Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fvga- CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCEEEEECCHHHHHHHHHC--CCCEEEEEEEEECCCCCCCCHHHHHCCCCCCEEEEEEEECCCCCCHHHHHHHHHHCCCCCCC-CCCCCCCHHHCCEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCEECCHHHCCHHHHCCCCCC-------------- >P1;d3pima1 -----------------------CCCCCCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHCCEEEEEEEEECCCC---CCCCCCCCCCEEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCC-----CHHHCCEEEECCHHHHHHHHHHHHHHHHHH---CC-CCCCEEEEEEEEEEHHHHHHHHCCCCCCCC-----CCCCCCCCCC >P1;d4gwba- ----------------------------------C---EEEEEEECCCCCCCC-HHH--CCCEEEEEEEEECCCCCCCCCC----CCCCCEEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCEECCEECHHHCEEEEECCHHHHHHHHHHHHHHHHHCCCC--CCCCCEEEECCCEEECCHHHCCHHHHCCCCCCCCCCCCCCCCCCCC PSA >P1;d1fvga- a41368702804a962907550533733037714b---9050000030152044006--3a103000000000404103392035460000000100032971407600810054140117-429b37610100000054890292058238622851687a6980402045b2602202560002023669358-------------- >P1;d3pima1 -----------------------a943076081569604000000450480273055515a4022030000006539---7500505330000000002395060440021006013008867-----850320000015a90393065028501573---a7-705030130430200730185207936308-----a040929287 >P1;d4gwba- ----------------------------------6---530000101020021-026--1700570300000063690539----917700000003033a61602300110020020045350882576220000011676036206701740582a504--a801031351680340387015204566b4433064188060558a Translating the sequences ***********************CCCCCCCCCCCC---**EEEEECCHHHHHHHHH*--CCCEEEEEEEEECCCCCCCC*****CCCCCCEEEEEEEECCCCCCHHHHHHHHHHCCCCCCC-C*CC**CHHHCCEE**CCHHHHHHHHHHHHHHHHHH**CCCCCCCCEE**CCC*EECCHHHCCHHHHCCCCCC-------------- -----------------------CCCCCCCCCCCC***EEEEEE*CCHHHHHHHHHH*******EEEEEEE**CCCC---C***CCCCCCEEEEEEEECCCCCCHHHHHHHH**CCCCCCCCC-----CHHHCCEEEECCHHHHHHHHHHHHHHHHHH---CC-CCCCEEEE***EEE**HHH**H***CCCCC-----CCCCCCCCCC ----------------------------------C---EEEEEEECC******-HHH--CCCEEEEEEEEECCCCCCCC*C----CCCCCEEEEEEEECCCCCCHHHHHHHHHH*CCCCCCC**CC**CHHHC*EEEECCHHHHHHHHHHHHHHHHH***C--CCCCCEEEECCCEEECCHHHCCHHHHCCCCCC****CCCCCCCCCC 55068.tem _________________________________ -----------------------CCCCCCCCCCCC---EEEEEEECCHHHHHHHHHH--CCCEEEEEEEEECCCCCCCC*C***CCCCCCEEEEEEEECCCCCCHHHHHHHHHHCCCCCCCCC*CC**CHHHCCEEEECCHHHHHHHHHHHHHHHHHH**CCCCCCCCEEEECCCEEECCHHHCCHHHHCCCCCC----CCCCCCCCCC Structural block scores 0 22 - 4.0 M 4.9 75.0 75.0 23 34 C 4.1 M 4.4 5.0 69.2 35 37 - 4.0 M 75.0 5.0 75.0 38 44 E 4.6 H 2.0 0.6 1.3 45 46 C 5.0 H 1.5 4.5 0.5 47 56 H 4.2 M 2.2 3.4 8.8 57 58 - 4.0 M 75.0 3.0 75.0 59 61 C 4.0 M 4.8 6.5 2.7 62 70 E 4.8 H 0.3 0.8 1.7 71 78 C 4.5 M 1.5 21.6 3.6 81 83 * 2.7 P 1.7 1.7 75.0 84 89 C 4.8 H 2.5 2.7 16.5 90 97 E 5.0 H 0.1 0.0 0.4 98 103 C 5.0 H 4.3 4.2 4.9 104 113 H 4.8 H 2.7 1.7 0.9 114 122 C 4.7 H 10.8 3.7 2.1 124 125 C 4.0 M 10.2 75.0 8.0 126 127 * 2.7 P 5.0 75.0 3.5 129 131 H 5.0 H 0.7 2.7 3.3 132 133 C 4.5 M 0.0 1.0 0.0 134 137 E 4.5 M 0.0 0.0 0.2 138 139 C 5.0 H 4.5 3.0 3.5 140 157 H 4.9 H 4.4 4.2 4.1 158 159 * 2.7 P 7.0 75.0 2.5 160 167 C 4.5 M 5.6 22.4 21.7 168 171 E 4.5 M 2.8 1.8 3.0 172 174 C 4.0 M 6.5 2.3 5.0 175 177 E 4.7 H 1.3 0.7 2.3 178 179 C 4.0 M 1.0 3.5 1.5 180 182 H 5.0 H 3.7 1.3 5.0 183 184 C 4.0 M 0.0 6.5 3.0 185 188 H 4.2 M 1.8 4.5 2.8 189 194 C 4.8 H 6.2 15.8 5.8 195 198 - 4.0 M 75.0 75.0 3.2 199 208 C 4.0 M 75.0 5.2 5.2 >>>>>>