Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ddza2 CCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCC---HHHHHHHHHHHHHHHHC-CCHHHHHCCCCCCCEEEEEECCCCCC--HHHHCCCCCCCEEEEEECCCCCCC----CCHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHCCCCC--CC----------CCHHHHCHHHHHHHHCCHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCEEEEEEECCCCCCCEEEEEECC--C--CCCCC---------------- >P1;d1ekja- ----------------------------------------CHHHHHHHHHHHHHHHCCCCC-HHHHHHHCCCCCCCEEEEEECCHHHC--HHHHCCCCCCCEEEEEEHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHHCC-CC-C-----CCCCCCHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCC-CCEEEEEEEECCCCEEEEEEE---CCCC-------CCCCCC--------- >P1;d1g5ca- ------------------------------------------------CHHHHHHHHCC--CCCCCHHHCC-CCCCEEEEEECCHHHCCHHHHHHCCCCCCCEEEEECCCCCC-------HHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHC--------------CCCHHHHHHHHHHH---C---CC-CCCHHHHHHHHHHHHHHCCCCCC------CCEEEEEEECCCCCCEEEEECCC--------------------------- >P1;d1ylka1 ----------------------------------------CHHHHHHHHHHHHHHCC--CCCCCCCCCC------CEEEEEECCCCCC--HHHHHCCCCCCEEEEEECCCCCC-------HHHHHHHHHHHHCCCCCEEEEEEECCCHHHCCCHHHHHHHHHHHHCC-------------------CCCCCCCCCC--------CHHHHHHHHHHHHHCCCCCCC------CCEEEEEEECCCCCCEEEECC----------------------------- >P1;d3eyxa- -----------------------------------------CHHHHHHHHHHHHHHHHHHC-HHHC-------CCCEEEEEECCCCCC---HHHHCCCCCCEEEEEEHHHCCCC----CCHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHCCCHHHCH-----HHCCHHHHHHCHHHHHHHHHCHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCC-CCEEEEEEECCCCCCEEEEEEECC--CCCC-------------------- >P1;d3lasa- -------------------------------------CCCCHHHHHCC-HHHHHHHHC-CCCCCCCCCC------CEEEEEECCCCCC--HHHHHCCCCCCEEEEEECCCCCC-------HHHHHHHHHHHHCCCCCEEEEEEECCCHHHCCCHHHHHHHC-CCCCC-------------------CCCCCCCCCC--------CHHHHHHHHHHHC-CCCCCCC--------EEEEEEECCCCCCCCC-------------------------------- >P1;d3qy1a- -----------------------------------------CHHHHHHHHHHHHHHHHHHC-CHHHHHHHCCCCCCEEEEEECCCCCC--HHHHHCCCHHHEEEEEECCCCCCC----CCHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHHCC--CC----------CCHHHHHHHHHHHHHHCHHHHHCC-CHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCEEEEEEECCCCCCEEECCCCCC--CHHHHHHHHHHHHHHHHHHHC--- >P1;d3teoa- --------------------------------------CHHHHHHHHHHHHHHHCHHH-HC---CCCCC------CEEEEEC-CCCCC--HHHHHCCCCCCEEEEECCCCCCC-------HHHHHHHHHHHHHCCCCEEEEEEECCCC-CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHH---HHCCCCCCC-CHHHHHHHHHCCCCCC------CCEEEEEEECCCCCCEECCCCCCCC-------------HHHCCCCCCCCC >P1;d3ucja- --------------------------------------CCC-CHHHHHHHHHHHHHHHHHC-CCCCHHHCCCCCCCEEEEEECCCCCC--HHHHCCCCCCCEEEEEECCCCCCC----CCHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHHCCCCCC----------CHHHHHCHHHHHHHHCCHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCEEEEEEECCCCCCEEEEEEEEC--CHHHHHHHCCCCHHHHHCHHHHCC >P1;d5swca1 ------------------------------------------CHHHHHHHHHHHHCHHHHC-HHHHHHHCCCCCCCEEEEEECCCCCC--HHHHHCCCCCCEEEEEECCCCCCCC-CCCCCHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHCCHHHHC-C-------CCHHHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHC-CCEEEEEEEECCCCEEEEEECCCCEEECCCCCCCCCCHHHCCCCC----- >P1;d6gwua- ----------------------------------CCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHC-CCCCCEEEEEECCCCCC--H-HHHCCCCCCEEEEEEHHHCCCC----CCHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHCC--CCC----------CCHHHHCHHHHHHHHCCHHHHHCCCCHHHHHC-CHHHHHHHHHHHHHCCHHHHHHHHC--CCEEEEEEECCCCCCEECCC-------------------CC--------- >P1;d6y04a- ---------------------------------------CCHHHHHHHHHHHHHHHCCCCCCCCCCCCC------CEEEEECCCHHHCCCHHHHCCCCCCCEEEEECCCCCCCCCCC---CHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHC--------------CCCHHHHHHHHHHHHHHH---CC-CCCHHHHHHHHHHHHHCCCCCCC------CCCEEEEEECCCCCCEEEEECCC--------------------------- >P1;d7coia- --------------------------------------CCCHHHHHHHHHHHHHHHHHHHC-CCHHHHHCCCCCCCEEEEEECCCCCC--HHHHCCCCCCCEEEEEEHHHCCCC----CCHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHCCC--CC----------CCHHHHHHHHHHHHHHCHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH-CCEEEEEEECCCCCCEEECCCCCC-----------HHHHHHHHHHHCC-- PSA >P1;d1ddza2 88a68a86878b857b86565775675577368b84878a7---87467657436722874-77235637738616000000443825--02602b365720321224000017----9288026204500562605401000127081046038a6--87----------9a3183054044046625b30772a6875311400110053007101219101800769290302010045c546247174386--6--658ab---------------- >P1;d1ekja- ----------------------------------------a89678662767446365564-7a4086376a590430000052a604--0592391644402222250000043389518c03720550046070520000001409205300825-06-a-----83829960520300460185057635b1-6795113400320052007102405103720369-704030002116777265252---9277-------9a889b--------- >P1;d1g5ca- ------------------------------------------------97857778778--6558220348-92611000007284077303611a16a53023133400206-------8601750170056480720100005805108365a532662577--------------93868508643774---0---84-15625610440064038195039------9010001003087072551462a--------------------------- >P1;d1ylka1 ----------------------------------------988777777789669b4--9094885076------410000072a407--04811a08551031133400004-------b701620240067280540200005709027373a842863468598-------------------61a6602008--------617810550063038267065------183050101218557174094----------------------------- >P1;d3eyxa- -----------------------------------------98967677677637516971-6a24-------b1300000042a405---2610a173940411325000055----84a60361055007627063000000140a00420047719613-----87b46a438406001501661695078387685215300210051007201717103700663-705020101406548255024016--9393-------------------- >P1;d3lasa- -------------------------------------9a788737779-688667839-a795686084------610000061a408--05712a18661023123600004-------b7016302500681505402000047090272649730751-766a5-------------------a258633119--------6156005603750-a196050--------8140110209658271-------------------------------- >P1;d3qy1a- -----------------------------------------a8a67867756546626976-644377588a9615100000543443--04801a187a40331214000