Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1b63a2 ---CCCC------CCCHHHHHHHHHHHHCC-------------------------CHHHHHHHHHHHHHHC--------------CCCEEEEEEC----HHHCCEEEEEECCCCCCHH--------HHHHHH-CCCCCCCCCCHHHHHCCC--CCCCCCCHHHHHHCCC------EEEEEEECCCCCCEEEEEEEC--CCC---EEEEEEECCC---CEEEEEEECCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCEEEEEECCCCCCCCCHHHHHHHC- >P1;d1q1da1 CHHHHCC------CCCHHHHHHHCCHHHHCCCCCEEECCCEEECCEEECCEEECHHHHHHHHHHHHHHHHHHHHCC---------CCCEEEEEEECC------CEEEEEEECCCCCCCCCCCCCCCHHHHHHHCCCCCCCCC---CCCCCC--CCCCCCCHHHHHHHC----EE-EEEEEEEECCCCEEEEEEEEC----CCCEECCCEEEECCCCCCEEEEEEEECHHHHCCCC-----CHHHHHHHHHHHHHHHHHCCCCEEEEC---CEECCCC----------------- >P1;d2hkja3 --------------CCHHHHHHHCHHHHCCCC-----------------H---HHHHHHHHHHHHHHHHHCCHHHC---------CCCEEEEEEEEEECCCCEEEEEEEECCCCCCHH--------HHHHHHHCCC----CC---CCCCCC--CCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCCEEEEEEEEEECCCCEEEEEEEEEEECCCCCCEEEEEEEEE------CC-----HHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCEEEECCCCC-----CCCCCCCC >P1;d3t0ha- -------CCEEEECCHHHHHHHHHHHH-------CCCC-------------CCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCEEEEEECC-----CCEEEEEECCCCCCHHHHHCHHHCCHHHHHHHHHHHHH-------CCCCHHHHHHHCCHHHHHHHC----EE-EEEEEEECCCC-CEEEEEECCC------CEEEEEECCCCCCCCEEEEEEEECHHHHHHHC---------HHHHHHHHHHHCCC-CCCCEEECCC------------------------- PSA >P1;d1b63a2 ---a7b8------a5442520151038207-------------------------2002004100230013--------------a054020403----7003400304050802548--------405620-53632921967a547829--3463620210000000------60200021692a702202059--870---9152472a06---4011120450032169348917858401740162037102742600020115b8533516207bd3667705a705- >P1;d1q1da1 88a9887------a26467302570791062286483525215867363804002001400120034012114427---------907401030449------41020403260130553b84833202120060511a157---695919--175592210000000----04-202020015932430303037----1074348181572693711030103010940a180-----7a3002004120140067199050215---8950758----------------- >P1;d2hkja3 --------------423036026225620026-----------------4---15002000200016002300138---------23040403053338a841030304030302428--------6017400408----78---998639--63272715110000000141a7103050024a29423304020239714051476816809ab42012100001------03-----06803980241067126803002030400556546142649-----71584377 >P1;d3t0ha- -------84462806730470052038-------5a18-------------6210002000440162066048306957631834870102030549-----6310101020101339403910429057107502621a-------8a0501302719000000000----06-301010221a3-710002050c------44020441a89718001202020288145005---------49206602961059-2a16060473------------------------- Translating the sequences ---****------CCCHHHHHHH*HHHH*C-------------------------*HHHHHHHHHHHHHH*--------------CCCEEEEEE*----****CEEEEEECCCCCCHH--------HHHHHH-CCC****CC******CCC--CCCCCCCHHHHHH*C*------EEEEEEECCCCC*EEEEEEEC--**C---EEEEEEE*CC---CEEEEEEE*C**************HHHHHHHHHHHHHHHHHCCCCEEEE**C***E***C****************- *******------CCCHHHHHHH**HHH*C************************HHHHHHHHHHHHHHHH**HH*C---------CCCEEEEEEE**------CEEEEEE*CCCCC**********HHHHHHHCCC****CC---**CCCC--CCCCCCCHHHHHHHC----**-EEEEEEE*CCCC*EEEEEEEC----C***E***EEE*CCCCCCEEEEEEEEC*******C-----*HHHHHHHHHHHHHHHHHCCCCEEEE*---**E***C----------------- --------------CCHHHHHHH*HHHH*C**-----------------*---*HHHHHHHHHHHHHHHH**HH*C---------CCCEEEEEEE*********EEEEEECCCCCCHH--------HHHHHHHCCC----CC---**CCCC--CCCCCCC*HHHHHH*********EEEEEECCCCC*EEEEEEE*****C***EEEEEEE*CCCCCCEEEEEEEE*------*C-----*HHHHHHHHHHHHHHHHHCCCCEEEE**C***E***C****-----******** -------******CC*HHHHHHH*HHH-------****-------------***HHHHHHHHHHHHHHHH**HH*C*********CCC*EEEEEE**-----*CEEEEEECCCCCCHH*********HHHHHH*******-------CCCC*******CCHHHHHHHC----**-EEEEEEECCCC-*EEEEEE*C*------*EEEEEE**CCCCCCEEEEEEEEC*******C---------HHHHHHHHHHH***-CCC*EEE**C------------------------- 55874-3.tem _________________________________ ---****------CCCHHHHHHH*HHHH*C**--****-----------*-***HHHHHHHHHHHHHHHH**HH*C---------CCCEEEEEEE**--****CEEEEEECCCCCCHH********HHHHHHHCCC****CC---**CCCC--CCCCCCCHHHHHHHC*---**-EEEEEEECCCCC*EEEEEEEC*-**C***EEEEEEE*CCCCCCEEEEEEEEC*******C-----*HHHHHHHHHHHHHHHHHCCCCEEEE**C***E***C****-----*******- Structural block scores 0 2 - 4.3 M 75.0 8.8 75.0 75.0 3 6 * 3.5 M 9.2 8.0 75.0 75.0 7 12 - 4.3 M 75.0 75.0 75.0 5.3 13 15 C 4.5 M 6.5 6.2 27.0 4.3 16 22 H 5.0 H 2.7 3.9 2.9 2.7 24 27 H 4.7 H 3.2 4.2 3.8 21.5 30 31 * 3.5 M 75.0 2.0 4.0 75.0 32 33 - 4.3 M 75.0 7.0 75.0 75.0 34 37 * 3.5 M 75.0 5.0 75.0 6.1 38 48 - 4.3 M 75.0 4.4 75.0 75.0 51 53 * 3.1 M 75.0 1.3 50.3 3.0 54 69 H 4.9 H 5.6 1.2 1.1 1.9 70 71 * 1.6 P 39.0 1.0 1.5 2.0 72 73 H 4.3 M 75.0 4.0 0.5 5.5 76 84 - 4.3 M 75.0 75.0 75.0 5.1 85 87 C 5.0 H 5.2 5.3 1.7 5.0 88 94 E 4.8 H 1.9 1.7 2.3 1.6 95 96 * 2.3 P 75.0 6.5 3.0 6.5 97 98 - 4.3 M 75.0 75.0 5.5 75.0 99 102 * 3.2 M 2.5 75.0 5.9 57.8 104 109 E 5.0 H 1.2 1.2 1.7 0.5 110 115 C 4.9 H 3.3 2.5 2.0 1.2 116 117 H 4.3 M 6.0 2.5 5.0 6.0 118 125 * 3.5 M 75.0 5.7 75.0 2.9 126 132 H 4.8 H 13.1 1.0 2.6 4.1 133 135 C 4.3 M 4.7 3.7 4.0 2.3 136 139 * 2.3 P 4.0 3.4 75.0 4.9 140 141 C 4.3 M 5.0 6.0 7.5 75.0 142 144 - 4.3 M 7.8 75.0 75.0 75.0 145 146 * 2.3 P 4.5 7.5 9.0 75.0 147 150 C 4.8 H 6.5 6.0 6.5 5.9 151 152 - 4.3 M 75.0 75.0 75.0 0.5 153 159 C 4.5 M 3.4 4.4 4.0 3.1 160 166 H 4.8 H 0.4 0.1 1.0 0.0 169 171 - 4.3 M 75.0 75.0 1.7 75.0 172 173 * 2.3 P 75.0 2.0 5.8 3.0 175 181 E 4.9 H 1.4 0.9 1.3 1.0 182 186 C 4.7 H 5.7 4.0 5.5 18.3 188 194 E 4.9 H 1.6 1.7 2.0 1.1 198 199 * 3.5 M 7.5 75.0 8.0 75.0 201 203 * 3.1 M 75.0 3.7 3.0 51.3 204 210 E 4.6 H 4.3 4.3 4.7 2.1 212 217 C 4.7 H 39.2 4.7 6.2 5.5 218 225 E 4.9 H 1.8 1.0 0.5 0.9 227 233 * 2.1 P 3.4 4.6 64.3 3.7 235 239 - 4.3 M 6.6 75.0 75.0 75.0 241 257 H 4.8 H 3.1 2.4 4.2 16.7 258 261 C 4.8 H 3.0 4.8 0.8 22.1 262 265 E 4.8 H 0.5 2.0 1.2 3.0 266 267 * 1.6 P 1.0 40.0 2.0 5.5 269 271 * 2.7 P 8.2 30.7 5.3 75.0 273 275 * 2.3 P 3.0 4.0 3.7 75.0 277 280 * 3.5 M 5.1 75.0 5.2 75.0 281 285 - 4.3 M 7.1 75.0 75.0 75.0 286 292 * 3.5 M 4.9 75.0 5.0 75.0 >>>>>>