Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1rcua- ------------------------------------------------------------------------------------------CEEEEEECCCCC------CCCCCHHHHHHHHHHHHHHHHCC-CEEEECCC-CCC-CHHHHHHHHCC--------CCEEEEECC-----CCCCCC---CCCEEEECCCCC--CCHHHHHCCCCEEEEECCC------HHHHHHHHHHHHC------------CCCEEEEC--CCCHHHHHHHHHCCCCCCCCCCCCCC--EEEEC---CHHHHHHHHHCC---------------------------------------------------------- >P1;d1t35a- ------------------------------------------------------------------------------------------CEEEECCCCCCC---------CCCHHHHHHHHHHHC-CCCC-CEEEECCCCCCC-CHHHHHC-CCC--------CCEEEC-CCCCCHHHH-CCC---CCCEECCCCCC---HHHHCC-CCCCEEEE-CCC------HHHHHHHHHHHHCCCCC------CCCCCEEEECHHHCCCC---CCHHHHHCCCCCCCHHHH--EEEEC---CHHHHHHCCCC----------------------------------------------------------- >P1;d1weha- ------------------------------------------------------------------------------------------CEEEEECCCCCC------CCC---HHHHHHHHHHHHHHHCC-CEEEECCC-CCC-CHHHHHHHHCC--------CCEEECCCHHHCCCCCCCCC---CCCEECCCCCHH--HHHHHHHHHEEEEEECCCC------HHHHHHHHHHHHHHHCC---CC--CCCCEEEC--HHHHHCCCCC-------CCCCHHHHCC--CEECC---CHHHHHHHHHCC---------------------------------------------------------- >P1;d2nx2a1 ------------------------------------------------------------------------------------------CEEEEEECCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCC-CCHHHHHHHHHHC---CCCCCCCCEEEEEECCCCCC---------CCCC-------HHHHHHHHHHHHHCCEEEECCC-CCCCCHHHHHHHHHHHHHHC------------CEEEEECCCCCCCCCHHHHHHHHHHHHH---HC---CCEEEEC-------HHHHHHHHHC------------------------------------------------------- >P1;d2q4oa- ----------------------C---------------------------------------------------------------CCCCCEEEEECCCCCC---------CCHHHHHHHHHHHHHHHHCC-CEEEECCCCCCC-CHHHHHHHHCC--------CCEEEEEECC-------------CCCEEEEECCC---HHHHCC-CCCCEEEECCCC------HHHHHHHHHHHHHHHHC------CCCCCEEEECHHHCCHHHHHHHHHHHHCCCCCHHHHCC--EEEEC---CHHHHHHHHHC----------------------------------------------------------- >P1;d3bq9a2 ---------------------CC---------------------------------------------------------------CCCCCEEEEECCCCCC------H-----HHHHHHHHHHHHHHHCC-CEEEECCC-CHHHCHHHHHHHHHHHHCCC-CCCCEEEEECCCCCCCC-CCCC---CCCEEEECCCHH--HHHHHHHHHCCEEEECCCC------HHHHHHHHHHHHHHCCH---HHCCCCCCEEEEECHHHHHHHHHHHHHHHH--HCCCCHHHH--CEEEEC--CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC------------------------------------- >P1;d3imka1 --------------------------------------------------------------------------------------------------------------------------------CCCCCEEECCCC-CCHHHHHHHHHHH---C-----CCCEECCCCHHHCCCCCCCCCCCCCCCC-----CCCHHHHHHHHHHCCCEEEEEEC-C----CCCHHHHHHHHHHHC------------CCEEEEECCC--CCHHHHHHHHHHHHHH---CCCCEEEEECCCCCCCCCHHHHCCHHHHHHC----------------------------------------------------- >P1;d3quaa- ----------------------------------------------------------------------------------------CCCEEEEECCCCCC----------CHHHHHHHHHHHHHHHHCC-CEEEECCCCCHHHHHHHHHHHHCC--------CCEEEEEEHHHCCCCC-CCC---CCCEEEEECCC---CCHHHHHHHCCEEEECCCC------HHHHHHHHHHHHHHHCC------CCCCCEEEECCCCCCHHHHHHHHHCCCCCCCCHHHHHC--CEEEC---CC-CHHHHHCC----------------------------------------------------------- >P1;d3uqza2 -------------------------------------------------------CEEECCCCCCCHHHHCCCCCCCEEEEEECHHHHHCCEEEEEECCCCC-----------HHHHHHHHHHHHCC--CCCCEEEECCC-CCHHHHHCCHHHH---------CCCEEEECCCC-CC---------CCCC-------HHHHHHHHHHHHHCEEEECCCC-CCCCCCCHHHHHHHHHHHHC------------CEEEEECCC------CCHHHHHHHHCCC----C---CEEEECCCCCCCCCCHHHHHHHHCCC-------EECCCHHHHHHHCCC------------------------------- >P1;d5wq3a- CCCCHHHHHHHHHHHHHHHHHHH---------------------------------------------------------------CCCCCEEEEECCCCCC------CCC---HHHHHHHHHHHHHHHCC-CEEEECCC-CCCCHHHHHHHHHCC-------CCEEEEEECCCC-----CCCC---CCCEEEEECCHH--HHHHHHHHCCCCEEECCCC------HHHHHHHHHHHHHHH-----CCCCCCCCEEEECHHHHHHHHHHHHHHCCCCCCCCHHHHHC--C-EEEC--CHHHHHHHHHHHHC---------C--------C------------------------------------- >P1;d6bcoa1 ----------------------CCCHHHHHCEEECCCEEECCCEEEEEECCCCCCCEEEEEEECCCCHHHHHHHHHH------CCCCCCCCCEEEEECCCCC------CCCCHHHHHHHHHCCHHHHHHHC-CEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEEHHHCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCC-CHHHHHHHHHHHCC--------CC--CEEECCCCHHHHHHHHHHHCCHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHHHHHHHCCCC PSA >P1;d1rcua- ------------------------------------------------------------------------------------------440000005651------876402714a4015003200749-13001303-300-20002004419--------340100007-----839007---302634516595--5004400630600000007------7600300510062------------42200001--70713035007703594104884324--02306---508400610569---------------------------------------------------------- >P1;d1t35a- ------------------------------------------------------------------------------------------911211127968---------c58116611440042-0759-110016174600-1210610-a5c--------140100-44b29a964-681---806522418ca---637635-73051100-029------bb04740732167127b------99432011010633067---736741749848752380--11415---70650173794----------------------------------------------------------- >P1;d1weha- ------------------------------------------------------------------------------------------610000025916------594---83184023002000319-01000300-500-10004003639--------35000000474278295207---303734407657--5107300930100000116------ab035105400632554---8c--50530001--4503b61738-------bb54680292--04404---546201600641---------------------------------------------------------- >P1;d2nx2a1 ------------------------------------------------------------------------------------------7300000031711607756186073023002630461077a043000002-1000000020006---129736a0301010004612---------5a25-------8522810670286046440237-64464860475005300560------------600000015a447305601710483568---68---0403302-------3751641567------------------------------------------------------- >P1;d2q4oa- ----------------------9---------------------------------------------------------------9070820001129956---------a7841271046006002616-010014189800-13005104759--------3400002277-------------82556332868---532531-72020000001a------b9036105200531468------61b3200001062407a237705511859827791472--02106---60650075026----------------------------------------------------------- >P1;d3bq9a2 ---------------------57---------------------------------------------------------------a460200000016708------9-----72270033002300335-00000000-41002000410460075582-ac111000005a33a71-5249---306335426437--500520023000000001a------a9055003300730367---806503020000007706940781296008--434770382--062106--52630054056208602500570a022530730------------------------------------- >P1;d3imka1 --------------------------------------------------------------------------------------------------------------------------------817063000001-2000100030057---3-----a16100300660503a95057918054a-----65555711250045040000001-6----a0d914303510764------------2312201057--2637700850571027---5805300010244661880471040034016----------------------------------------------------- >P1;d3quaa- ----------------------------------------------------------------------------------------66300000004848----------6860380046003300538-01000000520000100610285a--------140000006812a716-108---70542231775---901820483010000000a------aa035104510623356------71a3300000224408b208705922779825771175--04327---70-40073024----------------------------------------------------------- >P1;d3uqza2 -------------------------------------------------------7202395c401920370970084031626250076400000014804-----------aa037303700560--84600000000-7200330000293---------91400000000-16---------2241-------9a14820440075000002137-75715980163012001000------------300000105------a371170054072----c---04100026589562060025028691-------540740930164074------------------------------- >P1;d5wq3a- 75968844863377138704850---------------------------------------------------------------7905500001024928------783---73063025005301828-00000003-60011000200162a-------230000115498-----b207---205311605174--012400151040000000a------aa0360043016304-----56628700000024a306a2176048522858618761054--0-2206--61850173056417---------c--------b------------------------------------- >P1;d6bcoa1 ----------------------a557216303027795660300030203b19495020010018292630151018------4061a30610000102377------88068403510360004102747-000006015441030004005512874a7b77030000010010121940584918241806285787a98222002103000000303458a2a166011600330273527ba485960200000010-83830500150052--------60--01000126410200151378b85382066217774960252176036275001403964778304600770296085c Translating the sequences ------------------------------------------------------------------------------------------CEEEEE*CCCCC------******HHHHHHHHHHHHHH*CC-CEEEECCC-CC*-*HHHHHHHH**--------CCEEEE*C*-----***CCC---CCC*E***CC**--**HHHHH**CCEEEE*CCC------HHHHHHHHHHHH*------------CCCEEEE*--******HHHHHH******C*******--*EEEC---C***HHHHHH**---------------------------------------------------------- ------------------------------------------------------------------------------------------CEEEE**CCCCC---------***HHHHHHHHHHH*-**CC-CEEEECCC*CC*-*HHHHH*-***--------CCEEE*-C***C****-CCC---CCC*E***CC*---HHHH**-**CCEEEE-CCC------HHHHHHHHHHHH*****------**CCCEEEE********---**HH******C*******--*EEEC---C***HHH****----------------------------------------------------------- ------------------------------------------------------------------------------------------CEEEEE*CCCCC------***---HHHHHHHHHHHHHH*CC-CEEEECCC-CC*-*HHHHHHHH**--------CCEEE**C***C*****CCC---CCC*E***CC**--HHHHHHH****EEEE*CCC------HHHHHHHHHHHHH****---**--*CCCEEE*--**********-------**C*******--*EE*C---C***HHHHHH**---------------------------------------------------------- ------------------------------------------------------------------------------------------CEEEEE*CC***************HHHHHHHHHHHHHH*CC*CEEEECCC-CC***HHHHHHH*---*******C*EEEE*C***C*---------*CCC-------