Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1f7ua1 -CCHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCHHHCCCHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHHHHH-HHHH-HHH-------HCCCC-----CCC--HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d1ffya1 ---CHHHHHHHHHHHHCCCCCCHH-HH----CCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHIIIIIIHHH---------HHHHHHCCCCCCC-HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCC----CCCCHHHCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHEEEEEECCCCCCHHHHHHHCCCHHHHCCCCEEEECCCCCCCCEEE--CCEEEEEEECCCEECCCCCCEECCCEEECCEEEECHHHHHHHHCCC >P1;d1h3na1 --CHHHHHHHHHHHHHHHHCCCC--------CCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH---------H----------------CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCC-------CCHHHHCCCC-----CCHHHHC--------------------------------------------------------------------------------------------------------------------------- >P1;d1ilea1 --CHHHHHHHHHHHHHHHHHHCCCCCC----CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHH---------HHHHHHHCCC-CC-CCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCC------------------------------------------------------------------------------------------------------ >P1;d1iq0a1 CCCHHHHHHHHHHHHHHHHHHCCCC-----CCCHHHC-CHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHHHHH-HHHH-HHHCEECCEECCCCC-----CCC--CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC-------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d1ivsa2 ---CHHHHHHHHHHHHHCCCCC---------CCCC-CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHIIIIIHHH---------HHHHHHHCCC-------HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHC------CCCHHHCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHC----CCCCCCCEEEEEE-----CCHHHHH--CHHHHHHHHCCEECCCCCCCCEEEECCCEEEEECC-CCCC-------------------------------- >P1;d1pfva1 ------CHHHHHHHHHHHHHHC-----CCCCCC--C-CC--CHHHHHHHHHCHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------HHCHHHHCCCC---CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCC---CCC-CHHHH--CCCC-CCCCC--CCC---CCCCCCCHHHHHHHHHHHCC---------------------------------------------------------------------------------------------------- >P1;d1rqga1 ---CCCHHHHHHHHHHHHHHCC-----CCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------CCCHHHHCCC------CHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCC-----CC-CCCCCCCCCCC--CCC---CCCCCCCHHHHHHHHHHCCCCCCHH---------HHHHHHHHHCCHHHHHHHHHHHHC--------------------------------------------------CCHHHHHHHCCC >P1;d1u0bb1 --------------------------------------------CHHHHHHHCCCCCCCCCCCC-HHHHHHHHHHHHCC---------------------------CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHCCC---------------------------------------------CCCCCCCCCCHHHHHCCCHHHHHHHHCCCCCEEEEECCCEEEEEC----------------------------------------------- >P1;d2ct8a2 --CCCCHHHHHHHHHHHHHHHC-----CCEECCC------CCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-HHHH-HHH-------HHCHHHHCCC--C-CHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC---CCCCCC--CCCCCC-CEECC-----CCCCCCCCCC----------------------------------------------------------------------------------------------------------------C >P1;d2d5ba1 --CCCCCHHHHHHHHHHHHHHC-----CCCCCCCCC-----CHHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------HHCHHHHCCC----CHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCC--CCHHHHHCCCCC-CCCCCC--C--CCCCCCCCC------------------------------------------------------------------------------------------------------------------ >P1;d3kfla2 ---CCCHHHHHHHHHCC--CCC----CCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------HHCHHHHCC----CCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHCCCHHHCC-CCCCCCCCCCC--CCCCCCCCCCCCCCC--------------------------------------------------------------------------------------------------------------- >P1;d4qrea2 --CCCHHHHHHHHHHHHHHHHH-----CCEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------HHCHHHHCCC--HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCHHHHCHHHHCCCCCCCCCEECC--C--CCCCCCC-------------------------------------------------------------------------------------------------------------------- >P1;d5xgqa2 ---CCCCHHHHHHHHHHHHHHC-----CCCCCCCCC-CCHHHHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------HHCHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHCC-HHHCC--CCCCCCCCCC--CCC---CCCCCCCCC--------------------------------------------------------------------------------------------------------------- PSA >P1;d1f7ua1 -576730260012025203828d16795199055730748205504711a516914751874857610460016005-1026-038-------60705-----c28--862110000000501510350065184904575-------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d1ffya1 ---474137008301910830417-71----4154960330030000102300340270175855860764047004610270004---------0042005114673-521000020014001100100044259004500670241----94b20380931945--a245900630530260171045005503769408521201010021b627018207609414000300306247919b80751--71010105404274052061127806409a665005302801646a >P1;d1h3na1 --26b405600360494058172--------9182b719b3175013400610440350274755a40361058006-1016-027---------6----------------35013001100320000013123a20370041008-------740861b30a-----2378118--------------------------------------------------------------------------------------------------------------------------- >P1;d1ilea1 --26a2056016103721772707159----2244860093040000000200740481388a36760472056002101522006---------1056006612-74-65220000000300200010014234a103500460036237836720461a3291587345a820581564177267686859a97b------------------------------------------------------------------------------------------------------ >P1;d1iq0a1 b76463015000202211470aa19-----9348943-483087056407619713641776837720561026005-2028-047266ba7510303-----907--a113110031035016103600842a3813683-------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d1ivsa2 ---5830560053025237b18---------6655-64210050030200310750472287955840473075004410051003---------0030207600-------21014002500220010023244a20370045039------586048293093b--8638812630500110040043007709----0696581501037-----3170067--24710330040321794086034273750201004-8aa0-------------------------------- >P1;d1pfva1 ------127005200a302931-----a04017--8-13--36a207501611a50370185866850473046007-4035-006-------6420540175c---4695023000000000000000035447700640280042---706-38206--7113-52504--619---50689867875778678579---------------------------------------------------------------------------------------------------- >P1;d1rqga1 ---3840050042003102623-----a1500825a-2592065025108600750451387856940471045003-1016-006-------5150472088------83000000000000000000043156900540050040b3924-----38-15506272805--917---502868474740350036507b836---------70363015518594046005642a--------------------------------------------------c049107300aa >P1;d1u0bb1 --------------------------------------------455004002b0539493680-7912740580177a---------------------------8547605600450073037129665850120010015004617207671662026a---------------------------------------------bcbb6809477057228679506724805560304269c252227----------------------------------------------- >P1;d2ct8a2 --62850050013004003701-----a060647------5088018407710740472187757930331056003-2026-007-------8350420485--7-38a6034000000000000000044423930650070041a---822a71--61034a-50705-----8446015789----------------------------------------------------------------------------------------------------------------f >P1;d2d5ba1 --46930040073015003500-----914008238-----05604-901910760451595846830483026004-4027-006-------6350352366----5394031000000000000000037425a3032005103065a--064600361130-634603--9--918701499------------------------------------------------------------------------------------------------------------------ >P1;d3kfla2 ---18200500420037--910----485302815a-3696059016405901b40573275636840361035106-5018-006-------712047218----8598211000000000000000002533673064004003058a118778026-13209262607--116ac6402968a99--------------------------------------------------------------------------------------------------------------- >P1;d4qrea2 --57a30160054005102711-----a060221524319309a017304702730670186865950371027005-1025-006-------4040571285--b84672000000000000000000043139900720060040867622566108a00207942602--6--a16701a-------------------------------------------------------------------------------------------------------------------- >P1;d5xgqa2 ---2840160035005003731-----83500817a-35b5067007404802840693377815740360037005-6038-106-------6150361273a4a9435303000000000000000002433592036006003177a618-4910b--8307362804--818---901888968--------------------------------------------------------------------------------------------------------------- Translating the sequences -*****HHHHHHHHHHHHH**C*********CC****CC**HHHHHHHH**HHHHHHHHHH*CCHHHHHHHHHHHHH-HHHH-HHH-------*****-----***--**HHHHHHHHHHHHHHHHHHHH***C*******-------------------------------------------------------------------------------------------------------------------------------------------------------------- ---***HHHHHHHHHH*****C**-**----CCC***CC**HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH******HHH---------*HHHH********-*HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH***CC*----****H***CCCC**--*CC********************************************************************************--********************************************** --****HHHHHHHHHHHHH**C*--------CCC***CC**HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH---------*----------------****HHHHHHHHHHHHHHCCCCHHHHHHHH***CC-------**H***CCCC-----CC*****--------------------------------------------------------------------------------------------------------------------------- --****HHHHHHHHHHHHH**C*****----CCC***CC**HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH*H*****HH---------*HHHH*****-**-****HHHHHHHHHHHHHHHHHCCCC**HHHHHHHH*CC*********H***CCCC*****CC**************************------------------------------------------------------------------------------------------------------ ******HHHHHHHHHHHHH**C***-----*CC****-C**HHHHHHHH**HHHHHHHHHH*CCHHHHHHHHHHHHH-HHHH-HHH************-----***--**HHHHHHHHHHHHHHHHHHHH**CC*******-------------------------------------------------------------------------------------------------------------------------------------------------------------- ---***HHHHHHHHHHH****C---------CCC*-*CC**HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH******HHH---------*HHHH*****-------HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH**C------***H***CCCC**--*CC*************************----*************-----*******--***********************************-****-------------------------------- ------*HHHHHHHHHHHH**C-----****CC--*-CC--*HHHHHHHHH*HHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------***HHHH****---***HHHHHHHHHHHHHHHHHHH*CCCCHHHHHHHHHH*CC---***-**H**--CCC*-***CC--***---********************---------------------------------------------------------------------------------------------------- ---***HHHHHHHHHHHHH**C-----****CCC**-CC**HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------***HHHH***------*HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH*CC*****-----**-CCCC*****CC--***---*************************---------************************--------------------------------------------------************ --------------------------------------------*HHHHHHH*********CCC-HHHHHHHHHHHH**---------------------------****HHHHHHHHHHHHHHHHH*******HHHHHHHHHH**C*********H***CC---------------------------------------------*********************************************----------------------------------------------- --****HHHHHHHHHHHHH**C-----****CCC------**HHHHHHHHHHHHHHHHHH*CCCHHHHHHHHHHHHH-HHHH-HHH-------***HHHH***--*-***HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH*CC*---******--*CCCC*-***CC-----**********----------------------------------------------------------------------------------------------------------------* --*****HHHHHHHHHHHH**C-----****CCC**-----*HHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------***HHHH***----***HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH*CC***--****H***CCCC-****CC--*--*********------------------------------------------------------------------------------------------------------------------ ---***HHHHHHHHH**--**C----*****CCC**-CC**HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------***HHHH**----****HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH*CC*********H**-CCCC*****CC--***************--------------------------------------------------------------------------------------------------------------- --****HHHHHHHHHHHHH***-----****CCC***CC**HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------***HHHH***--*****HHHHHHHHHHHHHHHHHHHHCCCC**HHHHHHHH*CC*********H***CCCC*****CC--*--*******-------------------------------------------------------------------------------------------------------------------- ---****HHHHHHHHHHHH**C-----****CCC**-CC**HHHHHHHHH*HHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------***HHHH**********HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH*CC******-**H**--CCC*****CC--***---*********--------------------------------------------------------------------------------------------------------------- 47323.tem _________________________________ --****HHHHHHHHHHHHH**C*----****CCC***CC**HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHH-HHH-------***HHHH**********HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH*CC*********H***CCCC*****CC--***********************------------------------------------------------------------------------------------------------------- Structural block scores 0 1 - 4.7 H 40.0 75.0 75.0 75.0 9.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 2 5 * 2.2 P 5.8 22.5 5.9 5.1 4.8 22.8 75.0 22.5 75.0 5.2 5.5 21.5 6.4 22.2 6 18 H 4.7 H 1.8 3.2 3.2 3.0 1.4 2.9 2.5 1.3 75.0 1.2 1.8 13.2 1.8 1.8 19 20 * 1.4 P 5.0 1.5 4.5 4.5 3.5 6.2 6.0 4.0 75.0 3.5 2.5 5.0 4.0 5.0 23 26 - 4.3 M 5.8 22.5 75.0 5.5 40.0 75.0 75.0 75.0 75.0 75.0 75.0 57.2 75.0 75.0 27 30 * 3.0 P 6.0 75.0 75.0 75.0 58.5 75.0 3.6 4.1 75.0 4.1 3.5 4.0 4.1 4.0 31 33 C 4.7 H 3.3 3.3 6.0 2.7 5.0 5.7 27.7 3.3 75.0 5.7 3.3 3.7 1.7 3.0 34 36 * 2.5 P 3.3 6.3 6.8 6.0 5.3 28.7 52.7 30.2 75.0 75.0 28.7 30.2 3.7 30.8 37 38 C 4.5 M 5.5 1.5 5.0 0.0 39.5 3.0 2.0 3.5 75.0 75.0 75.0 4.5 2.0 4.0 39 40 * 2.3 P 5.0 1.5 7.2 6.0 5.5 0.5 75.0 5.5 75.0 40.0 75.0 7.5 6.0 8.2 41 60 H 4.8 H 4.4 1.6 2.6 2.0 4.5 2.5 3.9 3.3 14.5 3.9 7.3 4.0 3.8 3.9 61 63 C 4.9 H 5.7 6.0 5.3 7.2 5.7 7.0 6.3 6.7 4.7 6.3 5.7 4.7 6.7 5.3 64 76 H 5.0 H 2.8 3.9 3.7 3.5 3.2 3.6 3.8 3.3 9.7 3.1 3.4 3.3 3.4 3.1 78 81 H 4.3 M 2.2 2.5 2.0 2.0 3.0 1.5 3.0 2.0 58.9 2.5 3.2 3.5 2.0 4.2 83 85 H 4.7 H 3.7 1.3 3.0 2.0 3.7 1.0 2.0 2.0 75.0 2.3 2.0 2.0 2.0 2.3 86 92 - 4.8 H 75.0 75.0 75.0 75.0 6.9 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 93 95 * 2.3 P 4.3 50.0 52.0 50.3 1.3 50.0 4.0 3.7 75.0 5.3 4.7 3.3 2.7 4.0 96 99 H 4.5 M 38.8 1.5 75.0 2.8 38.2 1.2 2.2 3.2 75.0 1.5 2.5 3.2 3.2 2.5 100 109 * 3.0 P 41.1 10.7 75.0 18.2 40.2 38.8 26.9 47.4 47.4 27.1 33.2 33.9 20.1 5.8 110 129 H 4.9 H 1.2 0.7 8.4 0.8 1.8 8.5 0.5 0.1 3.5 0.7 0.4 0.2 0.1 0.3 130 133 C 4.5 M 5.0 2.5 1.8 2.5 6.1 2.8 4.0 3.2 4.5 3.5 4.0 3.2 2.8 3.0 134 143 H 4.5 M 25.9 3.6 3.0 3.4 25.7 3.5 3.4 2.9 1.0 3.3 3.0 3.0 3.3 3.1 145 146 C 4.6 H 75.0 3.0 4.0 1.5 75.0 6.0 3.0 2.0 5.0 2.5 1.5 1.5 2.0 2.0 147 155 * 2.9 P 75.0 36.4 59.6 4.9 75.0 52.1 36.0 36.6 4.1 29.4 20.8 6.2 5.3 14.2 157 159 * 2.4 P 75.0 3.7 5.0 3.7 75.0 4.7 27.0 28.7 1.3 52.0 3.0 27.7 6.2 28.8 160 163 C 4.5 M 75.0 5.5 6.2 6.1 75.0 5.2 21.0 2.8 41.6 2.0 1.2 1.5 0.5 21.5 164 168 * 2.9 P 75.0 33.9 75.0 4.8 75.0 34.5 18.0 5.0 75.0 19.5 18.8 5.0 5.6 5.2 169 170 C 4.5 M 75.0 3.0 2.5 4.5 75.0 4.5 2.0 2.5 75.0 2.5 1.5 3.5 1.0 2.0 171 172 - 4.2 M 75.0 7.0 7.5 9.2 75.0 8.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 173 195 * 3.3 M 75.0 2.4 65.7 5.6 75.0 2.3 15.3 13.4 75.0 44.7 44.9 30.2 50.7 39.1 196 298 - 4.5 M 75.0 4.9 75.0 74.4 75.0 34.0 73.0 44.9 44.5 74.5 75.0 75.0 75.0 75.0 >>>>>>