Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1c02a- -------------CCCCCCCCCHHHHHHHHHHHH--------------------------CCC-CHHH--HHHHHHH-----HHHHHHHHHHHHHHHC---------CCCHHHHHHHHHHH-HHHHHHCCCHHHH-HHHHHHHHHHCCCCCCCCCHHHHHCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHCCCC-------- >P1;d1i5na- --------------------------------------------------------------------CHHHHHHHH-----HHHHHHHHC-CHHHHHC--CCCCCCHHHHHHHHHHHHHH-HHHHHHCCCHHHH-HHHH-CCHHHHHHHCCC-----------------------------------CCCHHHHHHHHHHHH-CCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHC >P1;d1sr2a- ------------------------------------CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCHHHHH-----HCHHHHHHHHHHHHH----------CCCHHHHHHHHHHH-HHHHHHHCCHHHH-HHHHHHHHHHH--------------------------------------------CCCHHHHHHHHHHHHHHHHHHC------------------------ >P1;d1tqga1 ----------------------------------------------------------------------CHHHHHH-----HHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHH-HHHHHHCCCHHHH-HHHHHHHHHHHHHHCCCC----------------------------------CCCHHHHHHHHHHHHHHHHHHHHHCC----------------------- >P1;d1wn0a1 ------CHHHHHHHHHHCCCCC-HHHHHHHHHHCCC------------------------CCC-CHHH--HHHHHHH-----HHHHHHHHHHHHHCCCC--------CCCHHHHHHHHHHH-HHHHHHCCCHHHH-HHHHCHHHHHH--------------------------------------------CCCHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHC-------- >P1;d1y6da- --------------------------------------------------------------CCCCCCCCCHHHHHCHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC--------------------------------------CCCCCHHHHHHHHHHHHHHHCCCC----------------------- >P1;d2a0ba- ---------------CHHHHCCHHHHHHHHHH-----------------------------CCHHHHH--HHHHHHH-----HHHHHHHHHHHHHHH----------CCCHHHHHHHHHHH-HHHHHHCCCHHHH-HHHHHHCCC---CCC-----------------------------------------CHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHC-------- >P1;d2ooca1 -----------------------------------------------------------------CCCCHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCC-----CHHHHHHHH-HHHHHHHCCCCCC--CCCCCCC-----------------------------------------------CCCHHHHHHHHHHHHHHHHHHHH-----HHHCCCC----------- >P1;d4g78a1 CCHHHHHHHHHHHHHHHCCCCC-HHHHHHHCC--CC------------------------CCCCHHHH--HHHHHHH-----HHHHHHHHHHHHHHHCC--------CCCHHHHHHHHHHH-HHHHHHCCCHHHH-HHHHCHHHHHH--------------------------------------------CCCHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHCC PSA >P1;d1c02a- -------------8a0346003494068216629--------------------------a78-8303--7306700-----8305700750170037---------72507401710750-3a20580002001-1004100100445367017195007306857128c273665349340874a858306102101300100100020033-----201741a5b0-------- >P1;d1i5na- --------------------------------------------------------------------66973a901-----850372175-4630550--52872699203311712640-2930671a09203-3014-106013411697-----------------------------------a06891172024215-0360052138a7907892276008306714874 >P1;d1sr2a- ------------------------------------7ba959977877b4979ba99889a6456307757528504-----720250064056128----------97519303810660-2820470808302-82044036107--------------------------------------------4557730662063017106813------------------------ >P1;d1tqga1 ----------------------------------------------------------------------9856600-----840472076045005506684a--546204301600540-2910793928802-720570051035038763----------------------------------9077910870270075048105835a----------------------- >P1;d1wn0a1 ------a288107602866104-a50580064367d------------------------a38-8504--8206701-----72045007404720858--------a061a503720760-3910250105404-60054038208--------------------------------------------67539205810560383045027-----305602852a-------- >P1;d1y6da- --------------------------------------------------------------7058500462075504a607960272054206614640b624867a0173017101630045004300325028422350656306840a--------------------------------------825445004003730691035309----------------------- >P1;d2a0ba- ---------------64981032720563186-----------------------------3448705--5607603-----740492075038239----------79558303600750-3a30171004303-600420112---949-----------------------------------------5088404810540572065007-----0058108933-------- >P1;d2ooca1 -----------------------------------------------------------------8106285039609-7658406610660574087336046968-----535700720-2920590004700--0050269-----------------------------------------------63707404600750382056157-----7474987----------- >P1;d4g78a1 