Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3k7pa- -CCEEEEEEECCHHHHHHHHHHHHHHHCCCCEEEEECCCCCC-CCCCHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHCCCCCCEEECCCHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCC----------------------- >P1;d3sdwa- CCCEEEEEEECHHHHHHHHHHHHHHC-CCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHCC-CCEEEEEECCCHHHHHHHHCCCCCCEEECCCHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCC-CHHHHHHHHCCCCCCC-------------------- >P1;d4em8a1 ---CCEEEEECHHHHHHHHHHHHHHHHCC--CCEEECCCCCC-CCCCHHHHCHHHHCCCC---CCEEEEEECCCHHHHHHHCCCCCCCEEECCCC-CHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCC-CHHHHHHHHCC----------------------------- >P1;d4lfla- ---CEEEEEECCCCHHHHHHHHHHHHHCC--CEEEEC-CCCC-CC-CHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHCCCCCCCEEECCCHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHCC--------------------------- >P1;d4lflb- ---CEEEEEECHHHHHHHHHHHHHHHHCC--CEEEECCCCCC-CCCCHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHCCCCCCEEECCCHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC >P1;d6mu0a1 --CCEEEEEECHHHHHHHHHHHHHHHHCC--CEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHHHHHCCCCCCEEECCCC-CHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHC------------------------ PSA >P1;d3k7pa- -b534000001420281283026005305b505021100977-88285481056004101796050000004406201720471780202307468301200346301000001661b4850340011005182265a40655167565735787----------------------- >P1;d3sdwa- 47414000001310181054038406-39204705101075695748437004500530379-030000001506101710470580103102678403300336202000002750938502700330052207894b22-916753572756978e-------------------- >P1;d4em8a1 ---230000002101a0054006205939--16044130845-a8184472056006406---70100000140710262047376020220775-6055101462000000006706485036005200519254b-92566186547----------------------------- >P1;d4lfla- ---3200000075029004503720665a--170411-0683-29-54450044008503729060000006507100820473620102205437303300335103000001640b3a5026003500629243c-705661665487a--------------------------- >P1;d4lflb- ---54000000150072055017106939--17033200774-961343110040010012950500000036072005104714a010220464a503601232302000000550b3a503600420091826549805750574488a96588335367234754744779548d >P1;d6mu0a1 --b45000000210280084006304949--3604320199656a274371045006404663a000000-150510271047055010220539-603502346400000000670857402600460091a154c-5056506763782766------------------------ Translating the sequences -***EEEEEEC*HHHHHHHHHHHHHHHCC***EEEECCCCCC-CCCCHHHHHHHHHHHHH*CCCCEEEEEECCCHHHHHHHHCCCCCCEEECCCHHHHHHHHH**CCCEEEEECCCCCHHHHHHHHHHHHHCCCCCC*HHHHHHHHHHH****C*----------------------- ****EEEEEECHHHHHHHHHHHHHH*-CC***EEEECCCCCC*CCCCHHHHHHHHHHHHH*C-CCEEEEEECCCHHHHHHHHCCCCCCEEECCCHHHHHHHHH**CCCEEEEECCCCCHHHHHHHHHHHH*CCCCCC****-*HHHHHH****C****-------------------- ---C*EEEEECHHHHHHHHHHHHHHHHCC--C*EEECCCCCC-CCCCHHHH*HHHH****---CCEEEEEECCCHHHHHHH*CCCCCCEEECCC*-*HHHHHH**CCCEEEEECCCCCHHHHHHHHHHHHHCCCCCC-*HHHHHHHH**----------------------------- ---CEEEEEEC***HHHHHHHHHHHHHCC--CEEEEC-CCCC-CC-CHHHHHHHHHHHHH*CCCC*EEEEECCCHHHHHHH*CCCCCCEEECCCHHHHHHHHH**CCCEEEEECCCCCHHHHHHHHHHHHHCCCCC*-HHHHHHHHHHH**--------------------------- ---CEEEEEECHHHHHHHHHHHHHHHHCC--CEEEECCCCCC-CCCCHHHHHHHHHHHHH*CCCCEEEEEECCCHHHHHHHHCCCCCCEEECCCHHHHHHHHH**CCCEEEEECCCCCHHHHHHHHHHHHHCCCCCC*HHHHHHHHHH*****C************************ --*CEEEEEECHHHHHHHHHHHHHHHHCC--CEEEECCCCCC*CCCCHHHHHHHHHHHHH*CCCCEEEEE-CCCHHHHHHHHCCCCCCEEECCC*-*HHHHHH**CCCEEE**CCCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH****C------------------------ 89623.tem _________________________________ --*CEEEEEECHHHHHHHHHHHHHHHHCC--CEEEECCCCCC-CCCCHHHHHHHHHHHHH*CCCCEEEEEECCCHHHHHHHHCCCCCCEEECCCHHHHHHHHH**CCCEEEEECCCCCHHHHHHHHHHHHHCCCCCC*HHHHHHHHHHH****C*----------------------- Structural block scores 0 1 - 4.3 M 43.2 5.5 75.0 75.0 75.0 75.0 4 9 E 4.9 H 0.7 0.7 0.5 0.3 0.7 0.8 11 26 H 4.8 H 2.9 7.4 2.8 3.5 3.1 2.9 27 28 C 5.0 H 2.5 6.0 6.0 7.8 6.0 6.5 29 30 - 4.1 M 8.2 1.0 75.0 75.0 75.0 75.0 32 35 E 4.9 H 2.0 3.2 3.5 3.0 3.2 3.2 36 41 C 4.9 H 4.0 3.2 3.5 15.5 3.3 4.5 43 46 C 4.9 H 6.5 6.0 6.9 22.8 4.8 6.4 47 59 H 4.8 H 2.7 2.6 3.4 2.8 1.2 2.9 61 64 C 4.7 H 5.0 21.8 39.2 4.2 4.8 4.9 65 70 E 4.8 H 0.0 0.0 0.2 0.0 0.0 12.5 71 73 C 5.0 H 2.7 2.0 1.7 3.7 3.0 2.0 74 81 H 4.9 H 2.8 2.5 2.8 2.8 2.4 2.5 82 87 C 5.0 H 4.2 3.5 4.2 3.2 3.9 3.0 88 90 E 5.0 H 1.7 1.3 1.3 1.3 1.3 1.3 91 93 C 5.0 H 3.7 2.7 4.7 3.0 3.3 2.7 94 102 H 4.7 H 2.6 3.1 10.9 2.4 3.5 11.4 103 104 * 1.0 P 5.0 4.5 5.0 4.0 2.5 5.0 105 107 C 5.0 H 1.3 1.3 0.7 1.3 1.7 1.3 108 112 E 4.8 H 0.0 0.0 0.0 0.0 0.0 0.0 113 117 C 5.0 H 5.1 4.6 3.8 4.5 4.3 4.2 118 130 H 5.0 H 2.4 2.8 2.9 3.1 3.3 3.3 131 136 C 4.9 H 4.0 4.7 5.4 5.4 4.3 5.7 138 148 H 4.6 H 4.5 11.5 5.4 4.9 4.8 4.5 149 152 * 2.3 P 5.5 5.2 75.0 41.9 8.4 5.8 155 177 - 4.4 M 75.0 66.5 75.0 75.0 5.6 75.0 >>>>>>