Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ikpa2 -----------------------------------------------------------------------CCHHHCCCCCC------------------CCCCCCCCCCCCC-HHHHHHHHHHHHHCCEEEEEEEEECHHHHHHHHHCCCCCC----CCCCCHHHCCEEECCCHHHHHC---------CCCCCCCCCCCCCCCCEEEEEEEEHHHHHHEEECC-CCCCCCCHHHHHHHHHCCCCCCC----------CCEEEEECCC---------------------------------------CCCEEEEECHHHHHCCEEEECCCCCCCCCCCCCCCHHHCCHHHHCCCCCCCCCCCCC-------------------- >P1;d4dv8a1 CCHHHHHHHHHHHCHHHHHHCCHHHHHHHHHHHCCCCCCHHHHHHCCCHHHHHHHHHCCHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHCCCCCCCCCCCCC----------HHHHHHHHHHHHHCCCC-----CHHHHHHHHCCC---CCCCCCC---------------HHHHHHHHHHHHHHHHHCCCCCHHHHCC--CCCEEEEECHHHCC-------HHHHCCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCCEEECCCCCCCCCCCEEEEEECCC-CCCEEEECCCEEEECCCEEEEEEEEEEEEEC---CEEEEEEEEEEE---------------------------------------------------- >P1;d4gv2a2 -------------------------------CCCEEEECCC---------------------CCCCHHHHHHHHHHHCCC---------------------CCCEEEEEEEEEC-CCCHHHHHCCC-CCCEEEEEEECCHHHHHHHHHHCCCCC-CCCC---CCCCCCEEECCCHHHHHC---------CCCC-EEECC--EEEEEEEEEEEE---CCCEEEECCCCCCCCCCCC-----------CC----------CEEEECCCEEEC-HHHCEEEEEC---CEEEEECCCC--EEECHHHCCCCCCCCEEEECCHHH-EEEEEEEEEE----------------------------------------------------- >P1;d4k6lg- ---------------------------------------------------------------------------------------------------------CCEEEEEECCC--HHHHHHH----CCCCCCCCCCHHHHHCCCCCCCC----CC------CCCCEEEECCHHHHHHHHHHHHCCC------------CCCCCEEEEEEECCC--CEEE---CHHHHHHHHHCCC--CCCHHHHHHHH-------CCCEEEECCCCC-HHHEEEEEEEEECCCCCCEEEEE--EEECCCCCCCC----CCCCC-----CCCCCCCCCCCC-CCCCCEEECCCEEHHHCHHHCCCCCCCCCCCCCCCCCEEHHHHHHHHHCC >P1;d6ro0a- -------------------------------------------------------------------------------------------------------CCCCEEEEEECCC--HHHHHHH----CEECCCCCCCHHHHHCCCCEECC----EE------CCCEEEEECCHHHHHHHHHHHHHHHHHHHH---CCCCCCCEEEEEEEEECCC--CEEE---HHHHHHHHHHHHCHHHCCHHHHHHHH-------HCCEEEEECEEC-HHHEEEEEEEEEECCCCEEE-EE--EEECCCCCCCC----CCCCC-----CCCC-CCCCCCC-CCCCEEECCCCEEHHHHHHHCCCCC--------CCCEEEHHHCCC---CC >P1;d7aaca2 -------------------------------CCEEEEECCC---------------------C-CCHHHHHHHHHHCCCHHHC-----------------CEEEEEEEEEEEEE-CCHHHHHHHHCCCCCEEEEEEEECHHHHHHHHHHCCCCCCCCCCHHHCCCCCCEEECCCHHHHHH---------CCCC-CC--C--CCEEEEEEEEEE---CCCEEEECCCCC-CCCCCC-----------CC----------CEEEECEEEEEC-HHHCEEEC-------CEEECCCC--EEECC-CCCCCEEECEEEECCHHH-EEEEEEEEEEEEECC------------------------------------------------ PSA >P1;d1ikpa2 -----------------------------------------------------------------------52036014a89------------------9050348715507-2800150164058480100001004171067002a10656----b2b3864140020024130008---------7020a743a7764200100000026a21730151a-32291870493036008270505----------510000127a---------------------------------------d2562000014004500000000605498157a07794129706821a31a05482c-------------------- >P1;d4dv8a1 4667703750393049026518980480083028276173a812970589426301501071092068612610360184017826894386159646a478807----------87134103803760422-----202300661619---1847728---------------6852540450065048207330487026--50501202305733-------891076023a94945056a2175036916827112002010124807a810000303033-a04000089030001160404055051353a---820000020404---------------------------------------------------- >P1;d4gv2a2 -------------------------------4a06275199---------------------a28119204300540059---------------------b227035023030-76049305625-3a5010002016294185005400214-7a36---74003002000002202a---------6150-676ca--551020000000---0172331573569276139-----------c3----------300001043102-5962441605---7360200105--247189179050820000006320-0000000103----------------------------------------------------- >P1;d4k6lg- ---------------------------------------------------------------------------------------------------------37301000214--1900153----00510483320040000200232----64------40200000234a202100410154b------------808680200100029--4003---08200640373a1--70472043009-------407020017506-14102200206158854607439--5570b61666a----36028-----830480365778-2424000046100000004004180ac4a9a22a080410254058655a >P1;d6ro0a- -------------------------------------------------------------------------------------------------------9225201000322--1830057----0050338341001000030037c----51------600000002436103300642163227438---6986804140000200039--4012---0360064018528aa103a2005007-------514120034402-04002400213120666835-54--6570a51686b----55015-----9217-1a50a2a-0700101492201000011043b6b--------80904413633a---aa >P1;d7aaca2 -------------------------------4806377088---------------------9-420730360082010a628-----------------60507034024071-88068305624827221000201569508710360062268917376430010030000001004---------6050-66--b--834020000000---005134146433-27914a-----------b2----------300101062103-69535619-------a0400007--1581a-29a051600100005420-010300030406167------------------------------------------------ Translating the sequences -----------------------------------------------------------------------**HHH******------------------***C*********-****HHHHHHH***C*EE******CHHHHHHH***CCCCC----C*******CCEEE*CCHHHHH*---------**CC*****C**CC**EEEEEEEE******EEE**-C***CCC*********C******----------CC*EEEECC*---------------------------------------****EEEEC*******EEEE*******CC****************************-------------------- *************************************************************************HHH***************************C*----------***HHHHHHH***CC**-----C*HHHHHHH***---CC**CCC---------------HHHHHH***********CC********C--***EEEEE******-------****CCC*********C****************CC**EEECC**C******EEEE****C-C**E******EEE*C*C********EEEE**---***EEEE*****---------------------------------------------------- -------------------------------**********---------------------***********HHH****---------------------**C***EEEEEE*-C**HHHHH***-*CCEE*****CCHHHHHHH***CCCCC-*CCC---**CCCCEEE*CCHHHHH*---------**CC-****C--****EEEEEEEE---**CEEE***C***CCC***-----------**----------C**EE**C***C-HHH*EEEEE*---C****E****--EEEC***CCCC****EEEEC****-**EEEE****----------------------------------------------------- ---------------------------------------------------------------------------------------------------------**EEEEEE**C--HHHHHHH----C*******CCHHHHH*****CCC----CC------CCCCEEE*CCHHHHHH*********------------CC***EEEEEEE***--CEEE---C************--*C*********-------CC*EEEECC**C-HHH*EEEEE****C*C**E****--EEECC*CCCCC----****C-----************-CC************************************************ -------------------------------------------------------------------------------------------------------C***EEEEEE**C--HHHHHHH----CEE*****CCHHHHH******CC----**------CCC*EEE*CCHHHHHH**************---*C**CC**EEEEEEEE***--CEEE---****************C*********-------*C*EEEE*C**C-HHH*EEEEE****C*C**E*-**--EEECC*CCCCC----****C-----****-*******-CC***********************--------************---** -------------------------------**********---------------------*-*********HHH*******-----------------*******EEEEEE*-C**HHHHHHH***CCEE******CHHHHHHH***CCCCC**CCC*****CCCCEEE*CCHHHHHH---------**CC-**--C--CC**EEEEEEEE---**CEEE***C**-CCC***-----------**----------C**EE*E****C-HHH*EEE*-------C**E****--EEECC-CCCCC****EEEEC****-**EEEE*******CC------------------------------------------------ 