Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1u9ya1 ---------------------------------------------------------------CEEEEC-CCCHHHHHHHHHHC---CCCEECEEEEECCCCCEEEEEC--CCCC-----------CCEEEEECCCC-CHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCC-CC----CCCHHHHHHHHHHH-HCCEEEEEC-CCCHHHHHHCCCCEEEECCHHHHHHHHCCC-CC------- >P1;d1u9ya2 --------------------------------------------------------------CCEEEECCHHHHHHHHHHHHHH---CCCEEECC----------CCCC-CCCCC-----------CCCEEEEEEECC----CCHHHHHHHHHHHHCCCCCEEEEEEECCCC-------------------CCHHHHHHHHCCCEEEEECCCCC-------C-CEE-ECCHHHHHCCC------------- >P1;d1vcha1 CCEEEEECCEEEEECEEEEECCEEEECCCCCCCHHHHHHHHHHHHHHCCC-----------CCCEEEEECCCHHHHHHHHHHHH---CCCEEEECCCCCCCCCCCEEEECCCCEEEECHHHHHHHCCCEEEEEEEEEC----CCHHHHHHHHHHHHCCCEEEEEEEEEEC-CCCCCC-----CEEEEECCCC----------------------------------------------------------- >P1;d1vdma1 -----------------C-----CEEECC----HHHHHHHHHHHHHHHH-HH---------CCCEEEEECCCCHHHHHHHHHHCC--CCCEEEEEEECCC----CCCCCCCEEEECCC-C---CCCCCEEEEEEEEEC----CCHHHHHHHHHHHCCCCCEEEEEEEEECC-CCCCCCC----CCCEEC--C------------CEEECCCCC-------------CC------------C------CCCC >P1;d2h06a2 -----------------------------------------------------------CHHHCEEEECCHHHHHHHHHHHHHH---CCEEEEEEECC-----CCEEEE--CCCC-----------CEEEEEEEEEEC----CCHHHHHHHHHHHHCCEEEEEEEEEEECCC-------------------CCHHHHHHHCCEEEEEEECCCCCHHHHHHCC-CEEEECCHHHHHHHHHHHHHCCCCHHHC >P1;d3lrta1 ---------------------------------------------------------------CEEEEC-HHHHHHHHHHHHHC---CCCEECCEEEECCCCCEEEECC--CCCC-----------CCEEEEECCCC-C-HHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCC-CC----CCCHHHHHHHHHHH-CCCEEEEEC-CCCHHHHHHCCCEEEEECCHHHHHHHHCCCCCC------- >P1;d3lrta2 ----------------------------------------------------------------CEEECCCCCHHHHHHHHHHH---CCCEEEEEEEEECC-EEEEEEECCCCCC-----------CCEEEEEEEEEC----CCHHHHHHHHHHHHCCCCEEEEEEEEECCC-------------------CCHHHHHCC-CCCEEEEECCCCC-------C-CEE-ECCHHHHHHHHHHC---------- >P1;d5jsqa- -----------------CCCCCEEEEEEC----HHHHHHHHHHHHHHHHHHCHHHCCCCCCCCEEEEEECHHHHHHHHHHHHHHHHCCCCEEEEEE---------------------------CCCCCEEEEEEEEEC----CCHHHHHHHHHHHCCCCCEEEEEEEEECHHHCCCCC--CCCEEEEECC-C------------CCEECCCCCCCCCCCCCCCEEEEC------------HHHHHHHHHHC >P1;d5mp7a2 -----------------------------------------------------------CC-CEEEEECCHHHHHHHHHHHHHCC--CCCEEEEEECC------CEEEE--CCCC-----------CCEEEEEEEEEC----CCHHHHHHHHHHHHCCCCEEEEEEEEECCC-------------------CCHHHHHHHCCCCEEEEECCCCCCHHH-CCC-CEEEECCHHHHHHHHHHHHHC------C >P1;d5voga1 -----------------------CEEECC----HHHHHHHHHHHHHHCCCCC---------CCCEEEEEECCCHHHHHHHHHHH---CCCEEEEECCCCC----C-CCCCCCCCCCCC-CCCHHHCCCCEEEEEEEEC----CCHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCEEEEEEEC-C------------CEEECHHHCCCHHHHHHHCCCC------------------------- >P1;d6kp5a- ------------------------CEECC----HHHHHHHHHHHHHHCC----------CCCCCEEEEECCCCHHHHHHHHHHHCCC--CEEEEECCCCC----EECC------------------CCCEEEEEEEEC----CCHHHHHHHHHCC------CEEEEEEECC-----CCHHHCCEEEEECCCC------------CCEECHHHCC---------CCCCC------------CCC-------- >P1;d6nfea1 -------------------------------------------------------------CCEEEEEC-CCCC-CHHHHHHHH---CCCCCCEEEEECCCCCEEEEEC--CCCC-----------CCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCHHHCC----CCCHHHHHHHHHHHCCCCEEEEEC-CCCHHHHHHCCCCEEEECCHHHHHHHHHHCCCC------- >P1;d6nfea2 --------------------------------------------------------------CEEEEECCHHHHHHHHHHHHCCC--CCEEEEEEC-C------CCEEE--C-CC-----------CCEEEEEEEEEC----CCHHHHHHHHHHCC-CCCEEEEEEEEECCC-------------------CCHHHHHHCCCCCEEEEECCCCCCHHHHCCC-CEEEECCHHHHHHHHHHHC--------- PSA >P1;d1u9ya1 ---------------------------------------------------------------410010-11078505630794---a293060226359787030503--4a0b-----------45401000208-75840160044009303948074010101700407527467-9c----48150471075019-204303045-162560472091505375575887774885-8c------- >P1;d1u9ya2 --------------------------------------------------------------920000067b038405720984---a0630105----------5505-82807-----------724020114404----707600400630383606503010440207-------------------b8018404705055020143591-------9-107-65279767889------------- >P1;d1vcha1 b4340409a233615145368a551040504c287005100420463028-----------50400000152132005200822---9252010337535a0681041808654020237406506935000021104----6013040025006507070212000042-8a1b09-----0602440334----------------------------------------------------------- >P1;d1vdma1 -----------------8-----a33307----5640350056007605-81---------80300000070033005301710b--816133000322a----ab709814244408-b---706743000011203----70630520272067270551200000002-5061604----223261--6------------57000114a-------------66------------8------97ab >P1;d2h06a2 -----------------------------------------------------------758900000045b05a403540883---a0450103447-----680407--5706-----------820010013515----503501600730483305302040440406-------------------950364039130400201334807903880b-20726516556733851886a5636718 >P1;d3lrta1 ---------------------------------------------------------------420000-51047504630794---9263060726449788030605--4705-----------74403000206-5-a3115003300630681a062110201500407215558-cb----36110371044004-506402034-06465027106280405548a8668857a4a6b------- >P1;d3lrta2 ----------------------------------------------------------------1000055924a404630775---a68402032667aa-8240715691908-----------856030014405----715601400310375605403010340505-------------------c90394036-4034030133473-------7-105-54375764677797---------- >P1;d5jsqa- -----------------281a20542215----395027405a0055017408a19056a920000000470063006202710682a02034455---------------------------918822000000204----306403810561585703503000000148316391--9040200607-6------------450000002256621917100203------------57247656756 >P1;d5mp7a2 -----------------------------------------------------------c4-730000048a136405630773a--71520204358------85605--6808-----------820010016505----405501900520655906202010440304-------------------6301740271807303024248078a3-408-30416527677576867897a------c >P1;d5voga1 -----------------------752212----57205720660075084b3---------80400000083054005104521---8061230206477----4-7c5960367017-9038805642000011204----424203300620473606200000001063b17012ab0321004507-5------------370200181a749505630776------------------------- >P1;d6kp5a- ------------------------54406----6950561055006405----------8351800000192054009101810a19--73330209537----541d------------------904200011204----80b4071038105------0300000003-----504730332026073b------------2802003538---------b7997------------7aa-------- >P1;d6nfea1 -------------------------------------------------------------b7310010-5056-408831794---828217040556b778130705--2a08-----------8320200000396388006001300340375605500010160030731745976a----463204500640582505303045-0634904a20b050505646697676786597c------- >P1;d6nfea2 --------------------------------------------------------------740000067b03a506440464c--816202026-8------52506--7-16-----------923010013405----50790160092046-906103040340406-------------------a50063057140520001434808960690a-205355289766548778a--------- Translating the sequences ---------------------------------------------------------------*EEEE*-***HHHHHHHHHH*---CCCEE*EE**************--CCCC-----------CCEEEEE****-******HHHHHHHHHHH*CCCCEEEEE****CCC*******-**----**************-****EEE*C-CCC*******C*CEE***************-**------- --------------------------------------------------------------C*EEEE*C***HHHHHHHHHH*---CCCEEE**----------****-*CCCC-----------CC*EEEEEEE*C----CCHHHHHHHHHHH*CCCC*EEEEEEE*CCC-------------------C*************EEE*C*CCC-------C-CEE-***********------------- **************************************************-----------*C*EEEE*C***HHHHHHHHHH*---CCCEEEE*****************CC*************CCEEEEEEEEEC----CCHHHHHHHHHHH*CCC*EEEEEEEEEC-C*****-----*********C----------------------------------------------------------- -----------------*-----******----****************-**---------*C*EEEE*C***HHHHHHHHHH**--CCCEEEEE*****----**************-*---***CCEEEEEEEEEC----CCHHHHHHHHHHH*CCCCEEEEEEEEECC-*******----******--C------------*EEE*C*CC-------------**------------*------**** -----------------------------------------------------------*****EEEE*C***HHHHHHHHHH*---CC*EEEEE***-----******--CCCC-----------C*EEEEEEEEEC----CCHHHHHHHHHHH*CC**EEEEEEEEECCC-------------------C*************EEE*C*CCC*******C-CEE************************* ---------------------------------------------------------------*EEEE*-***HHHHHHHHHH*---CCCEE**E**************--CCCC-----------CCEEEEE****-*-****HHHHHHHHHHH*CCCCEEEEEE***CCC*******-**----**************-****EEE*C-CCC*******C**EE******************------- ----------------------------------------------------------------*EEE*C***HHHHHHHHHH*---CCCEEEEE******-*********CCCC-----------CCEEEEEEEEEC----CCHHHHHHHHHHH*CCCCEEEEEEEEECCC-------------------C********-****EEE*C*CCC-------C-CEE-**************---------- -----------------************----*****************************C*EEEE*C***HHHHHHHHHH****CCCEEEEE*---------------------------***CCEEEEEEEEEC----CCHHHHHHHHHHH*CCCCEEEEEEEEEC********--**********-C------------**EE*C*CCC*******C**EE**------------*********** -----------------------------------------------------------**-C*EEEE*C***HHHHHHHHHH**--CCCEEEEE***------*****--CCCC-----------CCEEEEEEEEEC----CCHHHHHHHHHHH*CCCCEEEEEEEEECCC-------------------C*************EEE*C*CCC****-**C-CEE******************------* -----------------------******----*******************---------*C*EEEE*****HHHHHHHHHH*---CCCEEEEE*****----*-*****CCCC***-*******CC*EEEEEEEEC----CCHHHHHHHHHH**CCCC*EEEEEEEE*CC******************-C------------*EEE****CC*********C**------------------------- ------------------------*****----****************----------***C*EEEE*C***HHHHHHHHHH****--CEEEEE*****----****------------------CC*EEEEEEEEC----CCHHHHHHHHH**------*EEEEEEECC-----***************C------------**EE****CC---------C****------------***-------- -------------------------------------------------------------*C*EEEE*-****-*HHHHHHH*---CCC***EE**************--CCCC-----------CCEEEEE****C******HHHHHHHHHHH*CCCCEEEEEE***CCC**********----*******************EEE*C-CCC*******C*CEE******************------- --------------------------------------------------------------C*EEEE*C***HHHHHHHHH***--CC*EEEEE*-*------*****--C-CC-----------CCEEEEEEEEEC----CCHHHHHHHHHH**-CCCEEEEEEEEECCC-------------------C*************EEE*C*CCC*******C-CEE****************--------- 