Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1euwa1 --CCCCEEEECCC---CCCCCCCCCCCCCCCC---CCEEEECCCCCCEEECCC--------------CEEEEEEEEEEECCCC--------------------------------------CEEEEEEECHHHHHHHCEEECCCCEEECCCCC---CEEEEEEEECCC--------------------CCEEECCCCEEEEEEEEECC---------CC-CCCCCCCC------------------------- >P1;d1f7da- -----CCEEC----------CCCCCCCC-C-C---CCEEEECCC--CEEECCC--------------CEEEEECCCEECC-CC--------------------------------------CEEEEEECCHHHHCC-CEEEE--CCEECCCCC---CCCEEEEEECCC--------------------CCEEECCCCEEEEEEEEECC-----------------------C--------CCCCCCCC---CC >P1;d1pkha- ------CCCCHHHHHHHHHCCCCEEECCCHHHCCCCCEEEECCCEEEEECC---CCCCCCCCCC--EEEEECC--CEEEEECCCCCCCHHHHHHHHHHHCCCEEEECCEEEEEEEEEECCCCEEEEEEECHHHHC-CCEECCCCCCEECCCC---EEEEEEEEEECC---------------------CCEEEECCCEEEEEEEEECCCCCC--CCCCCCC-----------------------C-------- >P1;d1sixa1 C-CCCCEEEECCC---C----CCCCCCCCCCC---CCEEEECCC--CEEECCC--------------CEEEEECCEEEEC-CC--------------------------------------CEEEEEECCHHHHHHHCEEECCCCEEEECCCC---CCCEEEEEECCCC-------------------CCEEECCCCEEEEEEEEECC---------CC-CCCCCCCHHHHC--------CCCCCCCC---CC >P1;d2bsya1 --CCCCEEEECCC-------CEEEEEEEC------CEEEEEECC--CEEECCC--------------CEEEEEEEEEEEC-CC--------------------------------------CEEEEEEEECC----CCEEEC--CEEECCCCC---CCEEEEEEECCC--------------------CCEEECCCCCEEEEEEEECC---------CCC--------------------------------C >P1;d2bsya2 ------------------------------------------CCCCCCCCC------------CCCCEEEECCC--CEEECCC-----------------------CEEEEEECCCCCCCCCEEEEEECCHHHHH-CCEEEC--CEECCCC------CEEEEEEECCC--------------------CCEEECCCCEEEEEEEEE-----HHHEECCCCCCEECCCCCCCCEEECCC----CCCCCCHHHCC >P1;d2qxxa- ------CCCCHHHHHHHHHCCCCEEECCCHHHEECCEEEEECCCCEEECCCCCCCCCCCCCCCHHHCEEECCCCCCCEEECCC-----------------------CEEEEECCCEEECCCCEEEEEECCHHHHC-CCEEECCCCCEECCCC---EECCEEEEEECCC--------------------CCEEECCCCEEEEEEEEECCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCC-------- >P1;d3lqwa- --CCCCEEEECC--------CCCCCEEC-CCC---CEEEEECCC--CEEECCC--------------CEEEEEEEEEEEC-CC--------------------------------------CEEEEEECCHHHHHHHCEEEC--CCEECCCCC---CEEEEEEEECCC--------------------CCEEEC-CCEEEEEEEEECC---------CC-CCCCCC--------------CCCC--------- >P1;d3t64a- ---CEEEEEECCHHHHHHHHCCCCCC---CCC---CEEEEECCC--CEEECCC--------------EEEEEECCEEEEEEEECCCCCCCC----------------------------EEEECEEEEECHHHHH-CCEEECCCCEEECCCCC---CCCEEEEEECCC--------------------CCEEECCCCEEEEEECCCCC---------CCEEEECCCCCCCCCCCCCCCC-------------- >P1;d3tq5a- -------------------CEECCCCCCCCCC---CCEEEECCC--CEEECHHH-------------CCEEECCCEECCC-CC--------------------------------------CEEEEEEECHHHHC--CEEEC--CEEECCCCC---CCCCEEEEECC---------------------CCEEECC--CEEEEEEEECC---------CCC--------------------------------C >P1;d4b0ha- --CCCCEEEECCCCCC-----CCCCC---CCC---CCEEEECCC--CEEECCC--------------CEEEEECCEEEECCC---------------------------------------CEEEEEEECCCHHHHHCEEECCCCEEECCCCCCCCCCCEEEEEECC----------------------CEEECCCCEEEEEEEEECC---------C---------------------CCCCCCCCC---CC >P1;d4gv8a- ---CCCCEEECC--------CCCCCCCC-CCC---CCEEEECCC--CEEECCC--------------CEEEEECCEEECC-C---------------------------------------CEEEEEEECHHHHCC-CEEEC--CEEEECCCC---CCCEEEEEECCCCCCCCEECCCCEECCCCCCCCCEEECCCCEEEEEEEEECC---------CCC------CCCCC---------------------- >P1;d4xjca- ------CCCCHHHHHHHHHCCCCEEECCCHHHCCCCCEEEECCCEEEEECCCCCCCCCCCCCCC--EEEEECCC-CEEEECCC-----------------------CEEEEEEEEEEECCCCEEEEEEECHHHHC-CCEEECC-CEEECCCC---EEEEEEEEEECCC--------------------CCEEEECCCEEEEEEEEECCCCC-CCCC--------CCCCCCCCCCCCCHHHCCC---------- >P1;d5y5qa- -CCCCCEEEECCC---CCCCCCCCCCCCCCCC---CCEEECCCC--CEEECCC--------------CEEEEECCEEEEECCC--------------------------------------CEEEEEECCHHHHHHHCEECC--CCEECCCCC---CCCEEEEEECCCC-------------------CCEEECCCCCCEEEEEEECC---------CCCEEEEEEECCCCC--------CEEEEEEE---EC >P1;d7n6sa1 CCCCCCEEEECCC---C------CCCCCCCCC---CEEEEECCCC-CEEECCC--------------CEEEEECCEEEEC-CC--------------------------------------CCEEEEECCHHHHHHHCEEECCCCEEECCCCC---CCCEEEEEECCC---------------------CEEEC-CCEEEEEEEE-CC---------CC-CCCCCCC-------------------------- PSA >P1;d1euwa1 --95b19474328---2037515319388ba2---901303001a92360538--------------5526020000030537--------------------------------------710030322a8118750010077406071948---73020103041a--------------------9413073134003021374a---------a6-a9aa49aa------------------------- >P1;d1f7da- -----18484----------9004b27b-7-4---702200046--4060739--------------4446020605050-47--------------------------------------843030542b80686-60604--906182955---640204020539--------------------95130665440030214638-----------------------a--------68a8ba9b---89 >P1;d1pkha- ------950459402711867501066247810586202000035022363---a855977a18--3561608--700000179390799438504954a014012050203030303025202020523a6169-560301488041a014---545050302055---------------------7112053624001010233a7639--3976889-----------------------a-------- >P1;d1sixa1 a-a4928273426---8----05507548bc4---702101003--7160628--------------7736040001030-39--------------------------------------511010322a5249644030482515171a45---7104020206388-------------------74040644540030126749---------57-997a29587639--------74b5b77c---86 >P1;d2bsya1 --3692747192a-------70635535a------a40000055--5150628--------------5422160305050-0b--------------------------------------6000303050a----410706--626184b55---730504050549--------------------76140747303010203649---------77a--------------------------------9 >P1;d2bsya2 ------------------------------------------261283489------------c4802001036--6030637-----------------------642404169607a48633200223aa038-540506--211028c------0070202053a--------------------720708474300101114-----45201797487063930478003345a----79b99479898 >P1;d2qxxa- ------9406484045019495070852459105750010102420113619839753606515720544518ac6114063a-----------------------34010003020502540103042177148-7204042791515120---301020201053a--------------------8415052425003010333b752943114---b7370334517202274525a3a7b-------- >P1;d3lqwa- --a561607536--------70450547-9c3---800200025--9050525--------------6645030000050-17--------------------------------------601030032a51496550506--595162945---720403040638--------------------851704-3650020213737---------58-9a7a6b--------------9aa9--------- >P1;d3t64a- ---03030002696046004808417---a64---500100019--7440836--------------332707020000012858b89888----------------------------54322010422b5079-12040279315184931---020301030537--------------------85360636420020105664---------6061512850395960306b5c-------------- >P1;d3tq5a- -------------------77609194679c2---801305057--63502294-------------4635040712050-48--------------------------------------a22020313a9368--60403--526172947---61040502058---------------------972406a--60010124759---------7bb--------------------------------b >P1;d4b0ha- --b582724145a705-----40857---a94---922102006--7040665--------------645502000004019---------------------------------------712010222b306841005046941417194398a31040103044----------------------6070842340030526747---------8---------------------b5896a5a9---9c >P1;d4gv8a- ---b91908325--------70560554-8b4---803000002--5230204--------------5736050000020-6---------------------------------------941030232aa0480-60607--366183656---6402050304197a58202218966185625920020430220030215639---------74a------b6bad---------------------- >P1;d4xjca- ------940609303721976504066167901395000010042002219961a752895506--465361a8-a3150534-----------------------44010003040502460103032277168-8406041-35516210---3020104030448--------------------8517031374001020152bab1-a428--------633371820216242548b---------- >P1;d5y5qa- -488616123416---9b6a005506547ab3---801100029--4460826--------------5416030000035016--------------------------------------a02020333a60497370402--616184a46---5203020404179-------------------84040457700020214738---------55777571754a978--------76655756---66 >P1;d7n6sa1 6a94918275361---f------419468982---802104021b-4240757--------------3535020000030-3a--------------------------------------632020423a7148745030172515162945---71040302063b---------------------41506-a450030006-5a---------96-a99a5ba-------------------------- Translating the sequences --***********---*****CC****C****---C*EEEECCC**CEEECCC--------------*EEEE****EEE**CC--------------------------------------CEEEEEE*CHHHH***CEEEC**C*EECCCCC---C**EEEEEECCC--------------------CCEEECCCCEEEEEEEEECC---------CC-********------------------------- -----*****----------*CC****C-*-*---C*EEEECCC--CEEECCC--------------*EEEE*C**EE**-CC--------------------------------------CEEEEEE*CHHHH**-CEEE*--C*EECCCCC---CC*EEEEEECCC--------------------CCEEECCCCEEEEEEEEECC-----------------------*--------********---** ------***************CC****C*******C*EEEECCC***EE*C---**********--**EEE**--*EEE**CC**************************************CEEEEEE*CHHHH*-*CEE*C**C*EECCCC---****EEEEEECC---------------------CCEEE*CCCEEEEEEEEECC****--***CC**-----------------------*-------- *-***********---*----CC****C****---C*EEEECCC--CEEECCC--------------*EEEE*C**EEE*-CC--------------------------------------CEEEEEE*CHHHH***CEEEC**C*EE*CCCC---CC*EEEEEECCC*-------------------CCEEECCCCEEEEEEEEECC---------CC-************--------********---** --***********-------*********------C*EEEE*CC--CEEECCC--------------*EEEE****EEE*-CC--------------------------------------CEEEEEE****----*CEEEC--C*EECCCCC---CC*EEEEEECCC--------------------CCEEECCCC*EEEEEEEECC---------CC*--------------------------------* ------------------------------------------CC**C***C------------*****EEE**C--*EE**CC-----------------------***************CEEEEEE*CHHHH*-*CEEEC--C*E*CCC------C*EEEEEECCC--------------------CCEEECCCCEEEEEEEEE-----******CC*******************----*********** ------***************CC****C*******C*EEEECCC***E**CCC***************EE***C***EE**CC-----------------------***************CEEEEEE*CHHHH*-*CEEEC**C*EECCCC---**C*EEEEEECCC--------------------CCEEECCCCEEEEEEEEECC*********---*************************-------- --**********--------*CC****C-***---C*EEEECCC--CEEECCC--------------*EEEE****EEE*-CC--------------------------------------CEEEEEE*CHHHH***CEEEC--C*EECCCCC---C**EEEEEECCC--------------------CCEEEC-CCEEEEEEEEECC---------CC-******--------------****--------- ---******************CC***---***---C*EEEECCC--CEEECCC--------------*EEEE*C**EEE************----------------------------***E*EEEE*CHHHH*-*CEEEC**C*EECCCCC---CC*EEEEEECCC--------------------CCEEECCCCEEEEEE***CC---------CC********************-------------- -------------------***C****C****---C*EEEECCC--CEEEC***-------------**EEE*C**E***-CC--------------------------------------CEEEEEE*CHHHH*--CEEEC--C*EECCCCC---CC**EEEEECC---------------------CCEEECC--*EEEEEEEECC---------CC*--------------------------------* --**************-----CC***---***---C*EEEECCC--CEEECCC--------------*EEEE*C**EEE**C---------------------------------------CEEEEEE*C**HH***CEEEC**C*EECCCCC***CC*EEEEEECC----------------------CEEECCCCEEEEEEEEECC---------C---------------------*********---** ---*********--------*CC****C-***---C*EEEECCC--CEEECCC--------------*EEEE*C**EE**-C---------------------------------------CEEEEEE*CHHHH**-CEEEC--C*EE*CCCC---CC*EEEEEECCC********************CCEEECCCCEEEEEEEEECC---------CC*------*****---------------------- ------***************CC****C*******C*EEEECCC***EE*CCC***********--**EEE**C-*EEE**CC-----------------------***************CEEEEEE*CHHHH*-*CEEEC*-C*EECCCC---****EEEEEECCC--------------------CCEEE*CCCEEEEEEEEECC***-****--------*******************---------- -************---*****CC****C****---C*EEE*CCC--CEEECCC--------------*EEEE*C**EEE**CC--------------------------------------CEEEEEE*CHHHH***CEE*C--C*EECCCCC---CC*EEEEEECCC*-------------------CCEEECCCC**EEEEEEECC---------CC*************--------********---** *************---*------****C****---C*EEEECCC*-CEEECCC--------------*EEEE*C**EEE*-CC--------------------------------------C*EEEEE*CHHHH***CEEEC**C*EECCCCC---CC*EEEEEECCC---------------------CEEEC-CCEEEEEEEE-CC---------CC-*******-------------------------- 51283.tem _________________________________ --*******************CC****C****---C*EEEECCC**CEEECCC--------------*EEEE*C**EEE**CC------------------------------------**CEEEEEE*CHHHH***CEEEC**C*EECCCCC---CC*EEEEEECCC--------------------CCEEECCCCEEEEEEEEECC---------CC*************--------********---** Structural block scores 0 1 - 4.6 H 75.0 75.0 75.0 42.8 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 39.5 8.2 2 20 * 2.9 P 16.1 53.1 19.4 31.1 31.2 75.0 19.3 34.6 6.6 67.8 23.5 38.4 19.3 16.2 31.7 21 22 C 4.5 M 3.0 0.0 2.5 2.5 3.0 75.0 2.5 2.0 4.0 3.0 2.0 2.5 2.5 2.5 75.0 23 26 * 1.6 P 4.0 6.1 3.2 4.2 4.0 75.0 5.0 3.5 21.8 5.8 23.8 4.0 4.0 4.0 4.5 28 31 * 2.1 P 8.0 40.2 5.0 