56399-1.tem _________________________________ -------------------------------**********---------------------*-*********HHH******------------------***C***EEEEEE**C**HHHHHHH***CCEE*****CCHHHHHHH***CCCCC-*CCC---**CCCCEEE*CCHHHHHH***********CC*****C**CC**EEEEEEEE*****CEEE**-C***CCC*********C*********-------CC*EEEECC**C-HHH*EEEEE****C*C**E****--EEECC*CCCCC****EEEEC****-**EEEE******-CC***********************------------------------- Structural block scores 0 30 - 4.5 M 75.0 4.4 75.0 75.0 75.0 75.0 31 40 * 3.4 M 75.0 4.7 5.3 75.0 75.0 5.1 41 61 - 4.5 M 75.0 3.8 75.0 75.0 75.0 75.0 64 72 * 3.2 M 59.1 3.6 3.1 75.0 75.0 2.8 73 75 H 4.3 M 3.0 3.0 3.0 75.0 75.0 3.3 76 81 * 2.9 P 5.4 2.3 27.3 75.0 75.0 3.2 82 99 - 4.5 M 75.0 5.9 75.0 75.0 75.0 71.3 100 102 * 2.9 P 4.7 7.7 29.5 75.0 75.0 3.7 104 106 * 1.9 P 5.0 52.3 3.3 28.3 3.0 3.3 107 112 E 4.2 M 4.2 75.0 2.2 0.7 0.5 2.8 113 114 * 3.0 P 38.5 75.0 37.5 1.5 2.5 38.0 116 117 * 2.7 P 0.0 4.0 3.0 75.0 75.0 4.0 118 124 H 4.9 H 2.4 2.7 4.1 2.7 3.4 4.3 125 127 * 2.9 P 5.7 5.3 27.7 75.0 75.0 4.7 128 129 C 4.4 M 4.0 2.0 7.8 37.5 37.5 4.5 130 131 E 4.1 M 0.5 2.0 0.5 2.5 2.5 1.5 132 136 * 1.9 P 0.2 75.0 0.4 3.2 3.4 0.4 137 138 C 4.3 M 2.0 1.0 3.5 2.5 2.5 3.0 139 145 H 4.7 H 3.1 2.6 4.1 0.6 0.1 5.1 146 148 * 1.0 P 4.2 5.3 3.0 0.7 1.0 3.0 149 153 C 4.4 M 3.6 46.8 1.4 31.4 34.5 2.0 156 158 C 4.2 M 53.8 5.7 6.5 28.3 27.0 5.7 159 161 - 4.1 M 5.5 75.0 75.0 75.0 75.0 5.3 162 163 * 3.4 M 7.0 75.0 5.5 75.0 75.0 3.5 164 167 C 4.3 M 2.2 75.0 0.8 1.5 1.5 0.2 168 170 E 4.5 M 0.7 75.0 0.7 0.0 0.0 1.0 172 173 C 4.5 M 3.0 75.0 0.0 2.5 3.0 0.0 174 179 H 4.9 H 2.0 5.0 2.8 3.2 2.7 0.8 180 190 * 3.1 M 62.0 3.1 62.0 16.0 3.0 61.9 191 192 C 4.2 M 1.0 3.5 2.5 75.0 3.5 2.5 193 197 * 3.0 P 7.0 3.6 21.3 75.0 47.8 47.4 199 200 * 3.4 M 6.5 1.0 75.0 75.0 7.0 75.0 201 202 C 4.3 M 3.0 40.5 5.0 4.0 4.0 5.5 203 204 * 1.4 P 0.0 40.0 0.5 7.0 2.5 2.0 205 212 E 4.8 H 0.4 1.6 0.2 1.4 0.8 0.2 213 217 * 2.7 P 5.3 3.6 45.2 32.2 32.4 45.0 219 221 E 4.5 M 2.0 75.0 2.7 1.0 1.0 2.7 222 223 * 3.4 M 5.8 75.0 3.0 75.0 75.0 2.5 226 228 * 1.3 P 4.3 3.3 6.7 3.3 3.0 27.0 229 231 C 4.1 M 5.3 4.3 5.0 3.3 3.3 6.0 232 240 * 2.3 P 2.8 5.2 51.4 20.2 5.1 51.7 242 250 * 2.6 P 27.1 4.5 60.1 3.2 3.1 59.8 251 257 - 4.5 M 75.0 4.9 75.0 75.0 75.0 75.0 258 259 C 4.3 M 3.0 1.5 1.5 2.0 3.0 1.5 261 264 E 4.5 M 0.2 0.8 0.2 0.5 0.8 0.5 265 266 C 4.1 M 4.5 0.5 3.5 4.0 3.5 4.0 267 268 * 1.4 P 42.8 3.0 0.5 2.5 2.0 0.5 271 273 H 4.2 M 75.0 8.5 6.7 2.0 1.3 6.7 275 279 E 4.3 M 75.0 0.6 3.0 1.2 1.6 19.2 280 283 * 3.2 M 75.0 1.5 57.5 3.0 1.8 75.0 287 288 * 1.9 P 75.0 2.0 1.0 5.0 7.0 2.0 290 293 * 2.1 P 75.0 2.0 1.5 5.8 22.2 1.8 294 295 - 4.5 M 75.0 4.5 75.0 75.0 75.0 75.0 296 298 E 4.5 M 75.0 1.0 4.3 5.7 6.0 4.7 299 300 C 4.2 M 75.0 0.5 4.5 5.8 5.2 5.8 302 306 C 4.2 M 75.0 2.8 4.4 5.9 6.5 5.3 307 310 * 2.7 P 6.6 2.5 2.5 75.0 75.0 1.8 311 314 E 4.1 M 0.5 3.5 0.0 2.8 2.8 0.2 316 319 * 3.2 M 1.2 58.9 2.8 75.0 75.0 2.8 321 322 * 1.0 P 2.5 1.0 0.0 5.5 5.5 0.5 323 326 E 4.1 M 0.0 0.0 0.0 3.0 21.0 0.8 327 332 * 1.4 P 1.8 14.2 25.7 6.0 6.4 2.2 334 335 C 4.3 M 8.5 75.0 75.0 3.0 3.5 6.5 336 358 * 3.4 M 4.8 75.0 75.0 1.5 2.5 75.0 359 383 - 4.2 M 61.3 75.0 75.0 5.4 35.9 75.0 >>>>>>