53271-3.tem _________________________________ ------------------------*****----****************------------*C*EEEE*C***HHHHHHHHHH**--CCCEEEEE******-*******-*CCCC-----------CCEEEEEEEEEC----CCHHHHHHHHHHH*CCCCEEEEEEEEECCC*******-**-********C*************EEE*C*CCC*******C*CEE******************------- Structural block scores 0 23 - 4.7 H 75.0 75.0 4.7 69.5 75.0 75.0 75.0 54.3 75.0 72.2 75.0 75.0 75.0 24 28 * 3.8 M 75.0 75.0 2.0 3.2 75.0 75.0 75.0 2.8 75.0 2.4 3.8 75.0 75.0 29 32 - 4.8 H 75.0 75.0 4.6 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 33 48 * 3.8 M 75.0 75.0 2.6 3.2 75.0 75.0 75.0 3.5 75.0 3.8 3.6 75.0 75.0 49 60 - 4.6 H 75.0 75.0 69.4 63.2 63.5 75.0 75.0 5.8 63.9 57.8 63.4 75.0 75.0 64 67 E 5.0 H 0.5 0.0 0.0 0.0 0.0 0.5 0.2 0.0 0.0 0.0 0.0 0.5 0.0 70 72 * 1.0 P 0.7 6.2 2.7 2.3 5.5 2.0 5.3 2.3 6.5 3.7 3.7 3.3 6.2 73 82 H 4.9 H 5.0 4.6 2.2 2.3 4.8 4.5 4.5 2.7 4.1 2.6 2.9 12.1 4.2 83 84 * 2.4 P 39.5 39.5 38.5 5.8 39.0 39.5 40.0 3.0 6.8 38.0 5.2 39.5 8.2 85 86 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 5.0 75.0 75.0 5.0 75.0 75.0 87 89 C 4.7 H 7.2 5.5 5.3 5.0 4.8 5.7 8.2 4.2 4.3 4.7 52.3 6.0 5.0 90 94 E 4.6 H 2.2 1.8 1.2 1.4 1.8 3.2 1.8 3.2 1.6 1.6 2.2 2.8 1.2 95 100 * 2.5 P 5.3 75.0 5.6 15.4 40.0 5.3 7.0 63.3 40.2 16.5 16.5 5.8 52.3 102 108 * 2.2 P 2.6 34.3 4.0 26.9 14.3 3.1 3.9 75.0 24.9 36.2 35.5 3.4 24.0 111 114 C 4.4 M 6.5 4.2 3.8 3.5 4.5 4.0 4.5 75.0 5.5 4.0 75.0 5.1 22.2 115 125 - 4.4 M 75.0 75.0 3.2 30.6 75.0 75.0 75.0 56.2 75.0 10.5 75.0 75.0 75.0 126 127 C 4.9 H 4.5 4.5 6.0 5.5 5.0 5.5 6.5 5.0 5.0 5.0 4.5 5.5 5.5 128 136 E 4.6 H 1.7 1.8 1.0 0.8 1.2 1.7 2.0 0.4 1.4 0.7 1.1 0.8 1.3 138 141 - 4.5 M 6.0 75.0 75.0 75.0 75.0 23.4 75.0 75.0 75.0 75.0 75.0 6.2 75.0 142 143 C 4.4 M 0.5 3.5 3.0 3.5 2.5 1.0 4.0 1.5 2.0 3.0 4.0 0.0 2.5 144 154 H 4.9 H 2.6 2.6 1.9 3.0 2.6 2.4 2.1 3.5 3.0 2.2 3.7 1.8 3.5 156 159 C 4.6 H 4.8 3.8 3.5 3.5 2.8 4.4 4.0 3.8 5.0 3.8 75.0 4.0 22.5 160 168 E 4.7 H 1.6 1.9 1.0 0.9 1.9 1.3 1.7 0.9 1.4 0.3 8.7 1.4 1.7 169 171 C 4.6 H 1.3 3.0 28.3 25.7 3.3 1.3 3.3 4.3 2.3 3.0 26.0 1.0 3.3 172 178 * 3.2 M 5.4 75.0 26.0 3.1 75.0 4.7 75.0 14.0 75.0 4.7 44.1 5.1 75.0 180 181 * 3.6 M 10.8 75.0 75.0 75.0 75.0 12.0 75.0 4.5 75.0 1.5 1.5 8.2 75.0 183 190 * 3.4 M 30.4 75.0 2.8 20.8 75.0 29.5 75.0 11.2 75.0 11.5 2.9 30.0 75.0 192 204 * 2.9 P 8.8 3.6 75.0 69.6 2.9 8.5 9.2 69.5 3.3 69.5 69.4 3.3 2.9 205 207 E 4.7 H 1.0 0.7 75.0 2.3 0.7 0.7 1.0 1.7 1.0 3.0 3.3 1.0 0.0 211 213 C 4.6 H 3.0 5.0 75.0 29.8 4.0 3.3 4.7 1.3 4.0 6.5 5.3 3.0 4.0 214 220 * 2.9 P 3.4 75.0 75.0 75.0 5.0 3.0 75.0 4.3 15.4 5.1 75.0 4.2 5.4 224 225 E 4.3 M 2.5 3.5 75.0 75.0 3.5 2.0 2.5 1.0 2.0 6.5 8.0 2.5 2.5 226 243 * 2.9 P 10.5 33.3 75.0 63.6 5.3 6.8 21.3 51.2 6.4 75.0 56.6 6.5 13.9 244 250 - 4.4 M 75.0 75.0 75.0 37.6 5.1 75.0 75.0 6.0 66.1 75.0 75.0 75.0 75.0 >>>>>>