Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1h7sa2 ----------------------------C------------------------EEE---C-CHHHHHHHHHHHHHHC----------------CCCEEEEEEEHHHCCEEEEEECCCCCC----HH----HCHHHHC---CCCCCCEEECCCCCHHHHHHHHC-EEEEEEECCCCCCCEEECCCCCCCC---CCEECCCC-----CEEEEEEECCCCCCHHHHHHHHHCHHHHHHCCHHHHHHHHHCCCCEEEEEEECCCCCEEEEEECCCCC-------CHHHHHHHHC >P1;d1i58a- ----CC--CEEECHHHHCCHHHHHHHHHHHC-CCCEEEEEECC-------CCEEE-HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCEEEEEEEEEEC-CEEEEEEEECCCCCC-------HHHHHHHHHHCCCCCHHHHCCCC---HHHHHHHHHCCCCCC---------------------------------------------------------CCCHHHHCCCHHHHHHHHHHHC-CCEEEEEEECCCEEEEEEEEECC------------------- >P1;d1s14a- ------------------------------------------------------CC---CCCCHHHHHHHHHHHHHHHHC--------C----CCCEEEEEECCC--CCEEEEECCCCCCCCCCCCCCCCHHHHHHH------------------CCHHHHHEEEEEEEEEECC--EEEEEEEECCEEEEEEEEEEE-CCCC---CCEEEEEEEECHH---HC-CCCCCCHHHHH--HHHHHHHHHCCCCEEEEEECCCC--EEEEEECCC------------------- >P1;d2e0aa2 CCCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCEEEE--CHHHHHHHHHHHHHHHHHHHH---HHCCC--CCCCCCEEEEEEECC-CEEEEEEEECCCCCC----------------------------------HHHHHHHCCCCCCCCC-----------------------------------------------------CCCCCCCCC-CCHHHHHHHHHHHC-CCEEEEEEECCCEEEEEEEEECCHHHCCCCCCCCCHHHHHHC >P1;d3cwva1 -------------CCHHHHHHHCCHHHHC------------------------CCC---HHHHHHHHHHHHHHHHHHHHC--------C----CCCEEEEEECCC--CCEEEEEEECCCC--------HHHHHHHHCCCCHHHCCCCCCCCCCCCHHHHHHCEEEEEEEEEECC--EEEEEEEECCEECCCCEEECCCCCCCCCCCEEEEEEEEECCC---CC-CCCCCCHHHHH--HHHHHHHHHCCCCEEEEEECC--CCEEEEEECCC------------------- >P1;d4k4oa1 ---------------CHHHHHHCHHHHHC------------------------CCC---HHHHHHHHHHHHHHHHHHHHC--------C----CCCEEEEEECCC--CCEEEEECCCCCCCCCCCCCCCCHHHHHHHC---------------CCHHHHHHCEEEEEEEEEECC--EEEEEEEECCEECCCCEEEEE-C--C---CCEEEEEEEECCC---CCCCCCCCCHHHHH--HHHHHHHHHCCCCEEEEEECCCCCCEEEEEECCC------------------- PSA >P1;d1h7sa2 ----------------------------7------------------------742---2-3010013100150192----------------a06405050442013202040405024----79----7085108---b5946752006397010000200-4030101277495014004470706---74474718-----401212064003347a1266037617922752720272026127250303025aa9855710708027-------559505a305 >P1;d1i58a- ----d8--62020250075047306420772-b0406031644-------90501-45106501600320043004720035830682917450302020554c-a30001040403037-------15501720384851788607707---665007111589037---------------------------------------------------------6162599a32124102720570-a0705060693801301030229------------------- >P1;d1s14a- ------------------------------------------------------25---443006001500580072055--------9----409402020277--300102020502419537846312013504------------------7341062043020402272--421200048382447154378-2b89---5200111020157---50-84470237501--74046205804704010403269--65561348b------------------- >P1;d2e0aa2 