Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1a3qa2 ------------------------------CCEEEEEECCCCCCCCCEE--C-------CCCCCCCCCCCCCCCC--------CCCCCCEEEEECCC------CCEEEEEEEECCCC----CCCCCC---CEEEEC-----------------CCCC-------------------CCCEEEEECCC-------------------CCEEECCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCC--------------------HHHHH----------------HHHHHHHHHH--C---CCCCCEEEEEEEEEEC-C---------------EECCCEECCC-EECCCCCCCC------------ >P1;d1bg1a2 --------------------CEE-EEEECCCCCCCCCEEECCCCEEEEEEECCCCHHHC---CCCEEEEEECC-------HHHCCC---------CCCCCCCEEEECCCEEECCCCCCCCCCEEEEEE-EEEEEECCCCCCCCCC----HHHCCC-----------------HHHCCCCEEEEEE---EEEC----------CEEEEEEEE-CCCCEEECCHHHHHHHHHHHHHHHHHCCCCCCCCHHH---CCCCEEHHHHH--HHHHHHHHHHCC-------CCCCHHHHHHHHHHHHCCC------------------CCCCCCEECHHHHCCCCCC---------CCCCCHHHHHHHHHHHHHHC >P1;d1eaqa- CCHHHHHCCCCCEECCCCCEEEC-CCCC----EEECCCCCC-CCCEEEECC---------------------------------------------------CCCCCCCEECCCCCCC----CCCCEE-CCEECC---------------CCEEECCCCEECCCCC------CCCCCCCEEEECC---C----------------CCEEEECCCCCEEEC---CCC----------------------------------------------------------------------------------------------------------------------------------------------- >P1;d1mnna- ----------------------------------CCEEEECCCCCEEEECCCCCCCCCCCCHHHCCCCCCCEEEE-----------ECCCEEECCCCCC----CCCEEEEEEEECCEEECCEEEEECCCCEEEEEEEECC-CCCHHHHHHCCEEECCCCEECC------------EEEEEEEEEECCCCCEECEEEECCCHHHCCEECCCCEECCCCCCCCHHHHHHCCCCCHHHHHHHHHHHEEEHHHCCH------HHCCCCCHHHHCCC--CEEECCEEEEEEEECCCCCCCCC--C---CCCCCEEEEEEEEEEE-CCCCCEEECCCCCCEEEEEEEEECCCEEEECCCHHHCHHHC-------- >P1;d1nfia2 --------------------------------CEEEEECCCCCCCCCCC--C-------CCCCCCCCCCCCCCCC--------CCCCCCEEEECCCC------CCEEEEEEEEECCC----CCCCCC---CEEECC-----------------CCC--------------------CCEEEEEECCC-------------------CCCCCCCCCEEECCCCCCHHHHCCCCCCCCCCCC---CCC--------------------CCCCC----------------C---------------CCCCCEEEEEEEEEEE-CC----------CCCEECCCCCCCCC-EECCCCC--------------- >P1;d1t4wa- -----CCEEEEEECHHHHC-CCCCEEEEECCCCCEEEEECCCCCEEEEEEEECCCCCCC---CCCEEEEEEEEECCCCCHHHHCCCCCCCCCCCHHHHHCCCCCCCCCCEEEE----CCC-CEEEEECCCCCEEEEECCC--CC-------CEEEE-EEEECCCHHHCCHHHHCCEEEEEEEEEC-----CC----------CC--EEEEEEEEEEEECC---CHHHHHHHHHHHHHHCC--------------------------------------------------------------------------------------------------------------------------------- >P1;d1uura2 ---------------CCCEEEEE-ECCCC--CEEECCCCCCCCCCEEEEECCC----------------------------------------------CCCEEEEEEEEEEEECC-----CCCCCEE-CCEECCCC------------CCCEEEC-CCEECCCC-------CCCCCEEEEEEEE---EECC----------CCEEEEECCCCCCCEEECCCCCHHHHHHHHHHHHHHCC-------------CCEEEHHHHH--HHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCC------------------C-----EEEHH------------------HHHHHHHHHHHHHHHHHHC >P1;d2as5m2 -------------------CCCCCCCCEECCEECCCCCCCCC-CCCCEE--C-------CCC-CCCCCCCCCC-------------CCCCEECCCCCCC----CCEEEEEEEEECCCC---CCCCCC--CEEEEECCC--------CCCCCCCEEEEEC----------------CEEEEEEEECHHH------------------CCEECCCCEEEEECCHHHHHCCC-------------------------------------------------------------CCCCCCC--C------CCEEEEEEEEEEE-EC----------CCEEEEE-EEEEEE-EECCC-HHHC------------ >P1;d3brfa2 -----------------------------------------------------CCCHHHHHHHHH-----------------------------CHHHH----CCEEEEECCCEEECCCCCCCCCCC---CCCEEEEECCHHHHHHHHHHHHHCCCC-------------------CEEEEEECCCC----CCCCEEECCC--------------------------------------------------CEEEEEECCCCCCCCCCCCC--------EECC----------------EEEEEECCCCEEEEEECC-----------------------CEEEECCCCCCCCCC-------------- >P1;d3d06a- ---------CCCCCCCCCCCEEECCCEEEECCCCEEEECCCCEEEEEECCCCCCC--------CCEEEEEEEECCHHHCC--------CCCCCCCCCC-----CCCCCCEEEE----CCCCCEEEECCCCCEEEEEECCCCCCC-------CCEEE-EEEECCCCCCC--CCCCCCEEEEEEEEC-----CC----------CC--EEEEEEE-EEEECC---CHHHHCCCCC---------------------------------------------------------------------------------------------------------------------------------------- >P1;d5qs9a- ----------------------------------------------------------------------------------------------------------------------------------CCEEEECCHHHHHHHHHHC--CEEECCCCCEEC------------CCCCEEEEECCCCCCEEEEEEEEEECCCCEEEEECCEEEEEE-----------------------------CCCCCCCCCCEECCCCCEEHHHHHHC--CEECCCCEEECCCCCC---------CCEECCCCCEEEEEEEEEECCCCCCCEEEEECHHH------CEEEECCCCCHHHHHHHHHHC-------- PSA >P1;d1a3qa2 ------------------------------a150505230445613024--6-------82579490010380aa--------99451010303857------84040201000479----835200---010346-----------------606b-------------------30304140769-------------------803160550204105896048302710344235a89a716--------------------98426----------------6037404722--6---8051210101010214-4---------------7609431032-0101539a05------------ >P1;d1bg1a2 --------------------603-42010583651300022835010003266446703---54070502013-------66668a---------426012305046843440117689941010205-70206348aab6477a----b56315-----------------3100002000315---0628----------b74573432-030000067573024000000003102b656416007---92340406401--600260145119-------8007895156105302687------------------a905a4705045003750a---------b4950002301730475568 >P1;d1eaqa- 9a6166627c6028071960100-5019----225165704-630100029---------------------------------------------------a176815040012964----a50706-624158---------------9420509302024508------9b43060502041---b----------------844603026403006---804----------------------------------------------------------------------------------------------------------------------------------------------- >P1;d1mnna- ----------------------------------8384771b171401001247381788383110200706516-----------6105002097757----0505020200230031894100015420000000306-2083960042101043463403------------00001020121567751902014586992765809113000190170520150150979547814930323147266------960ab800024038--550320010120101aa171539--7---9842400000000000-73e354382a2d70200100012024000126687131937-------- >P1;d1nfia2 --------------------------------70504210337624024--7-------72ca92a10203805c--------88751000305a26------35030200000368----421000---020367-----------------506--------------------30013380647-------------------5161407503030169622a70064036370002---835--------------------58606----------------9---------------a052400100020303-29----------76864a07221051-0205459--------------- >P1;d1t4wa- -----63505040258605-938400013057841000031424000205051188089---160303000011389382570041370107027613780948157000005----805-0837166990110304064--90-------73040-1010202292087823732000000001-----59----------77--21131202203017---7027225603761875b--------------------------------------------------------------------------------------------------------------------------------- >P1;d1uura2 ---------------39040405-52100--200744740968500020527b----------------------------------------------94508257405051426-----88b7305-42527168------------a740020-00203411-------9440010301060---4268----------87344150a4031000047782015000300232008c-------------7760717501--800351103017166891a8305683265015510a67------------------8-----60438------------------3067018500640265128 >P1;d2as5m2 -------------------8068627555c913042232036-514005--5-------93c-5350060489-------------8300010410769----741201000000398---824002--00003314b--------a9091a074375b----------------8130020303187------------------7041500000010254861383a-------------------------------------------------------------82a3808--8------3250400000405-3a----------7b87220-011073-01036-9519------------ >P1;d3brfa2 -----------------------------------------------------b68a88475357-----------------------------44854----4241306049502205cc445408---630103033600543567268838978-------------------8150301092b----a3a438091a--------------------------------------------------84134011650303382849--------3040----------------303030227551313609-----------------------70503666787897b-------------- >P1;d3d06a- ---------2274751926040306812106835000042440201031778039--------a0202010004498419--------7205007924-----9036000304----b2a8040456b5801000040762bb5-------81130-40101031818--910623000001002-----67----------57--3102110-103008---5096137349---------------------------------------------------------------------------------------------------------------------------------------- >P1;d5qs9a- ----------------------------------------------------------------------------------------------------------------------------------a180703548104403822--000003690550------------202020606506592302010104222b331515b6704609-----------------------------a349815b341605405260620176--40404703003684cb---------c1010134020103010334b18986443350530------200005723096057108738-------- Translating the sequences ------------------------------**********CC*C***E*--*-------****************--------**************------CC****EEE*****----C*****---CEEEE*-----------------****-------------------***EEEEEC**-------------------**E*******EE*C****HH********************--------------------*****----------------**********--*---****************-*---------------**********-**********------------ --------------------***-****************CC*C***E***********---***********-------******---------**************EEE*********C******-**EEEE**********----******-----------------*******EEEEE*---****----------******E**-****EE*C****HH***********************---***********--************-------*******************------------------*******************---------******************** ***********************-****----********C-*C***E***---------------------------------------------------*CC****EE*******----******-*CEE**---------------****************------*******EEEE*C---*----------------***E*******EE*C---***----------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------******CC*C***E***************************-----------*************----CC****EEE*******************EEEE*****-**********************------------****EEEEE***********************************C****HH**************************------**************--***********************--*---****************-*****************************************-------- --------------------------------********CC*C*****--*-------****************--------**************------CC****EEE*****----C*****---CEEE**-----------------***--------------------***EEEEEC**-------------------**********EE*C****HH**************---***--------------------*****----------------*---------------****************-**----------**************-*******--------------- -----**************-********************CC*C***E***********---*****************************************CC****EEE*----***-C********C*EEE*****--**-------*****-**********************EEEEEC-----**----------**--**E*******EE*C---*HH**************--------------------------------------------------------------------------------------------------------------------------------- ---------------********-*****--*********CC*C***E*****----------------------------------------------**********EEE****-----C******-*CEE****------------*******-********-------*******EEEEE*---****----------******E*******EE*C****HH**************-------------**********--**************************************------------------*-----*****------------------******************* -------------------*********************CC-C***E*--*-------***-**********-------------*************----CC****EEE******---C*****--**EEEE***--------*************----------------****EEEEEC***------------------**E*******EE*C****HH***-------------------------------------------------------------*******--*------*************-**----------*******-******-*****-****------------ -----------------------------------------------------************-----------------------------*****----CC****E***********C*****---C**EE**********************-------------------***EEEE*C**----**********--------------------------------------------------********************--------****----------------******************-----------------------***************-------------- ---------*******************************CC*****E*******--------*****************--------**********-----CC****EEE*----****C********CEEEE*********-------*****-***********--*********EEEEEC-----**----------**--**E****-**EE*C---*HH*******---------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------------C*EEE**************--************------------****EEEEEC***********************E*******E-----------------------------**************************--****************---------***********************************------*********************-------- 