Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1txoa- ------------------CEEEEEEEEECCCCCCCCCEEEEECC----------CEEEEEEC-CCCCHHHHHHHHHHHHHH--HHHC--C-CCC-CCCCC-CHHHHHHHHHHHHHHH-CCHHHCC-CCCEEEEEEEC---CEEEEEEECCCEEEEECCC-CEECCCCCCHHHHHHHCCCCCCCHHHH-------CCCCCCC-CCCCCC---------------CC-CEEEE-ECC-CCC-EEEEECHHHHCCCCC-CHHHHHCCC-----CCC-CHHHHHHHHHHCCCCCCEEEEEEEEEC--- >P1;d2j82a- --------------------CEEEEEEECCCCCCCCCEEEEEC---CCCC----CEEEEEEEE---CHHHHHHHHHHHHHH--HHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHC-------CCEECEEEEEECC-CCCEEEEEEECCCEEEEEC-CCEEECCCCCCC----------------------------CCCC-CCCC-----------------CCCEEEEEECC-CCC-EEEEECHHHHCCCCHHHHHHHHCCC-----CCC-CHHHHHHHHHHCCC-CCEEEEEEEC----- >P1;d2jfra- ---------------CCCCEEEEEEEEECCCCCCCCCEEEEEE------C----CEEEEEEEEC--CCHHHHHHHHHHHHH--HHHHH-------CCCHHHHHHHHHHHHHHHHHHHCCCC--CCCEECEEEEECCCHHHCCCEEEEECCCCEEEEECCEEEECCCCCCHHHHHHHCCCCCHHHHCC-------CCCCCCCCCCCCCCC--------------CCCCEEEECCCC-CCC-EEEEECHHHHCCCCHHHHHHHHCCC-----CHHHHHHHHHHHHHHCCCCCCEEEEEEEEC---- >P1;d2pk0a1 --------------------CEEEEEEECCCCCCCCCEEEEEEE-CCCCC----EEEEEEEEECCCCHHHHHHHHHHHHHH--HHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCEECEEEEEEEC---CEEEEEEECCCEEEEEECCEEEECCCCCCHHHHHHHCCCCCHHHHHC-------CCC-CCCCCCCCCCC--------------CCCCEEEEEECC-CCC-EEEEECHHHHCCCCHHHHHHHHCCC----CCHHHHHHHHHHHHHHCCCCCCEEEEEEECCC--- >P1;d3fxka1 CCEEEEEEEEEEEEEEEECCEEEEEEEEEEE-ECCCCEEEEEEEEECCC-EEEEEEEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEECEEEEEECC---CEEEEEEECCCEEEEEECCEEEEECCCCCCCCHHHH----HHHHHCCCCEECCEECCCCCCCCCEECHHHCCCCCCCHHHCCCCCCCEEEEEECCCCCEEEEEEECHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC >P1;d6ihra1 ---------------------CEEEEEECCCCCCCCCEEEEEEE-CCCCC----EEEEEEECCCCCCCHHHHHHHHHHHHH--HHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCEEEEEECC---CEEEEEEECCCEEEEECCCCEEECCCCCCHHHHHHHCCCCCHHHHHC-------CCCCCCCCCCCCCCC--------------CCCCEEEEEECC-CCC-EEEEECHHHHCCCCHHHHHHHHHCC----CCHHHHHHHHHHHHHHCCCCCCEEEEEEECCC--C >P1;d6jkva- ---------------CCCCEEEEEEEEECCCCCCCCCEEEEEE---HH-H----CEEEEEEEECCCCCHHHHHHHHHHHHH--HCCCC----CCHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCEECEEEEEEEC---CEEEEEEECCCEEEEEECCEEEECCCCCCHHHHHHCC---------C-------CCCCCCCCCCCCCCC--------------CCCCEEEEEECC-CCC-EEEEECHHHHCCCCHHHHHHHHCCC-----CHHHHHHHHHHHHHHCCCCCCEEEEEEEEE---- PSA >P1;d1txoa- ------------------170632252440665a3310313028----------20000010-3ab410440062015203--7217--9-61a-c7146-0280056017404652-966926a-10000000018---8600000000020001297-072006120413602569716797188-------3764463-610407---------------b1-07263-405-2b0-000000100041095-403800548-----606-006400410266904100000002048--- >P1;d2j82a- --------------------1701043330586a722032200---7873----100000104---860640050004303--7205731-97228414300440043017204652-------b100000000047-8443010000010200115-890720091128----------------------------a412-0004-----------------17040531706-790-000000200072085a301730357-----807-00640070028580-2000000012----- >P1;d2jfra- ---------------c77414611225340565a621021127------b----4000001035--830450072009203--85078-------55559102600450044035403b38--870000000000068c5a2200000000000104a79061203100400322478627466105-------274275133000444--------------90a021960905-6b0-0000002001240859502500309-----516500630170048291610000000203---- >P1;d2pk0a1 --------------------1510134340675a4210305426-06360----2000001052aa600140053006300--7604719-25739504710381036006503741686-828b00000000002c---64000000010200003a660541071104146329697279a6089-------287-4622100036a--------------709051444506-750-100000200051075930081075a----48076006300530274505200000003066--- >P1;d3fxka1 e752b91678172566773a04000000102-4472201320402088b-195100000010284260062027401520151940655bb8163810360051002500740353398895a36000000000004---920000000101000016770424081030348904----610470a0506a650426140010000262062ac36725010003040411813894010000002000620817600620153057295025003300330074904100000000045118 >P1;d6ihra1 ---------------------703223430853a5210202114-05592----2000001012b5610320072005204--7204837-60647503610371036005501440485a9258000000000319---70000000000100002795042005110402512659517796028-------285194143000376--------------705040330617-a16-000000200022054720261038b----3806600860152026380510000001309c--e >P1;d6jkva- ---------------b708716012323305758530021020---28-2----200000103177610320053005105--71935----a707700750460067009403812a839-3a5000000000028---56000000010200103c5806500611043165839---------a-------4865b6024000368--------------806023380704-380-0000002001400758303620379-----606600350082026490410000000104---- Translating the sequences ------------------***EEEEEEECCCCCCCCCEEEEE**----------*EEEEEE*-CCCC*HHHHHHHHHHHHH--HHH*--*-*CC-*****-*HHHHHHHHHHHHHHH-*C***CC-**CEEEEEE*C---CEEEEEEECCCEEEEE*CC-*EECCCCCCHHHHHHHC******HH**-------CCCCCCC-CCCCCC---------------CC-CEEEE-ECC-CCC-EEEEECHHHHCCCC*-*HHHHHCCC-----C**-*HHHHHHHHHHCCCCCCEEEEEEE***--- --------------------*EEEEEEECCCCCCCCCEEEEE*---****----*EEEEEEEE---C*HHHHHHHHHHHHH--HHH****-******HHHHHHHHHHHHHHHHHHH*-------CCEECEEEEEE*C-**CEEEEEEECCCEEEEE*-C*EEECCCCCC*----------------------------CCCC-CCCC-----------------CCCEEEEEECC-CCC-EEEEECHHHHCCCCHHHHHHHHCCC-----C**-*HHHHHHHHHHCCC-CCEEEEEEE*----- ---------------******EEEEEEECCCCCCCCCEEEEEE------*----*EEEEEEEEC--C*HHHHHHHHHHHHH--HHH**-------***HHHHHHHHHHHHHHHHHHH**C*--CCCEECEEEEE**C***C**EEEEECCC*EEEE*CC*EEECCCCCCHHHHHHHC******HH*C-------CCCCCCCCCCCCCC*--------------CCCCEEEE**CC-CCC-EEEEECHHHHCCCCHHHHHHHHCCC-----CHHHHHHHHHHHHHHCCCCCCEEEEEEE**---- --------------------*EEEEEEECCCCCCCCCEEEEEE*-*****----*EEEEEEEECCCC*HHHHHHHHHHHHH--HHH****-*CC***HHHHHHHHHHHHHHHHHHHH**C-**CCCEECEEEEEE*C---CEEEEEEECCCEEEEE*CC*EEECCCCCCHHHHHHHC******HH*C-------CCC-CCCCCCCCCC*--------------CCCCEEEEEECC-CCC-EEEEECHHHHCCCCHHHHHHHHCCC----*CHHHHHHHHHHHHHHCCCCCCEEEEEEE***--- *********************EEEEEEE***-*CCCCEEEEEE******-*****EEEEEEEECCC**HHHHHHHHHHHHH***********CC***HHHHHHHHHHHHHHHHHHHH**C***CCCEECEEEEEE*C---CEEEEEEECCCEEEEE*CC*EEE*CCCCC***HHHH----***HH*C********CCCCCCCCC**C****************CCCCEEEEEECC*CC**EEEEECHHHHCCCCHHHHHHHH********CHHHHHHHHHHHHHHCCCCCCEEEEEEE****** ---------------------*EEEEEECCCCCCCCCEEEEEE*-*****----*EEEEEE**CCCC*HHHHHHHHHHHHH--HHH****-*CC***HHHHHHHHHHHHHHHHHHHH**C***CCC**CEEEEEE*C---CEEEEEEECCCEEEEE*CC*EEECCCCCCHHHHHHHC******HH*C-------CCCCCCCCCCCCCC*--------------CCCCEEEEEECC-CCC-EEEEECHHHHCCCCHHHHHHHH*CC----*CHHHHHHHHHHHHHHCCCCCCEEEEEEE***--* ---------------******EEEEEEECCCCCCCCCEEEEEE---**-*----*EEEEEEEECCCC*HHHHHHHHHHHHH--H****----CC***HHHHHHHHHHHHHHHHHHHH****-*CCCEECEEEEEE*C---CEEEEEEECCCEEEEE*CC*EEECCCCCCHHHHHH*C---------C-------CCCCCCCCCCCCCC*--------------CCCCEEEEEECC-CCC-EEEEECHHHHCCCCHHHHHHHHCCC-----CHHHHHHHHHHHHHHCCCCCCEEEEEEE**---- 81606.tem _________________________________ ---------------******EEEEEEECCCCCCCCCEEEEEE*-*****----*EEEEEEEECCCC*HHHHHHHHHHHHH--HHH****-*CC***HHHHHHHHHHHHHHHHHHHH**C***CCCEECEEEEEE*C---CEEEEEEECCCEEEEE*CC*EEECCCCCCHHHHHHHC******HH*C-------CCCCCCCCCCCCCC*--------------CCCCEEEEEECC-CCC-EEEEECHHHHCCCCHHHHHHHHCCC----*CHHHHHHHHHHHHHHCCCCCCEEEEEEE***--- Structural