8672455158127603867105-84035125a--5b------------------------a5774402--7206800-----78048108602520669--------9171a502620670-3920570001303-7104604a308--------------------------------------------67548004600650561064028-----306401601442677a87 Translating the sequences -------------*********************--------------------------***-****--HHHHHHH-----HHHHHHHHHHHHHHH*---------CC*HHHHHHHHHHH-HHHHHHCCCHHHH-HHHH*HHHHH************************************************HHHHHHHHHHHHHHHHHHH*-----HHH*******-------- --------------------------------------------------------------------**HHHHHHH-----HHHHHHHH*-*HHHH**--*********HHHHHHHHHHH-HHHHHHCCCHHHH-HHHH-**HHHH******-----------------------------------******HHHHHHHHH-**HHHHHHH******HHH*************** ------------------------------------************************************HHHHH-----H*HHHHHHHHHHHHH----------CC*HHHHHHHHHHH-HHHHHH*CCHHHH-HHHH*HHHHHH--------------------------------------------*C*HHHHHHHHHHHHHHHHHH*------------------------ ----------------------------------------------------------------------*HHHHHH-----HHHHHHHHHHHHHHH*******--****HHHHHHHHHHH-HHHHHHCCCHHHH-HHHH*HHHHHH*******----------------------------------******HHHHHHHHHHHHHHHHHH**----------------------- ------****************-*************------------------------***-****--HHHHHHH-----HHHHHHHHHHHHH****--------CC*HHHHHHHHHHH-HHHHHHCCCHHHH-HHHH*HHHHHH--------------------------------------------*C*HHHHHHHHHHHHHHHHHHH*-----HHH*******-------- --------------------------------------------------------------*********HHHHH*******HHHHHHHHHHHHHH**********CC*HHHHHHHHH*H*HHHHHH*CC*HHH*HHHH*HHHHHH*****--------------------------------------**C**HHHHHHHHHHHHHHH****----------------------- ---------------*****************-----------------------------*******--HHHHHHH-----HHHHHHHHHHHHHHH----------CC*HHHHHHHHHHH-HHHHHHCCCHHHH-HHHH*H***---***-----------------------------------------C*HHHHHHHHHHHHHHHHHHH*-----HHH*******-------- -----------------------------------------------------------------*****HHHHHH**-***HHHHHHHHHHHHHHH**********-----*HHHHHHHH-HHHHHH*CC****--*******-----------------------------------------------*C*HHHHHHHHHHHHHHHHHHH*-----HHH****----------- **********************-*********--**------------------------********--HHHHHHH-----HHHHHHHHHHHHHHH**--------CC*HHHHHHHHHHH-HHHHHHCCCHHHH-HHHH*HHHHHH--------------------------------------------*C*HHHHHHHHHHHHHHHHHHH*-----HHH*************** 47226.tem _________________________________ ---------------*******-*********----------------------------**********HHHHHHH-----HHHHHHHHHHHHHHH**--***--*CC*HHHHHHHHHHH-HHHHHHCCCHHHH-HHHH*HHHHHH*****--------------------------------------**C*HHHHHHHHHHHHHHHHHHH*-----HHH*******-------- Structural block scores 0 14 - 4.5 M 66.2 75.0 75.0 75.0 32.8 75.0 75.0 75.0 4.5 15 21 * 3.6 M 2.3 75.0 75.0 75.0 3.9 75.0 4.4 75.0 4.3 23 31 * 3.6 M 4.7 75.0 75.0 75.0 4.3 75.0 4.2 75.0 4.3 32 59 - 4.7 H 70.0 75.0 17.9 75.0 65.3 75.0 75.0 75.0 70.2 60 69 * 3.0 P 26.4 61.2 5.3 75.0 26.4 17.9 25.6 39.2 18.9 70 76 H 4.7 H 3.3 5.6 4.4 4.9 3.4 3.6 3.9 4.4 3.3 77 81 - 4.5 M 75.0 75.0 75.0 75.0 75.0 5.5 75.0 20.4 75.0 82 96 H 4.9 H 3.1 8.7 3.2 3.5 3.3 3.6 4.2 4.1 3.8 97 98 * 2.5 P 41.0 2.5 75.0 2.5 6.5 5.0 75.0 5.0 7.5 99 100 - 4.0 M 75.0 75.0 75.0 6.0 75.0 5.8 75.0 4.5 75.0 101 103 * 3.6 M 75.0 5.0 75.0 7.5 75.0 4.0 75.0 3.3 75.0 104 105 - 4.0 M 75.0 4.5 75.0 75.0 75.0 7.0 75.0 7.5 75.0 107 108 C 4.2 M 4.5 9.0 8.0 5.0 5.2 5.2 8.0 75.0 5.0 110 120 H 4.9 H 2.9 2.5 3.4 2.1 3.8 2.6 3.4 16.3 3.6 122 127 H 5.0 H 4.8 4.5 3.8 4.7 3.3 2.7 4.1 4.5 4.3 128 130 C 4.7 H 0.0 3.8 2.7 4.7 0.3 1.0 0.3 0.0 0.0 131 134 H 4.6 H 0.8 3.5 3.2 4.5 3.2 2.2 2.5 2.8 1.8 136 139 H 4.7 H 1.2 2.0 3.5 3.5 2.8 2.8 2.5 20.0 3.0 141 146 H 4.4 M 0.8 1.8 2.8 1.5 3.5 3.3 25.7 40.3 4.2 147 151 * 3.4 M 5.0 4.2 75.0 4.6 75.0 5.7 34.4 75.0 75.0 152 189 - 4.6 H 4.9 69.5 75.0 67.6 75.0 75.0 75.0 75.0 75.0 190 191 * 2.6 P 1.5 7.0 39.5 7.0 40.5 5.0 75.0 40.5 40.5 194 212 H 4.9 H 0.7 6.3 3.5 3.7 3.4 2.8 3.5 3.3 3.0 214 218 - 4.7 H 75.0 6.7 75.0 75.0 75.0 75.0 75.0 75.0 75.0 219 221 H 4.4 M 1.0 6.3 75.0 75.0 2.7 75.0 1.7 6.0 3.0 222 228 * 2.9 P 5.6 3.7 75.0 75.0 4.8 75.0 4.6 36.1 2.3 229 236 - 4.4 M 75.0 4.6 75.0 75.0 75.0 75.0 75.0 75.0 6.4 >>>>>>