49417.tem _________________________________ ---------------********-****************CC*C***E***************************--------****************---*CC****EEE*********C******-*CEEEE**********-*******************-------*******EEEEEC**-****----------******E*******EE*C****HH**************---***-------**********--*******--***--****-*************--********************-**-----*******************-**************-------- Structural block scores 0 14 - 4.5 M 75.0 75.0 5.5 75.0 75.0 27.0 75.0 75.0 75.0 46.8 75.0 15 22 * 3.6 M 75.0 48.0 3.0 75.0 75.0 14.2 3.1 40.2 75.0 3.1 75.0 24 39 * 2.7 P 30.1 2.5 21.4 49.2 38.7 2.0 11.6 3.9 75.0 2.9 75.0 40 41 C 4.5 M 4.0 5.0 39.5 6.2 3.0 2.5 7.5 4.5 75.0 4.0 75.0 44 46 * 2.0 P 1.3 0.3 0.3 1.7 2.0 0.0 0.0 1.7 75.0 0.3 75.0 48 74 * 3.2 M 28.2 16.4 67.1 3.4 28.6 10.7 62.1 36.1 44.7 24.4 75.0 75 82 - 4.5 M 75.0 49.1 75.0 75.0 75.0 5.2 75.0 75.0 75.0 32.0 75.0 83 98 * 3.3 M 12.8 44.5 75.0 17.1 12.8 3.1 75.0 16.5 53.1 30.4 75.0 99 101 - 4.2 M 75.0 2.0 75.0 75.0 75.0 5.7 6.0 75.0 75.0 75.0 75.0 103 104 C 4.3 M 6.0 2.5 4.0 2.5 4.0 4.5 5.0 5.5 3.0 4.5 75.0 105 108 * 1.5 P 1.5 5.5 5.0 1.8 1.2 3.0 4.0 1.0 2.0 2.2 75.0 109 111 E 4.6 H 0.3 3.7 1.3 0.7 0.0 0.0 3.3 0.0 3.3 1.0 75.0 112 120 * 2.8 P 35.6 5.0 27.4 2.9 35.2 43.7 43.1 27.2 5.3 37.3 75.0 122 127 * 1.8 P 14.2 1.3 4.8 1.2 13.0 5.2 5.8 13.8 16.0 5.1 75.0 131 134 E 4.4 M 2.0 2.8 4.5 0.0 2.8 1.2 3.8 1.5 1.0 0.2 4.0 135 144 * 3.1 M 68.1 7.9 75.0 9.7 68.2 24.8 61.4 54.1 2.7 12.2 2.9 146 164 * 2.9 P 60.4 53.0 18.2 10.1 63.7 24.8 17.6 27.8 35.4 24.9 17.9 165 171 - 4.5 M 75.0 75.0 65.4 75.0 75.0 5.1 75.0 75.0 75.0 25.3 75.0 172 178 * 2.3 P 43.7 0.9 4.8 32.1 43.3 2.1 2.6 33.9 44.9 1.6 32.7 179 183 E 4.9 H 1.8 0.8 2.2 0.8 3.0 0.0 2.0 1.0 0.8 0.2 2.8 185 186 * 3.2 M 7.5 75.0 75.0 3.0 5.5 75.0 75.0 4.5 6.8 75.0 3.0 188 191 * 3.4 M 75.0 4.0 59.1 5.0 75.0 41.0 5.0 75.0 58.9 40.8 3.5 192 201 - 4.2 M 75.0 75.0 75.0 4.4 75.0 75.0 75.0 75.0 12.4 75.0 1.4 202 207 * 2.8 P 51.3 6.2 40.2 6.2 51.0 27.8 4.5 51.2 75.0 27.7 4.1 209 215 * 1.6 P 2.7 11.9 2.1 2.0 2.9 1.4 2.6 0.9 75.0 11.4 4.9 216 217 E 4.5 M 2.0 0.0 1.5 5.0 1.5 1.5 0.0 0.5 75.0 1.5 42.0 220 223 * 2.9 P 7.0 5.5 58.2 3.5 5.8 58.0 6.0 5.8 75.0 57.5 75.0 224 225 H 4.4 M 2.0 1.0 2.0 0.5 6.2 1.0 0.5 2.0 75.0 4.5 75.0 226 239 * 2.9 P 3.8 1.5 75.0 4.6 2.7 5.0 2.5 60.5 75.0 39.9 75.0 240 242 - 4.2 M 9.2 5.7 75.0 4.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 243 245 * 3.9 M 4.7 3.7 75.0 2.7 5.3 75.0 75.0 75.0 75.0 75.0 75.0 246 252 - 4.3 M 75.0 34.4 75.0 14.4 75.0 75.0 75.0 75.0 55.3 75.0 5.8 253 262 * 3.8 M 75.0 2.4 75.0 41.2 75.0 75.0 4.1 75.0 2.4 75.0 4.0 263 264 - 4.2 M 75.0 75.0 75.0 4.0 75.0 75.0 75.0 75.0 1.5 75.0 4.0 265 271 * 3.1 M 25.6 2.1 75.0 2.4 25.0 75.0 2.6 75.0 15.6 75.0 3.1 272 273 - 4.5 M 75.0 4.5 75.0 75.0 75.0 75.0 1.5 75.0 75.0 75.0 75.0 274 276 * 3.9 M 75.0 3.7 75.0 3.3 75.0 75.0 2.7 75.0 75.0 75.0 2.7 277 278 - 4.2 M 75.0 75.0 75.0 2.5 75.0 75.0 3.5 75.0 75.0 75.0 2.0 279 282 * 3.9 M 75.0 75.0 75.0 0.2 75.0 75.0 6.0 75.0 1.8 75.0 2.5 284 296 * 3.6 M 20.0 4.2 75.0 3.9 69.9 75.0 4.0 37.7 75.0 75.0 43.8 297 298 - 4.5 M 75.0 1.5 75.0 75.0 75.0 75.0 3.0 75.0 75.0 75.0 75.0 299 318 * 3.4 M 12.9 61.1 75.0 12.9 16.5 75.0 61.2 24.1 10.2 75.0 2.0 320 321 * 3.4 M 39.5 42.8 75.0 5.0 5.5 75.0 41.5 6.8 75.0 75.0 4.5 322 326 - 4.2 M 75.0 5.7 75.0 5.9 75.0 75.0 75.0 75.0 75.0 75.0 6.2 327 345 * 3.6 M 37.4 26.1 75.0 2.9 22.9 75.0 56.4 26.3 52.4 75.0 25.1 347 360 * 3.1 M 23.9 13.8 75.0 3.9 39.3 75.0 18.6 29.2 36.7 75.0 4.2 361 368 - 4.5 M 75.0 4.8 75.0 75.0 75.0 75.0 3.5 75.0 75.0 75.0 75.0 >>>>>>