Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1n55a- CCCCCEEEEECCC--CCCHHHHHHHHHHHHH-CCCCC--CCEEEEECCHHHHHHHHHHC---CCCCEEEEECCCCCC-CCCCCCCCCHHHHHHHCCCEEEECCHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEECCCHHHHHCC--CHHHHHHHHHHHHHCCCCHHHHHHEEEEECCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCEEEEECCCC-CCCHHHHHCCCCCCEEEECHHHHC-CCHHHHHHCCC--- >P1;d2h6ra- ----CCEEEECCCCHHHCCHHHHHHHHHHC-CHH---HHCCCEEEECCCCCHHHHHHHC------CCCCEECCCCCCCCCCCCCCCCHHHHHHCCCCEEEECCCCCC----CCHHHHHHHHHHHHHHCCEEEEEECC------------CHHHHHHCCC----------CCCEEEECCC---------------CCCHHHHHHHHHHC-----CCCEEEECCCCC-CHHHHHHHC-CCCCCEEECHHHHCCCCHHHHHHHHCC-- >P1;d2jgqa- ---CCEEEEECCC--CCCHHHHHHHHHHHHHHCCHHHCC--CEEEECCCCCCCCC-------CCCCCEECCCCCCCCCCCCCCCCCCHHHHHHCCCCEEEECCHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHCHHHHHHHHHHHHCCCCCC-----CCCEEEEECCHHHCCC--CCCHHHHHHHHHHHHHHCC--------CCCCEEEECCCC-CCCHHHHHCCCCCCEEEECHHHHCHHHHHHHHCCC---- >P1;d3kxqa- --CCCEEEEECCC--CCCHHH-HHHHHHHHHHHC------CEEEEECCCCCHHHHHHHHCC----CCEEEECCCCCCCCCCCCCCCCHHHHHHHCCCEEEECCHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEECCCC-CCC----CCHHHHHHHHHHHCC--CCCCCCCEEEEECCCC--------CHHHHHHHHHHHHHHHHHHHC--CCCCCCEEECCCCC--CCHHHHHCCCCCCEEEECHHHCCHHHHHHHHCCC---- >P1;d3taob- C-CCCEEEEECCC--CCCHHHHHHHHHHHHHHCCHHHHHCCEEEEECCHHHHHHHHHHHHHCCC-CCEEEECCCCCCCCCCCCCCCCHHHHHHCCCCEEEECCHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHC--CHHHHHHHHHHHHCCCCCHHHHCCCEEEECCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHCCCCEEECCCCC-CCCHHHHHCCCCCCEEEECHHHHCHHHHHHHHHHHHHCC >P1;d5csra- ---CEEEEEECCCCHHHCCHHHHHHHHHCC-CCC----CCEEEEEECCHHHHHHHHHHC------CCEECCCCCCCCCCCCCCCCCCHHHHHHHCCCEEEECCCCCC----CCHHHHHHHHHHHHHHCCEEEEEECC------------HHHHHHHHHH----------CCCEEEECCHHHCC-CCCCHHHCCCHHHHHHHHHHCCC-------CCEEEECCCCCCHHHHHHHHH-CCCCEEEECHHHHCCCCHHHHHHHHHCC- PSA >P1;d1n55a- a22410000002a--5286960481063027-19092--80200000239105202640---708302100200226-59a5bb42004604959050000001321575b0747500510010072702000000057a3275a--51581037104300820959107200000003101a4a7206274017007201710365148710770100000305-2920780182610000001a0036-53045002107--- >P1;d2h6ra- ----62000002839504396016004403-018---7290600000238005402760------b02000100221948a4bb42205605717050000113665----0899205300420681a020000036------------4840460061----------5050000128---------------96252006203843-----790400102b08-3a5067036-450400010650072a82372047016-- >P1;d2jgqa- ---4300000019--304694036006502840568247--30000034800261-------808201000210205467a2bb3300550783706000000142278580668305600620373903000000065821678993048403810920527-----1840000000220166--3065930760062028304--------980300000