Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1dk8a- CCC-CC-----CCHHHHHHH----CHHHHCCCHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH-HHCCCC-CCHHHHHCCHHHHHHHHH-HHHHCC--CCCCCCHHHHHHHHHHHHHCHHHHHCCC-------HHHHCCCCCCC-CCCCC--------------------------------------------------- >P1;d1fqia- CCCCCC-----CCCCHHHHC----CHHHHHCCHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHCCC-----HHHHHHHHHHHHH-HHCC-C-CCCCCCCCCCCC-CHHHH-HCC--C--CCCCCCHHHHHHHCCC--CCCHHHHHCC-------HHHH-CCCCCC-CC------------------------------------------------------ >P1;d1htjf- -------------CHHHHHH----CHHHHHHCHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHCCCC-----CCHHHHHHHHHHH-HHCCC--CCCCCCCCCC-CHHHHHH-HHHCCCC--CHHHHHHHHHHCC-HHH-HHHHHHHHHHHCCCHHHHCCCHHHHCC--------CCHHHHHHHHHHHHHHHHHHHHCC--CHHHHCC-CHHHHHCC-CCCCCC >P1;d1iapa- ----------------CCCC----CHHHHCCCHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHCCCC-----HHHHHHHHHHHHH-HHCCC--CCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCHHHHH-HHHHHHHHHHHCCCC--CCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHCCCCHHHHHHHHHHHHHHHHHCCCCC >P1;d2ihda- -----------CCCCCHHHC----CHHHHHC-CCHHHHHHHHHHH--CCCCHHHHHHHHHC-CCCCCC----HHHHHHHHHHHHH-HHCC-C-CCCCCCCCCHHHHHHHHH-HCC--C--CCCCCCHHHHHHHHHHHHHCHHHHHHCC-------HHHH-CCC------------------------------------------------------------ >P1;d2jnua1 ---------CCCCCHHHHHH----CHHHHHHCHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHH-HHCCC--CCCCCCCCCHHH-CCCCH-HHH--C--CCCCCCHHHHHHHHHHHHCCHHHHHCCC-------CCHH-HHHCCCCC------------------------------------------------------- >P1;d3v5wa1 CCCCCCCCCHHHHHHHHHHHCCCCCHHHHHCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCC----CHHHHHHHHHHHHCCHHHHHHHCCCC--CCCHHHHHHHHH-HHHCCC--CCCCCCHHHHHHHHHHHCCHHHHHHHHC-------HHHHHHHHHHHHHCCCC--------------------------------------------------- >P1;d6am3a- C---CC-----HHHHHHHHH----CHHHHHHCHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHCCCCC----HHHHHHHHHHHHH-HHCC-C-CCCCCCCCCHHHHHHHHH-HHC--C--CCCCCCHHHHHHHHHHHHHCHHHHHHCC-------HHHH-HHHHHC--------------------------------------------------------- PSA >P1;d1dk8a- da9-98-----356255026----508200639802830461057--5a114003014303803758469827680064036006-710658-b21006407891267053-106657--0815005600720571048610450182-------950468147ba-a998c--------------------------------------------------- >P1;d1fqia- ba9581-----532065038----505400516202620150067--39414302004302601636-----3951571037037-2002-8-c08350716c91-86068-517--9--1545003400820346--8621760181-------6206-737818-96------------------------------------------------------ >P1;d1htjf- -------------7276005----416401732000100010003--42520000010001001417-----8780471064027-10038--a02030806a-1186046-3086358--04b0056008307-506-700730352296a31560118108616--------d58842560036015205821874--8985281-54005214-43a174 >P1;d1iapa- ----------------8305----516501610000000010003--53800100000004108637-----6971272048026-50038--903040701890375075185870657406701850283059207-700630362285860--2147005707865aa7585036403820260084056437502a5a710520190015005318084 >P1;d2ihda- -----------a73055045----5064007-3901620450056--39223103013303-039097----9951583048006-3002-6-906440a068a0254038-407--a--1647005500840244047501350272-------9306-747------------------------------------------------------------ >P1;d2jnua1 ---------b7a44251048----507300528501520441055--58141006004104504707--5a65a50281047027-30026--c09430b062b9-03796-026--6--052500770175015504a601560270-------7306-50449978------------------------------------------------------- >P1;d3v5wa1 b868229692298028406859304065018385024103300265186051003012303602719----66951373057016381053028488--305a70277068-408775--0447004301730274039700740182-------82014000313364778--------------------------------------------------- >P1;d6am3a- c---38-----494054039----606500828403820460066--272021020133025027298----8730273047017-5102-7-909530907a70275056-328--9--0516004700830262057500450292-------9306-711682--------------------------------------------------------- Translating