.2 17.4 4.2 4.0 4.0 4.0 2.6 3.6 17.8 4.2 4.8 4.0 3.6 17.6 4.0 94 95 * 1.7 P 3.5 75.0 2.5 4.5 3.0 4.5 2.0 2.5 75.0 4.0 2.0 7.0 4.5 3.0 3.0 96 101 C 4.9 H 5.2 28.5 4.8 5.2 2.8 6.0 4.5 5.1 29.0 5.6 6.2 5.7 4.9 4.8 5.5 102 106 E 4.9 H 0.8 1.8 1.8 1.4 1.4 1.8 2.8 0.4 1.8 0.6 1.6 2.4 1.2 2.0 1.8 107 108 * 3.0 P 38.5 40.5 75.0 37.5 37.5 37.5 2.0 38.5 2.5 37.5 38.5 37.5 37.5 2.0 37.5 110 111 C 4.7 H 9.8 75.0 5.5 4.5 3.5 2.0 8.0 6.2 8.8 6.0 8.2 4.5 4.0 6.5 7.5 113 120 E 4.9 H 2.1 2.6 3.9 1.4 1.4 1.9 3.0 0.2 2.4 0.6 3.4 2.9 2.5 3.4 2.5 123 125 * 3.3 M 5.7 75.0 75.0 5.0 4.3 5.0 75.0 3.7 75.0 6.3 75.0 4.0 5.0 75.0 75.0 126 130 - 4.6 H 75.0 75.0 47.0 75.0 75.0 5.4 75.0 75.0 75.0 75.0 75.0 61.0 32.4 75.0 75.0 131 133 * 3.8 M 75.0 5.5 4.7 75.0 75.0 7.2 51.7 75.0 4.7 75.0 53.0 75.0 75.0 51.3 4.0 134 135 C 4.8 H 4.5 5.5 6.0 4.5 6.0 1.0 4.5 6.5 5.0 4.0 3.0 41.5 40.5 6.5 6.0 136 139 E 4.5 M 0.8 0.5 1.2 0.5 1.0 0.8 1.5 0.8 0.2 1.0 1.8 2.2 0.8 3.0 1.0 140 151 * 2.1 P 27.8 10.7 9.8 20.5 44.6 38.2 22.0 2.2 10.0 14.0 10.0 2.8 44.6 15.2 9.4 152 154 - 4.3 M 75.0 75.0 75.0 6.7 75.0 75.0 75.0 0.7 75.0 27.7 75.0 3.7 75.0 75.0 75.0 155 156 C 4.5 M 75.0 7.0 4.5 9.2 75.0 41.0 6.0 6.0 4.5 8.8 6.0 7.2 75.0 6.5 5.5 157 177 * 3.0 P 75.0 41.2 44.3 3.5 27.3 6.5 19.6 17.5 41.2 3.5 44.3 75.0 24.8 20.7 44.2 178 179 - 4.2 M 75.0 9.2 75.0 75.0 75.0 75.0 7.5 4.0 75.0 75.0 75.0 75.0 75.0 7.8 75.0 181 193 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 4.1 6.5 75.0 75.0 75.0 75.0 75.0 36.7 75.0 194 210 * 3.6 M 28.5 75.0 75.0 4.1 3.8 7.5 67.2 3.9 75.0 4.4 75.0 75.0 8.1 75.0 75.0 211 242 - 4.5 M 18.6 75.0 75.0 42.8 38.2 75.0 75.0 40.4 75.0 59.5 75.0 75.0 75.0 75.0 75.0 >>>>>>