105-2930760091b103000016203618402500720---- >P1;d3kxqa- --3620000003a--6073a3-2b3065017414------22000001490064057201c----70200021015439293bb3400460493205000001163167690619503400500140802000000058-42a----b15a10561075000--9a05193000000033--------938304800520273055217--a0370100003b03--b508710518402000029103619402500822---- >P1;d3taob- b-2420000003a--5275850380055029105861174040000013a00720171179591-405000210125498a4ba52004603927040000011431675b0838400500410171a03000000063a20657--813850271042005c0948401600000001004b3b4907182025004200910272037800770200000906-5a404700439200000039202506700500230044a >P1;d5csra- ---511000002829402984076008707-61a----a5030000013a005400746------404000100224559b4bb33003504639070000016654----1749501700620883a020000045------------4700740482----------80510001087066-b93101727361056037207b2-------c0300001005716005401a-1704000115c0042b622830661083- Translating the sequences ***CCEEEEECCC--CCCHHHHHHHHHHHHH-CC***--CCEEEEECC***HHHHHHH*---***C*EEEECCCCCC-CCCCCCCCCHHHHHH*CCCEEEECCHHHHH*CCCCHHHHHHHHHHHHHCCCEEEEEECCC*******--**HHHHHHHHHH**C**********EEEECCHHHCC***CCCHHHHHHHHHHHHHHHHHH********C*EEE*CCCC-CCCHHHHHCCCCCCEEEECHHHHC-**HHHHHH***--- ----C*EEEECCC****C*HHHHHHHHHH*-***---**CC*EEEECC***HHHHHHH*------CC**EECCCCCCCCCCCCCCCCHHHHHH*CCCEEEECC****----CCHHHHHHHHHHHHH*CCEEEEEECC------------*HHHHHH***----------CC*EEEECC*---------------***HHHHHHHHHH*-----CCC*EEECCCCC-C**HHHHHC-CCCC*EEECHHHHC***HHHHHH****-- ---CCEEEEECCC--CCCHHHHHHHHHHHHH*CC*****--*EEEECC*******-------***CCEE**CCCCCCCCCCCCCCCCHHHHHH*CCCEEEECCHHHHH*CCCCHHHHHHHHHHHHHCCCEEEEEECCC***********HHHHHHHH****C*-----*CC*EEEECCHHHCC*--CCCHHHHHHHHHHHHHH**--------CCC*EEE*CCCC-CCCHHHHHCCCCCCEEEECHHHHC***HHHHH***---- --*CCEEEEECCC--CCCHHH-HHHHHHHHH**C------CEEEEECC***HHHHHHH***----CCEEEECCCCCCCCCCCCCCCCHHHHHH*CCCEEEECCHHHHH*CCCCHHHHHHHHHHHHHCCCEEEEEECCC*-***----**HHHHHHHHHH**C--*****CC*EEEECC**--------CHHHHHHHHHHHHHHHHHH**--**CCC*EEECCCCC--CCHHHHHCCCCCCEEEECHHH*C***HHHHH***---- *-*CCEEEEECCC--CCCHHHHHHHHHHHHH*CC*****CCEEEEECC***HHHHHHH******-CCEEEECCCCCCCCCCCCCCCCHHHHHH*CCCEEEECCHHHHH*CCCCHHHHHHHHHHHHHCCCEEEEEECCC*******--**HHHHHHHHHH**C*******CC*EEEECCHHHCC***CCCHHHHHHHHHHHHHHHHHH******CCC*EEECCCCC-CCCHHHHHCCCCCCEEEECHHHHC***HHHHHH****** ---C*EEEEECCC****C*HHHHHHHHH**-*CC----*C*EEEEECC***HHHHHHH*------CCEE**CCCCCCCCCCCCCCCCHHHHHH*CCCEEEECC****----CCHHHHHHHHHHHHH*CCEEEEEECC------------HHHHHHHHHH----------CC*EEEECCHHHCC-**CC*HH***HHHHHHHHHH***-------CC*EEECCCCC****HHHHH*-CCCCEEEECHHHHC***HHHHHH*****- 51351.tem _________________________________ --*CCEEEEECCC--CCCHHHHHHHHHHHHH*CC*****CCEEEEECC***HHHHHHH*---**-CCEEEECCCCCCCCCCCCCCCCHHHHHH*CCCEEEECCHHHHH*CCCCHHHHHHHHHHHHHCCCEEEEEECCC*******--**HHHHHHHHHH**C*-*****CC*EEEECCHHHCC***CCCHHHHHHHHHHHHHHHHHH**--**CCC*EEECCCCC-CCCHHHHHCCCCCCEEEECHHHHC***HHHHHH****-- Structural block scores 0 1 - 4.3 M 6.2 75.0 75.0 75.0 43.2 75.0 3 4 C 4.5 M 2.5 40.5 3.5 4.0 3.0 3.0 5 9 E 4.9 H 0.0 0.4 0.0 0.0 0.0 0.2 10 12 C 5.0 H 4.2 3.3 3.3 4.5 4.5 3.3 13 14 - 4.1 M 75.0 6.0 75.0 75.0 75.0 5.5 15 17 C 4.4 M 5.0 3.0 2.3 4.3 4.7 2.0 18 30 H 4.7 H 4.0 8.5 3.8 9.8 3.8 10.1 32 33 C 4.3 M 5.0 4.5 2.5 2.5 2.5 5.8 34 38 * 3.3 M 32.2 46.8 5.4 75.0 4.6 62.1 39 40 C 4.2 M 4.0 4.5 75.0 38.5 2.0 2.5 41 45 E 4.8 H 0.4 1.2 0.6 0.4 0.8 0.6 46 47 C 5.0 H 1.0 1.0 1.5 0.5 0.5 0.5 48 50 * 1.0 P 4.3 3.7 4.0 4.3 4.5 4.5 51 57 H 4.5 M 2.7 3.4 33.4 3.4 2.6 2.9 59 61 - 4.2 M 75.0 75.0 75.0 29.5 7.0 75.0 62 63 * 3.4 M 3.5 75.0 4.0 75.0 5.0 75.0 65 66 C 4.8 H 1.5 5.8 1.0 3.5 2.0 2.0 67 70 E 4.3 M 0.8 0.5 0.2 0.5 1.2 1.0 71 86 C 5.0 H 9.1 4.5 4.3 4.3 4.7 4.5 87 92 H 5.0 H 3.8 3.8 4.2 3.8 3.7 3.0 94 96 C 5.0 H 4.7 4.0 4.3 2.3 3.7 5.3 97 100 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 101 102 C 5.0 H 0.0 1.0 0.0 0.5 0.5 0.5 103 107 H 4.1 M 2.4 19.0 3.2 3.4 3.0 19.2 109 112 C 4.7 H 5.9 39.5 4.8 5.2 6.1 39.5 113 125 H 5.0 H 2.3 3.7 3.5 2.5 2.5 3.8 126 128 C 4.7 H 3.0 3.8 4.0 2.7 3.8 4.5 129 134 E 5.0 H 0.3 0.3 0.5 0.3 0.5 0.3 135 137 C 4.8 H 1.7 28.0 2.0 1.7 2.0 28.0 138 144 * 3.0 P 6.4 75.0 5.3 35.6 4.8 75.0 145 146 - 4.5 M 75.0 75.0 9.0 75.0 75.0 75.0 147 148 * 2.7 P 3.0 75.0 1.5 6.2 4.5 75.0 149 158 H 4.7 H 3.2 3.3 3.9 4.0 3.2 3.6 159 160 * 2.7 P 0.0 75.0 2.5 0.0 0.0 75.0 164 168 * 3.3 M 4.8 75.0 60.2 5.1 5.0 75.0 169 170 C 4.5 M 4.5 2.5 6.0 6.0 3.5 4.0 172 175 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.2 176 177 C 5.0 H 0.0 1.5 0.0 0.0 0.0 0.5 178 180 H 4.2 M 1.3 52.7 1.3 27.0 0.3 5.0 181 182 C 4.3 M 5.8 75.0 3.5 75.0 7.8 6.0 183 185 * 3.4 M 7.2 75.0 52.0 75.0 6.2 31.8 186 188 C 4.3 M 2.7 75.0 3.0 53.0 5.3 1.3 189 206 H 4.6 H 2.9 23.4 11.4 3.2 2.5 3.9 207 208 * 3.0 P 2.5 39.0 75.0 4.0 1.5 75.0 209 210 - 4.1 M 7.5 75.0 75.0 75.0 7.5 75.0 211 212 * 3.4 M 0.5 75.0 75.0 5.2 0.0 75.0 213 215 C 4.6 H 4.7 5.3 5.7 3.3 4.7 29.2 217 219 E 5.0 H 0.0 0.3 0.0 0.0 0.0 0.0 220 224 C 4.8 H 1.6 4.3 1.2 3.5 3.0 1.2 226 228 C 4.1 M 4.3 6.2 4.7 30.5 6.5 2.3 229 233 H 5.0 H 3.2 3.2 2.6 3.2 2.2 2.0 234 239 C 4.8 H 2.8 15.7 4.2 3.3 3.0 16.2 240 243 E 4.9 H 0.0 0.2 0.0 0.0 0.0 0.2 245 248 H 4.9 H 3.4 2.8 2.8 3.2 3.2 4.4 250 252 * 1.3 P 27.7 6.8 4.3 4.7 4.3 6.5 253 258 H 4.9 H 1.8 3.0 2.3 2.5 1.2 3.5 259 262 * 2.0 P 20.8 3.5 38.0 38.5 1.8 3.8 263 264 - 4.3 M 75.0 75.0 75.0 75.0 7.2 39.0 >>>>>>