017----928902620550035060330000001909006102564--a4----------aa3373064037139506a10760-589434500000000000120042a10160065a290101020023a638135150305--668405710660175029603--- >P1;d3teoa- --------------------------------------a8985765687855665148-3a---32056------4000000-29305--04600908740021143b00202-------9401620150047450540100001508-256205620864486a4616736046a66747174485016322208---139194005-0552053057276034------6090503000072561160764659-------------5687969a99a8 >P1;d3ucja- --------------------------------------8a6-6777777787548614785-96237528a9490530000042a404--05912b133250220215000045----919900720550036170530100001608005101646584a----------a95084053018126826a308c-37a8611430031002300140000610260085a180101000030b658264217406--42a30872077607551668846f >P1;d5swca1 ------------------------------------------7998655777566944573-7a22771777570530000052a505--0571281352502113150000035-942d9a1273066006418064000000240900400061b707-9-------865a31520520470154045735a4-9b87227200210021005102615107621667-601010101228484130010864613837a815021463692b6----- >P1;d6gwua- ----------------------------------a9928c168646564778547404964968127839-d4905000000529400--2-9139233430221224000048----92a70182064005617064000000250900430069--735----------ca429305302813683595057465686104-0062004400430371710571296--60503020041955917717-------------------ca--------- >P1;d6y04a- ---------------------------------------5799658758787679737959a4793054------4000000729406a303921a0884203212530020324a5---4b005401600582906202000047081392408641673587--------------a587a5187749733550---36-08414710550050035065038------a0100010020670814613726--------------------------- >P1;d7coia- --------------------------------------96778746577777456517767-6924663897490620000042a503--13812a364340221214000026----a2a70482045005615063010000160b003300778--82----------ca4552061036029635a4077-17686103300110045014100211100401561-90613010040a5591480b1947-----------8933680296449-- Translating the sequences *****************************************---HHHHHHHHHHHHH***C-C**********CCCEEEEEECCCCCC--HHHH*CCCCCCEEEEEECCCCCCC----**HHHHHHHHHHHHCCCCCEEEEEEECCCHHH*******--**----------**********HHHHH**HHH**C*****HH****HHHHHHHHHHHHH*C***********CCEEEEEEECCCCCC*EE******--*--*****---------------- ----------------------------------------**HHHHHHHHHHHHHH****C-***********CCCEEEEEECC***C--HHHH*CCCCCCEEEEEE***CCCC******HHHHHHHHHHHHCCCCCEEEEEEECCCHHH***H***-**-*-----**************HHHHH**HHH**C*-***HH****HHHHHHHHHHHH**C**********-CCEEEEEEE*CCCC*EEE***---****-------******--------- ------------------------------------------------*HHHHHHHH**--*C********-*CCCEEEEEECC***C**HHHH*CCCCCC*EEEEECCCCCC-------HHHHHHHHHHHH**CCCEEEEEEECCC******H**********--------------***HHHHH**HHH*---*---**-***HHHHHHHHHHHHH*C*****------CCEEEEEEECCCCCCEEE*****--------------------------- ----------------------------------------**HHHHHHHHHHHHH**--*C*C******------CEEEEEECCCCCC--HHHH*CCCCCCEEEEEECCCCCC-------HHHHHHHHHHHHCCCCCEEEEEEECCCHHH***H*************-------------------*******C**--------*HHHHHHHHHHHHH