Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vema1 ------------------CEEEEEEEEECCC--CCCCCEEEEEECCHHHCCCCCCCCCE-ECEEEC----CCCEEEEEEEEEC--CCCEEEEEEEECCCC--CEEEECC-CCEEECCCCC----CCCEEEEEC------------- >P1;d2j43a1 ------------------CCCEEEEECCCCCCCCHHHEEEEEEECCCCCCC----CCCCCCCCCCCEECC--CCEECCEECCCCCCCEEEEEEEEC-----CC--CCCC-CCEEEECC----C-CCCEEEECCCC-CEECCC---- >P1;d2j43a2 ----------------CCCCCEEEEEEE-CCCCCCCCEEEEEEECCCCCCC----CCC-CCEECC-EEEC--CEEEEEEECC-CCCCCEEEEEEECCCCHHHH---CCCCCCEEECCC----C-CCCEEEEECCCCCCCCCCCCCC >P1;d2j73a- ----------------CC-CEEEEEEEE-CCCCCCCCEEEEEEEEECCCC------CC-EEECCC-EEEC--CEEEEEEEEC-CCCCEEEEEEEEC----CCC--EEEEEEEEEEECC----C-CEEEEEEECCCCCCCCCCC--- >P1;d3bmva2 ---------------CCCCEEEEEEEEECCC--CCCCCEEEEEECCHHHCCCCHH-HCCCCCCCCCCCC--CCCEEEEEEEEC--CCEEEEEEEEECCC---CC-EECCCCCEEEE-CCCC---CCEEEEEECCC----------- >P1;d3njxa2 -------------CCCHHHCCEEEEEEECCC---CCCCEEEEEECC----------CCEEEEECCC------CCEEECCCCCC---EEEEEEEEEC-------------CEEEEEEEEEECCCCEEECCEECCCC----------- >P1;d5ghla- -------------C-CCCCEEEEEEEEE-CC--CCCCCEEEEEECCHHHCCCCHH-HCE-ECCCC-CCCCCCCEEEEEEEEEC--CCEEEEEEEEECCCC--CE-EECCCCCEEEE-CCCCCCCCEEEEEEECC------------ >P1;d6j33a1 CCCCCCCCCCCCCCCCCCCCCEEEEEECCCCC-CHHHEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEC--CEEEEEEEC-CCCCCEEEEEEEECC--------EECCCCCEEEECC----CCCCCEEEECCCCCCCCC------ PSA >P1;d1vema1 ------------------9714020004805--16a60301000338401533188702-407436----9580143605000--657040200011876--8245307-8423165017----654414152------------- >P1;d2j43a1 ------------------284404014611ac2836201010373038409----941950245717639--113213030288818701000007-----71--6310-95260708----6-59830102671-724585---- >P1;d2j43a2 ----------------a36a94020004-186680a700020343067408----a42-704607-7549--4101120305-b90a200000012659cb61---320675050750----a-9221000236245004228287 >P1;d2j73a- ----------------a9-602020003-166681b30002010255776------90-822706-8849--1231040508-3406300000025----837--5301865040809----9-0814010227467035946--- >P1;d3bmva2 ---------------648b205030003807--08b9040100031610263428-7020507299437--441002406001--536050100122a9---83-5406aa31625-0289---8834141703a----------- >P1;d3njxa2 -------------9459a6214032406905---98481202043c----------726162706b------80605043033---7603000207-------------a740254706074a644837065348----------- >P1;d5ghla- -------------5-a23a504020204-08--09b6070300021850053628-602-60538-527ba611021416040--347040000115988--62-64068741726-03666946815081715------------ >P1;d6j33a1 ba7a697a79a3b41450886300010236ad-a39710020335a805003a25a74844834055368--300102060-644881000100373--------9320a56050209----728510010349465156------ Translating the sequences ------------------C**EEEEEEE*CC--CCCC*EEEEEECC***CC*****CC*-******----**C*EEEEEE**C--CC*EEEEEEE*****--*****CC-CCEEE**C**----C**EEEE*C------------- ------------------C**EEEEE***CC**C****EEEEEECC***CC----*CC*****CC*****--C*EE**EE**C**CCEEEEEEEE*-----**--**CC-CCEEEE*C----C-C**EEEE*CCC-******---- ----------------**C**EEEEEEE-CC**CCCC*EEEEEECC***CC----*CC-****CC-****--C*EEEEEE**-**CC*EEEEEEE********---*CC*CCEEE**C----C-C**EEEE*CCC*********** ----------------**-**EEEEEEE-CC**CCCC*EEEEEE*****C------CC-****CC-****--C*EEEEEE**-**CCEEEEEEEE*----***--*******EEEE*C----C-C**EEEE*CCC********--- ---------------***C**EEEEEEE*CC--CCCC*EEEEEECC***CC****-*C*****CC****--*C*EEEEEE**C--CCEEEEEEEE****---**-**CC*CCEEEE-C***---C**EEEE*CCC----------- -------------********EEEEEEE*CC---CCC*EEEEEECC----------CC*****CC*------C*EEE*****C---*EEEEEEEE*-------------***EEEE******C******EE*CCC----------- -------------*-***C**EEEEEEE-CC--CCCC*EEEEEECC***CC****-*C*-***CC-******C*EEEEEE**C--CCEEEEEEEE*****--**-**CC*CCEEEE-C****C*C**EEEE*CC------------ ******************C**EEEEEE**CC*-C****EEEEE*CC***CC*****CC*****CC*****--C*EEEEEE*-C**CCEEEEEEEE**--------**CC*CCEEEE*C----C*C**EEEE*CCC*****------ 49452.tem _________________________________ -------------*-***C**EEEEEEE*CC**CCCC*EEEEEECC***CC*****CC*****CC*****-*C*EEEEEE**C**CCEEEEEEEE*****-***-**CC*CCEEEE*C***-C*C**EEEE*CCC*******---- Structural block scores 0 12 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 8.7 15 17 * 2.7 P 75.0 75.0 29.5 31.5 6.0 8.2 5.2 3.0 19 20 * 1.0 P 4.0 6.0 9.8 3.0 1.0 1.5 2.5 7.0 21 27 E 4.9 H 1.4 2.7 1.4 1.0 1.6 2.7 1.7 0.9 29 30 C 5.0 H 2.5 5.8 4.5 3.5 3.5 2.5 4.0 8.2 31 32 * 3.6 M 75.0 7.2 6.0 6.0 75.0 75.0 75.0 44.2 33 36 C 4.4 M 5.9 4.8 6.4 5.9 7.1 24.0 6.6 7.4 38 43 E 5.0 H 0.7 2.0 1.5 0.5 0.8 1.5 1.7 1.3 44 45 C 4.7 H 3.0 1.5 1.5 3.5 2.0 7.8 1.5 7.8 46 48 * 1.7 P 4.0 5.0 5.7 6.3 2.3 75.0 4.3 4.3 49 50 C 4.6 H 3.0 4.5 4.0 40.5 4.0 75.0 2.5 0.0 51 55 * 3.4 M 4.6 61.8 62.1 75.0 18.4 75.0 18.8 6.2 56 57 C 4.7 H 3.5 2.5 3.0 4.5 3.5 4.5 3.0 5.5 58 62 * 1.5 P 17.6 4.0 18.4 18.8 2.8 4.4 17.6 5.4 63 64 C 4.7 H 3.5 6.0 3.5 3.0 5.5 3.0 5.5 2.0 65 69 * 2.5 P 61.2 5.2 20.0 20.8 19.6 62.3 20.1 5.4 74 79 E 4.7 H 3.2 2.0 1.2 2.2 2.0 3.0 2.3 1.5 80 81 * 1.4 P 0.0 1.0 2.5 4.0 0.0 1.5 2.0 37.5 83 84 * 3.4 M 75.0 8.0 10.2 3.5 75.0 75.0 75.0 4.0 85 86 C 4.7 H 5.5 4.5 5.2 3.0 4.0 41.0 3.5 8.0 87 94 E 4.9 H 1.6 1.0 0.4 0.6 1.6 1.4 1.5 0.6 95 99 * 2.9 P 4.6 61.4 6.9 61.0 19.7 61.4 6.2 47.0 101 103 * 3.4 M 28.3 27.7 27.3 28.3 28.7 75.0 27.7 75.0 105 106 * 2.0 P 4.0 4.5 39.0 4.0 4.5 75.0 5.0 6.0 107 108 C 4.4 M 3.5 0.5 1.0 0.5 3.0 75.0 3.0 1.0 110 111 C 4.3 M 6.0 7.0 6.0 5.5 6.8 5.5 5.5 5.5 112 115 E 4.8 H 3.0 3.8 3.0 3.0 3.5 2.8 4.0 1.8 118 120 * 3.6 M 27.7 75.0 75.0 75.0 6.3 4.3 5.0 75.0 125 126 * 1.0 P 4.5 8.5 2.0 4.5 5.5 6.0 4.5 3.0 127 130 E 4.8 H 2.5 1.0 0.2 1.2 2.5 4.0 3.5 0.2 132 134 C 4.7 H 50.7 4.7 3.7 4.3 4.5 5.0 27.0 5.7 135 141 * 3.6 M 75.0 15.1 2.4 4.9 75.0 75.0 75.0 24.7 142 145 - 4.6 H 75.0 75.0 6.2 57.8 75.0 75.0 75.0 75.0 >>>>>>