Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1dt9a1 -----------------------------CCEEEEEECCCCCCCEEEEE--CCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCCCCCEEEECC------CCCHHHHCC------CCCCCCCCCC-CCCEEECC------------CCCCHHHHHHHH--HHCCCCC------------------------------ >P1;d1fjgk- -------------------------CCCCCEEEEEEECCCCCCEEEEEC--CCC-CEEEEEECCCCCCCC--------HHHHCCHHHHHHHHHHHHHHHCC-------CCCEEEEEEE----CCCCCHHHHHHHHHCCCC----------EEEEEEECCCCCCCCCCCCHHHCCCC---------------------------------------------- >P1;d1vq8n1 CCCCCCCCCCHHHHCCCCCHHHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCCEEEEEEECHHHHHHC------CCCCCCCHHHHHHHHHHHHHHHHHC-------CCCCCEEECCCCCCCCCCHHHHHHHHHHHCCC----------CCCCC-------------HHHCCCHHHHHCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCC >P1;d2j01s1 ------------------------------CCEEECCCCCCCCCEEEEEC--CCCEEEEEECCCCCCCCC-----------CHHHHHHHHHHHHHHHHHHC-------CCCCCCCCCC------------------------------------------------------------------------------CCCCCCCCCCCCCCCCCC-------- >P1;d2qi2a2 --------------------------CCCCCCEEEEEECCCEEEEEEEC--CCCEEEEEEEECCHHH---------------HCCCHHHHHHHHHHHHHCCC--------CCEEEEECC------CHHHHHHHHHHHCC----------CCCCCCEECC------------CCCHHHHHHHHHC----HHHHHHHC-------------------------- >P1;d2vgna2 --------------------------CCCCCCEEEEEEECCEEEEEEEC--CCCEEEEEEEECCCCC---------------CCHHHHHHHHHHHHCCCCCCCC----CCCEEEEEECC------CHHHHC-CHHHHHHHHCCCHHHHCCCCCEEEECC------------CCCCHHHHHHHHCHHHHHHHHHHHC-------------------------- >P1;d4af1a2 -----------------------------CCEEEEEEECCCEEEEEEEE--CCEEEEEEEEECCCCCCCCCCCCCCCCCCCCC-CHHHHHHHHHHHHHHHHHCCC--CCEEEEEEEECH------HHHHHHHHC------CCCCHHHHCC-EEEEEECC------------CCCCCHHHHHHH--HCHHHHC------------------------------ PSA >P1;d1dt9a1 -----------------------------87310000026710000013--6c696335617280159769cb46a7427634765265014500430273016ba615060000005a------710550192------a402850367-14330809------------703580072017--5059506------------------------------ >P1;d1fjgk- -------------------------997165030206037a20303002--472-96016010432c298--------a6213460043003300740483-------4082040103----460602720060058260----------7056366537779b9a758a87499f---------------------------------------------- >P1;d1vq8n1 996aa484466465466153932761274a321010337c930503003518ba363413020640661a------0714112000000000000120365-------90840200114276761320100020024080----------80647-------------8a3019464020332287088498521bc80278040710470285035ca1b3 >P1;d2j01s1 ------------------------------823000734a5304040235--899824070203648356-----------54660063005201861275-------a25818122a------------------------------------------------------------------------------9485890204284521a9-------- >P1;d2qi2a2 --------------------------a9985210000033520100102--28505528217093aa---------------6817268006603740772a--------251000026------7004301710574b----------591501261a------------6155600670375----84058227-------------------------- >P1;d2vgna2 --------------------------b3294210000037200000001--8970343431539557---------------7587229005400503710517----60500000029------610610-8113500775827401775d1040707------------4053800540283792796178137-------------------------- >P1;d4af1a2 -----------------------------a2110000024530000002--5a725233518171368a6aa7b378769973-613570064017105610548--870400000027------700350177------7205770263-02632807------------805670054017--407a309------------------------------ Translating the sequences -----------------------------CC*EEEEE*CCC***EEEE*--CC**EEEE***CCCCC**C**************HH******HHHHH***C*******CCC**EEEEC*------C**HHHH**------**********-****EECC------------CCC**HHH*HHH--*******------------------------------ -------------------------****C**EEEEE*CCC**EEEEE*--CCC-*EEEEEECCCCC**C--------******HHHHHHHHHHHHHHH*C-------CCC**EEEE*----***C*HHHHH********----------*****EECC*************CC**---------------------------------------------- *****************************CC*EEEEE*CCC**EEEEE***CCC*EEEEEEEC******C------********HHHHHHHHHHHHHHH*C-------CCC**EEE*C*******C*HHHHH********----------*****-------------***CCC**HHH*HHH*************************************** ------------------------------C*EEE***CCC***EEEE**--CC*EEEEEE*CCCCC**C-----------***HHHHHHHHHHHHHHH*C-------CCC******C------------------------------------------------------------------------------******************-------- --------------------------***CC*EEEEE*CCC**EEEEE*--CCC*EEEEEEECC***---------------****HHHHHHHHHHHHH*C*--------C**EEEEC*------C*HHHHH*******----------******EECC------------CCC**HHH*HHH*----********-------------------------- --------------------------***CC*EEEEE**CC**EEEEE*--CCC*EEEEEEECCCCC---------------**HHHHHHHHHHHH****C***----CCC**EEEEC*------C*HHH*-***********************EECC------------CCC**HHH*HHH*************-------------------------- -----------------------------CC*EEEEE*CCC**EEEEE*--CC**EEEEEEECCCCC**C*************-*HHHHHHHHHHHHHH******--*C****EEEEC*------**HHHHH**------**********-****EECC------------CCC**HHH*HHH--*******------------------------------ 53137.tem _________________________________ --------------------------***CC*EEEEE*CCC**EEEEE*--CCC*EEEEEEECCCCC**C------********HHHHHHHHHHHHHHH*C***----CCC**EEEEC*------C*HHHHH***********************EECC------------CCC**HHH*HHH*-***********-------------------------- Structural block scores 0 25 - 4.6 H 75.0 72.5 5.6 75.0 75.0 75.0 75.0 26 28 * 3.1 M 75.0 5.7 4.3 75.0 9.5 5.5 75.0 29 30 C 4.6 H 7.5 5.5 6.8 41.5 6.5 6.5 6.2 32 36 E 4.8 H 0.2 2.2 1.0 2.0 0.2 0.2 0.2 38 40 C 4.9 H 5.0 6.8 9.5 6.5 3.7 4.0 3.7 41 42 * 1.0 P 0.5 1.0 1.5 1.5 1.0 0.0 1.5 43 47 E 4.8 H 0.2 1.2 1.6 2.0 0.4 0.0 0.0 49 50 - 4.4 M 75.0 75.0 3.0 40.0 75.0 75.0 75.0 51 53 C 4.6 H 8.2 4.3 10.0 30.7 5.0 8.0 7.5 55 61 E 4.7 H 4.4 3.3 2.7 3.3 4.3 3.3 3.9 62 66 C 4.4 M 3.2 4.3 3.2 4.2 6.6 5.8 3.6 67 68 * 2.5 P 8.0 5.5 3.5 4.0 75.0 75.0 9.2 70 75 - 4.2 M 8.9 75.0 75.0 75.0 75.0 75.0 8.2 76 83 * 2.8 P 5.0 22.1 2.0 48.8 58.0 57.8 15.5 84 98 H 4.6 H 2.9 2.3 0.4 2.7 3.8 3.5 3.1 101 103 * 3.5 M 2.3 75.0 75.0 75.0 53.5 4.3 3.0 104 107 - 4.4 M 7.2 75.0 75.0 75.0 75.0 75.0 41.5 108 110 C 4.5 M 3.7 4.0 5.7 5.8 50.7 3.7 3.7 111 112 * 1.0 P 0.0 1.0 2.0 4.5 3.0 0.0 0.0 113 116 E 4.5 M 0.0 1.2 0.8 3.2 0.0 0.0 0.0 119 124 - 4.4 M 75.0 39.2 4.8 75.0 75.0 75.0 75.0 127 131 H 4.4 M 2.2 2.2 0.2 75.0 1.6 16.4 1.8 132 154 * 3.0 P 25.8 34.7 34.4 75.0 35.1 4.2 25.6 155 156 E 4.4 M 4.0 6.0 75.0 75.0 4.0 3.5 5.0 157 158 C 4.4 M 4.5 4.0 75.0 75.0 5.8 3.5 3.5 159 170 - 4.5 M 75.0 8.3 58.0 75.0 75.0 75.0 75.0 171 173 C 4.5 M 3.3 6.7 3.3 75.0 4.0 3.0 4.3 174 175 * 1.8 P 6.5 15.8 5.0 75.0 5.5 5.5 6.5 176 178 H 4.4 M 2.3 75.0 2.0 75.0 2.0 1.7 1.7 180 182 H 4.4 M 2.7 75.0 2.7 75.0 3.3 3.3 2.7 185 195 * 3.1 M 30.0 75.0 5.8 75.0 23.7 5.5 30.3 196 221 - 4.3 M 75.0 75.0 4.7 26.6 75.0 75.0 75.0 >>>>>>