****HHHHHHH**CCEEEE*CC-******HHHHHHHHHHHHH*------------C*EEEE*********HHHHHH*******---**---**EEE**-------HHHHH*****------------------------------------------------------- ----------------------*---------------------------------------------------------------****CEEEEE*CCCCC---------***HHHHHHHHHHHHHH*CC-CEEEECCC*CC*-*HHHHHHHH**--------CCEEEE****-------------CCC*E***CC*---HHHH**-**CCEEEE*CCC------HHHHHHHHHHHHH****------**CCCEEEE*********HHHHHH******C*******--*EEEC---C***HHHHHH*----------------------------------------------------------- ---------------------**---------------------------------------------------------------****CEEEEE*CCCCC------*-----HHHHHHHHHHHHHH*CC-CEEEECCC-C****HHHHHHHH*******-**CCEEEE*C***C***-*CCC---CCC*E***CC**--HHHHHHH**CCEEEE*CCC------HHHHHHHHHHHHH****---*****CCCEEEE*********HHHHHH***--*C*******--*EEE**--C***HHHHHH***********************------------------------------------- --------------------------------------------------------------------------------------------------------------------------------*CC*CEEE*CCC-CC***HHHHHHHH---*-----*CCEE***C***C*****CCC***CCC*-----C****HHHHHHH**CCEEEE**C-*----***HHHHHHHHHHH*------------CCEEEE****--***HHHHHH*******---*******EE*C***C***HHHH*********----------------------------------------------------- ----------------------------------------------------------------------------------------**CEEEEE*CCCCC----------**HHHHHHHHHHHHHH*CC-CEEEECCC*C****HHHHHHHH**--------CCEEEE*****C****-CCC---CCC*E***CC*---**HHHHH**CCEEEE*CCC------HHHHHHHHHHHHH****------**CCCEEEE*********HHHHHH******C*******--*EEEC---C*-*HHHHH**----------------------------------------------------------- -------------------------------------------------------***********************************CEEEEE*CCCCC-----------*HHHHHHHHHHH**--CC*CEEEECCC-CC***HH**HHHH---------*CCEEEE*C**-C*---------*CCC-------****HHHHHHH**C*EEE**CC-*******HHHHHHHHHHHH*------------C*EEEE***------**HHHH******C----*---**EEEC***C*****HHHH*******-------***************------------------------------- ***********************---------------------------------------------------------------****CEEEEE*CCCCC------***---HHHHHHHHHHHHHH*CC-CEEEECCC-CC***HHHHHHHH**-------*C*EEEE*C***-----*CCC---CCC*E***CC**--HHHHHHH**CC*EEE*CCC------HHHHHHHHHHHHH**-----*****CCCEEEE*********HHHHHH******C*******--*-EE**--C***HHHHHH****---------*--------*------------------------------------- ----------------------*******************************************************------*******C*EEEE*CCCCC------******HHHHHHH**HHHHH**C-CEEEE*CC*CC***HHHHHHHH**********CCEEEE*****C*****CCC***CCC*E***CC*************CCEEEE**CC********HHHHHHHHHHH************CCCEEEE****-****HHHHHH****--------**--*EEEC*******HHHHHH************************************************************ 102405.tem _________________________________ ----------------------*---------------------------------------------------------------****CEEEEE*CCCCC------******HHHHHHHHHHHHHH*CC-CEEEECCC*CC***HHHHHHHH**-*-----*CCEEEE*C***C*****CCC--*CCC*E***CC****HHHHHHH**CCEEEE*CCC*----*HHHHHHHHHHHHH****---**-**CCCEEEE*********HHHHHH******C*******--*EEEC*--C***HHHHHH*******---------------*------------------------------------- Structural block scores 0 21 - 4.8 H 75.0 75.0 75.0 75.0 75.0 71.8 75.0 75.0 75.0 5.5 75.0 23 