Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1cwva1 --------CEEEEEEE-------CCCEECCCCCCEEEEEEEECCCCCCCCCC-EEEEECCC-CCCCCEEEEECCCCCEEEEEECCCCCEEEEEEEEECC---EEE---EEEEEEECC-- >P1;d1cwva2 ---CCCHHHC-EEEEE-------CCEEECCCCCCEEEEEECCCCCCCCCCCC-CEEEEECC--CEEC--CCEECCCCEEEEEEECCCCEEEEEEEEECCEEEEEE---EEEEEEE---- >P1;d1cwva3 CCCCCCCCCC-EEEEC-------CCEEECCCCCCEEEEEECCCCCCCCCCCCCCEEEEEEECCCEEC--CCEECCC-CEEEEEECCCCEEEEEEEEECCEEC---HHHCEEEEEECC-- >P1;d1cwva4 --CCEE-----EEEE-CCEEECCCCCCCCCCCCCCEEEEEECCCHH--HHHH--EEEEECCCCCEEEC-C-------CCEEEECCCCCCCEEEEEEECCCCCCEE---EEEECC----- >P1;d1f00i1 ---CEE---E-EEEEC-------CCEEECCCCCCEEEEEEEEE-CCEECCCC-EEEEEEC--CCEECCCEEECCCCCEEEEEEECCCCEEECEEEEECCCCCCEE---CCCEEEEC--- >P1;d1f00i2 -CCEECC---CCEEECCCCCEE---CCCCCCCCCCEEECCEE---C--CCCC--EEEEECCCCCEEECCC-------CCEEEECCC--CCEEEEEEECCC--EEE---EEEECCC--CC >P1;d6tpla1 CCCCEE---E-EEEEC-------CCEEECCCCCCEEEEEEEEE-CCEECCCC-EEEEEEEECCCEECCCEEECCCCCEEEEEEECCCCEEEEEEEECCCCCCCEE---CCCEEEECCCC PSA >P1;d1cwva1 --------16080615-------a3404051853020204022857643462-60304074-b08485253605990104060207559403020408b---564---42505068b-- >P1;d1cwva2 ---9312950-60607-------57607041842050304030793554383-80605072--1915--92535860201050208677503050407b880908---3250506---- >P1;d1cwva3 1477035a50-60606-------36604031853040303010755620690960603377170714--9263388-1020403085576030002189450---681545010566-- >P1;d1cwva4 --2601-----0032-cc7547286720791878140101038638--3056--06070625620506-9-------503040279085501030405876b532---106060----- >P1;d1f00i1 ---670---5-51706-------46506062932030302017-ca832492-3020706--3181577435079704050402076486030003129478245---05504069--- >P1;d1f00i2 -806056---850233a75846---90477095654020607---6--0568--2606065581040679-------603020366--36040004054b--441---4170950--97 >P1;d6tpla1 a77230---5-50706-------4a304051932030301033-678423b2-505092464708054b5390896040503030865870200030a51b8246---0d105054798 Translating the sequences --------***EEEE*-------CC*EECCCCCCEEEEEEE***CC**CCCC-*EEEE*C*-CC**C****E*CCC**EEEEE*CCCCEEEEEEEEECC---*EE---*EEEEEE**-- ---C******-EEEE*-------CC*EECCCCCCEEEEEE****CC**CCCC-*EEEEEC*--CEEC--**E*CCC**EEEEE*CCCCEEEEEEEEECC****EE---*EEEEEE---- ***C******-EEEE*-------CC*EECCCCCCEEEEEE****CC**CCCC**EEEEE***CCEEC--**E*CCC-*EEEEE*CCCCEEEEEEEEECC***---****EEEEEE**-- --*C**-----EEEE-*******CC***CCCCCC*EEEEEE*****--****--EEEEEC**CCEE**-*-------**EEEE*CCCC**EEEEEEECC****EE---*EEE**----- ---C**---*-EEEE*-------CC*EECCCCCCEEEEEEE**-CC**CCCC-*EEEEEC--CCEEC****E*CCC**EEEEE*CCCCEEE*EEEEECC****EE---***EEEE*--- -******---**EEE*******---***CCCCCC*EEE**E*---C--CCCC--EEEEEC**CCEE****-------**EEEE*CC--**EEEEEEECC*--*EE---*EEE***--** ***C**---*-EEEE*-------CC*EECCCCCCEEEEEEE**-CC**CCCC-*EEEEE***CCEEC****E*CCC**EEEEE*CCCCEEEEEEEE*CC****EE---***EEEE**** 49373.tem _________________________________ -**C***-**-EEEE*-------CC*EECCCCCCEEEEEEE***CC**CCCC-*EEEEEC**CCEEC****E*CCC**EEEEE*CCCCEEEEEEEEECC****EE---*EEEEEE**-- Structural block scores 1 2 * 3.4 M 75.0 75.0 5.5 38.5 75.0 4.0 7.0 4 6 * 2.4 P 75.0 2.0 2.7 25.3 27.3 3.7 26.0 8 9 * 3.1 M 3.5 2.5 2.5 75.0 40.0 75.0 40.0 11 14 E 4.9 H 3.8 3.0 3.0 1.2 3.2 2.5 3.0 16 22 - 4.3 M 75.0 75.0 75.0 7.1 75.0 16.5 75.0 23 24 C 4.6 H 6.8 6.0 4.5 7.0 5.0 75.0 7.2 26 27 E 4.2 M 2.0 3.5 2.0 1.0 3.0 2.0 2.0 28 33 C 5.0 H 3.7 3.2 3.3 6.7 3.7 5.7 3.3 34 40 E 4.7 H 1.1 1.7 1.4 1.0 1.1 2.4 1.0 41 43 * 2.0 P 4.0 3.3 2.7 5.7 27.7 52.3 27.0 44 45 C 4.4 M 6.0 6.0 5.0 5.5 11.5 40.5 6.5 46 47 * 2.5 P 5.0 5.0 4.0 75.0 5.5 75.0 6.0 48 51 C 4.6 H 3.8 4.5 3.8 3.5 4.2 4.8 4.6 54 58 E 4.9 H 1.4 2.2 2.4 2.6 1.8 2.8 3.2 60 61 * 2.5 P 39.5 38.5 4.0 3.5 75.0 5.0 5.0 62 63 C 4.8 H 5.8 38.0 3.5 4.0 2.0 4.5 3.5 64 65 E 4.6 H 6.0 5.0 4.0 2.5 4.5 2.0 4.0 67 70 * 2.3 P 3.8 40.2 40.2 41.2 5.2 24.2 5.9 73 75 C 4.4 M 7.7 6.3 6.3 75.0 7.7 75.0 7.7 76 77 * 2.0 P 0.5 1.0 38.0 40.0 2.0 40.5 2.0 78 82 E 4.8 H 2.0 1.2 1.2 1.4 1.8 1.0 1.6 84 87 C 4.8 H 4.2 5.2 4.5 6.0 4.2 40.5 4.8 88 96 E 4.7 H 2.4 2.7 2.1 2.0 2.3 1.9 2.2 97 98 C 5.0 H 9.8 9.2 8.5 6.5 5.5 4.5 7.8 99 102 * 2.1 P 57.5 6.2 21.0 7.4 5.2 41.4 5.6 103 104 E 4.6 H 5.0 4.0 75.0 2.5 4.5 2.5 5.0 105 107 - 4.6 H 75.0 75.0 5.0 75.0 75.0 75.0 75.0 109 114 E 4.4 M 3.0 3.0 2.5 14.5 3.3 3.7 4.1 115 116 * 3.4 M 9.8 75.0 6.0 75.0 42.0 75.0 5.5 117 118 - 4.2 M 75.0 75.0 75.0 75.0 75.0 8.0 8.5 >>>>>>