b939d7513805015106600630271056429500716164507267a6704040--018203300210015002500---4506a--699122060304069-640204020501035----------------------------------9711a51065731719-----------------------------------------------------82b620206-15100303630332-3040207075a6014110402045951745597868737698 >P1;d3cwva1 -------------9b30570187136206------------------------543---560002001100600451056--------a----307200020237--5000000002605--------382035005020066858594000623000000002602000027a--8042050570304c8184179358033938200202010069---10-854a0427203--730560057145040000157--7a54441346c------------------- >P1;d4k4oa1 ---------------a1760177166309------------------------533---470003002200660082174--------8----508503000157--20010203050261b62a7374120024016---------------321000000021010301296--401301064082597074269-1--b---4601102040056---00784370619300--640650066255050102041aa56534723389------------------- Translating the sequences ----------------------------*------------------------***---*-*HHHHHHHHHHHHHH*----------------CCCEEEEEE*****C*EEEEECCCCCC----**----H*HHHH*---***************HHHHHH**-EEEEEEE*CC****EEE***CC***---**E***C*-----C*EEEEEE**C************C*HHHHH**HHHHHHHHHCCCCEEEEEE*CCC**EEEEEECCC**-------********** ----**--********H**HHH**HHHH***-***********-------*****-***HHHHHHHHHHHHHHHHHH**C********C*******EEEEEE*C-****EEEEECCCCCC-------***HHHHHH**************---**HHHHHH*******---------------------------------------------------------CCC**HH*****HHHHHHHHHC-CCEEEEEE*CCC**EEEEEE*CC------------------- ------------------------------------------------------**---****HHHHHHHHHHHHHHHHC--------C----CCCEEEEEECC*--C*EEEEECCCCCC**********HHHHHH*------------------**HHHH***EEEEEEE*CC--**EEE***CC********E**-C***---C*EEEEEE**C**---**-CCCCCCHHHHH--HHHHHHHHHCCCCEEEEEE*CCC--EEEEEECCC------------------- ****************H**HHH**HHHH****************************--*HHHHHHHHHHHHHHHHHHHH---*****--****CC*EEEEEECC-****EEEEECCCCCC----------------------------------*HHHHHH*********-----------------------------------------------------*CCCCCC**-****HHHHHHHHHC-CCEEEEEE*CCC**EEEEEE*CC******************* -------------***H**HHH**HHHH*------------------------***---HHHHHHHHHHHHHHHHHHHHC--------C----CCCEEEEEECC*--C*EEEEE**CCCC--------**HHHHHH*******************HHHHHH***EEEEEEE*CC--**EEE***CC********E***C******C*EEEEEE**C**---**-CCCCCCHHHHH--HHHHHHHHHCCCCEEEEEE*C--**EEEEEECCC------------------- ---------------*H**HHH**HHHH*------------------------***---HHHHHHHHHHHHHHHHHHHHC--------C----CCCEEEEEECC*--C*EEEEECCCCCC**********HHHHHH**---------------**HHHHHH***EEEEEEE*CC--**EEE***CC********E**-C--*---C*EEEEEE**C**---***CCCCCCHHHHH--HHHHHHHHHCCCCEEEEEE*CCC**EEEEEECCC------------------- 