Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1x9ya2 -----------------------------CCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCEECCCCCCCCEEEEEEECCEEEEEEEEEECC---HHHHHCCCCCCCEEEEEECCCHHHHHHCCCCCCEEEEEEECCEEEEEEC--C--EEEEEEECC--CCCCCCCCCCCCCCCHHHHHHCCEEECCCCC >P1;d2bk7b1 -------------------------------CCC-------CCC-CHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEEEEC----------CCEEEEEEEEEEEECCCC--------------------------------CCEEEEEE---EEEEECCC---CCCCCEEEEEEC--CCCCCC---------------------- >P1;d2bk7b2 ----------CHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHH-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEECCC----------CCCEEEEEEEEEEECCCC---------------------------------CEEEEEE---EEEEECC---CEEEEEEEEECCC------------------------------ >P1;d2ch9a1 CCCCCCCCCC----------------CCCCCEEC-------CCC-CHHHHHHHHHHHHHHHHHCCCC-EEEEEEEEEEEEEEEC------------CCEEEEEEEEEEEEEEECC----C----------CCCHHHCCCCCCCCCCCEEEEEE---EEEEEHHH--CEEEEEEEEEE-------------------------------- >P1;d2gu3a1 ---------------------------------------------CCCHHHHHHHHHHCC-----------CCCEEEEEEEEEE-----------CCEEEEEEEEECCC--------------------------------------CCEEEE---EEECC---CC---CEEEEECC-------------------------------- >P1;d2gu3a2 --------------------------------------------CCCCHHHHHHHHHHHC-----------CEEEEEEEEEEEC------------CCEEEEEEEEECC--------------------------------------CCEEEE---EEECC---CC---CCCEEEECCC------------------------------ >P1;d2octa- -----------------------------CC-CCCCCCEECCHHHHHHHHH-HHHHHHHHH---CCCCCCCCCCEECC-------------CCC----CEEEEEEEEECC---C-------------------------------CCEEEEEE---EEECCC--CCCCEEEEEEEEEECC------------------CCCCCCC---- >P1;d3mwza1 ------------------------------CCCCCCCCEEECCCCCCCCCC-CHHHHHHHHHCCCCCCEEEEEEEC-CEEEEEC------------CCEEEEEEEEEEEEEEECC--C------------CCCCCCCCCCC---CCCEEEEEE---EEEECC----CCEEEEEEEECCC------------------------------ >P1;d4eyca1 --------------------------------------------CCCCHHHHHHHHHHHHHHHCCC-CEEEEEEEECCCCCC--C----------CCCCCEEEEEEEEEEEEECCCC--------------CCHHHCCCCC---CCCEEEEEE---EECCCCCCC-----CCEEEEECCCC---------------------------- >P1;d4it7a- ----------------------------CCCEEC-------CCC-CHHHHHHHHHHHHHHHHHCCCC-EEEEEEEEEEEEEECC------------CCEEEEEEEEEEEEEEECCCCCCC---------------CCCCCC---CCCCEEEEE---EEEEECCC--CEEEEEEEEEEEC------------------------------ >P1;d4n6ob1 ----------------------------CCEEEE-------CCC-CHHHHHHHHHHHHHHHHHCCCC-EEEEEEEEEEEEEEEC------------CCEEEEEEEEEEEEEEECCCCCCC----------CCCHHHCCCCCC-CCCCEEEEEE---EEEEEHHH--CEEEEEEEEEEEC------------------------------ >P1;d5o46a- ------------------------------C---CCCCEEECCCCCHHHHHHHHHHHHHCC---CCCCEEEEEEEEEEEEEEEC------------CCEEEEEEEEEEEEEEECCC-C------------CCCCCCCCCCC---CCCCEEEEE---EEEEECCC--CEEEEEEEEECCCCCCC-------------------------- >P1;d5zc1a- ------CCCC----------------CCCCCCCC-------CCC-HHHHHHHHHHHHHHCHHHHC---CCCCCEEEEEEEEEEC------------CCEEEEEEEEECC--------------------------------------CEEEEE---EEEECCHHHCCCEEEEEEEEEECCCCCCCCC---------------------- >P1;d6uioa- --------------------------CCCCEEEC-------CCC-CHHHHHHHHHHHHHHHHHCCCC-EEEEEEEEEEEEEEEC------------CCEEEEEEEEEEEEEEECCCCCCC---------------CCCCCCCCCCCCEEEEEE---EEEEEHHH--CEEEEEEEEEEEC------------------------------ >P1;d6ztka- ------------------------------------CCEEECCC-CHHHHHHHHHHHHCCC---CCCCEEEEEEEEEEEEEEEC------------CCEEEEEEEEEEEEEEEHHHCC------------CCCCCCCCCCC---CCCCEEEEE---EEEEEHHH--CEEEEEEEEEECC------------------------------ PSA >P1;d1x9ya2 -----------------------------a404010354810740553057416a304720785a3a4490400400000518063370000000178703000103058---a805947677060406039100730171175835000021820200108--8--905505446--7a80796964929038705840653020374 >P1;d2bk7b1 -------------------------------762-------63a-6730660063016402a53048714061560340124638----------b50521403010304467--------------------------------82512030---300315bb---5a7836091807--bb1699---------------------- >P1;d2bk7b2 ----------8aa84561057037497317375024a8781488-145004005700840284347ba1706041045050442c----------563000301020213357---------------------------------6410010---1011108---6717046266396------------------------------ >P1;d2ch9a1 a99678b2a8----------------98491792-------939-3860550011004411954a26-1101126028051275------------703201030201105142a----6----------a470670a40a798455516030---10310567--9455032170a-------------------------------- >P1;d2gu3a1 ---------------------------------------------0275a4025107658-----------3056347066368-----------da560120003268--------------------------------------766010---10238---60---71355436-------------------------------- >P1;d2gu3a2 --------------------------------------------87a4189027304741-----------9037176042766------------9642110303287--------------------------------------725130---40037---99---4816264275------------------------------ >P1;d2octa- -----------------------------88-7754954817781367269-639840855---b6818828184357-------------556----415352424547---a-------------------------------a6110311---225569--838838535645a166------------------9493772---- >P1;d3mwza1 ------------------------------7186aa918645497584165-0030014204728c2731000370-5010057------------a020230304005051619--6------------a164860807a---b28424040---102228----77471340807a4------------------------------ >P1;d4eyca1 --------------------------------------------8517156005600440095294-910021381394b27--a----------543550500020210506281a--------------6648708339---a06412046---30111257c-----72909065758---------------------------- >P1;d4it7a- ----------------------------d83894-------838-3850560073018401873c56-5302236035041276------------72330204020020814275a2b8---------------a1834b---807432030---10421765--a335041661676------------------------------ >P1;d4n6ob1 ----------------------------685783-------639-47606700620075104a3b45-3003227136021373------------b032030102010063526aa267----------71717707408b-9643505060---30221377--9637037590863------------------------------ >P1;d5o46a- ------------------------------b---969288272672840560014001435---8b290100035044011275------------912002040200305052c7-3------------9145860843a---b23104030---10112464--95141550814936487-------------------------- >P1;d5zc1a- ------b87a----------------94835a24-------806-89148302520484068318---8709404043002163------------9120000002036--------------------------------------752000---1041258a8a3617053045b2769260851---------------------- >P1;d6uioa- --------------------------bc891a61-------937-5a40440062004311642b28-2004237134021275------------a3110203040110608274ac58---------------c04618668443513010---20003057--5707025460666------------------------------ >P1;d6ztka- ------------------------------------92773738-5781471013002325---ac262120017034021387------------90211304010030505196b2------------a066a606167---a73422040---30100576--a335046082884------------------------------ Translating the sequences -----------------------------************C****HHHHHHHHHHHHH*H***CCC***EEE******EE**C************CCEEEEEEEEEE**---********************************C**EEEEE***EEEE**--*--*EEEEEE**--C****************************** -------------------------------***-------C**-CHHHHHHHHHHHHH*H***CCC***EEEEEEEEEEEE***----------*C*EEEEEEEEEE*****--------------------------------CC*EEEEE---EEEE****---*****EEEE**C--******---------------------- ----------*******************************C**-*HHHHHHHHHHHHH*H***CCC***EEEEEEEEEEEE*C*----------*CCEEEEEEEEEE*****---------------------------------C*EEEEE---EEEE***---**EEEEEEEE**C------------------------------ **********----------------********-------C**-CHHHHHHHHHHHHH*H***CCC-**EEEEEEEEEEEE*C------------CCEEEEEEEEEE*******----*----------***************CC*EEEEE---EEEE****--**EEEEEEEE*-------------------------------- ---------------------------------------------C**HHHHHHHHHH**-----------***EEEEEEEE**-----------*C*EEEEEEEE***--------------------------------------**EEEE---EEE**---**---*EEEEE**-------------------------------- --------------------------------------------*C**HHHHHHHHHHH*-----------*EEEEEEEEEE*C------------CCEEEEEEEEE**--------------------------------------**EEEE---EEE**---**---***EEEE**C------------------------------ -----------------------------**-*********C****HHHHH-HHHHHHH*H---CCC*******EE**-------------***----*EEEEEEEEE**---*-------------------------------CC*EEEEE---EEE***--****EEEEEEEE**C*------------------*******---- ------------------------------***********C***C*****-*HHHHHH*H***CCC***EEEEE*-*EEEE*C------------CCEEEEEEEEEE*******--*------------***********---*CC*EEEEE---EEEE**----**EEEEEEEE**C------------------------------ --------------------------------------------*C**HHHHHHHHHHH*H***CC-***EEEEEE******--*----------*CC**EEEEEEEE*********--------------**********---*CC*EEEEE---EE*******-----**EEEE**C**---------------------------- ----------------------------******-------C**-CHHHHHHHHHHHHH*H***CCC-**EEEEEEEEEEEE*C------------CCEEEEEEEEEE************---------------******---*CC*EEEEE---EEEE****--**EEEEEEEE**C------------------------------ ----------------------------******-------C**-CHHHHHHHHHHHHH*H***CCC-**EEEEEEEEEEEE*C------------CCEEEEEEEEEE************----------************-**CC*EEEEE---EEEE****--**EEEEEEEE**C------------------------------ ------------------------------*---*******C***CHHHHHHHHHHHHH**---CCC***EEEEEEEEEEEE*C------------CCEEEEEEEEEE********-*------------***********---*CC*EEEEE---EEEE****--**EEEEEEEE**C****-------------------------- ------****----------------********-------C**-*HHHHHHHHHHHHH*H***C---*****EEEEEEEEE*C------------CCEEEEEEEEE**--------------------------------------*EEEEE---EEEE********EEEEEEEE**C********---------------------- --------------------------********-------C**-CHHHHHHHHHHHHH*H***CCC-**EEEEEEEEEEEE*C------------CCEEEEEEEEEE************---------------**********CC*EEEEE---EEEE****--**EEEEEEEE**C------------------------------ ------------------------------------*****C**-CHHHHHHHHHHHH***---CCC***EEEEEEEEEEEE*C------------CCEEEEEEEEEE**********------------***********---*CC*EEEEE---EEEE****--**EEEEEEEE**C------------------------------ 54403.tem _________________________________ ----------------------------*************C***CHHHHHHHHHHHHH*H***CCC***EEEEEEEEEEEE*C-----------*CCEEEEEEEEEE**********-*----------***********---*CC*EEEEE---EEEE*****-**EEEEEEEE**C*----------------------------- Structural block scores 0 27 - 4.7 H 75.0 75.0 30.3 46.4 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 60.7 70.5 75.0 28 40 * 3.5 M 8.9 58.8 4.9 42.8 75.0 75.0 16.6 17.0 75.0 43.9 43.2 33.1 42.9 43.1 48.3 42 44 * 2.7 P 3.7 29.5 30.3 29.0 75.0 52.7 5.3 6.7 52.7 28.7 29.0 5.0 27.0 28.3 28.7 46 58 H 4.8 H 4.3 3.2 2.8 2.6 4.2 4.6 11.0 8.2 3.0 3.6 3.5 2.5 3.8 2.9 2.8 61 63 * 2.7 P 6.7 6.2 5.0 6.0 75.0 75.0 75.0 4.3 5.3 6.0 5.8 75.0 4.0 4.0 75.0 64 66 C 4.6 H 8.0 4.0 7.5 6.2 75.0 75.0 8.5 7.5 29.3 7.8 6.8 7.2 52.7 7.2 8.3 67 69 * 2.2 P 5.7 4.0 6.2 25.7 75.0 75.0 5.7 3.7 3.3 27.7 26.0 3.3 30.0 25.7 3.0 70 81 E 4.5 M 1.2 2.7 2.4 2.3 9.8 10.1 28.2 7.6 4.3 2.3 2.5 1.7 2.2 2.4 1.9 84 94 - 4.7 H 1.7 68.9 69.3 75.0 75.0 75.0 56.0 75.0 69.1 75.0 75.0 75.0 75.0 75.0 75.0 96 97 C 4.7 H 7.5 2.5 4.5 3.5 7.8 7.5 75.0 5.2 3.5 4.5 5.8 5.0 5.0 6.8 4.5 98 107 E 4.9 H 1.4 1.9 0.8 1.2 2.0 2.4 3.5 1.4 1.9 1.4 1.2 1.0 0.7 1.2 1.2 108 117 * 2.8 P 27.1 39.6 39.4 24.9 68.3 68.2 54.6 18.3 10.8 4.2 4.5 11.2 68.1 5.1 4.2 120 129 - 4.8 H 3.6 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 130 140 * 3.3 M 2.9 75.0 75.0 5.4 75.0 75.0 75.0 5.5 11.7 37.5 4.5 5.3 75.0 37.0 5.4 141 143 - 4.3 M 4.3 75.0 75.0 8.0 75.0 75.0 75.0 75.0 75.0 75.0 31.8 75.0 75.0 6.7 75.0 145 146 C 4.5 M 4.0 5.0 40.5 5.0 75.0 75.0 8.2 5.0 3.0 3.5 3.5 2.5 75.0 3.5 5.0 148 152 E 4.9 H 0.6 1.2 0.4 2.0 2.6 2.2 1.2 2.0 2.6 1.6 2.2 1.4 1.4 1.0 1.6 153 155 - 4.8 H 3.3 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 156 159 E 4.8 H 0.8 1.5 0.8 1.2 1.5 1.8 3.5 1.2 1.2 1.8 1.8 0.8 1.5 0.5 1.0 160 164 * 2.4 P 33.2 20.8 31.8 18.6 47.8 48.2 34.6 47.0 5.5 18.8 18.6 18.2 6.7 18.0 18.6 166 167 * 2.4 P 42.0 40.0 6.5 6.5 75.0 75.0 8.0 7.0 75.0 6.8 7.5 7.0 4.5 6.0 6.8 168 175 E 4.6 H 3.6 5.6 4.0 2.9 12.9 13.2 4.9 3.4 22.1 3.2 4.2 3.1 3.1 3.0 3.5 176 177 * 1.8 P 75.0 4.0 6.0 42.8 40.5 4.5 5.8 8.8 5.5 6.5 7.0 6.5 6.8 6.0 8.0 180 208 - 4.6 H 4.6 61.1 75.0 75.0 75.0 75.0 58.3 75.0 72.7 75.0 75.0 67.9 58.0 75.0 75.0 >>>>>>