the sequences ***-**-----****HHHH*----CHHHH**CHHHHHHHHHHHH*--*CC*HHHHHHHHHHHH**CC*****HHHHHHHHHHHHH-HHCC**-CC*****CCHHHHHHHHH-H****C--CCCCCCHHHHHHHHHHHH**HHHHH**C-------HHHH*******-*****--------------------------------------------------- ******-----****HHHH*----CHHHHH*CHHHHHHHHHHHHH--*CCCHHHHHHHHHHHH*CCC-----HHHHHHHHHHHHH-HHCC-*-CCCCCCCCC***-*HHHH-H**--C--CCCCCCHHHHHHH***--***HHHHH*C-------HHHH-******-**------------------------------------------------------ -------------**HHHH*----CHHHHH*CHHHHHHHHHHHHH--*CCCHHHHHHHHHHHH*CCC-----**HHHHHHHHHHH-HHCC*--CCCCCCCCC*-*HHHHHH-H****C*--C****HHHHHH**-HHH-*HHHHHH*********HH*********--------************************--*******-********-****** ----------------****----CHHHH**CHHHHHHHHHHHHH--*CCCHHHHHHHHHHHH*CCC-----HHHHHHHHHHHHH-HHCC*--CCCCCCCCCHHHHHHH********C********HHHHH**HHHHH-*HHHHHH********--**H**************************************************************** -----------*****HHH*----CHHHHH*-**HHHHHHHHHHH--*CCCHHHHHHHHH*-**CCC*----HHHHHHHHHHHHH-HHCC-*-CCCCCCCCCHHHHHHHHH-H**--C--CCCCCCHHHHHHHHHHHH**HHHHHH*C-------HHHH-***------------------------------------------------------------ ---------******HHHH*----CHHHHH*CHHHHHHHHHHHHH--*CCCHHHHHHHHHHHH*CCC--***HHHHHHHHHHHHH-HHCC*--CCCCCCCCCHHH-****H-H**--C--CCCCCCHHHHHHHHHHHH**HHHHH**C-------**HH-********------------------------------------------------------- ***************HHHH*****CHHHHH*CHHHHHHHHHHHHH******HHHHHHHHHHHH*CCC----*HHHHHHHHHHHH**HH*****CCCC--CCCHHHHHHHHH-H****C--CCCCCCHHHHHHHHHHH***HHHHHH*C-------HHHH*************--------------------------------------------------- *---**-----****HHHH*----CHHHHH*CHHHHHHHHHHHHH--*CCCHHHHHHHHHHHH*CCC*----HHHHHHHHHHHHH-HHCC-*-CCCCCCCCCHHHHHHHHH-H**--C--CCCCCCHHHHHHHHHHHH**HHHHHH*C-------HHHH-******--------------------------------------------------------- 48097.tem _________________________________ ***-**-----****HHHH*----CHHHHH*CHHHHHHHHHHHHH--*CCCHHHHHHHHHHHH*CCC*---*HHHHHHHHHHHHH-HHCC**-CCCCCCCCCHHHHHHHHH-H****C--CCCCCCHHHHHHHHHHHH**HHHHHH*C-------HHHH*************--------------------------------------------------- Structural block scores 0 2 * 3.7 M 11.0 10.3 75.0 75.0 75.0 75.0 8.5 54.2 4 5 * 3.4 M 8.5 4.5 75.0 75.0 75.0 75.0 2.0 5.5 6 10 - 4.5 M 75.0 75.0 75.0 75.0 75.0 48.7 5.6 75.0 11 14 * 2.0 P 4.0 2.5 39.8 75.0 5.1 5.1 4.8 4.2 15 18 H 4.6 H 3.0 3.5 3.2 21.5 3.5 2.5 4.5 3.0 20 23 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 4.2 75.0 25 29 H 4.9 H 2.0 1.8 2.4 2.6 2.0 2.0 2.4 2.2 32 44 H 4.9 H 4.1 2.8 0.5 0.3 3.2 3.1 2.6 3.6 45 46 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 3.0 75.0 48 50 C 4.6 H 4.2 4.7 3.0 3.7 4.3 4.3 3.7 3.0 51 62 H 4.9 H 2.2 2.0 0.2 0.5 7.7 1.8 1.6 1.6 64 66 C 4.9 H 6.7 5.0 4.0 5.3 6.0 4.7 5.7 6.0 68 70 - 4.4 M 7.7 75.0 75.0 75.0 75.0 30.2 75.0 75.0 72 84 H 4.9 H 3.5 3.9 4.2 4.2 4.5 4.0 4.1 3.8 86 87 H 5.0 H 4.0 1.0 0.5 2.5 1.5 1.5 4.5 3.0 88 89 C 4.7 H 3.0 1.0 1.5 1.5 1.0 1.0 2.5 1.0 90 91 * 2.9 P 6.5 41.5 41.5 41.5 40.5 40.5 1.5 41.0 93 101 C 4.8 H 3.5 4.7 3.3 2.7 4.4 5.1 20.7 4.7 102 110 H 4.5 M 4.6 13.9 12.4 4.9 4.5 13.6 5.3 4.7 113 116 * 2.2 P 4.2 39.5 4.2 5.0 39.2 39.5 5.5 40.0 118 119 - 4.5 M 75.0 75.0 41.5 6.0 75.0 75.0 75.0 75.0 120 125 C 4.4 M 2.3 2.5 15.1 3.0 3.0 2.0 2.5 2.0 126 137 H 4.7 H 3.1 15.0 9.6 4.1 3.0 3.5 2.8 3.1 138 139 * 1.6 P 7.0 7.0 41.0 41.0 6.0 8.2 8.0 6.0 140 145 H 4.8 H 1.8 2.8 2.2 2.0 1.8 2.3 2.0 1.8 148 154 - 4.4 M 75.0 75.0 5.2 14.9 75.0 75.0 75.0 75.0 155 158 H 4.4 M 4.5 3.5 2.0 20.5 4.5 4.0 2.8 4.5 159 171 * 2.6 P 13.2 32.6 36.9 5.6 59.1 32.4 3.5 42.3 172 222 - 4.3 M 75.0 75.0 12.6 3.6 75.0 75.0 75.0 75.0 >>>>>>