Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1enfa2 --CEEEEEEEEEEEEEECC----EECCCEE---EEEEECEEEHHHHHHHHHHHHHHHHCCCCC--------------CCCCCEEEEEEEECCCCEEEEECCCCCC--CCHHHHHHHHCCCCEEEHHHEEEEEEEEEC-- >P1;d1esfa2 ------CCEECCEEEEECC----EEEC-CCHHHCEECCCEEEHHHHHHHHHHHHHHHHCCCCCHHH-----------CCCCCEEEEEEECCCCCCEEEECCCCCC--CCHHHHHHHHCCCCEEECCCC-EEEEEEECC- >P1;d1et9a2 --CC--CCEEEEEEEEECC----EECCCEE---EEECCCEEEHHHHHHHHHHHHHHHCCCCCC-------------CCCCCCCEEEEEEECCCEEEEEECCCCCC--CCHHHHHHHHCCCCEEECCCE-EEEEEEC--- >P1;d1ty0a2 ----------CEEEEEECC----EEEEEEE-CCCCCCCCEEEHHHHHHHHHHHHHHHHCCCCC-------------C-CCCCEEEEEEEECCCEEEEEECCCCCCC-CCHHHHHHHHHHCCEEEHHHEEEEEEEEEC-- >P1;d1v1oa2 ----CCCCEEEEEEEEEEEC-CEEEEEEEE---EEECCCEEEHHHHHHHHHHHHHHHCCCCCC----------------CCCCEEEEEEECCCEEEEEECCCCCC--------HHHCC--CEEEC-CEEEEEEEEE-CC >P1;d2rdha2 --CC-CCCEEEEEEEEEECCCCCEEEEEEE---EEECCCEEEHHHHHHHHHHHHHHHCCCCCC----------------CCCCCEEEEEECCCCEEEEECCCCCC--------HHHCC--CEEEHHHEEEEEEEE---- >P1;d3ea6a2 --CEEEEEEECCEEEEECC----EEEEECC-CCCEEEECEEEHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCC-CCCHHHHHHHHCCCCEEEHHHE-EEEEEEECCC >P1;d3seba2 CCCEEEEEEEEEEEEEECC----EEEEEEE---EEEEECEEEHHHHHHHHHHHHHHHHCCCCC-------------CCCCEEEEEEEEEEC-CEEEEEECCCCCCCCCCHHHHHHHHHHCCEEECCCE-EEEEEEEEC- >P1;d4o1na2 --CCCCCCCCCEEEEEC------CCCEEEE---CCCCCCEEEHHHHHHHHHHHHHHHHCCCCC----------------CCCCCCEEEEECCCCEEEECCCCCCC--------HHHCC--CEEEHHHEEEEEEECC--- >P1;d4ohja2 ----CCCCEECCCEEEECC----EECCCCC---CEECCCEECHHHHHHHHHHHHHHHHCCCCCC---------------CCCEEEEEEEECCCCEEEEECCCCCC--------HHHCC--CCEEHHHEEEEEEEEE--- PSA >P1;d1enfa2 --750aa424030403158----8538505---050643303142006401720474150469--------------8280680503020679652415038446--978731543188943050760340204054-- >P1;d1esfa2 ------b434040403248----953a-05661030868603043006301710475140437798-----------7070460402050583931616034397--988944663086954030890-300030439- >P1;d1et9a2 --79--872604050514a----7727714---040655703042004302610576160339-------------9666088140204179b651406015708--779913683177836130660-3040605--- >P1;d1ty0a2 ----------150302155----8446507-70080858603052007301420474260348-------------a-1616704020017aa85342602348b9-178863563176843042830430102043-- >P1;d1v1oa2 ----586636050502236b-a95845935---05053850306201750162047710038a----------------70553403052667761306009707--------7831c--64070-4062050505-29 >P1;d2rdha2 --5a-a202605020246589874644556---120755603063009501630456260378----------------928a1404021487743204055804--------8812b--540404605303081---- >P1;d3ea6a2 --861b9533030204049----9455442-a50105435030420054017002420003080c7606727250826000340502023788642316004608-5575a23573076844020550-3020504189 >P1;d3seba2 cc471b9634050401159----8263414---05054450305300730154035536034a-------------851306704030228-a63261601499a98478882662186945010630-602030545- >P1;d4o1na2 --b9478553040102a------8453555---16045970306401750133047626036b----------------63652502031688643406038907--------8823a--6314046063020307--- >P1;d4ohja2 ----198533050603157----8718450---261665603012006201610363030466a---------------62511303011687722615047a08--------6b726--7304046053030308--- Translating the sequences --******EE*EEEEEECC----EE***EE---*EE**CEEEHHHHHHHHHHHHHHHHCCCCC--------------**CCC*EEEEEEECCC*EEEEECCCCCC--******HHH*C**CEEE***E*EEEEEEE*-- ------**EE**EEEEECC----EE**-******EECCCEEEHHHHHHHHHHHHHHHHCCCCC***-----------**CCC*EEEEEE*CCC**EEEECCCCCC--******HHH*C**CEEE****-EEEEEEE**- --**--**EE*EEEEEECC----EE***EE---*EECCCEEEHHHHHHHHHHHHHHH*CCCCC-------------***CCC*EEEEEEECCC*EEEEECCCCCC--******HHH*C**CEEE***E-EEEEEE*--- ----------*EEEEEECC----EE***EE-*****CCCEEEHHHHHHHHHHHHHHHHCCCCC-------------*-*CCC*EEEEEEECCC*EEEEECCCCCC*-******HHH****CEEE***E*EEEEEEE*-- ----****EE*EEEEEE***-**EE***EE---*EECCCEEEHHHHHHHHHHHHHHH*CCCCC----------------CCC*EEEEEEECCC*EEEEECCCCCC--------HHH*C--CEEE*-*E*EEEEEEE-** --**-***EE*EEEEEE*C****EE***EE---*EECCCEEEHHHHHHHHHHHHHHH*CCCCC----------------CCC**EEEEEECCC*EEEEECCCCCC--------HHH*C--CEEE***E*EEEEEE---- --******EE**EEEEECC----EE*****-***EE**CEEEHHHHHHHHHHHHHHHHCCCCC****************CCC*EEEEEEECCC*EEEEECCCCCC-*******HHH*C**CEEE***E-EEEEEEE*** ********EE*EEEEEECC----EE***EE---*EE**CEEEHHHHHHHHHHHHHHHHCCCCC-------------***C***EEEEEEEC-C*EEEEECCCCCC********HHH****CEEE***E-EEEEEEE**- --*********EEEEE*------*****EE---***CCCEEEHHHHHHHHHHHHHHHHCCCCC----------------CCC***EEEEECCC*EEEE*CCCCCC--------HHH*C--CEEE***E*EEEEE**--- ----****EE***EEEECC----EE*****---*EECCCEE*HHHHHHHHHHHHHHHHCCCCC*---------------CCC*EEEEEEECCC*EEEEECCCCCC--------HHH*C--C*EE***E*EEEEEEE--- 54334.tem _________________________________ --******EE*EEEEEECC----EE***EE---*EECCCEEEHHHHHHHHHHHHHHHHCCCCC-------------***CCC*EEEEEEECCC*EEEEECCCCCC--******HHH*C**CEEE***E*EEEEEEE**- Structural block scores 0 1 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 12.5 75.0 75.0 2 7 * 2.4 P 6.2 52.6 30.2 75.0 29.2 17.2 6.8 6.4 7.4 28.8 8 9 E 4.5 M 3.0 3.5 4.0 75.0 4.5 4.0 3.0 3.5 4.0 3.0 11 16 E 4.8 H 1.8 2.2 2.5 1.8 2.3 2.2 1.5 1.8 2.9 2.5 17 18 C 4.4 M 6.5 6.0 7.2 5.0 4.5 5.5 6.5 7.0 75.0 6.0 19 22 - 4.5 M 75.0 75.0 75.0 75.0 26.5 8.0 75.0 75.0 75.0 75.0 23 24 E 4.7 H 6.5 7.0 7.0 6.0 6.5 5.0 6.5 5.0 6.0 7.5 25 27 * 1.2 P 5.3 29.5 5.3 5.0 6.0 4.3 4.7 4.3 4.3 4.3 28 29 E 4.1 M 2.5 2.5 2.5 3.5 4.0 5.5 3.0 2.5 5.0 2.5 30 32 - 4.3 M 75.0 4.3 75.0 27.3 75.0 75.0 30.2 75.0 75.0 75.0 34 35 E 4.5 M 2.5 1.5 2.0 4.0 2.5 1.0 0.5 2.5 3.0 3.5 36 38 C 4.4 M 4.3 7.3 5.3 7.0 5.3 5.7 4.0 4.3 6.0 5.7 39 41 E 4.9 H 2.0 3.0 3.3 3.0 2.7 3.0 2.7 2.7 3.3 3.0 42 57 H 4.9 H 2.7 2.6 2.6 2.6 3.1 3.1 1.9 2.8 3.1 1.9 58 62 C 5.0 H 4.8 3.6 4.2 4.2 4.3 4.8 2.2 4.7 5.3 3.8 63 75 - 4.6 H 75.0 59.5 75.0 75.0 75.0 75.0 4.8 75.0 75.0 70.0 76 78 * 3.4 M 28.3 27.3 7.0 28.8 75.0 75.0 2.7 4.7 75.0 75.0 79 81 C 4.8 H 4.7 3.7 4.7 4.3 4.0 6.3 1.0 3.0 5.0 4.3 83 89 E 4.8 H 1.4 1.6 1.7 1.0 2.4 1.7 1.7 1.6 1.9 1.3 90 92 C 4.9 H 7.3 5.3 9.2 9.3 6.3 6.3 7.7 31.2 7.3 7.0 94 98 E 4.9 H 3.4 3.4 3.2 4.0 3.2 2.6 3.2 3.6 3.4 3.2 99 104 C 5.0 H 4.2 4.3 3.5 4.8 3.8 3.7 3.0 5.6 4.5 4.9 105 106 - 4.5 M 75.0 75.0 75.0 42.0 75.0 75.0 40.0 8.5 75.0 75.0 107 112 * 3.0 P 5.8 7.0 6.0 5.5 75.0 75.0 5.4 6.2 75.0 75.0 113 115 H 5.0 H 4.0 5.0 5.7 4.7 6.0 5.7 5.0 4.7 6.0 8.2 118 119 * 3.0 P 8.5 7.5 7.5 7.0 75.0 75.0 7.0 7.5 75.0 75.0 121 123 E 4.9 H 2.7 2.3 3.3 2.3 3.7 2.7 2.0 2.0 2.7 2.3 124 126 * 1.2 P 4.3 5.7 4.0 4.3 26.3 3.3 3.3 3.0 3.3 3.3 129 135 E 4.9 H 2.1 1.4 2.6 1.4 2.4 12.9 2.0 2.3 2.1 2.4 136 137 * 3.6 M 39.5 6.0 75.0 39.0 38.5 75.0 4.5 4.5 75.0 75.0 >>>>>>