55874-2.tem _________________________________ -------------***H**HHH**HHHH*------------------------***---HHHHHHHHHHHHHHHHHHHHC--------C----CCCEEEEEECC***C*EEEEECCCCCC----**-***HHHHHH**--**********---**HHHHHH***EEEEEEE*CC--**EEE***CC********E**-C*-*---C*EEEEEE**C**---***CCCCCCHHHHH**HHHHHHHHHCCCCEEEEEE*CCC**EEEEEECCC------------------- Structural block scores 0 12 - 4.3 M 75.0 37.0 75.0 5.8 75.0 75.0 13 15 * 3.2 M 75.0 2.3 75.0 2.3 7.8 53.5 17 18 * 2.7 P 75.0 6.0 75.0 6.0 6.0 6.5 19 21 H 4.3 M 75.0 3.7 75.0 2.0 3.0 2.7 22 23 * 2.7 P 75.0 1.5 75.0 1.5 4.0 4.0 24 27 H 4.3 M 75.0 3.0 75.0 2.5 2.8 3.8 29 52 - 4.2 M 75.0 27.6 75.0 4.4 75.0 75.0 53 55 * 1.6 P 4.3 25.3 27.3 1.3 4.0 3.7 56 58 - 4.4 M 75.0 3.3 75.0 50.0 75.0 75.0 59 78 H 4.7 H 12.7 2.1 2.5 1.6 1.8 2.4 80 87 - 4.2 M 75.0 4.4 75.0 31.3 75.0 75.0 89 92 - 4.1 M 75.0 4.2 75.0 6.2 75.0 75.0 93 95 C 4.4 M 5.5 1.0 4.3 1.3 3.3 4.3 96 101 E 5.0 H 2.3 2.3 1.3 2.2 0.7 1.3 102 103 C 4.3 M 4.0 8.2 4.5 7.5 2.5 3.0 104 106 * 3.2 M 1.0 29.5 52.3 28.3 52.3 52.3 109 113 E 5.0 H 1.2 1.0 0.6 1.2 0.0 0.6 114 119 C 4.8 H 2.5 2.8 2.2 2.3 2.2 2.7 120 123 - 4.1 M 75.0 75.0 4.5 75.0 75.0 5.1 124 125 * 3.4 M 8.0 75.0 7.5 75.0 75.0 8.8 127 129 * 2.9 P 75.0 3.7 3.3 75.0 28.7 4.0 130 135 H 4.5 M 3.5 2.2 1.8 75.0 1.7 1.3 136 137 * 2.6 P 41.5 6.0 39.5 75.0 2.5 3.5 138 139 - 4.1 M 75.0 6.5 75.0 75.0 1.0 75.0 140 149 * 3.4 M 5.0 5.1 75.0 75.0 5.1 75.0 150 152 - 4.1 M 6.0 75.0 75.0 75.0 2.0 75.0 153 154 * 2.3 P 3.5 6.0 75.0 42.0 2.5 2.5 155 160 H 4.8 H 0.5 2.3 3.5 4.2 0.0 0.2 161 163 * 1.3 P 25.0 4.7 2.0 3.7 0.7 0.7 164 170 E 4.2 M 1.3 34.9 1.6 14.7 1.1 0.9 172 173 C 4.3 M 7.0 75.0 4.5 75.0 8.8 7.5 174 175 - 4.5 M 6.5 75.0 75.0 75.0 75.0 75.0 176 177 * 2.7 P 2.5 75.0 3.0 75.0 4.0 2.0 178 180 E 4.3 M 1.7 75.0 1.0 75.0 2.0 1.3 181 183 * 2.7 P 2.7 75.0 1.3 75.0 3.3 2.3 184 185 C 4.3 M 3.5 75.0 5.5 75.0 3.5 2.0 186 193 * 3.0 P 31.1 75.0 4.4 75.0 5.1 5.2 195 196 * 2.7 P 5.5 75.0 7.5 75.0 8.0 7.5 202 204 - 4.5 M 75.0 75.0 75.0 75.0 5.0 75.0 207 212 E 4.3 M 2.0 75.0 0.5 75.0 0.7 0.7 213 214 * 2.7 P 2.0 75.0 1.0 75.0 0.5 2.0 216 217 * 2.7 P 3.0 75.0 6.0 75.0 7.5 5.5 218 220 - 4.5 M 7.2 75.0 75.0 75.0 75.0 75.0 221 223 * 2.9 P 3.0 75.0 26.7 52.7 25.3 2.3 224 229 C 4.4 M 3.8 15.8 4.2 3.9 5.2 4.7 230 234 H 4.3 M 5.4 6.7 3.2 17.4 2.8 2.6 235 236 * 3.4 M 3.5 1.5 75.0 0.5 75.0 75.0 237 245 H 5.0 H 3.1 3.1 4.0 2.3 3.7 3.7 246 249 C 4.8 H 3.0 21.4 2.8 20.0 2.5 3.0 250 255 E 5.0 H 1.8 3.0 1.5 2.2 0.8 1.3 257 259 C 4.7 H 8.7 6.7 5.7 7.2 52.3 7.3 260 261 * 1.9 P 8.5 0.5 75.0 0.5 8.8 5.5 262 267 E 5.0 H 4.2 1.2 4.3 1.7 3.5 4.0 268 270 C 4.7 H 2.7 4.3 7.8 2.0 7.5 6.7 271 289 - 4.2 M 30.6 75.0 75.0 6.3 75.0 75.0 >>>>>>