Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1uuna- ----------------------CEEEEEEEECCCCCEEEEEEEEEEEEEECCCCCCC---CCEEEEEEEEEEEEEECCCHHHCEEEEEEEEEEECC---------------------EEEEEEEEEECCC--CCCEECCCCCCCCCCCCCCEECCCCCCEEEEEEEEEECCC---------------------------------------------------------------------------------------------------CEEEEEEEEEEECCEEEEEEEEEEEEECCEECCCEEEEEEEEEECCCCEEEEECCCEECC----- >P1;d4i0na- ------------CCEEEC--CCEEEEEEEEEEEC-CCEEEEEEEEEECC-----CCCEEEEEEEEEEEEECCCEEEECC---CEEEEEEEEEEEEEEEEECCCCC-CCCEEECCCEECCCEEEEEEEECCCCC-----------------------EEEEEEEEEECCCEEEEEEEC--CCEEEEEEEEC--CCCCC--CCCC--CCCC-CCCCCCCCCCCCC-----CCCCCCCC-CCCCHHHHCEECCEEEEEEEEECCC--CEEEEEEEEEEEEEEEEEEEEC--C--EEEEECCCC--C-EEEEEEEEEECC----CCCCCCC--------- >P1;d4iyaa- -----------CCEEEEECCEEEEEEEEEEEECCCCEEEEEEEEEEECC------CCEEEEEEEEEEEEECCCEEEEHHHCCCCEEEEEEEEEEEEEEECC--CCEEEEEEECCCCCCCCEEEEEEEEECCCEEEEEECCC----CCC-------CCCEEEEEEEECCCEEEEEEE-EECCEEEEEEEECEEEECC--EEECC--C-------CCCCCC-CCCCC--CCHHHHCCCHHHCCHHHHCEECCCEEEEEEEECCCC-CEEEEEEEEEEEEEEEEECC-C--CCCCCCCEEEEEEEEEEEEEEEEEEECC----CCCCCC---------- >P1;d6rhvg- --------------------CEEEEEEEEEEECCCCEEEEEEEEEEECC-----CCCEEEEEEEECCEEECCCEECCCCCCCE-EEEEEEEEEEEEEEECCCCCCEEEEEEECCCCCCCCEEEEEEEEE---EECCEEC---------CEECCEEEEEEEEEEECCCCCEEEEECCCCCCCEEEEEEEECCEEECC-EEECCCCCCCCCCCCCCCCCCCCCCCCCC---HHHCCCCHHHCCHHHHCEECCCEEEEEEEECCC-CCEEEEEEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEE-EEEEEEEEEECCCCEEEEEEECC--------- >P1;d6rhvh- ----------CC---CCCCCCEEEEEEEEEEECCCCEEEEEEEEEEECC-----CCCEEEEEEEEEEEEECCCEEEECCCCCCCEEEEEEEEEEEEEEEE-CCCCEEEEEEECCCCCCCCEEEEEEEEE---EECCCCC---------CCCCCEEEEEEEEEEECCCCCEEEEECCCCCCCEEEEEEEECEEEECC-EEEECCCC---------CCCCC-CCCCCCCCCHHHHCCCHHHCCHHHHCEECCCEEEEEEEECCC--CEEEEEEEEEEEEEEEEECCCC----CCCCCEEEEEEEE-EEEEEEEEEECCCCEEEEEEEEEECCCCCCCC >P1;d6u2sa- -----CEEECCCEEEECCCCEEEEEEEEEEEECCCCEEEEEEEEEEEEC-----CCCEEEEEEEEEEEEECCCCCCCCC-CCCEEEEEEEEEEEEEEEEE-CCCCEEEEEEECCCCCCCCEEEEEEEEECCCEEEEEE-------CCC-------CCCEEEEEEEECCCEEEEECCCCCCCEEEEEEEECCEEECCEEEECCC--CCCC-CCCCCCCCCCCCCCC---CHHHCCCCHHHCCHHHHCEECCCEEEEEEEECCCC-CCEEEEEEEEEEEEEEEEEECC--C--CEEEEEEEEEEE-EEEEEEEEEECCCCEEEEEEEEEEECCCCC-- >P1;d7ahla- CHHHHCCCCCCC---CCCCCCCCEEEEEEEEECCCCEEEEEEEEEECCC-----CCCCEEEEEEEEEEECCCCCCC--CCCCC-CEEEEEEEEEEEEEC-CCCCCCEEEEEECCCCCCCCEEEEEEEEE---EEECCEECC----CCCEECCEEEEEEEEEEEECCCCCEEEEEE-CCCCCEEEEEEEECCEEECCEEEECCC--CCCC-CCCCCCCCCCCCCCCC---HHHCCCCHHHCCHHHHCCCCCCEEEEEEECCCCCCCEEEEEEEEEEEEEEEEEEECC----CCEEEEEEEEEEE-EEEEEEEEEECCCCEEEC-------------- PSA >P1;d1uuna- ----------------------a343465470a6804010103506043390a574a---202103020503040777628806020100010305---------------------5529396777468--785735a0579775606752632b694968684948b04b---------------------------------------------------------------------------------------------------664541135915527552328835253650273060400010407292302041943702----- >P1;d4i0na- ------------b0761e--66042263447158-80503030100306-----31a4000002051302041426176---6503010000020103061a885-00340003b43585706550506141a-----------------------082126070501303030359--85200010403--51765--3439--2648-6100100053458-----56050027-67007001800601000002024b1--5603030102030020305259--7--20207070a--8-344350020106----710526b--------- >P1;d4iyaa- -----------d8449078b030024405251b7110303030000508------1a330000103230503051433894973000200000000060a1--730402210069626575022100041307044351a8----b49-------a12031405080520102036-48531020003036092a7--b1606--3-------540002-84295--6722300276b6004003500800000000054c38-83030301000100001075-9--9995200705351547410204050309----202b56---------- >P1;d6rhvg- --------------------653343615152ab380402030202226-----b394010203042502040742a781462-01020000030102041b59402045154469a895958577455---6476777---------7748a766664756454b243042323c71561000030202206129-63040542272ba7120000044464946---044001469702910070180602010003482-695040003030000104031585ba40100020354545-2300000101077180633543d--------- >P1;d6rhvh- ----------b6---8304828525462514096050205020000307-----9182100002040103040602227748000101000000000204-a38403033143469bba2745475677---8756859---------a8768686876647565d4a3043500a7167420000030520607b-45240635---------40013-a13805496133000627300830480190602000004481--6504010100000000003078----8407050341510-0302010200048160722645024a11259a >P1;d6u2sa- -----9672491856603b4011140204032a8060405010000407-----4282000001021303020771758-38540301000202040304-50a2040411004952577402130406450808289-------64b-------a85041304060320303159817634000002025050797131207--3746-5220000037363b4---30050005275015002430702000000053a28-7403030202010020005359--8--102040434402-0101000201048140703735371765b3-- >P1;d7ahla- 92787c498567---8328d09354452535289210402030101207-----b3b2110104031404050344--69a5b-000100010202040-2aa0405034273579a996766555665---77688736a----8a7766795686858555759455043303-a165240003030220505c9021427--3557-5100000035464832---00700043b601830380160602020105291951504020000001000305248----8101040546434-140524040107824065-------------- Translating the sequences ----------------------*EEEEEEEE*CCCCEEEEEEEEEEE*******CCC---**EEEEEEEE***EE**CC***C*EEEEEEEEEE**---------------------***EEEEEEE***--***************************EEEEE********---------------------------------------------------------------------------------------------------*EEEEEEEEEEE*********EEEEEE**EE***EEEEEEEEE*CCC*EE**********----- ------------******--**EEEEEEEEEE*C-C*EEEEEEEEEECC-----CCCEEEEEEEEEEEEECCCEE**CC---C*EEEEEEEEEEEEEEE**CCCC-***EEECCC**CCCEEEEEEEE*****-----------------------**EEEEEE**CCCEEEEE**C--CCEEEEEEEEC--**CC*--**CC--C***-***CCCCCC*CCC-----*****CCC-**CCHHHHCEECC*EEEEEEEECCC--CEEEEEEEEEEEEEEEEEE**C--*--*EEEE****--*-EEEEEEEEEECC----*******--------- -----------***********EEEEEEEEEECCCCEEEEEEEEEEECC------CCEEEEEEEEEEEEECCCEE*****CCC*EEEEEEEEEEEEEEE**--CC*EEEEEECCCCCCCCEEEEEEEEE***EE*******----***-------***EEEEEE**CCCEEEEE**-**CCEEEEEEEEC*EEECC--EE*CC--C-------CCCCCC-CCCCC--**HHH*CCCHHHCCHHHHCEECCCEEEEEEEECCC*-CEEEEEEEEEEEEEEEEE**-C--*******EEEEEEEE*EEEEEEEEEECC----******---------- --------------------**EEEEEEEEEECCCCEEEEEEEEEEECC-----CCCEEEEEEEE**EEECCCEE**CC*CC*-EEEEEEEEEEEEEEE**CCCC*EEEEEECCCCCCCCEEEEEEEEE---EE*****---------**********EEEEEE**CCCEEEEE**C**CCEEEEEEEEC*EEECC-*EE*CC**C*******CCCCCC*CCCCC*---HHH*CCCHHHCCHHHHCEECCCEEEEEEEECCC-*CEEEEEEEEEEEEEEEEEE*********EEEEEEEEEEE-EEEEEEEEEECCCC*EE******--------- ----------**---*******EEEEEEEEEECCCCEEEEEEEEEEECC-----CCCEEEEEEEEEEEEECCCEE**CC*CCC*EEEEEEEEEEEEEEE*-CCCC*EEEEEECCCCCCCCEEEEEEEEE---EE*****---------**********EEEEEE**CCCEEEEE**C**CCEEEEEEEEC*EEECC-*EE*CC**---------CCCCC-CCCCC****HHH*CCCHHHCCHHHHCEECCCEEEEEEEECCC--CEEEEEEEEEEEEEEEEE***C----*****EEEEEEEE-EEEEEEEEEECCCC*EE*************** -----*****************EEEEEEEEEECCCCEEEEEEEEEEE*C-----CCCEEEEEEEEEEEEECCC****CC-CCC*EEEEEEEEEEEEEEE*-CCCC*EEEEEECCCCCCCCEEEEEEEEE***EE****-------***-------***EEEEEE**CCCEEEEE**C**CCEEEEEEEEC*EEECC**EE*CC--C***-***CCCCCC*CCCCC---*HHH*CCCHHHCCHHHHCEECCCEEEEEEEECCC*-C*EEEEEEEEEEEEEEEEE**C--*--*EEEEEEEEEEE-EEEEEEEEEECCCC*EE*************-- ************---********EEEEEEEEECCCCEEEEEEEEEE*CC-----CCC*EEEEEEEEEEE*CCC***--C*CCC-*EEEEEEEEEEEEE*-*CCCC*EEEEEECCCCCCCCEEEEEEEEE---EE*******----*************EEEEEE**CCCEEEEE*-C**CCEEEEEEEEC*EEECC**EE*CC--C***-***CCCCCC*CCCCC*---HHH*CCCHHHCCHHHHC**CCCEEEEEEE*CCC**CEEEEEEEEEEEEEEEEEE**C----**EEEEEEEEEEE-EEEEEEEEEECCCC*EE*-------------- 56959.tem _________________________________ ----------************EEEEEEEEEECCCCEEEEEEEEEEECC-----CCCEEEEEEEEEEEEECCCEE**CC*CCC*EEEEEEEEEEEEEEE**CCCC*EEEEEECCCCCCCCEEEEEEEEE***EE*******----*************EEEEEE**CCCEEEEE**C**CCEEEEEEEEC*EEECC**EE*CC--C***-***CCCCCC*CCCCC*--*HHH*CCCHHHCCHHHHCEECCCEEEEEEEECCC*-CEEEEEEEEEEEEEEEEEE**C--****EEEEEEEEEEE-EEEEEEEEEECCCC*EE**********----- Structural block scores 0 9 - 4.4 M 75.0 75.0 75.0 75.0 75.0 40.3 7.2 10 21 * 2.9 P 75.0 29.3 11.9 63.4 23.0 4.5 23.5 22 31 E 4.9 H 4.7 3.3 2.3 3.3 3.4 1.7 3.8 32 35 C 4.8 H 6.1 24.0 5.1 8.2 5.0 6.1 5.0 36 46 E 4.9 H 1.8 1.4 1.3 1.4 1.1 1.3 