Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1u0ta- ----CEEEEEECCC---CCCCHHHHHHHHHHHCCCCEEEEE-------------------CCCEEEEECHHHHHHHCCHHH-----HCCCEEEEECCCCCCCC--CEEHHHHHHHHHHHHHCCCEEEEECCEEEEEEECCEEEEEEEECCEEEEECCCCC------------------CCEEEEEECCCCEEEEEEECEEEEECCHH--HHC-HHHHCCCCCCCCCCCCEEEEEECCCCC--------------------CCCCEEECCCCCEEEEECCCCCCEEEEECCCEEEEECCCCEEEEEECCCCEEEEECCCCCHHHHHHHHHCCCCCCCCC >P1;d1z0sa- ----CEEEEEECCC-------CCHHHHHHHHHHCCCEEEEEC--------CCCHHHHH--CCEEEEEECHHHHHHHHCCCC-----CCCCEEEEECCCCCCCC--CCCCCCCHHHHHHHHHHC-CEEEECCEEEC------CEEEEEECCEEEEEECCCC------------------CCEEEEEEECCEEEEEEEECEEEEEECHH--HHC-HHHHCCCCCCCCCCCCEEEEEECCCCC--------------------CCCCEEECCCCCEEEEEE----EEEEEECCCEEEEEE--EEEEEEECCCCEEEECCC--CHHHHHHHHHHCC-----C >P1;d2bona1 ----CCEEEEECC---CCCCCHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHCCCCCCHHHHHHHHHH--CEEEEEEEEEECC--------CCEECCEEEEEEEEECCCHHHHHHHHHCCCEEEEECEEEEEEECC-EEEEEEECEEEEE-CCCCCCCCCCCCC---CCCCCCCCEEEEEECC--CCCCHHHHHHHHC--CC--CCCCEEEEEEC---EEEEEEE---EEEEEEECC---EEEEE-EEEEEEEEEEEEEEEECC--CCCCCC------------- >P1;d2qv7a1 ---CEEEEEEECCCCCCCCHHHHHHHHHHHHHHCCEEEEEEECCCCCHHHHHHHHCC-CCCCEEEEECCHHHHHHHHHHHCCCC--CCCEEEEECC-CCCHHHHHCCCCCCC-CHHHHHHH--CCEEEEEEEEC----------CCCCCCEEEECCCCC----CCCCCCCCCC----CCCEEEEEEECC-EEEEEEEEEEEEE-CCCCCCCC-CCCC---CCCCCCCCEEEEEEECCCHHHHHHC-CCHHH--CCHHHCCCEEEEEEC---EEEEECC---CC-CCEECC---EECCC-CCEEEEEEEEEEEEECCCCCCCCCCC------CCCCCCC >P1;d3s40a- CCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHCC-CCCEEEEEECHHHHHHHHHHHCCCC--CCCEEEEEECCCCCHHHHHCCCCCCHHHHHHHHCC--CCCCCEEEEEEC---------CEEECCEEEECC-----------CCCC-----CCCCEEEEEEECC-EEEEEEEEEE-EE-CCCEECCEECCCC---CCCCCCCCEEEEEEEC---CCHHHHHHHCCCCCCCCCCCCCEEEEEEC---EEEEEEC---CCCEEEEC-----CCEE-CCEEEEEEEEEECCCCCCCC------------------- >P1;d4wera1 ----CEEEEEECCCCCCCCHHHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE-CCHHHHHHHHHHHCCCC--CCCEEEECCCCCCCHHHHHCCCC-CHHHHHHCCCC--CCEEEEEEEEEC---------CEEE-CEEEECCCCCCCCHHHHHHCCC-----CCCCEEEEEEECC-EEEEEEECCEEEE-CCCCCCCCCCCCC---CCCCCCCCEEEEEECCCCCCHHHHCHHHHHHCCCCCC--CCEEEEEEC---EEEEEEC-CCCCCEEEECC---EEEEE-CCEEEEEEEEEEEEECC---------------------- PSA >P1;d1u0ta- ----5101000769---a467a1075037308649080646-------------------5100000153a1014002029-----5612000003ba21001--023295066008403666083361000301034d883356410010000221399------------------a503040027b853360104000000000--004-504719042051a56000000180a3b--------------------5282131619040004068b475030300943505022203010431b51040021b2571661135339486ab893 >P1;d1z0sa- ----4400001469-------a40950260066190904318--------91376028--050000001240005001404-----60110000223920100--013198067505510653-63160000206------207a110020000203599------------------72040004059743150504000000000--005-40371804213047400000026074b--------------------938143250755020207----602010082645615--650205319310100418--6056405721772-----f >P1;d2bona1 ----630000048---a05a48606710670475a150222309699106620640294904000000427001500310180a6a93000000102b42000700603a52670042005--2904400002047--------7400000000002753b8a3246014600505608236030505b-1426560000000-0020122702003---9030114401010032--8605870150069--95--a3870363303---3040505---760001006---74325-570304026520501018--904016------------- >P1;d2qv7a1 ---553010003271185716951670364048260505123087a7002500450a-5b050000002080022001000358--b214000000-941000510403982-30050026--44004000026----------a51001200003379----5263110a05----761060503149-7315540110000-00028709-4005---6030010300000036089932b60-51186--540170830214304---504050b---47-000101---76056-07070501531030000254709206------42901d7 >P1;d3s40a- 8260740000032801a8839502750252058306605224178a510271046106-50400000024b112200300042a--72010000004931100200103381250051026--151160000304---------621001302025-----------9418-----918213040415b-7515540110-00-0012101420100---5030340200000012---70480057026653593548a30203306---4030407---96380701-----3a15-06040503631050113863------------------- >P1;d4wera1 ----650000134912aa617721630362057209503144088a70035103500667110000-0337003201100033b--42030000013a32010300a12-52660087042--962330000205---------a710-21010139a8b49297989433-----b45112030305a-9543150010200-0020191457102---6071322400000040370830450462278004743--a20113206---6140305-a6591303119---88334-05050400561040013---------------------- Translating the sequences ----CEEEEEECCC---CC**HHHHHHHHHHH*CCCEEEEE-------------------CC*EEEEECHHHHHHH**HH*-----*CC*EEEEECCCCC***--C*****HHHHHHHHHH**C*EEEE**EEE***********EEECCEEEE*CCCCC------------------CCEEEEEE*CC*EEEEEEECEEEEE*C**--**C-*******CCCCCCCC*EEEEEECCCCC--------------------C***EEEC****EEEEEC***CC*EEEECC***EEE***C*EEEEE****EEEE*CC**C****************** ----CEEEEEECCC-------**HHHHHHHHHHCCCEEEEE*--------***HHH**--CCEEEEEECHHHHHHHH***C-----CCC*EEEEECCCCC***--CCCCCC*HHHHHHHHH**-CEEEE**EEEC------****EEECCEEEE**CCCC------------------CCEEEEEEECC*EEEEEEECEEEEE*C**--**C-*******CCCCCCCC*EEEEEECCCCC--------------------C***EEEC****EEEEE*----**EEEECC***EEEE--**EEEEE****EEEECCC--C************-----* ----C*EEEEECC---CCC**HHHHHHHHHHH*CCC*EEEEECCCCCHHHHHHHHH***CCCEEEEEECHHHHHHHHHHH**CC**CCCEEEEEECCCCCHHHHHCCCCCCHHHHHHHHHH--C*EEEEEEEEEC*--------C*EECCEEEE*****C*******************CEEEEEEECC-EEEEEEECEEEEE-CCC**CCC*CCCC---CCCCCCCCEEEEEE*C--CC**HH*******--CC--**CCEEEEEEC---EEEEEE*---***EEEECC---EEEE*-**EEEEEEEEEEEEE*CC--C*****------------- ---**EEEEEECCC**CCC**HHHHHHHHHHHHCC*EEEEEECCCCCHHHHHHHH**-*CCCEEEEE*CHHHHHHHHHHHC*CC--CCCEEEEE*C-CCCHHHHHCCCCCC*-*HHHHHHH--CCEEEEEEEE*----------C***CCEEEE*CCCC----**********----*CCEEEEEEECC-EEEEEEE*EEEEE-CCC**CCC-CCCC---CCCCCCCCEEEEEEECCC****HH*-*****--CC****CCEEEEEEC---EEEEE*C---CC-**EECC---EE***-C*EEEEEEEEEEEEECCC**C*****------******* ****C*EEEEECCC**CCC**HHHHHHHHHHHH*CC*EEEEECCCCCHHHHHHHHH**-CCCEEEEEECHHHHHHHHHHHC*CC--CCCEEEEEECCCCCHHHHHCCCCCCHHHHHHHH**--CC***EEEEEEC---------CEEECCEEEE*C-----------****-----**CCEEEEEEECC-EEEEEEE*EE-EE-CCC**CC**CCCC---CCCCCCCCEEEEEEEC---C**HH*********CC****CCEEEEEEC---EEEEEEC---CC*EEEEC-----**E*-C*EEEEEEEEEE***CCC**------------------- ----CEEEEEECCC**CCC**HHHHHHHHHHHH*CCEEEEEECCCCCHHHHHHHHH***CCCEEEE-*CHHHHHHHHHHHC*CC--CCCEEEE**CCCCCHHHHHCCCC-CHHHHHH****--CCEEEEEEEEEC---------CEEE-CEEEE*CCCCC***********-----**CCEEEEEEECC-EEEEEEEC*EEEE-CCC**CCC*CCCC---CCCCCCCCEEEEEE*CCCCC**HH*********CC**--CCEEEEEEC---EEEEEEC-**CC*EEEECC---EEEE*-C*EEEEEEEEEEEEECC---------------------- 111331.tem _________________________________ ----CEEEEEECCC**CCC**HHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHH***CCCEEEEEECHHHHHHHHHHHC*CC--CCCEEEEEECCCCCHHHHHCCCCCCHHHHHHHHHH--CCEEEEEEEEEC---------CEEECCEEEE*CCCCC---********-----**CCEEEEEEECC-EEEEEEECEEEEE-CCC**CCC*CCCC---CCCCCCCCEEEEEEECCCCC**HH*******--CC****CCEEEEEEC---EEEEEEC---CC*EEEECC---EEEE*-C*EEEEEEEEEEEEECCC**C*****------*-----* Structural block scores 0 3 - 4.4 M 75.0 75.0 75.0 57.5 4.0 75.0 5 10 E 4.9 H 0.3 0.8 0.5 0.7 0.7 1.0 11 13 C 4.8 H 7.3 6.3 29.0 4.0 4.3 5.3 14 15 * 3.4 M 75.0 75.0 75.0 1.0 0.5 1.5 16 18 C 4.4 M 29.8 75.0 5.2 6.7 8.8 9.0 19 20 * 1.9 P 6.5 75.0 7.2 3.5 6.0 4.0 21 32 H 4.8 H 4.2 4.0 4.3 4.4 3.4 3.5 33 35 C 4.5 M 4.3 3.3 5.5 2.7 3.0 3.7 36 41 E 4.7 H 16.5 4.2 2.3 2.7 3.2 2.8 42 46 C 4.3 M 75.0 75.0 6.6 6.5 6.3 6.7 47 55 H 4.3 M 75.0 27.9 2.8 1.8 2.4 1.9 56 58 * 2.7 P 75.0 28.3 5.0 30.2 27.0 4.0 59 61 