Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hcda- ----CCCCEEECC-CCCEEEEECC--EEEEECCC-CCCCCCCEEEEEC--CEEEEECCCCCEEEEEECCEEEEECCCCCCCCCCEEEEEC-CEEEEECCC-CCEEEEC-HHHCEEEE-CCCCCCCCCEEECC--- >P1;d3llpa1 CCCCCCEEEEECC-CCCEEEECCHHHCEEEEECCC-CHHHCEEEE--CCCCCCEEECCCCCEEEECCCCCEEEEECCCCHHHCEEEEECCCCCEEEEECCCCCEEEEE-CC-EEEEEECCCCHHHCCEEEECCCC >P1;d3llpa2 ------CEEEEECCCCEEEEEEC-CCEEEEEECCCCCHHHCCEEEECC--CCEEEECCCCCEECC--CCC---EECCCCHHHCCEEEEC---CEEEECCC-CCCEEEECCCCEEEEC----CHHHCEEEEEC--- >P1;d3llpa3 ----CCEEEEECC-CCCEEECCC--CCCEEEECCC-CHHHCEEEEECCCCCCEEEECCCCCEEEECCCCCEEEEECCCCHHHCCEEEEEC-CEEEEECCC-CCEEEEC-CCCCEEEEECCCCHHHCCEEEECC-- >P1;d3llpa4 ----CCEECCEEC-C-EEEEECC--CCEEEEECCC-C---CEEEEEEC--CEEEEECCCCCEEEECCCCCEEEEECCCC---CCEEEEECCCEEEEEEC--CEEEEEC-CCCCEEEEECCCCHHHCEEC------ PSA >P1;d1hcda- ----b34101108-96110014ab--51621628-6a92750405a2c--b32003288551000288671514774882310050764c-940102068-6120005-7a751114-87447600044377--- >P1;d3llpa1 baa6633000203-793100034a93601032881-762030024--bc3902102013420000477080405578338404011472b6a4100102326210044-46-705073691684130415412a7 >P1;d3llpa2 ------62002032274101138-a4200043762789203032381b--933002014821021--406---0279447100071464---50004016-24201057a4020308----c8622022493--- >P1;d3llpa3 ----733000303-485000041--6700052864-481010212438867300040443300112a9330403188389301050464b-940004034-7400105-a703010528909a6020315624-- >P1;d3llpa4 ----487020505-8-4200248--3200054a95-4---4040465a--7020011985410328b841030438843---4050553996300031c--8510321-a5120203178266402032------ Translating the sequences ----CC**EEECC-CCCEEEE*C*--*EEEE*CC-*C***C*EEEE*C--C*EEEECCCCCEEEE**CC*EEEE*CCCC***CCEEEEEC-CEEEEECCC-CCEEEEC-***CEEEE-CCCC***CCEEE*C--- ****CCEEEEECC-CCCEEEECC***CEEEEECCC-CHHHCEEEE--C**CC*EEECCCCCEEEECCCCCEEEEECCCCHHHC*EEEE*C*C*EEEE*CC*CCEEEE*-CC-*EEEEECCCCHHHCCEEEEC*** ------*EEEE*C*CC*EEEE*C-*C*EEEEECCC*CHHHC*EEEE*C--CCEEEECCCCCEE**--CCC---EECCCCHHHCCEEEE*---*EEEECCC-CC*EEE**CCC*EEE*----CHHHC*EEEEC--- ----CCEEEEECC-CCCEEE*CC--CC*EEEECCC-CHHHCEEEEE*C**CCEEEECCCCCEEEECCCCCEEEEECCCCHHHCCEEEEEC-CEEEEECCC-CCEEEEC-CCCCEEEEECCCCHHHCCEEEEC*-- ----CCEE**E*C-C-*EEEECC--CCEEEEECCC-C---CEEEEE*C--C*EEEECCCCCEEEECCCCCEEEEECCCC---CCEEEEEC*CEEEEE*C--C*EEEEC-CCCCEEEEECCCCHHHC*E*------ 50405.tem _________________________________ ----CCEEEEECC-CCCEEEECC--CCEEEEECCC-CHHHCEEEEE*C--CCEEEECCCCCEEEECCCCCEEEEECCCCHHHCCEEEEEC-CEEEEECCC-CCEEEEC-CCCCEEEEECCCCHHHCCEEEEC--- Structural block scores 0 3 - 4.5 M 75.0 9.6 75.0 75.0 75.0 4 5 C 4.5 M 7.2 4.5 75.0 5.0 6.0 6 10 E 4.5 M 1.4 1.0 2.0 1.2 2.8 11 12 C 4.4 M 4.0 1.5 1.5 1.5 2.5 14 16 C 4.4 M 5.3 6.3 4.3 5.7 29.0 17 20 E 4.9 H 0.5 0.2 0.8 0.0 1.0 21 22 C 4.4 M 7.2 3.5 5.5 2.5 6.0 23 24 - 3.8 M 43.2 9.8 42.8 75.0 75.0 25 26 C 3.9 M 40.0 4.5 3.0 6.5 2.5 27 31 E 4.8 H 3.2 1.2 1.4 1.4 1.8 32 34 C 4.8 H 28.3 5.7 5.0 6.0 8.2 37 39 H 4.1 M 6.0 2.7 3.7 3.0 75.0 41 45 E 4.7 H 3.9 16.2 3.2 1.8 2.8 48 49 - 3.8 M 75.0 7.8 75.0 7.0 75.0 50 51 C 4.4 M 7.2 4.5 6.0 5.0 3.5 52 55 E 4.9 H 1.2 1.2 1.2 1.0 0.8 56 60 C 5.0 H 5.6 2.0 3.0 2.8 5.4 61 64 E 4.8 H 0.2 0.0 1.0 0.5 1.5 65 69 C 4.5 M 6.2 5.2 32.0 5.5 6.5 70 74 E 4.6 H 3.6 2.8 45.4 1.6 2.0 75 78 C 5.0 H 6.8 5.2 6.0 6.8 5.8 79 81 H 4.1 M 2.0 4.0 2.7 4.0 75.0 82 83 C 4.8 H 0.0 2.0 0.0 0.5 2.0 84 88 E 4.8 H 4.4 3.0 4.4 3.8 3.6 92 96 E 4.8 H 1.4 1.2 1.8 1.6 1.2 97 99 C 4.4 M 4.7 1.7 2.3 2.3 29.5 101 102 C 4.8 H 3.5 4.0 3.0 5.5 6.5 103 106 E 4.9 H 0.5 1.2 0.8 0.2 1.5 109 112 C 4.2 M 7.4 23.0 4.1 5.1 4.6 113 117 E 4.7 H 16.4 3.0 17.2 1.6 1.2 118 121 C 4.6 H 5.8 5.5 59.4 6.5 5.8 122 124 H 4.5 M 4.3 4.3 5.3 5.5 3.3 125 126 C 4.4 M 0.0 1.5 1.0 1.0 1.0 127 130 E 4.5 M 4.5 3.5 4.2 3.8 38.8 132 134 - 4.3 M 75.0 6.5 75.0 51.3 75.0 >>>>>>