*C*****------CCEEEEEEECCCCCCEEE***----------------------------- -----------------------------------------*HHHHHHHHHHHHHHH***C-****-------CCCEEEEEECCCCCC---HHH*CCCCCCEEEEEE***CCCC----**HHHHHHHHHHHHCCCCCEEEEEEECCCHHH***H********-----**************HHHHH**HHH**C*****HH****HHHHHHHHHHHH**C**********-CCEEEEEEECCCCCCEEE******--****-------------------- -------------------------------------*****HHHH**-HHHHHHHH*-*C*C******------CEEEEEECCCCCC--HHHH*CCCCCCEEEEEECCCCCC-------HHHHHHHHHHHHCCCCCEEEEEEECCCHHH***H*******-*****-------------------*******C**--------*HHHHHHHHHHH*-*C*****--------EEEEEEECCCCCC***-------------------------------- -----------------------------------------*HHHHHHHHHHHHHHH***C-C**********CCCEEEEEECCCCCC--HHHH*CCC***EEEEEECCCCCCC----**HHHHHHHHHHHHCCCCCEEEEEEECCCHHH***H***--**----------**********HHHHH**HHH**C*-***HH****HHHHHHHHHHHHH*C***********CCEEEEEEECCCCCCEEE******--*********************--- --------------------------------------****HHHHHHHHHHHH*HH*-*C---*****------CEEEEE*-CCCCC--HHHH*CCCCCCEEEEE*CCCCCC-------HHHHHHHHHHHH*CCCCEEEEEEECCC*-****H******************************HH**HHH**C**---HH*******-*HHHHHHHH*C*****------CCEEEEEEECCCCCCEE********-------------************ --------------------------------------***-*HHHHHHHHHHHHHH***C-C**********CCCEEEEEECCCCCC--HHHH*CCCCCCEEEEEECCCCCCC----**HHHHHHHHHHHHCCCCCEEEEEEECCCHHH***H*******----------**********HHHHH**HHH**C-****HH****HHHHHHHHHHHHH*C***********CCEEEEEEECCCCCCEEE******--************************ ------------------------------------------*HHHHHHHHHHHH*H***C-***********CCCEEEEEECCCCCC--HHHH*CCCCCCEEEEEECCCCCCC*-*****HHHHHHHHHHHCCCCCEEEEEEECCCHHH**********-*-------************HHHHH**HHH**C*-***HH****HHHHHHHHHHHH**C**********-CCEEEEEEE*CCCC*EEE***************************----- ----------------------------------********HHHHHHHHHHHHHHH*****C*******-**CCCEEEEEECCCCCC--H-HH*CCCCCCEEEEEE***CCCC----**HHHHHHHHHHHHCCCCCEEEEEEECCCHHH***H**--***----------**********HHHHH**HHH**C*****HH**-*HHHHHHHHHHHHH*C*********--CCEEEEEEECCCCCCEE***-------------------**--------- ---------------------------------------***HHHHHHHHHHHHHH****C*C******------CEEEEE*CC***C**HHHH*CCCCCCEEEEE*CCCCCCC***---*HHHHHHHHHHHCCCCCEEEEEEECCC******H**********--------------***HHHHH**HHH*****---**-***HHHHHHHHHHHHH*C*****------CC*EEEEEECCCCCCEEE*****--------------------------- --------------------------------------****HHHHHHHHHHHHHHH***C-C**********CCCEEEEEECCCCCC--HHHH*CCCCCCEEEEEE***CCCC----**HHHHHHHHHHHHCCCCCEEEEEEECCCHHH***H***--**----------**********HHHHH**HHH**C-****HH****HHHHHHHHHHHHH*C**********-CCEEEEEEECCCCCCEEE******-----------*************-- 53056.tem _________________________________ --------------------------------------****HHHHHHHHHHHHHHH***C*C**********CCCEEEEEECCCCCC--HHHH*CCCCCCEEEEEECCCCCCC----**HHHHHHHHHHHHCCCCCEEEEEEECCCHHH***H**********-------**********HHHHH**HHH**C*****HH****HHHHHHHHHHHHH*C**********-CCEEEEEEECCCCCCEEE******--**-*-----**********----- Structural block scores 0 37 - 4.8 H 7.2 75.0 75.0 75.0 75.0 73.3 75.0 75.0 75.0 75.0 67.9 75.0 75.0 