Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1muga- ------------------------------------------------------CCCCCCCCCCCEEEEECCCCHH-HHHHCCCCCCC------------------------------------CCCHHHHHHHCC-CCCCCCC-----------HHHHHHHH-H---HCEEEEECCCCCC-C------CHHHCC----HHHHHHHHHHHHHHHHHHCCCEEEEEC-HHHHHHHH----CCC-CCCCEEEEEEEC--CEEEEEECCCCCCCC--C--CHHHHHHHHHHHHHHCCC-------------------------------- >P1;d1oe4a- -----------CCCHHHHHHHHHHHHHHHHCCCCCCCCCEEECHHHHCHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHH-C-------------------CHHHHHC-----CEEEEECCCCEEECCCCCEECHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEC-HHHHHHHHHHHHHC--------------CCCCEEEEECCCCCCCHHHCCCHHHHHHHHHHHH-CCHHHHC------------------------------ >P1;d1vk2a- ----------------CCCCCCCHHHHHHCCC------------CCHHHHCCCCCCCCEECCCCCEEEEECCCCCC-CC-CCCCCCCC------------------------------------CCCHHHHHHHCC------CC--------------HHH---------CEEEECCCCCC-H------HHCCCC----HHHHHHHHHHHHHHHHHHCCCEEEEEC-HHHHHHCCC---CCCCCCCCCCCEEC-HH-HCEEEEECCHHHHHHCCCHHHHHHHHHHHHHHHCCCC--------------------------------- >P1;d1wywa- ------------------------------------------------CCHHHCCCCCCCCCCCCEEEEECCCCHH-HHHHCCCCCCC------------------------------------CCCHHHHHHHCC-CCCCCCC-----------HHHHHHHHHH---HCEEEEECCCCCC-C------CHHHCC----HHHHHHHHHHHHHHHHHHCCCEEEEEC-HHHHHHHHHHCCCCCCCCCCEECCCCCCCCCCEEEEECCCCCCCCCCC--CHHHCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC >P1;d2c53a- CHHHHCCCCCCHHHHHHHHHHHHCHHHHHHHHHHHHHHH--HCCEECCHHHCCCHHHHCCHHHCCEEEEECCCCCCCCCCCCCCCCCC----------------------------CC-CCCHHHHHHHHHHHHHCC--------------CCCCCCCHHHCC-----CCEEEEECCCCEECC----------CCCCCC-CCHHHHHHHHHHHHHHC-CCCEEEEECHHHHHHCC--CC------------------CCEEEEECCCCCCC-CCCCCCCCHHHHHHHHHHC-----CCCCCCCCC---------------------- >P1;d2hxma2 ---------CCHHHHHHHHHHCCCHHHHHHHHHHHHHHH--HCCEECCHHHCCHHHCCCCHHHCCEEEEECCCCCCCCCCCCCCCCCCC---------------------------CC-CCCHHHHHHHHHHHHHCC------------CCCCCCCCCCHHHHH----CCEEEEECCCCEECC----------CCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECHHHHHHCCCCCC-----------------CCCEEEEECCCCCCCHHHCCCCCCHHHHHHHHHHH----CCCCCCCCCCC--------------------- >P1;d2q07a2 ----------------------------------------------------------------------------------------------------------------------------CHHHHHHHHHCCCCCCEEEEEECCCCCCHHHCHHHHHHHHHCCCCCEEEEECCCCEEEHHHCCC--------CCCHHHHHHHHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHC----------------CCCCEEEECCCCCCCC--------HHHHHHHHHHHCCC---------------------------------C >P1;d4wpka1 -CCCCHHHHCCHHHHHHCHHHH--HHHHHHHHHHHHHHH-HCCCCCCCHHHCCHHHH-CCHHHCCEEEEECCCCCCCCCCCCCCCCCCC---------------------------CCCCCCHHHHHHHHHHHHHHC-------------CCCCCCCCCHHHHC----CCEEEEECCCCCCCC----------CCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHCC-----------------CCEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHH----CCCCCCCCCCC--------------------- PSA >P1;d1muga- ------------------------------------------------------b0920038b0100002100664-01953401068------------------------------------612004004407-0084406-----------26206502-7---2700001008530-7------448406----693046006604730673705000003-36001100----648-c195251b440c--b0300000203272a--3--73860053046017409a-------------------------------- >P1;d1oe4a- -----------b40085008105501840781807740522010070024004500440075504000002002220000000010008204800705480870a8105736050180655251023004005500-8-------------------8083007-----400010000000018606303065037a13460072026100300530605100002-82016203700475--------------91a060500120249378079a049404730781-9029305------------------------------ >P1;d1vk2a- ----------------8737637512670537------------61602721750010434270500000300566-10-62500219------------------------------------201045006419------07--------------175---------00000000110-4------a44605----790283116004300810701000001-60001103a---88491842082271-7b-912000012045027596b703620260075037328--------------------------------- >P1;d1wywa- ------------------------------------------------7a367350732056b0000001100a44-0064530103a------------------------------------911006004307-0077416-----------16207500b5---1300001008501-6------c15a07----583055206401630362705000000-3500510060118693c08124076403a190200000302482a610--20500102034033211634a59294a95477372647805633665877 >P1;d2c53a- 809704506056404500430194860870283066228--616010456200000320508602000015102264b2021001006----------------------------b2-811420630160047037--------------214b40105500-----500000100000457----------564304-16053002400650284-64100000183028301--77------------------60101534402492-9670380600340163068-----a48407030---------------------- >P1;d2hxma2 ---------12a2057304d12a4810770492166127--646010368101100411407602000014102435920010010056---------------------------91-81171041006006803a------------907419001023006----200000100000217----------545205753016006200720284273000000293039006a044-----------------9302024124035a107770190500450282067----1a394050460--------------------- >P1;d2q07a2 ----------------------------------------------------------------------------------------------------------------------------a93075026308161600000121b663054092054036507030000001275000151077--------a138930550181025005409060000002c12370054038----------------50b0703100696135--------a601640283072a---------------------------------b >P1;d4wpka1 -096608520280018108614--b30550262077178-494811074a3003004-2516502000003001365b20220000045---------------------------817921810520060025019-------------36507402011006----300000100000418----------552305945035003100520081b330000001820360461087-----------------c403004132034920867046140044028406a----2a184070407--------------------- Translating the sequences ------------------------------------------------------*****C***CCEEEEECCCC**-****CCCCCCC------------------------------------***HHHHHHH*C-*******-----------***HHHHH-*---*CEEEEECCCC**-C------****CC----***HHHHHHHHHHHHHHHCCCEEEEE*-HHHHHH**----***-************--C*EEEEECCCCCCC*--C--***HHHHHHHHHH*****-------------------------------- -----------************************************************C***CCEEEEECCCC*******CCCCCC****************************************HHHHHHH**-*-------------------*HHHHH*-----CEEEEECCCC***C**********CC*******HHHHHHHHHHHHHHHCCCEEEEE*-HHHHHH********--------------**CCEEEEECCCCCCC***C*****HHHHHHHHH-*******------------------------------ ----------------****************------------*******************CCEEEEECCCC**-**-*CCCCCCC------------------------------------***HHHHHHH*C------**--------------HHH---------*EEEECCCC**-*------****CC----***HHHHHHHHHHHHHHHCCCEEEEE*-HHHHHH***---**************-**-*CEEEEECC********C*****HHHHHHHHHH****--------------------------------- ------------------------------------------------***********C***CCEEEEECCCC**-****CCCCCCC------------------------------------***HHHHHHH*C-*******-----------***HHHHH**---*CEEEEECCCC**-C------****CC----***HHHHHHHHHHHHHHHCCCEEEEE*-HHHHHH************************CCEEEEECCCCCCC***C--***H*HHHHHHHH************************************* ***************************************--******************C***CCEEEEECCCC*******CCCCCCC----------------------------**-********HHHHHHH*C*--------------*******HHH**-----*CEEEEECCCC***C----------CC****-**HHHHHHHHHHHHHH*-CC*EEEE**HHHHHH**--**------------------CCEEEEECCCCCCC-**C*****HHHHHHHHHH*-----*********---