1.2 47 48 C 4.4 M 3.5 3.0 4.0 4.0 3.5 3.5 3.5 49 53 - 4.6 H 5.5 75.0 75.0 75.0 75.0 75.0 75.0 54 56 C 4.9 H 7.2 4.8 28.8 7.8 6.0 4.7 8.7 57 69 E 4.7 H 18.5 1.3 1.5 1.8 1.0 0.9 1.6 70 72 C 4.6 H 1.0 1.7 1.0 1.3 1.3 0.7 1.7 73 74 E 4.2 M 2.0 3.0 3.0 5.5 3.0 7.0 3.5 75 76 * 1.4 P 7.0 3.5 3.5 6.2 2.0 4.0 39.5 77 78 C 4.4 M 6.5 6.5 5.5 7.5 4.5 6.5 40.5 80 82 C 4.4 M 5.3 52.0 6.7 4.0 4.0 5.3 9.0 84 98 E 4.8 H 15.8 0.7 0.5 0.6 0.3 1.0 0.7 99 100 * 2.8 P 75.0 3.5 5.8 2.5 39.5 39.5 38.5 101 104 C 4.5 M 75.0 7.9 40.0 7.4 6.4 4.4 6.2 106 111 E 4.5 M 75.0 1.2 1.5 2.8 2.3 1.7 3.5 112 119 C 4.5 M 48.4 4.9 5.1 6.9 7.2 4.9 7.3 120 128 E 4.9 H 6.4 3.8 1.6 6.1 5.8 2.2 5.7 129 131 * 3.5 M 52.7 2.0 1.3 75.0 75.0 3.0 75.0 132 133 E 4.2 M 7.5 42.8 3.5 5.0 7.5 4.0 7.0 134 140 * 2.4 P 5.1 75.0 5.1 26.3 26.1 36.0 6.9 141 144 - 4.6 H 7.5 75.0 75.0 75.0 75.0 75.0 75.0 145 157 * 2.7 P 5.3 64.1 43.3 22.5 23.0 43.8 7.2 158 163 E 4.9 H 6.8 3.0 2.2 5.2 5.7 2.0 5.8 164 165 * 1.0 P 6.5 2.5 4.0 7.8 9.2 3.0 7.0 166 168 C 4.6 H 7.8 1.3 2.3 3.0 5.8 1.7 4.7 169 173 E 4.6 H 33.1 1.2 0.6 2.2 2.4 1.4 2.0 174 175 * 2.1 P 75.0 4.0 4.5 7.8 5.2 7.0 39.0 177 178 * 2.5 P 75.0 75.0 6.0 3.0 3.5 4.0 3.5 179 180 C 4.6 H 75.0 6.5 4.0 3.5 5.5 4.5 3.5 181 188 E 4.6 H 75.0 0.9 0.8 0.6 0.6 0.8 1.2 191 193 E 4.3 M 75.0 27.0 3.7 2.3 2.0 1.7 1.7 194 195 C 4.6 H 75.0 6.5 8.8 5.5 9.2 8.0 8.8 196 197 * 3.4 M 75.0 40.0 75.0 40.5 39.5 4.0 4.5 198 199 E 4.3 M 75.0 39.0 6.2 1.5 3.5 2.0 1.5 201 202 C 4.6 H 75.0 6.0 3.0 2.5 3.0 3.5 4.5 203 204 - 4.2 M 75.0 75.0 75.0 3.0 4.0 75.0 75.0 206 208 * 3.1 M 75.0 6.0 75.0 6.8 75.0 5.7 5.7 210 212 * 3.1 M 75.0 2.3 75.0 3.3 75.0 3.0 2.0 213 218 C 4.6 H 75.0 1.0 1.8 0.7 13.8 0.5 0.5 220 224 C 4.5 M 75.0 33.4 5.6 5.4 4.5 5.5 5.0 226 227 - 4.4 M 75.0 75.0 40.5 75.0 6.5 75.0 75.0 229 231 H 4.3 M 75.0 3.7 2.3 2.7 2.3 1.7 2.3 233 235 C 4.6 H 75.0 3.0 3.0 1.7 2.0 1.7 1.3 236 238 H 4.3 M 75.0 29.3 7.8 7.3 4.0 4.7 6.8 239 240 C 4.6 H 75.0 0.0 0.0 1.0 0.0 0.5 0.5 241 244 H 4.6 H 75.0 2.0 1.8 2.5 3.8 1.8 3.5 246 247 E 4.3 M 75.0 0.0 0.0 0.5 0.5 1.5 0.5 248 250 C 4.5 M 75.0 2.3 2.7 4.7 5.0 3.0 4.0 251 258 E 4.6 H 75.0 0.5 0.6 0.8 0.8 0.6 1.2 259 261 C 4.6 H 75.0 5.5 6.5 4.7 4.3 5.2 4.0 265 282 E 4.8 H 27.8 1.6 1.1 1.3 0.8 1.2 1.1 283 284 * 1.4 P 3.5 3.5 40.0 3.0 3.5 4.0 3.0 286 287 - 4.2 M 5.0 75.0 75.0 8.2 75.0 75.0 75.0 288 291 * 2.4 P 3.8 39.8 8.0 3.9 40.5 39.8 39.8 292 302 E 4.4 M 4.2 16.8 2.9 2.5 2.4 2.1 2.8 304 313 E 5.0 H 1.5 2.2 1.9 0.7 0.8 0.5 2.1 314 317 C 4.6 H 4.5 39.0 39.8 3.8 3.2 3.2 4.2 319 320 E 4.3 M 1.5 41.0 38.5 3.0 3.5 3.5 3.0 321 330 * 2.5 P 3.2 32.5 40.0 33.1 3.6 4.2 68.0 331 335 - 4.4 M 75.0 75.0 75.0 75.0 5.5 33.9 75.0 >>>>>>