Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1g3pa1 -----------CCC-HHHHHCC---------CCEEE--EEECCCCCCCCCCEEEECCEEEEEEEEEEEC----CCCCEEEE-EEEEEEECCC----------------------------------------- >P1;d1g3pa2 CCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECC-EEEEEECCEEEEEEE-EEEECCCC----CEEEEEEEECCCHHHHHHHHCCCCCCCCCCCCCCCCCEECCCCCCEEEECCCCCCC >P1;d2x9ba- -----------CCC-HHHHHHC---------CCEEE--EECCCEECC-CCEEEEECCEEEEEEEEEEEE----CCCCEEEE-EEEEEEECC------------------------------------------ >P1;d4eo1a- -----------CCCHHHHHHHC---------CCEEE--EECCCEECCCCCEEEEECCEEEECCCCEEEC----CCCCCEEEEEEEECCCCCCC---------------------------------------- PSA >P1;d1g3pa1 -----------b28-5850482---------a5357--416a054986651205557010104aa2705----c8555050-2040324279----------------------------------------- >P1;d1g3pa2 b5b885572576160346613134b5073959242368224200201a-230106b46000227-43468998----6541320200104500511481407500549a93a691608220886658042aa8 >P1;d2x9ba- -----------a19-6950583---------92385--216b0455c-9411045760003169a1706----6c450242-40503412b------------------------------------------ >P1;d4eo1a- -----------b5766550673---------75275--62890562ba643202489010303b91716----ca7530407305021630a8---------------------------------------- Translating the sequences -----------CCC-HHHHH*C---------CCEEE--EE*CC**CCCCC*EEEECCEEEEEEE*EEE*----CCCC*EEE-EEEE***CC*----------------------------------------- ***********CCC*******C*********CCEEE****CCCEE*CC-*EEEEECCEEEEEEE-EEE*****----*EEE*EEEE*********************************************** -----------CCC-HHHHH*C---------CCEEE--EECCCEECC-CCEEEEECCEEEEEEE*EEE*----CCCC*EEE-EEEE***CC------------------------------------------ -----------CCC*HHHHH*C---------CCEEE--EECCCEECCCCCEEEEECCEEEE****EEE*----CCCC*EEE*EEEE***CC**---------------------------------------- 50176.tem _________________________________ -----------CCC*HHHHH*C---------CCEEE--EECCCEECCCCCEEEEECCEEEEEEE*EEE*----CCCC*EEE*EEEE***CC**---------------------------------------- Structural block scores 0 10 - 4.3 M 75.0 6.8 75.0 75.0 11 13 C 5.0 H 7.2 4.3 6.8 7.8 15 19 H 4.3 M 4.4 4.0 5.0 4.4 22 30 - 4.3 M 75.0 5.3 75.0 75.0 31 32 C 5.0 H 7.8 5.5 5.5 6.0 33 35 E 5.0 H 5.0 3.0 5.3 4.7 36 37 - 4.3 M 75.0 7.0 75.0 75.0 38 39 E 4.3 M 2.5 2.0 1.5 4.0 40 42 C 4.8 H 5.5 2.0 5.8 5.7 43 44 E 4.3 M 4.5 1.0 4.5 5.5 45 49 C 4.4 M 6.8 17.7 21.1 6.8 50 54 E 4.9 H 2.6 2.0 2.2 2.2 55 56 C 5.0 H 6.0 7.8 6.5 8.5 57 63 E 4.7 H 2.4 2.4 2.7 2.6 65 67 E 5.0 H 3.0 3.7 2.7 3.0 69 72 - 4.3 M 75.0 8.5 75.0 75.0 73 76 C 4.3 M 7.6 75.0 6.9 8.8 78 80 E 5.0 H 1.7 3.3 2.7 1.3 82 85 E 5.0 H 1.5 1.0 2.2 2.0 86 88 * 1.0 P 3.0 0.3 2.7 3.0 89 90 C 4.3 M 4.5 4.5 6.8 1.5 91 92 * 2.9 P 42.0 0.0 75.0 9.2 93 132 - 4.3 M 75.0 4.9 75.0 75.0 >>>>>>