Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1jhsa- CCCEEEEEHHHCEEEEECCCEEEHHHCCCCCC-----CEEEEEECCCCCCCCCCCCCC------CCEEEEEEEE------CCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEEEEEE-CCCEEEEEEEEEEECCCCCCCCCCEEEEEEEEEEHHHCEEEEEEEEEECCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCEECCHHHHC >P1;d1tu1a1 ------------CEEEECCCC-----EEEECCCCCCCCCEEEEECCCC-------CCC------CEEEEEEEEC------CCCCCCHHHHHHHHHHHHHH--HCCCCEEEEEEEEEECCEEEEEEEEEEEEC------CEEEEEEEEEECC--CCCEEEEEEEEC--------------HHHHHHHHHHHHHHHHCCCCCCC---- >P1;d1v2ba- ------------CCCCCCCCCCCCCCCCEECCCCCCCEEEEEEEC----------CEE------EEEEEEEEEE------CCCCHHHHCCHHHHHHHHHHHCCCCEEEEEEEEECCCCC-CEEEEEEEEC---------CCEEEEEEEEEE--CCEEEEEEEEEE--HHHCCC-----------CCCHHHHHHHHCCCCC------ >P1;d2i8ga- ---------------CCHHHCCCCC--CCCCCCCCCCCCCCCCCHHHHHHHHCCCCEEEEECCCCCCEEEEECCCCCCCEEECCCCCHHHHHHHHHHHCCCCCCEEECCCC---------CCEEEEEEEC----------CEEEEEEEE----CCEEEEEEECCC-----------------CHHHHHCCHHHHHHHCC------- PSA >P1;d1jhsa- 0a0571701c100100002603324668b16b-----62110405079839290a053------603030114a------21b4b6046004400463058720571511435207-99410000012430669639696240100000018928100000030207a912730899620a007100500230066071556820c >P1;d1tu1a1 ------------485444a86-----556227a78585545651856a-------908------5021313236------50aa5618700641164146--726907345346471683500100022559------7640000200032--472021010302--------------49116504670675066260686---- >P1;d1v2ba- ------------616392a6003006a0652a8626504021126----------836------3010000128------1a26065065157007507401b27625248275588c9-0010202056---------604101000006--873000000003--69326a-----------914430540042062b------ >P1;d2i8ga- ---------------8605726241--600775290757050063940392052a53121075051200001083a8301100128558404500430048960570662b---------9042031067----------900100014----551000030226-----------------617200503300742a2------- Translating the sequences *****************CCC*******C**CC-----C*EEEEEC**********C**------C*EEEEEEE*------CCCCCCHHHHHHHHHHHHHH*CC**EEEEEEEEE**-CC**EEEEEEEE***********CEEEEEEEE*****CEEEEEEEEE*******************HHHHHHHHHHHH*C**C****** ------------*****CCCC-----****CCCCCCCC*EEEEEC***-------C**------C*EEEEEEE*------CCCCCCHHHHHHHHHHHHHH--*C***EEEEEEE***CC**EEEEEEEE***------***EEEEEEEE**--CC*EEEEEEEE*--------------****HHHHHHHHHHHH*CCCC**---- ------------*****CCCC******C**CCCCCCC**EEEEEC----------C**------**EEEEEEE*------CCCC**HH**HHHHHHHHHH*CCC*EEEEEEEEE***CC-*EEEEEEEE*---------*CEEEEEEEE**--CCEEEEEEEEE*--******-----------***HHHHHHHH*CCCC------ ---------------*****C****--C**CCCCCCCC*****************C********C**EEEEE**********CCCC*HHHHHHHHHHH***CCC*EE****---------**EEEEEEE*----------CEEEEEEEE----CCEEEEEEE***-----------------*HHHHH**HHHHH**CC------- 55724.tem _________________________________ ------------*****CCCC******C**CCCCCCCC*EEEEEC**********C**------C*EEEEEEE*------CCCCCCHHHHHHHHHHHHHH*CCC*EEEEEEEEE***CC**EEEEEEEE***------**CEEEEEEEE**--CCEEEEEEEEE*--******------****HHHHHHHHHHHH*CCCC**---- Structural block scores 0 11 - 4.3 M 3.8 75.0 75.0 75.0 12 16 * 1.8 P 0.2 5.0 5.0 47.8 17 20 C 4.3 M 2.0 7.1 4.6 3.5 21 26 * 2.5 P 4.0 63.3 3.2 27.2 28 29 * 1.0 P 6.2 4.0 5.5 0.0 30 37 C 4.5 M 49.8 6.6 4.9 5.2 39 43 E 4.3 M 1.2 4.2 1.2 2.2 45 54 * 3.1 M 5.8 54.6 75.0 4.5 56 57 * 1.0 P 4.0 4.0 4.5 2.0 58 63 - 4.3 M 75.0 75.0 75.0 2.5 66 72 E 4.8 H 1.7 2.1 0.6 0.4 74 79 - 4.3 M 75.0 75.0 75.0 4.2 80 85 C 4.5 M 6.0 6.2 4.2 2.0 86 99 H 4.8 H 2.6 3.5 3.7 3.0 101 103 C 4.3 M 3.0 28.0 4.8 5.0 105 113 E 4.3 M 3.2 4.6 4.6 28.6 114 116 * 2.7 P 27.3 4.0 7.0 75.0 117 118 C 4.3 M 9.0 7.0 10.8 75.0 119 120 * 2.2 P 2.5 4.0 37.5 42.0 121 128 E 4.9 H 0.9 0.6 1.2 2.0 129 131 * 2.7 P 3.0 6.3 52.0 52.3 132 137 - 4.3 M 6.5 75.0 75.0 75.0 138 139 * 2.9 P 7.5 6.5 40.5 75.0 141 148 E 5.0 H 0.6 0.2 0.8 0.8 149 150 * 2.3 P 0.5 2.5 3.0 75.0 151 152 - 4.3 M 8.5 75.0 75.0 75.0 153 154 C 4.7 H 5.0 5.5 7.5 5.0 155 163 E 4.8 H 0.4 1.0 0.3 0.9 165 166 - 4.3 M 3.5 75.0 75.0 75.0 167 172 * 3.5 M 5.4 75.0 6.1 75.0 173 178 - 4.3 M 5.7 75.0 75.0 75.0 179 182 * 3.2 M 2.6 3.8 75.0 57.8 183 194 H 4.6 H 2.0 4.3 9.1 2.3 196 199 C 4.3 M 3.2 3.5 4.9 22.4 200 201 * 3.5 M 5.5 7.0 75.0 75.0 202 205 - 4.3 M 5.6 75.0 75.0 75.0 >>>>>>