Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2hq2a2 -------CHHHHHHHHCCCCCCCCHHHHHHCCCCHHHHHHHHCCCCEEEECCC-HHHHHHHHHHHCCEEEEEECCCEEEEEEECCCCEECC-CCEEECCCCCCCEEECHHHEEEEEEEEECCCCCEEEEEEEECCCCEEEEEECCC-CCC---HHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHCCCCCCHHHHHHHCCCCCEEEECCCHHHHHHHHHHHHCCCEEEEEECCCEEEEEEECCCCEEECCEEEEECCCEEEEECHHHCCEEEEEEEECCCEEEEEEEECCCCCEEEEEEECCCCCCCCCCCCCCHHHCC >P1;d2hqva1 CCCCHHHHHHHHCCHHHHHHCCCCCCCC-----CHHHHHCCCCCCCEEEEEHHHHHHHHH-CCCCCCCC-CEECCCCEECCCCCCCCEEEECCEEEECCCCCCCEEECHHHCCEEEEEEEC-CCCEEEEECC-CCCCCCEEECCCCCCCCHHHHHHHHHHHHHC------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PSA >P1;d2hq2a2 -------6a5175266096379322400940a150030031019230410767-1350061057083040201062010203240451609-d6030425550002050b4021100041a4bb551000000510200010102b-806---4910780185021b81771827992747502740470742950980062b082260062058600150746003500730463513020200240020000240515768b210040660103034a1012000020109750000000097433001010228e5803a5030078026 >P1;d2hqva1 ba89b86768665677458339605a27-----3257007208b7102405384065008-53a06402-1647ca646534160080946a1403067b062355242650440100126-ac34000005-8944121120254a704ab0274038217a2------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Translating the sequences -------*HHHHHHHH****CCCCHHHH*****CHHHHHHHHCCCCEEEE***-HHHHHH*HHHHCCEE*EEECCCEEEEEEECCCCEE**-C*EEECCCCCCCEEECHHHEEEEEEEEEC*CCCEEEEEEE*CCCCEEEEEECCC-CCC---HHHHHHHHHHH************************************************************************************************************************************************************************* *******HHHHH**HHHHHHCCCC****-----CHHHHH***CCCCEEEEEHH*HHHHHH-****CC**-*EECCC*EE****CCCCEEEE*CEEEECCCCCCCEEECHHH**EEEEEEEC-CCCEEEEE**-CCCC**EEE*CCC*CCC***HHHHHHHHHH*------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 144064.tem _________________________________ -------HHHHHHHHHHHHHCCCCHHHH-----CHHHHHHHHCCCCEEEEEHH-HHHHHH-HHHHCCEE-EEECCCEEEEEEECCCCEEEE-CEEEECCCCCCCEEECHHHEEEEEEEEEC-CCCEEEEEEE-CCCCEEEEEECCC-CCC---HHHHHHHHHHH------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Structural block scores 0 6 - 3.0 P 75.0 9.2 7 19 H 3.9 M 5.1 6.0 20 23 C 5.0 H 5.2 4.5 24 27 H 3.0 P 1.5 6.1 28 32 - 3.0 P 4.9 75.0 34 41 H 4.2 M 0.9 2.9 42 45 C 5.0 H 3.8 6.9 46 50 E 4.6 H 2.4 2.2 51 52 H 3.0 P 6.5 5.5 54 59 H 5.0 H 2.5 3.2 61 64 H 3.0 P 3.0 4.6 65 66 C 5.0 H 5.5 5.0 67 68 E 3.0 P 2.0 1.0 70 72 E 4.3 M 1.0 3.7 73 75 C 5.0 H 2.7 10.0 76 82 E 3.6 M 1.1 4.1 83 86 C 5.0 H 3.2 3.5 87 90 E 4.0 M 4.0 4.8 93 96 E 4.5 M 2.2 1.8 97 103 C 5.0 H 3.0 5.1 104 106 E 5.0 H 0.7 4.0 108 110 H 5.0 H 5.2 4.3 111 119 E 4.6 H 1.0 1.3 122 124 C 5.0 H 9.3 8.7 125 131 E 4.4 M 0.9 1.3 133 136 C 5.0 H 2.0 6.2 137 142 E 4.0 M 0.3 1.2 143 145 C 5.0 H 4.5 3.7 147 149 C 5.0 H 4.7 3.7 150 152 - 3.0 P 75.0 7.3 153 163 H 4.8 H 3.9 4.2 164 332 - 3.0 P 3.2 75.0 >>>>>>