Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1a2pa- ------------------CCCCHHHHHHHHHHHCCCCCCEECHHHHHHHCCCHHHCCHHHHCCCCEEEEEEECCCCCCCCCCC---------CCCEEEEECCCCCC----------CCCCCEEEEEC-CC--CEEEECCCCC---CCEECC--- >P1;d1aqza- ----CEEEEEEECCCEEEEEEEHHHHHHHHHHCCCCCC----CCCCCCCEEEC-CCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEEEC-CCCCCCEEECCC-- >P1;d1i0va- ---CCCEEEC-------CEEECHHHHHHHHHHHC-CCCCCCCCCCCCCCC-CC-C--CCC---------CCCCC-----------------CCCEEEEECCCCCCCCCC-C-----CCCCEEEEEECC-CCEEEEEECCCCC--CCCEECC--- >P1;d1t2ha- ---------------CCCCEEEHHHCCHHHH----------HHHHHHHCCCC----CCCC------CCCEECCCCCCCCCCCC--------CCCEEEEECCCCCCC----------CCCCCEEEEECCCC--CEEEECCCCC---CCEEEECCC >P1;d3agna- CCCCCEEEEC-------CEEEEHHHHHHHHHHHHHHHHCCCCHH--HCCEEEC-CCHHHC---------CCCCCC----------------CCCEEEEECCC-CCCCCC-CCCCCCCCCCEEEEEECCCCCEEEEEECCCCCCCCCCEECC--- PSA >P1;d1a2pa- ------------------5416186006203755600b0014486068680569702028207a300022517186740477b---------c1404100050867----------72432000005-52--3013054527---807512--- >P1;d1aqza- ----560305044b965615042950370067033212----41307003103-1013270645ab59228074a603740403a506598020000000147045063737793291310000001472400000003-673896153096-- >P1;d1i0va- ---b252405-------a4505794076017302-2257a6421b66005-07-2--927---------1a0a2-----------------856120000257784093-b-----91a300000057-3520300035b0a--d815509--- >P1;d1t2ha- ---------------c16b624186037204----------70074286909----1339------5026116087710593a--------831031100525b39----------81463000108698--1101034627---602404495 >P1;d3agna- 6b23a40506-------845056820630060045148765404--a004707-569a19---------09130b----------------92620000025-b04050-4aa86571640000014850700000035b0a8a721330c--- Translating the sequences ------------------****HHHHHHHHHHHC*CCCC**CHH**H**C*C***CC***************CCC***CCCCC---------CC*EEEE*CCCCCC----------CCCC*EEEEEC-CC--*EEEECCCCC---CCEECC--- ----C*EEE*********EEEEHHHHHHHHHH*C*CCC----*****CC***C-CCCCCC*********CCCCC****CCCCC********CC*EEEEECCCCCCCCCC*C*****CCCCEEEEEE*CCCCEEEEEE*C-CC**CC*EECC*-- ---*C*EEE*-------CEEE*HHHHHHHHHHHC-CCCC**C*****CCC-CC-C--CCC---------CCCCC-----------------CCCEEEEECCCCCCCCCC-C-----CCCCEEEEEECC-CCEEEEEECCCCC--CCCEECC--- ---------------**C*EEEHHH**HHHH----------*HH**H*CC*C----CCCC------*****CCCC***CCCCC--------CCCEEEEECCCCCCC----------CCCC*EEEEECCCC--*EEEECCCCC---CCEE***** ****C*EEE*-------CEEEEHHHHHHHHHHH*****C**CHH--HCC***C-CC***C---------CCCCCC----------------CCCEEEEECCC-CCCCCC-C*****CCCCEEEEEECCCCCEEEEEECCCCC**CCCEECC--- 53933.tem _________________________________ ----C*EEE*-------CEEEEHHHHHHHHHHHC*CCCC**CHH**HCCC*CC-CCCCCC------***CCCCCC***CCCCC--------CCCEEEEECCCCCCCCCC-C-----CCCCEEEEEECCCCCEEEEEECCCCC--CCCEECC--- Structural block scores 0 3 - 4.3 M 75.0 75.0 59.1 75.0 5.6 6 8 E 4.2 M 75.0 1.0 2.0 75.0 1.7 10 16 - 4.3 M 75.0 5.6 75.0 55.5 75.0 18 21 E 4.2 M 4.0 2.5 3.5 5.9 3.5 22 32 H 4.8 H 3.5 3.5 4.0 16.5 2.8 35 38 C 4.1 M 2.9 20.0 4.0 75.0 5.0 39 40 * 3.0 P 0.5 75.0 8.2 75.0 5.5 42 43 H 3.8 M 6.0 2.5 1.5 0.0 2.0 44 45 * 2.1 P 3.0 1.5 8.8 5.5 75.0 47 49 C 4.0 M 7.3 1.0 1.7 7.7 1.3 51 52 C 3.9 M 5.5 1.5 3.5 42.0 3.5 54 59 C 4.1 M 3.2 2.3 28.3 27.7 6.8 60 65 - 3.8 M 3.8 6.2 75.0 75.0 75.0 66 68 * 3.0 P 0.7 5.3 75.0 2.3 75.0 69 74 C 4.4 M 4.0 5.2 16.5 3.7 4.1 75 77 * 3.0 P 5.7 3.0 75.0 5.0 75.0 78 82 C 4.2 M 5.9 3.0 75.0 5.5 75.0 83 90 - 4.5 M 75.0 5.8 75.0 75.0 75.0 91 93 C 4.7 H 29.5 0.7 6.3 4.0 5.7 94 98 E 4.9 H 1.8 0.0 0.6 1.0 0.4 99 108 C 4.7 H 25.1 3.0 4.5 26.1 10.2 111 115 - 3.8 M 75.0 5.6 75.0 75.0 8.0 116 119 C 5.0 H 4.0 3.5 5.9 4.8 4.5 120 125 E 4.8 H 0.3 0.0 0.0 0.7 0.2 126 130 C 4.5 M 32.4 3.6 19.0 21.2 4.8 131 136 E 4.7 H 13.7 0.0 0.8 13.0 0.0 137 141 C 4.8 H 4.6 18.2 6.0 4.4 6.0 142 143 - 3.8 M 75.0 5.5 75.0 75.0 9.2 144 146 C 4.6 H 27.7 5.3 7.5 27.0 3.3 147 148 E 5.0 H 6.0 4.0 5.0 3.0 3.0 149 150 C 4.5 M 1.5 4.5 4.5 2.0 6.2 151 153 - 4.3 M 75.0 52.0 75.0 6.0 75.0 >>>>>>