Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2qrda- C--------------------------------------CCCCCEEEECCHHHHHHHHHHHHHHHCCEECCCCCCCCCCHHHEEEEEEECHHHHHCCCCEEEEEEEEEEEEE--CCEEEEEEEEEEEEECC--CCCCCCHHHHHHHHHHHHHHC- >P1;d2v8qa1 ----------------------------------------CCCCEEECCCHHHHHHHHHHHHHHCCCEEEEEE-------CCEEEEEEECCCCC-----CEEEEEEEEEEC-CC-CCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHCCC--C >P1;d3osea- ---------------------------------CCCCCCCCCCCCEECCCHHHHC-CHHHHHHHCCCEEEEEE-------CCEEEEEECCCCCC-----CCEEEEEEEEEE-HHHCEEEEEEEEEECC--------HHHHHHHHHHHHHHCC--- >P1;d3t4na- CCCCCCHHHCHHHHHHHHHHHCCCHHHHCCCCCCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHHCCEECCCC-----CCCCEEEEEECCC-------CCEEEEEEEEEEEE--CCEEEEEEEEEEEECCC--C-CCHHHHHHHHHHHHHHHHCC PSA >P1;d2qrda- d--------------------------------------aa4922728a6258106501700740907277292aba5992230604040360677a550203010206557--87313031524727269--ba6661156027403821769- >P1;d2v8qa1 ----------------------------------------b77344456828611750240087190539536-------85205040517926-----640401020553-69-711002072397ab89973537611660175038403--b >P1;d3osea- ---------------------------------2652946a90412084615700-304800671a0926457-------7120202336487a-----430202000040-5949300020643526--------8722770166029401--- >P1;d3t4na- 9aa888666579464663587837407788697698996894a235373729700840270088190626927-----a55410504064a-------55202020206548--a51020307145348ba--6-64831550175046216847 Translating the sequences *--------------------------------------CCCCCEEE*CCHHHHHHHHHHHHHH*CCEE*************EEEEEE*C**********EEEEEEEEEEE*--*CEEEEEEEEEE***CC--C*****HHHHHHHHHHH****- ----------------------------------------CCCCEEECCCHHHHHHHHHHHHHH*CCEE****-------CCEEEEEE*CC***-----CEEEEEEEEEE*-**-C*EEEEEEEE****CC**C***HHHHHHHHHHHH***--* ---------------------------------******CCCCC*EECCCHHHH*-*HHHHHHH*CCEE****-------CCEEEEEE*CC***-----C*EEEEEEEEEE-***CEEEEEEEEEE**--------*HHHHHHHHHHHHH**--- ***************************************CCCCCEEECCCHHHHHHHHHHHHHH*CCEE****-----**CCEEEEEE*CC-------*CEEEEEEEEEEE*--*CEEEEEEEEEE***CC--C-**HHHHHHHHHHHHH***** 103243.tem _________________________________ *--------------------------------******CCCCCEEECCCHHHHHHHHHHHHHH*CCEE****-----**CCEEEEEE*CC***----*CEEEEEEEEEEE****CEEEEEEEEEE***CC--C***HHHHHHHHHHHHH***** Structural block scores 1 32 - 4.3 M 75.0 75.0 75.0 6.5 33 38 * 3.5 M 75.0 75.0 4.7 7.8 39 43 C 4.9 H 7.2 20.7 5.9 6.7 44 46 E 4.8 H 3.7 4.0 1.0 3.7 47 49 C 4.8 H 8.2 6.3 6.0 5.7 50 63 H 4.9 H 3.3 3.6 8.3 3.9 65 66 C 5.0 H 4.5 4.5 5.2 4.5 67 68 E 5.0 H 4.5 4.0 5.5 4.0 69 72 * 1.0 P 6.2 5.8 5.5 6.0 73 77 - 4.3 M 7.9 75.0 75.0 75.0 78 79 * 3.5 M 9.0 75.0 75.0 7.8 80 81 C 4.3 M 2.0 6.5 4.0 4.5 82 87 E 5.0 H 2.2 1.8 1.5 1.7 89 90 C 4.7 H 1.5 4.0 5.0 7.2 91 93 * 2.3 P 4.0 5.7 8.5 75.0 94 97 - 4.3 M 7.4 75.0 75.0 75.0 100 110 E 4.9 H 2.2 2.2 1.0 2.1 111 114 * 3.2 M 41.2 41.2 23.2 42.1 116 125 E 4.9 H 2.9 2.5 2.3 2.3 126 128 * 1.4 P 3.7 9.7 27.7 5.0 129 130 C 4.3 M 7.5 8.5 75.0 11.0 131 132 - 4.3 M 75.0 8.0 75.0 75.0 134 136 * 2.3 P 7.5 5.0 52.7 28.3 137 149 H 4.8 H 3.5 3.7 4.1 3.6 150 154 * 2.5 P 19.6 32.9 45.2 5.2 >>>>>>