C 4.8 H 27.0 26.7 4.3 5.5 3.0 3.0 62 67 E 4.7 H 0.2 0.0 0.0 0.0 0.0 12.5 69 79 H 4.8 H 2.1 1.5 1.7 1.2 2.2 1.5 82 83 C 4.3 M 75.0 75.0 5.2 6.5 6.2 7.2 84 85 - 4.5 M 75.0 75.0 8.2 75.0 75.0 75.0 86 88 C 4.8 H 4.0 2.3 4.0 4.8 3.0 2.0 89 94 E 4.6 H 0.3 0.5 0.2 0.7 0.2 0.5 95 99 C 4.9 H 5.6 3.2 3.9 17.8 3.4 3.9 100 104 H 4.2 M 30.2 30.2 1.4 1.2 0.6 0.8 105 110 C 4.5 M 3.5 3.7 4.1 4.0 2.5 15.6 111 120 H 4.5 M 3.3 3.5 2.6 9.3 2.2 3.5 121 122 - 4.1 M 6.0 4.0 75.0 75.0 75.0 75.0 123 124 C 4.3 M 4.0 40.5 5.5 4.0 3.0 7.5 125 133 E 4.6 H 1.8 1.3 1.1 1.3 1.2 1.1 135 143 - 4.3 M 5.3 51.0 67.4 75.0 75.0 75.0 145 147 E 4.4 M 1.7 0.7 1.3 2.0 1.0 2.7 148 149 C 4.8 H 0.5 1.0 0.0 0.5 0.5 38.5 150 153 E 5.0 H 0.0 0.0 0.0 0.5 1.2 0.5 155 159 C 4.2 M 4.8 5.2 3.4 19.4 61.0 8.4 160 162 - 4.1 M 75.0 75.0 10.0 75.0 75.0 5.0 163 170 * 3.0 P 75.0 75.0 3.2 3.6 40.2 6.5 171 175 - 4.3 M 75.0 75.0 2.0 46.0 75.0 75.0 176 177 * 3.0 P 75.0 75.0 3.0 41.0 5.0 7.8 178 179 C 4.8 H 7.8 4.5 5.0 3.5 5.0 3.0 180 186 E 4.9 H 1.3 1.1 2.4 2.1 1.9 1.3 187 188 C 5.0 H 9.2 7.0 8.2 6.5 8.2 7.8 190 196 E 5.0 H 2.6 2.6 3.4 3.6 3.9 3.9 198 202 E 4.8 H 0.0 0.0 0.0 0.2 15.2 0.6 204 206 C 4.4 M 0.0 0.0 0.7 0.0 0.3 0.7 207 208 * 2.7 P 75.0 75.0 0.5 5.0 1.5 0.5 209 211 C 4.2 M 1.3 1.7 3.7 5.3 1.7 4.7 213 216 C 4.1 M 4.0 3.5 1.2 2.2 0.2 2.5 217 219 - 4.1 M 3.3 3.0 75.0 75.0 75.0 75.0 220 227 C 5.0 H 4.2 3.1 2.8 1.6 2.1 3.1 228 234 E 4.7 H 0.1 0.3 0.7 0.4 0.1 0.6 235 239 C 4.5 M 6.6 5.7 33.2 6.4 46.8 3.6 240 241 * 2.7 P 75.0 75.0 2.5 2.5 2.0 1.5 242 243 H 4.3 M 75.0 75.0 7.5 8.8 4.0 4.5 244 250 * 2.8 P 75.0 75.0 3.0 13.7 3.7 4.1 251 252 - 4.1 M 75.0 75.0 75.0 75.0 4.0 0.0 253 254 C 4.3 M 75.0 75.0 7.0 4.5 7.0 5.5 255 258 * 3.4 M 75.0 75.0 40.9 2.0 5.0 39.2 259 260 C 4.7 H 40.0 42.0 7.5 5.5 6.8 6.2 261 266 E 4.5 M 2.8 3.5 2.5 1.7 1.3 1.2 268 270 - 4.1 M 3.3 4.0 75.0 75.0 75.0 75.0 271 276 E 4.8 H 1.3 1.5 2.0 2.3 1.8 2.3 278 280 - 4.2 M 7.8 75.0 75.0 75.0 75.0 30.5 281 282 C 4.2 M 6.0 40.5 6.5 5.5 7.5 7.0 284 287 E 4.8 H 1.5 0.8 0.2 0.2 3.8 1.8 288 289 C 4.8 H 4.5 4.0 3.0 0.5 38.0 5.0 290 292 - 4.1 M 4.0 4.0 75.0 75.0 75.0 75.0 293 296 E 4.3 M 1.8 4.2 4.0 4.5 22.4 5.5 301 313 E 4.6 H 2.3 1.9 2.2 1.9 2.2 1.9 314 316 C 4.5 M 4.8 4.3 3.0 0.7 4.0 26.3 317 318 * 3.4 M 3.5 75.0 75.0 4.5 4.5 75.0 320 324 * 2.7 P 3.0 3.0 2.2 3.4 75.0 75.0 325 330 - 4.1 M 4.5 4.8 75.0 75.0 75.0 75.0 332 336 - 4.1 M 9.0 75.0 75.0 5.1 75.0 75.0 >>>>>>