Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ydxa1 ----------CCCCCCCCCCCC--EEEEHHHHE-EEEECC-CC-H--HHCCC---CCCEEEECCCC-----------CCC--CEEC--------CCCCCCCCEEEECCC-CCCCEEECCCCCEECCCEEEEEECCCCCCCHHHHHHHHH-CCHHHHHCCCCCCCCCCCCHHHHHHCEEE---ECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--HHHHHHCC >P1;d1ydxa2 ---------------CCHHHHC--CEEEHHHCC-EEEECCCCC-H--HHCCC---CCCEEEECCCC-----------CCC--CEEC--------CCCCCCCEEEEECCCCCCCCEEEECCCCEECCCEEEEECC--CCCCHHHHHHHHH-HHHHHHHHCCCCC-CCCCCHHHHHCCEEE---CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---------- >P1;d1yf2a1 CCCCCCCCCCCCCCCCC---CC--CCEEHHHHEEEEEECCCC--CCCHHHCC---CCCEEEECHHHHHCCC--CEECCCC--EEECHHHHHCCCCCCCCCCCEEEECCC-CCCCEEEECCCCEECCCEEEEEEC-CCCCCHHHHHHHHH-HCHHHHHCCCCCCCCCCCCHHHHHCCEEC---CC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC >P1;d1yf2a2 -----------CCCCCC---CC--EEEEHHHHE-EEEECCCCC-CCCHHHCC---CCCEEEECHHHHHCCCCCCEECCCC--CEECHHHHHHCCCCCCCCCCEEEECCC-CCCCEEEECCCCEECCCEEEEEECCCCCCCHHHHHHHHH-HCHHHHHHHHCCCCCCCCCHHHHHHCEEE---EC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC----- >P1;d2ih2a2 ------------CCCCHHHHHHHHCCEEHHHHEEEEECCCHHHHHHCCCCCCCCCCCEEECCCHHH--EECCEECCCCCCCCCEEEHHHHHHCC-HHHHCCEEEECCCCCCCCCEEEECCCCCC-CCCEEEEECCCEEECHHHHHHHHCCHHHHHHHHHHHCCCCCCCCHHHHCCCEECCCCEEEC----------------------------------------------------- PSA >P1;d1ydxa1 ----------63a8634ab0a2--483306400-708516-07-9--83248---90713113354-----------925--5407--------632186610000018-50020111583000083000060466a402330010103-722a504820789a927062820381403---00763900532085527746676747656676775665448358574--a9148859 >P1;d1ydxa2 ---------------3a53a86--751404600-913606626-9--9626a---92820020565-----------937--3209--------92309750000106ba020102005630100500000429--b701001000103-9228613678838-836144830261604---1086381047104760672356486787876658566567877797b---------- >P1;d1yf2a1 a8998682576297035---71--702304500540520020--6a476126---b060000326005918--0305a15--44036500751a013036600000049-420100004550001610000114-89502140011104-83497036317987765072840251502---10-428405640654266468738777867687666775687575669b69959a8b >P1;d1yf2a2 -----------2bb25b---91--755204410-502506305-89486017---a08100021600251a870503705--630276016629042047600000036-600300004560001510000305778502020001101-823a503940099a753044730260600---20-527305630874356576556866676466757875573475a4689ab----- >P1;d2ih2a2 ------------1535970663196234015004052004363058170057855ac120000380--03546010871309010249405503-90057400000263505000030750000-220000233b705053940191014a60270063006a54730448003500056610437----------------------------------------------------- Translating the sequences ----------*CCCCCC***CC--*EEEHHHHE-EEEECC-CC-H--HHCCC---CCCEEEEC***-----------CCC--CEEC--------CCCCCCCCEEEECCC-CCCCEEE*CCCCEECCCEEEEEECCCCCCCHHHHHHHHH-*CHHHHH*CCCCCCCCCCCHHHHH*CEEE---EC*CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCC--******** ---------------CC****C--CEEEHHH**-EEEECCCCC-H--HHCCC---CCCEEEEC***-----------CCC--CEEC--------CCCCCCC*EEEECCC*CCCCEEEECCCCEECCCEEEEE*C--CCCCHHHHHHHHH-H*HHHHHHCCCCC-CCCCCHHHHHCCEEE---*C*CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCC---------- ***********CCCCCC---CC--C*EEHHHHE*EEEECCCC--**CHH*CC---CCCEEEECHHH****C--***CCCC--*EECHHHHH*CCCCCCCCCCEEEECCC-CCCCEEEECCCCEECCCEEEEEEC-CCCCCHHHHHHHHH-HCHHHHH*CCCCCCCCCCCHHHHHCCEE*---*C-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH***C********** -----------CCCCCC---CC--*EEEHHHHE-EEEECCCCC-**CHH*CC---CCCEEEECHHH****C*****CCCC--CEECHHHHH*CCCCCCCCCCEEEECCC-CCCCEEEECCCCEECCCEEEEEECCCCCCCHHHHHHHHH-HCHHHHHH**CCCCCCCCCHHHHH*CEEE---EC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCC*****----- ------------CCCC********C*EEHHHHE*EEE*CC****H*C**CCC***CC*EE**CHHH--**C*****CCCC**CEE*HHHHH*CC-****CC*EEE*CCC*CCCCEEEECCCC**-CC*EEEEECCC***CHHHHHHHH**H*HHHHHH***CCCCCCCCHHHH*CCEE****E**C----------------------------------------------------- 116734.tem _________________________________ -----------CCCCCC***CC--CEEEHHHHE-EEEECCCCC-H*CHHCCC---CCCEEEECHHH--**C--***CCCC--CEECHHHHH*CCCCCCCCCCEEEECCC-CCCCEEEECCCCEECCCEEEEEECCCCCCCHHHHHHHHH-HCHHHHHHCCCCCCCCCCCHHHHHCCEEE---EC*CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCC--***----- Structural block scores 0 10 - 4.4 M 68.7 75.0 7.1 75.0 75.0 11 16 C 4.5 M 5.8 52.2 4.3 7.2 16.3 17 19 * 3.0 P 7.3 6.2 75.0 75.0 4.3 20 21 C 4.2 M 6.2 7.0 4.0 5.0 4.5 22 23 - 4.5 M 75.0 75.0 75.0 75.0 5.0 25 27 E 4.6 H 4.7 3.3 1.7 4.0 3.0 28 31 H 4.9 H 2.5 2.5 2.2 2.2 1.5 34 37 E 4.9 H 5.0 4.8 2.8 3.0 1.8 38 42 C 4.5 M 17.8 4.0 15.4 2.8 3.2 47 48 H 4.5 M 5.5 7.5 6.5 7.0 3.5 49 51 C 4.6 H 4.7 6.2 3.0 2.7 4.0 52 54 - 4.5 M 75.0 75.0 75.0 75.0 6.0 55 57 C 4.8 H 5.3 6.3 5.8 6.2 8.0 58 61 E 4.8 H 1.5 1.0 0.0 0.2 0.5 63 65 H 3.8 M 4.0 5.3 2.7 2.3 3.7 66 67 - 3.8 M 75.0 75.0 2.5 1.0 75.0 68 69 * 3.0 P 75.0 75.0 5.0 3.0 1.5 71 72 - 3.8 M 75.0 75.0 75.0 7.5 5.0 73 75 * 3.0 P 75.0 75.0 1.0 1.7 0.3 76 79 C 4.8 H 22.8 23.5 5.4 3.8 4.8 80 81 - 4.5 M 75.0 75.0 75.0 75.0 4.5 83 84 E 5.0 H 2.0 1.0 2.0 1.5 0.5 86 90 H 4.2 M 75.0 75.0 3.6 4.0 4.4 92 101 C 4.5 M 18.3 18.5 3.0 3.4 10.3 102 105 E 4.9 H 0.0 0.2 0.0 0.0 0.0 106 108 C 5.0 H 3.0 5.8 4.3 3.0 3.7 110 113 C 5.0 H 1.8 0.8 1.8 2.2 1.2 114 117 E 4.9 H 0.8 0.5 0.0 0.0 0.8 118 121 C 5.0 H 4.0 3.5 3.5 3.8 3.0 122 123 E 4.5 M 0.0 0.5 0.0 0.0 0.0 124 126 C 4.8 H 3.7 1.7 2.7 2.3 26.3 127 132 E 4.8 H 1.0 1.0 0.3 0.5 0.8 133 139 C 4.6 H 4.6 25.5 14.7 4.9 4.5 140 148 H 4.9 H 1.2 0.6 1.3 0.6 3.1 152 157 H 4.8 H 4.9 4.3 4.8 5.1 2.5 158 168 C 4.7 H 5.5 11.9 5.5 4.7 3.9 169 173 H 4.9 H 3.0 3.4 3.2 3.2 3.0 174 175 C 4.4 M 4.5 3.5 3.0 3.0 2.5 176 178 E 4.6 H 2.3 3.3 2.3 2.0 1.7 179 181 - 4.5 M 75.0 75.0 75.0 75.0 4.3 186 224 H 4.5 M 5.1 5.3 5.6 5.3 75.0 226 228 C 4.2 M 5.3 9.2 5.7 6.5 75.0 229 230 - 3.8 M 75.0 75.0 10.2 7.0 75.0 231 233 * 3.0 P 6.8 75.0 8.0 10.3 75.0 234 238 - 3.8 M 6.8 75.0 8.8 75.0 75.0 >>>>>>