------------------- ---------******************************--******************C***CCEEEEECCCC*******CCCCCCC*---------------------------**-********HHHHHHH*C*------------**********HHHH*----*CEEEEECCCC***C----------CC*******HHHHHHHHHHHHHHHCCC*EEEE**HHHHHH******-----------------*CCEEEEECCCCCCC***C*****HHHHHHHHHH*----***********--------------------- ----------------------------------------------------------------------------------------------------------------------------***HHHHHHH*C**********************HHHHH******CEEEEECCCC*********--------******HHHHHHHHHHHHHHHCCCEEEE****HHHHH******----------------**CCEEEE*CCCCCCC--------*HHHHHHHHHH***---------------------------------* -*********************--***************-*****************-*C***CCEEEEECCCC*******CCCCCCC*---------------------------***********HHHHHHH***-------------*********HHHH*----*CEEEEECCCC***C----------CC*******HHHHHHHHHHHHHH*CCCEEEEE**HHHHHH******-----------------*C*EEEEECCCCCCC***C*****HHHHHHHHHH*----***********--------------------- 52141.tem _________________________________ ---------******************************--******************C***CCEEEEECCCC*******CCCCCCC*---------------------------**-********HHHHHHH*C********------********HHHHH**---*CEEEEECCCC***C------****CC*******HHHHHHHHHHHHHHHCCCEEEEE**HHHHHH*********-**********-***CCEEEEECCCCCCC***C*****HHHHHHHHHH****************--------------------- Structural block scores 0 8 - 4.3 M 75.0 75.0 75.0 75.0 4.3 75.0 75.0 12.3 9 38 * 3.2 M 75.0 8.6 37.6 75.0 3.7 4.2 75.0 8.4 39 40 - 4.5 M 75.0 2.0 75.0 75.0 75.0 75.0 75.0 39.5 41 58 * 2.5 P 55.4 1.7 14.8 32.1 2.0 2.4 75.0 7.3 60 62 * 1.7 P 7.5 5.7 4.3 7.5 4.7 4.3 75.0 4.0 63 64 C 4.7 H 0.5 2.0 2.5 0.0 1.0 1.0 75.0 1.0 65 69 E 4.7 H 0.4 0.0 0.0 0.2 0.2 0.2 75.0 0.0 70 73 C 4.7 H 1.8 1.0 2.0 2.9 2.0 1.8 75.0 1.0 74 80 * 2.0 P 14.3 0.6 24.1 13.3 3.9 3.3 75.0 4.2 81 87 C 4.7 H 3.1 0.1 2.7 3.2 1.1 1.0 75.0 0.9 89 115 - 4.7 H 75.0 3.7 75.0 75.0 75.0 75.0 75.0 75.0 116 117 * 3.4 M 75.0 4.0 75.0 75.0 6.8 5.0 75.0 4.5 119 126 * 2.5 P 48.0 2.9 47.2 48.2 3.1 2.9 49.7 3.5 127 133 H 5.0 H 1.7 2.0 2.7 1.9 2.6 2.9 3.3 1.9 136 143 * 3.6 M 12.1 66.6 57.1 12.5 66.5 66.9 1.8 66.8 144 149 - 4.6 H 75.0 75.0 75.0 75.0 75.0 64.0 3.6 75.0 150 157 * 3.0 P 48.1 66.6 75.0 48.0 12.3 2.8 3.6 3.4 158 162 H 4.6 H 2.6 2.2 32.6 2.4 2.0 1.0 2.4 0.4 163 164 * 3.4 M 41.0 41.0 75.0 8.2 75.0 40.5 5.5 40.5 165 167 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 2.3 75.0 170 174 E 4.9 H 0.2 0.2 0.0 0.2 0.2 0.2 0.0 0.2 175 178 C 5.0 H 3.2 0.0 0.2 3.2 0.0 0.0 3.8 0.0 179 181 * 1.6 P 26.0 0.0 25.3 25.3 3.0 1.0 0.0 1.7 183 188 - 4.4 M 75.0 3.8 75.0 75.0 75.0 75.0 15.8 75.0 189 192 * 3.4 M 5.0 3.5 6.1 7.2 75.0 75.0 75.0 75.0 193 194 C 4.7 H 3.0 1.5 2.5 3.5 5.5 4.5 75.0 5.0 195 201 * 2.3 P 45.4 4.5 45.1 45.1 13.3 3.9 15.6 4.0 202 216 H 5.0 H 3.5 1.9 2.5 2.9 2.6 2.5 2.4 1.9 217 219 C 4.9 H 4.0 3.7 2.7 4.0 28.3 4.0 5.0 5.8 220 224 E 4.8 H 0.0 0.2 0.0 0.0 0.2 0.0 0.0 0.0 225 226 * 2.2 P 39.0 38.5 38.0 37.5 0.5 1.0 1.0 0.5 227 232 H 5.0 H 1.8 3.2 1.3 2.3 4.0 4.0 4.2 3.2 233 241 * 2.5 P 35.3 11.2 28.7 3.4 43.3 27.7 27.2 27.9 243 252 * 3.9 M 5.5 75.0 3.5 4.5 75.0 75.0 75.0 75.0 254 256 * 3.4 M 54.2 28.3 31.2 4.8 75.0 53.0 26.7 54.2 257 258 C 4.5 M 5.8 5.2 5.0 4.5 3.0 1.5 5.8 2.0 259 263 E 4.9 H 0.6 2.2 0.4 0.4 2.0 1.8 2.2 1.6 264 270 C 4.8 H 2.3 3.0 2.0 2.7 3.6 3.6 4.3 3.3 271 273 * 2.3 P 53.5 5.0 7.0 5.8 30.0 4.7 75.0 4.7 275 279 * 2.0 P 33.6 6.5 5.5 31.4 3.4 3.0 62.1 3.0 280 289 H 4.9 H 2.5 10.9 2.5 1.3 2.3 2.7 3.0 2.8 290 305 * 3.2 M 53.5 43.9 57.5 5.2 30.9 21.8 62.2 22.1 306 326 - 4.7 H 75.0 75.0 75.0 5.3 75.0 75.0 72.0 75.0 >>>>>>