Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1w5fa2 CCCHHHHHHHHHHHHC--CCCCCEEEEEEEEC-------CCHHHHHHHHHHCCCCCC--CCHHHCCEEEEEEEECCCCCHHHHHHHHHHHHCCCC----CCCEEEEEEEECC----------CCCCCEEEEEEEEECCCCC----HHHH---------------------C--------------------------------- >P1;d2btoa2 C---CCHHHHHHHHCCCCCCCCCEEEEECCCCCC-----CCCHHHHHHHHCCHHHCCCCCCHHHCCEEEEEEEEEEC---CCHHHHHHHHHCC--CCCCCCCCCCEEEEEECCCCC--------CCCEEEEEEEEECCHHH----HHHHHHHHHHHHHCCCCCHHHHHCCCCC--HHHHHHHHHHHHHHHHHHHHHCC------ >P1;d2r7512 -----CCHHHHHHHHC--CCCCCEEEEEEEEC-------CCHHHHHHHHHHHCCCCC-CCCHHHCCEEEEEEEECCCCCCCHHHHHHHHHHHHCC----CCCEEEEEEEECC----------CC-CCEEEEEEEEECCCCCCEEE--CC---------------------EEECC-------------------------CCCC >P1;d2vapa2 ---CCCCHHHHHHHHC--CCCCEEEEEEEECC-------CCHHHHHHHHHHCCCCCC--CCHHHCCEEEEEEEECCCCCHHHHHHHHHHHHHHCC----CCCEEEEEEEECC----------CC-CCCEEEEEEEECCHHHEEEECC-----------------------EEEEC----------------------------- >P1;d3cb2a2 CCCCCCHHHHHHHHCCCCCCCCCEEEEECCC-------CCCCHHHHHHHCCC-CCCCCCCC-CCCCEEEEEEEEEC-CCHHHHC-CCCCC----CCCCCCCCCCCC-CEEECCC------------CCEEEEEEEEHHHHH----HHC--CCCCCC--CCCCCCHHHHCCCCCCCCHHHHHHC-CCC-CHHHHHHCCCHHHCCC >P1;d3ryca2 CCCCCCHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHCCCHHHCCCCCCHHHCCEEEEEEEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCEEEEEEEEEHHHHH----HHHHHHHHHHHHHCCCCCCHHHHCCCCC--HHHHHHHHHHHHHHHHHHHHHHCC----- >P1;d3rycb2 CCCCCCHHHHHHHHCCCCCCCCCEEEEECCCCCC----CCCCHHHHHHHCCCHHHCCCCCCHHHCCEEEEEEEEEECCCHHHHHHHHHHHHHHCHHHCCCCCCCCEEEEEECCCCC--------CCCEEEEEEEEEHHHHH----HHHHHHHHHHHHHCCCCCCHHHHCCCCC--HHHHHHHHHHHHHHHHHHHHHHHCC-CCC >P1;d6rvqa2 -----CCHHHHHHHHC--CCCCCEEEEEEEEC-------CCHHHHHHHHHHCCCCCC--CCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHC----CCCEEEEEEEECC----------CC-CCEEEEEEEEECC------------------------------------------------------------------ PSA >P1;d1w5fa2 8677974765656057--a0712050615068-------83003400460053a918--150640610202010056058802630160076204----9a07234422636----------9048620504010030654----7615---------------------8--------------------------------- >P1;d2btoa2 b---5779624740215970641030300457aa-----54a36700740074a10527020280300000041408---a627710481488--03406917230535569833b--------63800040200001017----2156607634661674261776398a34--58516861765582063069034------ >P1;d2r7512 -----38785367045--a0623030405056-------b80055005600532737-4170350320103030086179621750084058402----6809024525626----------a2-84002010300305622145--ca---------------------75156-------------------------a94a >P1;d2vapa2 ---4b27875356056--b2722140405175-------a61055006600909606--050510800204010077055820650274058504----8a06122116538----------91-98204030200006830573ba-----------------------94657----------------------------- >P1;d3cb2a2 958b37894267701406605410404054b-------ba380520044005-92051a1c-9a201000103065-277a606-11604----607103139350-0114678------------912030200101003----414--70a264--288170885677b71b617416663-845-2072045016761589 >P1;d3ryca2 691057982477001249405320304006163b5ab3a33606600620065930739041761100200030508067950870277058849060074194705221688608299c5b5260520030100000024----22557077357616844707755a8a39--496157728625603830981268----- >P1;d3rycb2 db2156a9725840123940542040300469ac----66050350073014480051803066020000003030906784066207502872773006227a10413148832a--------b1a10030200000003----3154517624762886470775398a38--4651567267256017304622745-39a >P1;d6rvqa2 -----18772367036--c4b52063604158-------b70014005600617a4a--24074061000201007705a710730152038308----3b0a124136346----------92-b630104010041------------------------------------------------------------------ Translating the sequences *******HHHHHHH*C--CCCCCEEEEE***C-------CC*HHHHHHH**C***CC--CCHHHCCEEEEEEEE**CCCHHHHHHHHHHHH***C----CCC***EEEEE*C----------***CCEEEEEEEEE*****----****---------------------*--------------------------------- *---*C*HHHHHHH*C**CCCCCEEEEE***C**-----CC*HHHHHHH**C***CC**CCHHHCCEEEEEEEE**C---**HHHHHHHHH**--****CCC***EEEEE*C****--------*CCEEEEEEEEE*****----****************************--***********************------ -----C*HHHHHHH*C--CCCCCEEEEE***C-------CC*HHHHHHH******CC-*CCHHHCCEEEEEEEE**CCC**HHHHHHHHHH***C----CCC***EEEEE*C----------**-CCEEEEEEEEE*********--**---------------------*****-------------------------**** ---**C*HHHHHHH*C--CCCC*EEEEE***C-------CC*HHHHHHH**C***CC--CCHHHCCEEEEEEEE**CCCHHHHHHHHHHHH***C----CCC***EEEEE*C----------**-CC*EEEEEEEE***********-----------------------*****----------------------------- *****C*HHHHHHH*C**CCCCCEEEEE***-------*CC*HHHHHHH**C-**CC**CC-**CCEEEEEEEE**-CCHHHH*-*****----C****CCC****-*EE*C**------------C*EEEEEEEE*****----***--******--*************************-***-**************** *****C*HHHHHHH*C**CCCCCEEEEE***C*******CC*HHHHHHH**C***CC**CCHHHCCEEEEEEEE**CCCHHHHHHHHHHHH***C****CCC****EEEE*C*************CCEEEEEEEEE*****----****************************--************************----- *****C*HHHHHHH*C**CCCCCEEEEE***C**----*CC*HHHHHHH**C***CC**CCHHHCCEEEEEEEE**CCCHHHHHHHHHHHH********CCC***EEEEE*C****--------*CCEEEEEEEEE*****----****************************--*************************-*** -----C*HHHHHHH*C--CCCCCEEEEE***C-------CC*HHHHHHH**C***CC--CC***CCEEEEEEEE**CCCHHHHHHHHHHHH***C----CCC***EEEEE*C----------**-CCEEEEEEEEE**------------------------------------------------------------------ 55307.tem _________________________________ *****C*HHHHHHH*C**CCCCCEEEEE***C**----*CC*HHHHHHH**C***CC**CCHHHCCEEEEEEEE**CCCHHHHHHHHHHHH***C****CCC***EEEEE*C****------***CCEEEEEEEEE*****----******************************************************--*** Structural block scores 0 4 * 3.0 P 7.4 48.3 75.0 48.1 7.3 4.2 6.6 75.0 7 13 H 5.0 H 5.0 4.6 5.1 4.9 5.0 4.0 5.0 4.6 16 17 * 3.4 M 75.0 7.0 75.0 75.0 3.0 6.5 6.0 75.0 18 22 C 4.9 H 4.1 3.6 4.3 4.9 3.2 2.8 3.0 7.0 23 27 E 5.0 H 2.4 1.2 1.4 1.8 1.6 1.4 1.4 3.0 28 30 * 1.0 P 3.7 3.0 3.3 4.3 6.8 2.3 3.3 3.3 32 33 * 3.9 M 75.0 10.5 75.0 75.0 75.0 7.2 11.5 75.0 34 37 - 4.7 H 75.0 75.0 75.0 75.0 75.0 7.5 75.0 75.0 39 40 C 5.0 H 5.5 4.5 9.8 8.2 6.8 3.0 3.0 9.2 42 48 H 5.0 H 2.4 3.9 3.0 3.1 2.1 2.9 2.6 2.3 49 50 * 1.0 P 0.0 0.0 0.0 0.0 0.0 0.0 0.5 0.0 52 54 * 1.2 P 7.5 5.2 4.0 5.0 28.7 5.7 4.0 6.2 55 56 C 5.0 H 4.5 2.5 5.0 3.0 2.5 3.5 2.5 7.2 57 58 * 3.1 M 75.0 4.5 39.5 75.0 5.8 6.0 4.5 75.0 59 60 C 5.0 H 3.0 1.0 4.0 2.5 6.8 2.0 1.5 3.0 61 63 H 4.3 M 3.3 3.3 2.7 2.0 31.5 4.7 4.0 3.7 64 65 C 5.0 H 3.0 1.5 1.5 4.0 1.0 1.0 1.0 3.0 66 73 E 5.0 H 0.8 0.6 1.1 0.9 0.6 0.6 0.4 0.5 74 75 * 1.0 P 2.5 2.0 4.0 3.5 5.5 2.5 1.5 3.5 76 78 C 4.7 H 3.7 52.7 4.7 4.0 28.0 4.7 5.0 4.0 79 90 H 4.7 H 3.4 10.5 3.9 3.7 16.0 4.8 3.9 3.3 91 93 * 1.9 P 2.7 30.3 4.0 4.3 75.0 6.7 5.7 3.7 95 98 * 3.4 M 75.0 1.8 75.0 75.0 2.0 1.5 2.5 75.0 99 101 C 5.0 H 6.5 5.3 4.7 6.2 2.3 4.0 3.3 4.8 102 104 * 1.0 P 4.0 4.0 3.7 3.0 5.7 6.7 6.2 4.5 105 109 E 4.7 H 3.6 3.6 4.4 3.0 15.4 2.0 1.8 3.4 112 115 * 3.6 M 75.0 6.4 75.0 75.0 41.2 5.5 5.9 75.0 116 121 - 4.7 H 75.0 75.0 75.0 75.0 75.0 8.2 75.0 75.0 122 124 * 3.1 M 4.3 52.0 29.2 28.3 75.0 4.3 53.8 28.7 125 126 C 4.8 H 7.0 5.5 6.0 8.5 42.0 2.5 5.8 8.8 127 135 E 4.9 H 1.3 0.7 0.7 1.2 1.0 0.7 0.7 1.0 136 140 * 1.4 P 3.6 1.8 3.2 3.4 0.8 1.2 0.6 46.0 141 144 - 4.3 M 75.0 75.0 3.0 3.8 75.0 75.0 75.0 75.0 145 198 * 3.3 M 68.6 8.6 66.1 66.3 12.5 7.7 7.3 75.0 199 200 - 4.3 M 75.0 75.0 42.8 75.0 3.5 75.0 40.0 75.0 201 203 * 3.9 M 75.0 75.0 7.8 75.0 7.3 75.0 7.5 75.0 >>>>>>