9.0 58.9 75.0 4.8 24.9 23.9 7.6 24.6 24.6 5.5 8.0 6.8 32 34 - 4.5 M 75.0 75.0 4.3 75.0 75.0 75.0 4.0 75.0 75.0 75.0 75.0 75.0 4.3 75.0 75.0 37 40 E 4.8 H 1.8 1.0 0.5 1.0 0.0 75.0 0.5 0.5 0.2 2.2 1.2 0.8 0.2 0.5 1.8 41 43 C 4.9 H 0.3 3.3 1.0 1.0 3.3 27.7 2.0 2.3 3.3 4.0 2.0 0.7 1.3 3.7 1.0 44 45 * 3.9 M 9.8 75.0 2.5 75.0 75.0 1.5 1.0 75.0 75.0 75.0 75.0 75.0 1.0 75.0 43.2 47 49 E 4.5 M 3.0 2.0 3.7 2.3 2.0 5.0 3.3 1.7 2.7 2.7 1.3 1.7 1.7 3.3 2.0 50 52 C 4.7 H 5.3 6.3 51.0 5.3 5.3 53.0 6.0 4.0 5.7 4.3 5.7 2.0 8.0 5.3 6.3 53 66 - 4.5 M 75.0 75.0 21.4 75.0 75.0 55.3 4.2 75.0 75.0 69.9 75.0 75.0 15.2 75.0 75.0 68 71 E 4.7 H 3.2 3.5 3.2 4.0 2.2 0.2 3.5 3.8 3.0 3.5 3.5 4.0 3.8 2.8 3.2 74 75 * 1.8 P 0.0 3.0 41.0 0.0 1.5 75.0 9.2 0.0 1.0 4.0 0.0 0.0 42.8 0.0 0.0 76 78 E 4.6 H 1.0 3.3 0.0 1.3 3.3 3.0 2.0 1.7 0.0 2.3 1.3 0.7 3.0 1.0 1.0 79 80 * 2.1 P 2.5 37.5 0.0 37.5 37.5 3.0 3.0 37.5 0.5 37.5 0.5 37.5 2.5 2.5 37.5 81 82 C 4.7 H 5.0 5.5 4.0 6.0 5.8 5.0 6.8 4.0 5.0 6.0 42.0 40.5 3.5 3.5 6.8 83 118 - 4.5 M 75.0 75.0 3.5 75.0 75.0 49.6 48.4 75.0 60.2 75.0 75.0 75.0 48.5 75.0 75.0 119 120 * 4.0 M 75.0 75.0 3.5 75.0 75.0 6.0 3.5 75.0 4.5 75.0 75.0 75.0 3.0 75.0 75.0 122 127 E 4.9 H 1.2 2.5 1.5 1.0 1.0 1.7 1.3 0.7 1.5 1.5 1.0 1.7 1.2 1.2 1.8 130 133 H 4.7 H 5.1 6.4 5.9 5.4 40.1 6.0 4.8 5.1 5.9 7.1 5.1 6.2 5.2 5.1 5.6 134 136 * 2.3 P 6.7 29.7 29.7 6.3 51.3 29.3 30.0 6.7 28.3 52.7 4.3 27.7 30.3 6.3 6.3 138 140 E 4.9 H 0.3 2.0 1.0 1.0 2.3 1.7 1.3 1.7 1.3 1.3 1.7 2.0 2.0 1.3 1.0 142 143 * 3.4 M 7.0 75.0 6.0 5.0 75.0 75.0 4.5 75.0 8.0 75.0 7.5 75.0 38.0 75.0 4.5 146 147 E 4.9 H 3.0 3.5 2.5 3.0 3.5 0.5 3.0 3.0 3.0 3.5 2.5 3.5 3.0 3.5 3.0 148 152 C 4.8 H 5.8 5.8 18.1 5.5 6.7 34.5 16.6 5.2 5.0 5.8 4.8 5.6 16.8 6.5 5.2 153 155 - 4.6 H 75.0 75.0 51.7 75.0 75.0 75.0 51.0 75.0 75.0 75.0 9.2 75.0 51.0 75.0 75.0 156 157 C 4.2 M 5.0 5.0 4.5 4.0 5.0 37.5 0.5 4.5 1.0 3.5 2.0 5.0 1.0 3.5 4.0 159 164 E 5.0 H 1.0 1.3 1.7 1.3 2.3 1.8 0.8 1.8 1.2 1.8 1.3 1.7 1.3 1.5 1.5 165 167 C 4.9 H 5.2 5.7 28.3 5.7 6.0 6.2 6.2 5.7 5.0 29.3 27.7 4.7 5.3 4.0 6.8 168 187 - 4.8 H 75.0 75.0 75.0 71.7 75.0 75.0 75.0 75.0 75.0 75.0 75.0 5.1 75.0 71.7 75.0 188 189 C 4.8 H 6.5 7.0 4.0 5.5 6.5 4.5 6.0 6.5 6.5 8.0 40.5 1.0 6.5 6.0 39.5 190 192 E 5.0 H 1.3 1.3 1.0 1.3 1.7 2.3 2.0 2.7 3.0 2.0 2.3 0.7 2.7 1.3 2.0 193 196 C 4.7 H 3.5 5.2 4.0 4.8 5.2 5.8 3.2 22.0 4.8 41.6 4.2 2.2 3.5 5.8 23.9 197 205 E 4.8 H 2.2 2.2 1.2 2.6 1.7 1.2 1.7 2.2 1.8 2.3 3.0 2.1 1.4 1.8 9.9 206 207 C 4.8 H 7.2 5.5 6.8 6.5 6.5 75.0 7.2 5.0 5.0 7.0 5.5 6.0 6.8 5.5 7.8 208 216 - 4.4 M 75.0 75.0 21.6 75.0 75.0 27.1 4.0 75.0 75.0 75.0 75.0 75.0 21.9 75.0 75.0 217 218 C 4.5 M 8.2 75.0 7.0 6.0 7.0 8.0 75.0 6.5 3.0 9.2 41.5 5.5 75.0 5.0 7.5 219 231 * 3.3 M 34.6 70.0 64.8 12.3 70.0 4.5 9.9 44.6 4.6 70.1 75.0 45.3 31.4 6.5 39.7 232 239 - 4.3 M 75.0 75.0 75.0 75.0 75.0 21.9 3.4 75.0 14.1 75.0 67.1 75.0 2.8 75.0 75.0 240 247 * 3.7 M 75.0 9.4 66.9 8.2 75.0 24.9 33.4 42.4 75.0 75.0 7.9 75.0 49.8 5.9 75.0 248 250 - 4.8 H 75.0 75.0 75.0 75.0 75.0 8.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 251 252 * 3.8 M 75.0 8.5 75.0 7.0 42.0 8.5 75.0 75.0 75.0 43.2 10.8 75.0 75.0 6.0 75.0 >>>>>>