Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2byoa1 --CCHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCCCCEEEEEEEEECC---CCEEEEEEEEC-----CEEEEEEEEECCEEEEEEC--CEEEEEEEHHH---HHHHCC---CCCCCCC--CCEEEEEEEEEEECCEEEEEEEEEECHHHHHHHCC--CCC-CCEEEEEEEECC------CCCCEEEEEEECC-CEEEEEEEECCC-CCCCCC----------------- >P1;d2w7qa- CCCCCCCHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCEEEEEEEEEEECCC--EEEEEECCC-------CCEEEEEEC--CEEEE-CCCCEEEECC--C--CCC-----CCHHHHHHCCCCCCCCEEEEEEEECCEEEEEEEECC--------------CCCCCEEEEE-EEC--------CEEEEEEEECCCCCEEEEEEECCCCCCCCHHHHCCCCCCCCEEECC-- >P1;d3ksna- --------CHHHHHHHHHHCCCEEEEEEEEEEEC-----CCEEEEEEEEECCC--EEEEEEEEC-------CCEEEEECCCEEEEEE-HHHCEEEEEEHHH--CCC-----CCHHHHHHHCCC--CCCCEEEEEECC--EEEEEECCC-------------CCCEEEEEEE-ECC-------CCCEEEEEEEECCCCEEEEEEEEEEECCCCHHHHCCCCCCCCEEEECCC >P1;d3mh9a1 CCCCCCHHHHHHHHHHHHHHCCEEEEEEEEECCCCCC-CEEEEEEEEECC---CCEEEEEEEEEE--CCEEEEEEEEEECCEEEEEEE-CCEEEEEEEHHHCCCHHHHHCCCCCHHHHHH--CEEEEEEEEEEEECCEEEEEEEEEECHHHHHHHCHHHCCC-CCEEEEEEEECC------CCCCEEEEEEEEECCEEEEEEEECCC-CCCCCCCCCCC------------ >P1;d3wjta- -CCCCCCCHHHHHHHHHHHCCCEEEEEEEEEEEEC--CEEEEEEEEEEECCC---CEEEEEECCCCC----EEEEEEEECCEEEEEE-CCCCEEEECCHHH--HHHHHCCCCCCHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEC-------------C-EEEEEEECCEECCCC----CCEECEEEEECC-CEEEEEEEEEEEEE---------------------- >P1;d4qa8a- CCCCHHHHHHHHHHHHHHHCCCEEEEEEEEEC-CCCC-CEEEEEEEEEECCCCCEEEEEEEEECCCCCCCCEEEEEEEECCEEEEEEC--CEEEEEEEHHHCCCHHHCCCCCCCHHHHHH--CCEEEEEEEEEECCCCEEEEEEEEEEHHHHCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCEEEEEEEEC-CEEEEEEEECCC-CCCCCCCCC-C------------ PSA >P1;d2byoa1 --65892173056017325a08012121408990a12350431303234a---85006450118-----9688041314c5610034a--78366141378---369629---d642909--70680544a44607925023031312380043524--918-742511210046------a332102320608-823034104516-591906----------------- >P1;d2w7qa- b84a3918902830271077081040503241410657757445040203194--20212157a-------73300006a--04110-2667200532--a--102-----70000000190811960005293ac63050102036--------------a370610501-057--------55043021228863414060580159a05876072b739c17549a-- >P1;d3ksna- --------92372037004508103020406166-----75704020105172--200021564-------6422100427011512-2746603032076--124-----430000001048--910707092ba4--60506258a-------------a370430102-016-------602054000146764313071470849a18973071824bc0836452c >P1;d3mh9a1 b7933807500850284068060030414057906b2-41441312011a---921033613225--cb66471501039a3000057-8971454550677451220054830002005--4077070431461695500304050419003503530819-850502010128------b721001030428ab30221102617-2909095084c------------ >P1;d3wjta- -a147491660661264047195020506010219--937170502030538---505130238986----3202010568403003-6775545483027--002831904000411420000013809717036622032042629-------------c-68050506b02491a----10002503020b-91404060370709---------------------- >P1;d4qa8a- 78448705610550093039151020515057-09a0-30542503011877b40202371431787b5805725100097211236c--881543550584350111036860000001--5068001365572ab340030324060810220046006c89605020100039379963601003010428-903010305716-590913828-e------------ Translating the sequences --CC***HHHHHHHHHHHHCCCEEEEEEEEEE*CCCC*CEEEEEEEEE*C---**EEEEEEEEC-----**EEEEEEEECCEEEEEE*--C*EEEEEEHHH---HHH**C---C******--CC***EEEEEEEECC*EEEEEEEEEC*********--**C-C*EEEEEE*ECC------*CCCEEEEEEE*C-CEEEEEEEECCC-CCCC**----------------- *CCC***HHHHHHHHHHHHCCCEEEEEEEEEE*CCCC*CEEEEEEEEEE*CC*--EEEEEE**C-------**EEEEEEC--*EEEE-**C*EEEE**--*--C**-----CC*HHHHH***CC***EEEEEEEECC*EEEEEEE**--------------C*C**EEEEE-E*C--------C*EEEEEEE*C*C*EEEEEEECCC*CCCC****C*C**********-- --------*HHHHHHHHHHCCCEEEEEEEEEE*C-----**EEEEEEEE*CC*--EEEEEEEEC-------**EEEEE*CCEEEEEE-****EEEEEEHHH--C**-----CC*HHHHHH**C--****EEEEEECC--EEEEEE**C-------------C*C*EEEEEE-ECC-------CCCEEEEEEE*C*C*EEEEEEE****CCCC****C*C************ *CCC***HHHHHHHHHHHH*CCEEEEEEEEE**CCCC-CEEEEEEEEE*C---**EEEEEEEE**--****EEEEEEEECCEEEEEE*-*C*EEEEEEHHH**CHHH**C*CCCHHHHHH--C****EEEEEEEECC*EEEEEEEEEC*************C-C*EEEEEE*ECC------*CCCEEEEEEE***CEEEEEEEECCC-CCCC****C*C------------ -CCC****HHHHHHHHHHHCCCEEEEEEEEEE**C--**EEEEEEEEEECCC---*EEEEEE*C***----EEEEEEEECCEEEEEE-**C*EEEE**HHH--*HHH**C*CCCHHHHHH**CC******EEEE*CC**EEEEEEEEC-------------C-**EEEEE**E*C***----CC*E*EEEEE*C-CEEEEEEEE*****---------------------- *CCC***HHHHHHHHHHHHCCCEEEEEEEEE*-CCCC-CEEEEEEEEEECCC***EEEEEEEEC*******EEEEEEEECCEEEEEE*--C*EEEEEEHHH**CHHH**C*CCCHHHHHH--CC***EEEEEEE*CC*EEEEEEEEE**************C*C*EEEEEE*ECC*******CCCEEEEEEE*C-CEEEEEEEECCC-CCCC****C-C------------ 89392.tem _________________________________ *CCC***HHHHHHHHHHHHCCCEEEEEEEEEE*CCCC*CEEEEEEEEEECCC***EEEEEEEEC*----**EEEEEEEECCEEEEEE***C*EEEEEEHHH--CHHH**C*CCCHHHHHH**CC***EEEEEEEECC*EEEEEEEEEC*********--**C*C*EEEEEE*ECC------*CCCEEEEEEE*C*CEEEEEEEECCC*CCCC****C*C------------ Structural block scores 1 3 C 4.4 M 28.7 7.5 75.0 6.3 5.2 5.3 4 6 * 1.9 P 6.3 4.3 75.0 3.7 6.7 5.0 7 18 H 4.9 H 3.3 3.9 9.3 3.8 3.5 3.1 19 21 C 4.8 H 6.2 5.0 4.3 4.7 5.7 5.0 22 31 E 4.9 H 2.8 2.0 1.7 2.4 1.9 2.6 33 36 C 4.4 M 3.4 3.0 57.8 4.9 40.0 4.9 39 48 E 4.8 H 2.3 3.1 2.6 1.8 2.5 2.1 49 51 C 4.2 M 53.5 4.3 4.3 53.5 5.3 7.3 52 54 * 3.4 M 29.3 51.3 50.7 28.7 75.0 5.2 55 62 E 4.8 H 2.1 2.5 2.0 2.4 2.4 2.8 65 68 - 4.1 M 75.0 75.0 75.0 43.5 41.0 7.9 69 70 * 3.4 M 7.5 75.0 75.0 6.0 75.0 4.0 71 78 E 4.7 H 3.6 2.4 2.4 2.6 1.6 2.5 79 80 C 4.8 H 8.8 42.8 4.5 9.8 7.0 8.0 81 86 E 4.8 H 2.3 13.5 1.7 1.3 1.7 2.5 87 89 * 3.2 M 53.5 27.7 28.0 30.0 29.3 54.2 92 97 E 4.7 H 3.5 2.0 2.3 4.0 4.8 3.8 98 100 H 4.5 M 6.0 53.5 4.3 4.3 3.0 4.3 101 102 - 4.1 M 75.0 75.0 75.0 5.5 75.0 3.5 104 106 H 4.2 M 6.0 25.7 27.0 1.7 3.3 0.7 107 108 * 2.7 P 4.0 75.0 75.0 0.0 2.0 0.5 111 113 C 4.4 M 54.5 2.3 2.3 3.7 1.3 4.7 114 119 H 4.4 M 5.0 0.2 0.2 1.2 2.0 0.2 120 121 * 3.4 M 75.0 4.5 2.0 75.0 0.0 75.0 122 123 C 4.6 H 3.5 4.5 41.5 2.0 0.0 2.5 124 126 * 1.3 P 4.7 5.3 28.3 4.7 1.3 4.7 127 134 E 4.6 H 4.7 3.7 4.6 3.2 4.4 3.6 135 136 C 5.0 H 8.0 9.2 7.2 7.5 6.0 11.0 138 146 E 4.7 H 2.0 1.9 11.9 1.9 2.3 1.8 148 156 * 3.4 M 3.2 75.0 75.0 2.9 75.0 1.9 157 158 - 4.1 M 75.0 75.0 75.0 1.5 75.0 3.0 159 160 * 3.4 M 5.0 75.0 75.0 4.5 75.0 3.0 165 170 E 4.8 H 2.0 2.2 1.7 1.3 2.7 1.3 173 174 C 4.5 M 5.0 6.0 3.5 5.0 3.0 1.5 175 180 - 4.3 M 75.0 75.0 75.0 75.0 40.9 7.2 182 184 C 4.5 M 2.7 28.3 2.7 3.3 0.3 2.3 185 191 E 4.9 H 2.0 1.7 1.4 1.1 1.7 1.1 196 203 E 4.9 H 2.1 2.9 2.9 1.4 2.2 1.5 204 206 C 4.1 M 4.0 3.0 5.0 4.7 4.7 4.7 208 211 C 4.5 M 6.0 6.1 7.1 5.0 58.5 5.8 212 215 * 2.3 P 39.0 5.2 4.8 3.5 75.0 3.5 219 230 - 4.2 M 75.0 18.2 5.9 75.0 75.0 75.0 >>>>>>