Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1nzia1 ------------CCCCEEEEECCCCC-CCCCCCEEEEEEEECCCCEEEEEEEE---EEECCC-CH--HHCCCEEEEEC-------CCEEECCEECCCCCCCCCCEEEEECCCEEEEEEEECCCCCCCCCEEEEEEEEEEC >P1;d1sfpa- CCEEC--CCCEEECCCEEEEECCC------CCCCEEEEEEECCCCCEEEEEEE---EEECCC-------CCEEEEEECCCC-CCCEEEEEC---------EEEEEEEECCCCEEEEEEEECCCC-CCCCCEEEEEEECCC >P1;d1sppb- CEEEHHHHCCEEECCCEEEEECCC------CCCCEEEEEEECCCCCEEEEEEE---EEECCC-------C-CEEEEECCCC-CCCEEEEEC---------EEEEEEEECCCCEEEEEEECCCC--CCCCCEEEEEEECC- >P1;d1szba1 C---CCC----CCCCCEEEEECCCCC-CCCCCCCEEEEEEECCCCCEEEEEEE---EEECCC-CC--CCCCCEEEEECC----CCEEEEECCCCCCCCCCCCCCCCEECCCCEEEEEEECCCCCCCCCCEEEEEEEEEC- >P1;d2qqma3 -----CCCC-EEECCCCEEEECCCCC-CCCCCCCEEEEEEECHHHCCEEEEEE---EEECCC-CCCCCCCCCEEEEECCCCCCCCEEEEECCC------CCCC--EEEECCCEEEEEEECCCC--CCCCEEEEEEE---- >P1;d3dema3 -------CCCCCCCCCEEEEECCCCC-CCCCCCCEEEEEEECCCCCEEEEEECC-C-CCCCC-CCCCCCCCCEEEEEEC----CEEEEEECCC------CCCC--CEECCCCEEEEEEECCCC--CCCCCCEEEEEEE-- >P1;d4lora3 -------CCCCEECCCEEEEECCCCC-CCCCCCCEEEEEEECCCCEEEEEECCHHH-EEECCCCCCCCC-CCEEEEEEC----CEEEEEECEE------CCCCCCEEECCCCEEEEEEECCCC--CCCCEEEEEEEEEEC >P1;d6fzvd1 C---CCCCC-EEEECCEEEEECCCCC-CCCCCCEEEEEEEECCCCCCCEEEEE---EEECCC-CC--CCCCCEEEEEECCCCCCEEEEEECCC------CCCC--CEECCCCEEEEEEEECC---CCCCEEEEEEECCC- >P1;d6fzvd2 -------CC-CEECC-CCEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCEEE---EEECCC-CC--CCCCCEEEEECCCCCCCCCCEEECCC------CCCC--CCCCCCCCCEEEEEECCC--CCCCEEEEECC-CC- PSA >P1;d1nzia1 ------------a3558440302625-70044736542803039a30020201---303037-1b--a1550002031-------32321004692c6796320352505526040104048608762300003140385 >P1;d1sfpa- 45524--80096065320000017------48636030003058a33030307---707054-------940101001364-b28434612---------6747152408922000204066a2-80370303030265a >P1;d1sppb- a61300621865075762102027------60656010203067803030304---709096-------c-0200011375-a37338522---------56781513087320002030898--90260305060246- >P1;d1szba1 9---988----847837440102b17-97073726482616029b34030405---402004-08--90660204010c----b6414300023859193007a721306b3404020301851866030010312039- >P1;d2qqma3 -----9b13-6617776550502a15-97054616030103049974020406---502005-1eb770440200001151882742342028------9506--506064120000020597--71350010507---- >P1;d3dema3 -------33b2535966540202704-64044637040305088b230505047-4-03024-3776802402040519----9742032019------8218--517082330302030396--5725003000509-- >P1;d4lora3 -------35b8536847550302716-8603573503140309aa30000307683-0102724b7981-40201030c----b552041038------004155605052440202050479--825300405030374 >P1;d6fzvd1 c---84820-9828742650002405-a8035a45030202048c45030204---303017-28--318500010015582a5942432015------a518--52705943000203048---8124002030005a- >P1;d6fzvd2 -------40-86258-9470302825974024338040102048a53040606---704006-1a--8164000000915a28aa42342029------960b--45509a430003050497--73160010400-97- Translating the sequences ------------*CCCEEEEECCCCC-CCCCCC*EEEEEEECCCC*EEEEEEE---EEECCC-C*--**CCCEEEEEC-------**EEECC*******CCCC***EE*CCCEEEEEEE*CCC**CCCCEEEEEEEE*** *****--CC**EECCCEEEEECCC------CCCCEEEEEEECCCCCEEEEEEE---EEECCC-------CC*EEEEECC**-*C*EEEEEC---------******EECCCCEEEEEEE*CCC*-CCCC*EEEEEEE*** ********C**EECCCEEEEECCC------CCCCEEEEEEECCCCCEEEEEEE---EEECCC-------C-CEEEEECC**-*C*EEEEEC---------******EECCCCEEEEEEE*CCC--CCCC*EEEEEEE**- *---***----**CCCEEEEECCCCC-CCCCCCCEEEEEEECCCCCEEEEEEE---EEECCC-CC--CCCCCEEEEECC----C*EEEEECC*******CCCC***EECCCCEEEEEEE*CCC**CCCCEEEEEEEE**- -----**CC-*EECCC*EEEECCCCC-CCCCCCCEEEEEEEC***C*EEEEEE---EEECCC-CC**CCCCCEEEEECC****C*EEEEECC*------CCCC--*EE*CCCEEEEEEE*CCC--CCCCEEEEEEE---- -------CC****CCCEEEEECCCCC-CCCCCCCEEEEEEECCCCCEEEEEE**-*-**CCC-CC**CCCCCEEEEE*C----C*EEEEECC*------CCCC--*EECCCCEEEEEEE*CCC--CCCC**EEEEEE*-- -------CC**EECCCEEEEECCCCC-CCCCCCCEEEEEEECCCC*EEEEE*****-EE*CC*CC**CC-CCEEEEE*C----C*EEEEEC**------CCCC***EECCCCEEEEEEE*CCC--CCCCEEEEEEEE*** *---***CC-*EE*CCEEEEECCCCC-CCCCCC*EEEEEEECCCCC**EEEEE---EEECCC-CC--CCCCCEEEEE*C****C*EEEEECC*------CCCC--*EECCCCEEEEEEE*CC---CCCCEEEEEEE***- -------CC-*EECC-**EEECCCCC*CCCCCC*EEEEEE*CCCCC****EEE---EEECCC-CC--CCCCCEEEEECC****C***EEECC*------CCCC--***CCCC**EEEEE*CCC--CCCCEEEEE**-**- 49854.tem _________________________________ *---***CC**EECCCEEEEECCCCC-CCCCCCCEEEEEEECCCCCEEEEEEE---EEECCC-CC--CCCCCEEEEECC**-*C*EEEEECC*------CCCC***EECCCCEEEEEEE*CCC--CCCCEEEEEEEE**- Structural block scores 1 3 - 4.4 M 75.0 4.0 3.3 75.0 75.0 75.0 75.0 75.0 75.0 4 6 * 3.6 M 75.0 51.3 2.0 8.3 31.8 75.0 75.0 6.7 75.0 7 8 C 4.4 M 75.0 4.0 1.5 75.0 2.0 3.0 4.0 1.0 2.0 9 10 * 2.9 P 75.0 4.5 7.0 75.0 40.5 6.8 9.8 42.0 41.5 11 12 E 4.1 M 42.8 3.0 2.5 6.0 3.5 4.0 4.0 5.0 4.0 13 15 C 4.8 H 4.3 4.7 6.3 6.0 7.0 6.7 6.0 6.3 29.3 16 20 E 4.8 H 3.8 0.4 2.2 3.2 4.2 3.4 4.0 2.6 4.6 21 25 C 4.8 H 3.0 31.6 31.8 4.3 3.7 2.6 3.2 2.2 3.4 27 33 C 4.6 H 3.6 35.1 34.6 5.0 4.6 3.9 4.6 5.9 3.3 34 40 E 5.0 H 4.0 1.7 1.7 4.7 1.9 2.7 2.3 1.7 2.1 41 45 C 4.7 H 5.1 5.3 4.2 5.1 5.8 5.9 6.6 5.7 5.5 46 52 E 4.6 H 0.7 2.3 1.9 2.3 2.3 2.4 1.4 2.0 2.7 53 55 - 4.5 M 75.0 75.0 75.0 75.0 75.0 28.7 5.7 75.0 75.0 56 58 E 4.6 H 2.0 4.7 5.3 2.0 2.3 26.0 25.3 2.0 3.7 59 61 C 4.9 H 3.3 3.0 5.0 1.3 1.7 2.0 3.0 2.7 2.0 63 64 C 4.4 M 6.2 75.0 75.0 4.0 7.8 5.0 7.8 5.0 5.8 65 66 - 4.0 M 75.0 75.0 75.0 75.0 9.2 6.5 8.0 75.0 75.0 67 71 C 4.5 M 4.3 32.6 47.5 4.2 3.0 2.8 17.6 3.4 3.8 72 76 E 5.0 H 1.0 0.4 0.6 1.4 0.4 2.2 1.2 0.2 0.0 77 78 C 4.3 M 38.0 2.0 2.0 6.2 1.0 5.0 6.2 3.0 5.0 79 80 * 3.2 M 75.0 5.0 6.0 75.0 3.0 75.0 75.0 6.5 7.8 85 89 E 4.8 H 2.2 3.6 4.2 2.4 3.0 2.2 2.4 3.0 3.0 90 91 C 4.7 H 0.0 38.5 38.5 0.0 1.0 0.5 1.5 0.5 1.0 93 98 - 4.4 M 7.1 75.0 75.0 5.8 75.0 75.0 75.0 75.0 75.0 99 102 C 4.4 M 5.0 23.0 23.2 2.5 5.0 4.8 1.2 6.1 6.6 103 105 * 2.5 P 2.7 4.3 4.7 6.5 51.7 51.7 5.3 51.7 51.3 106 107 E 4.7 H 3.5 3.0 2.0 2.0 3.0 4.0 2.5 4.5 5.0 108 111 C 4.8 H 3.0 4.8 4.5 5.1 2.8 3.2 2.8 4.5 5.9 112 118 E 4.9 H 2.1 1.1 1.0 1.9 0.6 1.6 1.9 1.1 1.6 120 122 C 4.9 H 6.0 7.5 8.3 4.7 7.0 6.0 6.7 29.0 6.7 123 124 - 4.2 M 4.0 38.5 75.0 4.5 75.0 75.0 75.0 75.0 75.0 125 128 C 5.0 H 4.5 4.5 4.2 3.8 4.0 4.8 4.5 3.8 4.2 129 136 E 4.7 H 1.0 1.4 2.0 0.9 11.0 1.0 1.5 0.6 10.0 137 138 * 1.9 P 5.5 5.5 5.0 6.0 75.0 42.0 5.0 7.8 8.0 >>>>>>