block scores 0 14 - 4.6 H 75.0 75.0 75.0 75.0 6.1 75.0 75.0 15 20 * 3.2 M 38.8 62.7 5.9 62.7 5.6 75.0 5.8 21 27 E 4.9 H 3.4 2.6 2.9 2.4 0.6 3.0 2.4 28 36 C 4.8 H 4.3 4.8 4.4 4.4 10.8 4.2 4.0 37 42 E 4.9 H 1.5 1.2 2.2 2.3 1.7 1.0 0.8 45 49 * 2.9 P 75.0 20.0 62.3 3.0 20.5 4.2 32.4 50 53 - 4.6 H 75.0 75.0 75.0 75.0 4.0 75.0 75.0 55 62 E 4.8 H 9.5 0.6 0.5 0.8 0.4 0.2 0.5 63 66 C 4.5 M 7.2 58.2 40.8 7.2 5.0 6.1 5.2 68 80 H 5.0 H 2.1 1.9 2.5 1.7 2.3 1.9 1.8 81 82 - 4.6 H 75.0 75.0 75.0 75.0 3.0 75.0 75.0 83 85 H 4.3 M 3.3 3.0 4.3 4.3 4.3 3.0 5.7 86 89 * 2.1 P 41.5 4.0 41.2 5.2 6.9 5.5 39.5 92 93 C 4.3 M 5.8 4.5 75.0 6.0 3.5 3.0 8.8 94 96 * 1.5 P 31.5 4.7 28.3 5.7 4.0 5.3 4.7 97 116 H 4.9 H 6.8 2.5 2.9 3.0 2.4 2.5 3.1 117 118 * 2.1 P 42.0 75.0 7.2 7.0 8.5 6.0 9.2 120 122 * 2.7 P 5.7 75.0 52.7 28.3 8.2 7.2 29.0 123 125 C 4.7 H 30.5 29.2 5.0 6.5 3.0 4.3 5.2 126 127 E 4.2 M 0.5 0.0 0.0 0.0 0.0 0.0 0.0 129 134 E 4.9 H 0.0 0.0 0.0 0.0 0.0 0.5 0.0 137 139 - 4.3 M 75.0 29.0 8.5 75.0 75.0 75.0 75.0 141 147 E 4.9 H 0.9 0.6 0.6 0.6 0.3 0.0 0.9 148 150 C 5.0 H 0.0 0.3 0.0 0.3 0.3 0.0 0.3 151 155 E 4.9 H 0.6 0.8 0.2 0.4 0.2 0.2 0.6 157 158 C 4.8 H 8.0 41.5 8.8 8.2 6.5 8.0 8.8 160 162 E 4.9 H 3.0 3.0 2.3 3.0 2.0 2.0 3.7 163 168 C 4.9 H 1.5 2.2 1.0 1.7 2.7 1.2 1.3 169 175 H 4.4 M 3.0 65.4 2.1 4.1 4.0 2.9 4.3 177 182 * 2.8 P 6.5 75.0 5.5 7.4 38.7 6.3 75.0 183 184 H 4.4 M 4.0 75.0 3.5 3.0 5.5 3.0 75.0 187 193 - 4.6 H 75.0 75.0 75.0 75.0 4.6 75.0 75.0 194 207 C 4.7 H 9.0 33.7 3.0 8.3 1.4 3.4 4.0 209 222 - 4.6 H 75.0 75.0 75.0 75.0 4.1 75.0 75.0 223 226 C 4.8 H 21.9 20.8 4.9 4.0 0.8 3.0 3.5 227 232 E 4.8 H 16.2 3.3 4.5 3.8 3.0 2.7 3.8 233 234 C 5.0 H 2.5 3.0 2.5 3.0 2.0 4.0 2.0 236 238 C 4.9 H 4.5 5.3 5.8 4.0 4.3 5.8 3.7 240 244 E 5.0 H 0.0 0.0 0.0 0.2 0.0 0.0 0.0 246 249 H 5.0 H 0.2 0.5 0.8 0.5 0.5 0.5 0.8 250 253 C 5.0 H 3.5 4.2 3.5 3.2 4.0 2.2 2.8 254 261 H 4.8 H 11.9 3.7 3.2 3.2 2.8 2.8 3.4 262 264 C 4.5 M 5.7 5.0 4.0 7.5 3.0 7.5 6.3 265 268 - 4.6 H 75.0 75.0 75.0 75.0 3.5 75.0 75.0 271 284 H 4.8 H 7.4 7.8 2.9 2.8 1.9 3.0 2.7 285 290 C 4.9 H 3.3 15.0 3.2 2.7 3.0 2.8 3.0 291 297 E 5.0 H 0.3 0.1 0.3 0.4 0.0 0.6 0.1 298 300 * 2.0 P 4.0 50.7 26.0 4.0 3.0 7.2 26.3 301 303 - 4.5 M 75.0 75.0 75.0 75.0 3.3 54.8 75.0 >>>>>>