Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ng6a- CCHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCC >P1;d1zq1c1 CCHHHHHHHHHCCC---CCCHHHHHHHHH----CCCCCC------------CCCCC--------------------------------------------------------------------------------------------C >P1;d2d6fc1 CCHHHHHHHHHHCC---CCCHHHHHHHHHCC-CCCCCC-----------CHHHHHCCCCHHHHHCC----------------------------------------------------------------------------------- >P1;d2f2ab1 CCHHHHHHHHHHCC---CCCHHHHHHHCCCHHHHHHHHHHHCCC---CCHHHHHHHHHCHHHHHHHCC-------------CCCCCCCC------CCHHHHHHHHHHHCC------CCCCHHHHHHHHHHHHHCCCCCCCHHHHCCCCC PSA >P1;d1ng6a- 471363057128516759-497324005602520571178484b6079631260004004614632773486957721650552061057003a217596058206601852a0845933b501a30453040301783067003750c >P1;d1zq1c1 49665107303965---817887036006----83b14f------------a8586--------------------------------------------------------------------------------------------e >P1;d2d6fc1 38665246403664---b0767103401719-208509-----------46550361056456778----------------------------------------------------------------------------------- >P1;d2f2ab1 495a6036404872---90588005100677400400340184a---043430051015403612886-------------93805706------042710050061155------85067730660037005917603510676b353 Translating the sequences CCHHHHHHHHHH*****C-CHHHHHHHHH*********************HHHHH****HHHHH************************************************************************************C CCHHHHHHHHH*CC---CCCHHHHHHHHH----******------------*****--------------------------------------------------------------------------------------------C CCHHHHHHHHHHCC---CCCHHHHHHHHH**-******-----------*HHHHH****HHHHH**----------------------------------------------------------------------------------- CCHHHHHHHHHHCC---CCCHHHHHHH*****************---***HHHHH****HHHHH****-------------********------***************------********************************C 89095.tem _________________________________ CCHHHHHHHHHHCC---CCCHHHHHHHHH***************---***HHHHH****HHHHH****-------------********------***************------********************************C Structural block scores 0 1 C 5.0 H 5.5 6.5 5.5 6.5 2 11 H 4.9 H 3.6 4.0 4.2 4.7 12 13 C 4.3 M 3.0 5.5 5.0 4.5 14 16 - 4.3 M 6.0 75.0 75.0 75.0 17 19 C 4.8 H 29.3 5.3 6.2 4.7 20 28 H 4.8 H 4.0 4.2 3.2 3.1 29 43 * 2.3 P 4.4 48.3 37.3 3.5 44 46 - 4.3 M 4.3 75.0 75.0 75.0 47 49 * 3.1 M 6.0 75.0 51.3 2.3 50 54 H 4.3 M 1.8 21.3 3.8 2.4 55 58 * 2.0 P 1.0 57.8 3.0 1.8 59 63 H 4.3 M 4.2 75.0 5.6 2.8 64 67 * 2.9 P 4.8 75.0 41.2 6.0 68 80 - 4.3 M 4.8 75.0 75.0 75.0 81 88 * 3.5 M 3.0 75.0 75.0 4.8 89 94 - 4.3 M 3.8 75.0 75.0 75.0 95 109 * 3.5 M 4.3 75.0 75.0 2.5 110 115 - 4.3 M 4.9 75.0 75.0 75.0 116 147 * 3.5 M 3.7 75.0 75.0 4.2 >>>>>>