38 41 * 3.0 P 25.1 42.1 75.0 41.8 58.5 8.4 58.9 8.9 24.9 75.0 6.9 24.0 7.2 42 56 H 4.7 H 14.8 5.8 34.3 7.4 6.1 11.1 6.2 5.6 6.3 6.7 5.4 6.8 5.7 57 59 * 1.7 P 5.7 5.3 30.0 53.0 7.3 31.5 7.3 28.7 6.3 5.3 6.3 7.0 6.7 63 72 * 2.0 P 5.1 6.0 11.6 33.4 54.1 33.2 6.5 39.1 5.7 5.5 13.1 32.8 5.8 73 75 C 4.6 H 4.3 4.3 3.0 51.3 5.2 52.0 4.0 51.3 4.7 4.0 4.7 51.3 5.0 76 81 E 4.9 H 0.0 0.5 0.2 0.2 0.0 0.2 0.2 0.0 0.5 0.5 0.0 0.0 0.3 82 87 C 4.7 H 4.3 4.6 4.7 5.1 4.2 4.9 3.8 15.7 4.1 4.6 3.3 4.7 4.1 88 89 - 4.6 H 75.0 75.0 5.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 6.8 75.0 90 93 H 4.9 H 2.0 4.0 2.5 3.2 21.0 3.2 3.0 2.5 3.8 3.2 21.8 3.5 3.2 95 100 C 4.9 H 5.8 4.7 6.0 4.9 5.8 5.4 6.8 4.7 4.2 4.0 4.0 5.4 5.1 101 106 E 4.9 H 1.7 1.7 2.0 1.8 1.8 1.8 1.7 1.8 1.2 1.3 1.5 2.2 1.3 107 113 C 4.5 M 1.7 1.3 12.4 11.9 2.1 12.1 1.7 12.9 2.0 1.1 2.3 1.4 1.7 114 117 - 4.5 M 75.0 5.8 75.0 75.0 75.0 75.0 75.0 75.0 75.0 23.2 75.0 23.6 75.0 118 119 * 2.9 P 5.5 3.0 75.0 75.0 6.0 75.0 5.5 75.0 5.0 7.8 5.5 75.0 6.2 120 131 H 5.0 H 3.3 3.9 3.3 3.3 3.6 3.5 3.3 2.7 3.3 4.2 3.6 3.0 3.8 132 136 C 4.9 H 3.8 3.6 5.0 4.4 4.2 3.8 2.8 4.2 3.8 3.8 4.0 5.0 3.6 137 143 E 5.0 H 0.9 0.3 0.4 0.9 0.4 0.9 0.4 0.7 0.6 0.6 0.6 0.6 0.6 144 146 C 5.0 H 3.0 1.7 4.3 4.0 1.7 3.7 3.3 2.0 2.3 2.0 2.3 3.7 2.3 147 149 H 4.4 M 3.0 3.7 2.0 3.7 3.5 3.7 3.0 28.3 2.7 3.0 3.0 4.0 3.8 150 152 * 1.0 P 3.3 2.7 5.7 5.7 2.0 5.0 2.3 4.3 2.0 1.3 2.3 5.0 2.0 154 163 * 2.2 P 41.5 33.1 5.3 6.0 18.8 12.0 40.5 4.9 26.9 26.6 40.5 5.5 40.7 164 170 - 4.3 M 75.0 35.1 75.0 46.0 36.5 45.9 75.0 5.4 75.0 55.6 75.0 75.0 75.0 171 180 * 2.4 P 4.3 3.4 54.5 75.0 4.2 75.0 4.7 5.7 4.5 3.4 4.9 54.9 4.6 181 185 H 4.5 M 3.6 3.8 5.4 75.0 2.6 75.0 4.6 4.8 3.6 3.4 4.0 6.3 4.0 186 187 * 1.0 P 4.0 2.5 5.0 3.5 3.5 6.2 2.5 2.5 5.0 2.0 5.5 7.0 4.5 188 190 H 4.6 H 6.5 6.0 5.7 7.5 6.7 6.3 5.8 3.3 6.5 5.3 6.3 6.7 6.5 191 192 * 1.2 P 3.5 4.0 39.5 1.0 3.5 3.0 3.5 2.0 4.0 4.0 2.5 3.0 3.5 194 198 * 2.6 P 6.7 19.6 60.0 46.6 6.4 47.0 19.4 46.6 20.7 21.5 5.8 46.0 19.4 199 200 H 4.3 M 4.0 3.0 6.0 75.0 3.5 75.0 3.5 2.0 3.5 4.5 3.5 4.5 3.5 201 204 * 1.9 P 1.5 2.0 21.8 57.8 2.2 57.8 2.2 5.8 2.0 2.8 19.8 21.8 1.5 205 217 H 4.8 H 1.5 1.7 2.7 3.0 1.5 8.7 0.2 8.1 1.1 1.1 2.0 2.4 1.3 220 229 * 2.0 P 4.1 3.6 40.1 39.9 3.3 39.5 4.0 39.5 3.9 4.1 11.3 39.7 1.9 231 232 C 4.8 H 4.5 3.5 4.5 4.5 3.5 75.0 4.5 3.0 4.0 3.0 3.0 5.2 4.5 233 239 E 5.0 H 0.9 1.3 0.3 1.4 1.3 2.1 0.6 2.4 0.3 0.6 1.4 0.3 1.6 240 245 C 4.9 H 6.1 4.8 4.2 4.7 4.5 5.0 5.4 3.3 5.6 4.7 5.5 3.8 5.6 246 248 E 4.6 H 4.3 4.3 4.0 4.0 4.0 3.3 3.0 2.7 4.0 1.3 5.0 3.7 4.3 249 254 * 2.2 P 4.8 39.0 16.4 39.7 2.2 75.0 2.3 4.7 3.3 3.2 51.3 15.7 5.4 255 256 - 4.5 M 75.0 5.5 75.0 75.0 75.0 75.0 75.0 42.0 75.0 3.5 75.0 75.0 75.0 257 258 * 3.7 M 40.5 7.0 75.0 75.0 6.0 75.0 6.0 75.0 3.0 5.5 75.0 75.0 75.0 261 265 - 4.2 M 22.0 75.0 75.0 75.0 75.0 75.0 2.6 75.0 3.4 4.9 75.0 75.0 75.0 266 275 * 3.7 M 75.0 35.6 75.0 75.0 75.0 75.0 4.2 27.5 5.0 5.0 62.3 75.0 5.4 276 280 - 4.4 M 75.0 75.0 75.0 75.0 75.0 75.0 45.6 9.4 9.7 75.0 75.0 75.0 33.4 >>>>>>