Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1d7la2 CEEEEEEEEEEEEEEEECCCCCCC---------CCEEECCCC-CCEEEEEEEC------CEEEEEEEECC---------------------CCCHHHCC---HHHHHHHHHHCCCHH---HHCCCC-CCCEEEEEEEEEEEEEEEC >P1;d1n4wa2 ------CCCCCEEEEEECCCCCCCCCCCCCCCCCEEEECCCCCCCEEEEEECCCCCCCCCEEEEEEEECCC----CCCCEEEECCCCEEEECCCHHHH-HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEECCCCCCCCC--- >P1;d2voua2 ----CEEEEEEEEEEEECCCCCCHHHHHHH-CCCCEEEEEC-CEEEEEEEECCCCCCCCCEEEEEEEEECCCCHHHHHHC-CCCCCCCCCCEECHHHCCHHHHHHHHHHHCCCC-----HHHHHHH-H-HCCCCEEEEEEEC---- >P1;d3c96a2 -----CEEEEEEEEEEEEEC------CCCC-CCCCEEEECCCCCEEEEEECCCCHHHCCEEEEEEEEEEHH---HHCC---------CCCCCCC---CC---HHHHHHHHCCCCCCC--CCHHHHH-H-CCCEEEEEEEEC----- PSA >P1;d1d7la2 67453753730300020515103a---------94361b385-3200012579------84010103055---------------------92738508---394008104500497---117606-2480352517534647459 >P1;d1n4wa2 ------2140001000202776437391889399136338b688005033121845823301100020506----56075763788875658186920-530290057104821976a090346129c59300115227377b--- >P1;d2voua2 ----88027300040306493069901840-496426273b-9430003228088ca66610102020618769705700-30568733771062b104550374036505907-----6014100-2-4076020113197---- >P1;d3c96a2 -----945701102010518------8046-384526342975020204042a35989501020101022a---52bb---------a157967---07---385015203a19396--0706400-5-41440141332a----- Translating the sequences ******EEEEEEEEEEECCCCCC*---------CCEEE*CCC-C*EEEEEE*C------CEEEEEEEE*C---------------------CCCHHHCC---HHHHHHHH**CC***---*H****-**C**EEEEEEEE****** ------*****EEEEEECCCCCC********CCC*EEE*CCCCC*EEEEEECCC***CCCEEEEEEEE*C*----****************CCCHHH*-***HHHHHHHH*******************CCCEE*********--- ----**EEEEEEEEEEECCCCCC*******-CCCCEEE**C-C**EEEEEECCC***CCCEEEEEEEE*C**********-************CHHHCC***HHHHHHHH**CC-----**H****-*-*CC**EEEEEE**---- -----*EEEEEEEEEEE**C------****-CCCCEEE*CCCCC*EEEEE*CCC***CC*EEEEEEEE***---****---------****CCC---CC---HHHHHHHH**CC***--**H****-*-CCCEEEEEEEE*----- 54373-3.tem _________________________________ ----**EEEEEEEEEEECCCCCC*******-CCCCEEE*CCCCC*EEEEEECCC***CCCEEEEEEEE*C*---******-**********CCCHHHCC***HHHHHHHH**CC***--**H****-**CCCEEEEEEEE***--- Structural block scores 0 3 - 4.3 M 5.5 75.0 75.0 75.0 4 5 * 2.9 P 5.0 75.0 8.0 42.0 6 16 E 4.7 H 2.1 0.9 1.7 1.9 17 22 C 4.4 M 2.5 4.3 4.7 39.8 23 29 * 2.6 P 65.8 5.6 4.4 34.7 31 34 C 4.5 M 40.8 5.5 5.8 5.0 35 37 E 5.0 H 3.3 4.0 3.3 3.7 39 43 C 4.4 M 18.8 8.3 20.5 4.6 45 50 E 4.9 H 1.3 2.0 1.2 1.7 51 53 C 4.5 M 30.3 3.7 5.3 5.2 54 56 * 2.3 P 75.0 5.7 10.3 7.3 57 59 C 4.3 M 52.7 2.7 6.0 4.7 60 67 E 5.0 H 1.1 0.5 0.8 0.6 71 73 - 4.3 M 75.0 75.0 7.3 75.0 74 79 * 2.9 P 75.0 16.3 3.2 30.0 81 90 * 3.0 P 75.0 6.3 4.9 47.4 91 93 C 4.5 M 6.0 5.7 2.3 7.3 94 96 H 4.3 M 5.3 5.7 4.8 75.0 97 98 C 4.3 M 4.0 37.5 2.0 3.5 99 101 * 3.5 M 75.0 2.7 3.3 75.0 102 109 H 5.0 H 3.1 3.0 3.5 3.0 110 111 * 1.0 P 4.5 6.0 7.0 6.8 112 113 C 4.3 M 0.0 1.5 3.5 5.0 114 116 * 2.3 P 6.7 7.3 75.0 6.0 117 118 - 4.3 M 75.0 5.2 75.0 75.0 119 120 * 1.6 P 38.0 4.5 3.0 3.5 122 125 * 1.0 P 4.8 3.2 1.2 2.5 127 128 * 2.2 P 3.0 8.8 38.5 40.0 129 131 C 4.3 M 3.7 4.0 3.7 3.0 132 139 E 4.3 M 4.0 2.6 1.8 2.2 140 142 * 2.3 P 5.7 8.5 30.3 53.5 143 145 - 4.3 M 6.0 75.0 75.0 75.0 >>>>>>