Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2wasa- -C--CEEEEEEEHHHCCCCC----HHHHHHHCCHHHHHHHHCCC---CHHHHHHHHHHHHHHHHHHHC--------CCCCCEEEEEECCEEEEEEECHHHHHHHHCCCC-CEEEEEEE-CCCEEEEEEEECC--------------- >P1;d2wdsa- CEEEEEEEEEEEHHHHHHHHHHC-CCHHHHHCCHHHHCCCCCCC---CCHHHHHHHHHHHHHHHHHCCCC--C--CCCHHHEEEEECCCCCEEEEECHHHHHHHHHHCCCEEEEEEEE-ECCEEEEEEEEEE--------------- >P1;d3hqja- -CEEEEEEEEEEHHHHHHHH----C-----CCCHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHEEEEECCCCCEEEEECHHHHHHCC--CC-EEEEEEEE-ECCEEEEEEEEECC-------------- >P1;d3otaa1 --CCEEEEEEEEHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHCCCCCCC--CCCHHHEEEEECCCCCEEEEECHHHHHHHHHCCCCEEEEECCC-CCCEE-EEEEEEC--------------- >P1;d4mrta1 ----CEEEEEECCCCCC----HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHC--------CCHHHCCEE-CCCCCEECCC----CCCC------EEEEEEE---CCEEEEEEEC----------------- >P1;d4mrta2 ---CCEEEEEEECCCCC-------CHHHHHHCCHHHHHHHHCCCC--CHHHHHHHHHHHHHHHHHHHCC----HHHCCHHHCEEEECCCCCEEEEC----CCCC------CCEEEEECCCCCEEEEEEECCCCCCCCCCCCCHHHHC >P1;d5xuka- ----CEEEEEEEHHHHHHHCCCCCHHHHHHHCCHHHHHHHCC------CHHHHHHHHHHHHHHHHHCCCCCCC--CCCHHHEEEEECCCCCEEEEEC---HHHHHHCCCCCEEEEEEE-ECCEEEEEEEEC---------------- PSA >P1;d2wasa- -c--4707151717506395----98307600184039105718---63310000010002005500a--------252430102187989160614891573078290-70708074-7b84040506073--------------- >P1;d2wdsa- 4871360715151a803751994-862386003a7014389777---0a454000020003002500953--b--b16331010324bb77240516a40372087390640607183-a9a5030504026--------------- >P1;d3hqja- -d723618171515814984----8-----50153057307------833431000300020025015931a969743253010215867626051687038307--81-60506173-ac840204040426-------------- >P1;d3otaa1 --6136071714057155418866492068002a801850582a---74021003020002000500815258--a061510305449886140706a40452176470861608192-79750-0404036--------------- >P1;d4mrta1 ----6654235076615----99338821730469225505729765410110000010030007639--------493550155-588764405a----1681------6061739---a660504069----------------- >P1;d4mrta2 ---77616154517837-------354056601a5027204729a--5345000102000200040376----56826065010414b67806081----7928------7040511625973000100155907a939846a9678 >P1;d5xuka- ----57171604176058418675761066004880393078------623200001000200050071619a--6052520604229986160505---9922961a0870806174-a98605030505---------------- Translating the sequences -*--*EEEEEEEHHH*****----*HHHHHHCCHHHHHHH*CCC---CHHHHHHHHHHHHHHHHHH*C--------CC***EEEEE*CC**EEEEEC***HHH****CC-*EEEEEE*-*CCEEEEEEEE**--------------- *****EEEEEEEHHH********-**HHHHHCCHHHH****CCC---C*HHHHHHHHHHHHHHHHH*C**--*--*CCHHHEEEEECCCCCEEEEEC***HHH****CC**EEEEEE*-*CCEEEEEEEE**--------------- -****EEEEEEEHHH*****----*-----*CCHHHHHHH*------CHHHHHHHHHHHHHHHHHH**********CCHHHEEEEECCCCCEEEEEC***HHH**--CC-*EEEEEE*-*CCEEEEEEEE***-------------- --***EEEEEEEHHH**********HHHHHHCCHHHHHHH**CC---CHHHHHHHHHHHHHHHHHH*C*****--*CCHHHEEEEECCCCCEEEEEC***HHH****CC**EEEE***-*CCEE-EEEEE**--------------- ----*EEEEEE******----****HHHH**CCHHHHHHH*CCC****HHHHHHHHHHHHHHHHHH*C--------CCHHH**EE-CCCCCEE***----****------*EEEEEE---CCEEEEEEE*----------------- ---**EEEEEEE*****-------*HHHHHHCCHHHHHHH*CCC*--CHHHHHHHHHHHHHHHHHH*C*----***CCHHH*EEEECCCCCEEEE*----****------**EEEEE***CCEEEEEEE****************** ----*EEEEEEEHHH**********HHHHHHCCHHHHHHH*C------*HHHHHHHHHHHHHHHHH*C*****--*CCHHHEEEEECCCCCEEEEEC---HHH****CC**EEEEEE*-*CCEEEEEEEE*---------------- 56214.tem _________________________________ -****EEEEEEEHHH**********HHHHHHCCHHHHHHH*CCC---CHHHHHHHHHHHHHHHHHH*C*****--*CCHHHEEEEECCCCCEEEEEC***HHH****CC**EEEEEE*-*CCEEEEEEEE**--------------- Structural block scores 1 4 * 2.9 P 41.6 4.8 6.4 21.2 57.8 41.0 57.5 5 11 E 4.9 H 4.0 3.6 4.1 3.7 3.6 4.0 3.7 12 14 H 4.2 M 4.3 6.5 4.7 4.0 6.3 5.3 4.7 15 24 * 2.4 P 33.2 12.1 33.4 4.8 33.0 53.8 5.1 25 30 H 4.4 M 4.0 4.2 63.3 4.2 4.8 4.3 3.2 31 32 C 5.0 H 0.5 1.5 0.5 1.0 2.0 0.5 2.0 33 39 H 4.8 H 3.6 4.8 3.3 4.6 4.1 3.8 4.4 41 43 C 4.4 M 5.3 7.0 75.0 6.8 6.0 6.0 52.7 44 46 - 4.5 M 75.0 75.0 75.0 75.0 6.0 53.5 75.0 48 65 H 5.0 H 1.1 2.0 1.4 1.1 1.1 1.2 1.2 68 72 * 3.2 M 75.0 33.9 6.5 4.2 75.0 61.2 5.5 73 74 - 4.2 M 75.0 75.0 7.5 75.0 75.0 5.5 75.0 76 77 C 5.0 H 3.5 3.5 3.5 3.0 6.5 4.0 2.5 78 80 H 4.6 H 3.0 2.3 3.3 2.3 4.3 3.7 3.0 81 85 E 4.7 H 0.8 1.2 0.8 2.4 17.2 1.2 2.4 86 90 C 4.8 H 8.2 8.2 6.4 7.0 6.8 7.3 6.8 91 95 E 4.7 H 2.8 2.4 2.8 2.4 4.7 3.0 2.4 97 99 * 3.1 M 6.0 4.8 5.0 4.8 75.0 75.0 75.0 100 102 H 4.2 M 5.0 4.0 4.7 3.7 5.0 6.0 6.7 103 106 * 2.4 P 4.2 4.5 39.2 4.5 56.5 58.2 4.5 107 108 C 4.4 M 4.5 4.5 4.5 3.5 75.0 75.0 5.2 109 110 * 2.4 P 41.0 5.0 40.5 7.0 40.5 41.0 7.5 111 116 E 4.8 H 3.7 3.7 3.2 4.2 4.3 1.8 3.7 120 121 C 5.0 H 9.8 9.8 10.2 8.0 8.2 8.0 8.5 122 129 E 4.9 H 2.4 2.1 1.8 11.0 3.8 0.6 2.4 130 131 * 2.1 P 5.0 4.0 3.0 4.5 75.0 5.0 40.0 132 146 - 4.6 H 75.0 75.0 70.4 75.0 75.0 7.1 75.0 >>>>>>