85 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 40.0 75.0 10.1 86 89 * 3.4 M 75.0 75.0 75.0 75.0 4.0 5.1 75.0 40.5 3.2 5.2 3.6 91 95 E 4.7 H 0.8 1.2 0.2 0.6 0.6 0.0 75.0 0.0 0.0 0.2 0.2 97 101 C 4.7 H 3.4 6.4 4.6 2.4 6.2 4.4 75.0 4.8 3.4 5.0 3.8 102 107 - 4.8 H 75.0 75.0 75.0 4.3 75.0 75.0 75.0 75.0 75.0 75.0 75.0 108 113 * 3.3 M 4.5 41.8 40.5 4.7 41.8 64.0 75.0 52.3 64.2 40.5 5.7 114 127 H 4.7 H 2.7 7.5 2.2 2.1 2.4 2.1 75.0 2.4 8.5 2.5 1.8 129 130 C 4.9 H 6.5 7.0 5.0 8.8 3.5 4.0 4.0 5.5 6.0 5.0 5.5 133 136 E 5.0 H 1.0 0.5 0.2 0.8 0.5 0.0 0.8 0.2 0.0 0.0 0.0 137 139 C 4.9 H 2.0 4.7 1.0 0.7 4.3 0.0 0.3 0.0 0.0 1.0 2.3 141 142 C 4.8 H 1.5 3.0 2.5 0.5 4.0 2.5 1.0 1.0 4.5 3.0 4.0 143 145 * 1.6 P 25.7 25.3 25.3 0.0 25.3 0.7 0.3 0.0 1.0 0.7 1.3 146 153 H 4.8 H 1.2 11.9 1.6 1.0 2.5 1.9 1.9 2.2 2.1 1.1 1.8 154 155 * 2.4 P 5.0 8.8 6.0 75.0 7.0 0.0 75.0 7.8 75.0 6.2 1.5 158 162 - 4.3 M 75.0 75.0 75.0 5.4 75.0 20.1 75.0 75.0 75.0 75.0 8.0 164 165 C 4.8 H 3.5 2.5 4.0 1.5 3.5 1.0 3.5 2.5 2.5 1.5 1.5 166 169 E 4.8 H 0.2 0.2 0.0 0.5 0.0 0.2 1.0 0.0 0.0 0.2 0.0 172 174 * 1.6 P 52.3 5.8 5.0 3.3 29.7 6.2 4.0 5.0 25.0 7.0 0.3 176 180 * 3.0 P 34.0 20.9 6.2 60.4 75.0 19.7 5.5 19.9 61.2 62.3 3.4 181 183 C 4.5 M 2.3 5.0 3.0 75.0 75.0 5.0 4.0 3.0 75.0 3.0 4.3 184 185 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 5.0 75.0 75.0 75.0 6.5 187 189 C 5.0 H 1.7 4.7 2.0 5.8 5.0 3.0 3.0 4.0 2.3 2.3 4.7 192 194 * 2.4 P 3.3 2.3 2.7 75.0 2.7 3.7 75.0 2.0 75.0 2.3 2.7 195 196 C 4.5 M 5.5 10.2 6.5 75.0 7.0 5.0 40.5 7.0 75.0 3.0 6.5 197 200 * 2.8 P 41.0 58.9 40.5 4.2 58.2 40.0 5.0 57.5 6.1 40.2 8.1 201 207 H 4.4 M 1.9 15.0 2.3 3.4 13.4 1.7 2.3 3.4 2.6 1.1 3.3 208 209 * 1.0 P 4.5 5.0 6.0 7.0 4.5 2.5 4.5 5.5 6.0 3.0 1.5 210 211 C 4.7 H 3.0 2.5 0.5 2.0 1.0 0.0 2.0 0.5 0.0 2.0 1.5 212 215 E 4.9 H 0.0 0.5 0.0 3.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 217 219 C 4.7 H 2.3 3.7 2.7 28.3 3.8 3.8 25.3 3.5 28.3 3.5 1.0 221 224 - 4.2 M 75.0 75.0 75.0 4.5 75.0 75.0 75.0 75.0 4.5 75.0 6.9 226 238 H 4.9 H 2.3 4.9 3.8 3.2 3.5 3.5 4.0 3.7 1.7 3.6 2.9 239 242 * 2.7 P 75.0 5.4 4.0 56.2 4.8 4.0 57.2 4.2 56.2 38.5 4.2 243 245 - 4.8 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 6.8 246 247 * 3.9 M 75.0 75.0 10.2 75.0 75.0 4.0 75.0 75.0 75.0 5.5 7.2 249 250 * 3.0 P 75.0 9.0 40.0 75.0 3.5 2.5 75.0 4.0 75.0 5.0 7.0 251 253 C 4.7 H 2.7 3.0 2.7 27.0 5.5 1.7 26.7 5.5 26.0 2.3 2.7 254 257 E 5.0 H 0.0 0.5 0.2 0.0 0.0 0.0 1.2 0.0 0.0 0.0 0.0 258 266 * 1.8 P 18.8 11.2 20.1 3.8 3.6 3.7 19.3 3.7 50.7 4.3 10.9 267 272 H 4.5 M 3.7 28.8 40.5 3.3 4.5 5.5 4.5 4.8 4.9 5.0 1.8 273 278 * 1.7 P 3.7 5.5 53.8 4.3 5.3 27.0 2.5 5.8 2.7 5.2 26.2 280 286 * 2.3 P 4.7 4.7 4.4 55.6 5.3 4.4 34.7 4.7 66.1 4.4 54.4 287 288 - 4.5 M 75.0 75.0 75.0 37.5 75.0 75.0 1.5 75.0 37.5 75.0 75.0 290 292 E 4.8 H 1.7 2.0 2.7 2.0 1.0 3.0 0.3 3.0 0.3 26.3 0.3 295 296 - 4.2 M 75.0 75.0 75.0 75.0 75.0 75.0 5.0 75.0 5.5 75.0 4.0 298 300 * 1.7 P 4.0 3.7 4.0 75.0 3.7 3.7 5.7 26.3 6.7 4.7 1.0 301 306 H 4.6 H 2.0 4.5 2.2 16.2 2.3 2.3 2.7 2.0 1.7 2.7 1.7 307 313 * 3.0 P 55.7 64.9 54.3 24.7 65.1 3.4 2.0 64.9 4.4 34.7 7.2 314 328 - 4.3 M 75.0 75.0 75.0 75.0 75.0 3.3 75.0 75.0 37.1 70.8 4.3 330 366 - 4.8 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 63.4 75.0 4.2 >>>>>>