Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1k2yx1 ----------CCCCCHHH-CCCCCEEEECC-CCCCHHHHHHHHHHH--HHHHHHC--C--CCCEEEEECCCCCHHHHHHHHHHHHHCCCCC-----EEEEEC--------------CHHHHHHHHHHCCCCEEEEECCCCCC--C-CEEEEEEECC--CCCCC----CHHHHCCCCCCCCC-----------------------CCCCEECC- >P1;d1k2yx2 -----------------------------------CCHHHHHHHHHCCCCC---------CCEEEEECCCC----HHHHCHHHHHHHCCCEEE---EECCCC-CCCCCCCCCCC--CCCCHHHHHHHHCCCEEEEECCCCC--------CEEEEECCCCEE---------------------------------------------------- >P1;d1k2yx3 ----------------------------------CHHHHHHHHHHH--HHHHCC-------CCEEEEEC------CCCHHHHHHHHHCCCE-----EEEECC--------------CHHHHHHHHHHHCCCEEECCC-----------CCEEECCCCCCCCCHHHHHHHHHHHHHC-C-CCHHHHHHCC------------------------ >P1;d6y8ya1 CCCCCCCEEEECCCCCCCCCCCCCEEEEHHHHHHCCCHHHHHHHHH--HHCCCHHHHC--CCEEEEEECCCCCHHHHHHHHHHHHHHCCCC-----EEEEEEEEE----------CCHHHHHHHHHHHCCCEEEEECC-CCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCCCEEEEECCCCCCCCEEEEEECC >P1;d6y8ya2 -----------------------------------CHHHHHHHHHHCCHHHHHHHHCCCCCCCEEEECCCC----CCHHHHHHHCCCCCCC-CHHHEECCCCCCCHHHCCCCCCCCCCHHHHHHHHCCCCCEEEEECCCCC--------CEEEEEHHHCCC---------------------------------------------------- >P1;d6y8ya3 ----------------------------------CHHHHHHHHHHH--HHHCHHHHHH--CCCCEEEEC------CCCCHHHHHHHHHCCC-----EEEECC--------------CCHHHHHHHHCCCCCEEEECC-----------CEEEECC--CCCCCHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHC------------------- PSA >P1;d1k2yx1 ----------03a04780-04572031329-730536001200100--0020253--a--1540000225192057017300500130200-----220751--------------62650471085390700000003916--7-7200030102--57039----50570410876049-----------------------a193892b- >P1;d1k2yx2 -----------------------------------99862783559492a7---------83300000011----610631161172180701---512144-99345270507--740502830574a043010102717--------533303670746---------------------------------------------------- >P1;d1k2yx3 ----------------------------------911420000052--007438-------81200005------70476048205a4906-----124364--------------948504710752b02000027-----------44000514271533aa116602741187-3-5768602551------------------------ >P1;d6y8ya1 68a214254370922a5040ab510325063037591002000000--0200869615--7110000043140065003100000001302-----300003405----------07473037206839030000020-927145b1100000025804604a9216602510471850210370706068495331305c1a8303020393 >P1;d6y8ya2 -----------------------------------08a505724a5571b735970389a42602000010----5103205502173040-59800460845b833887240447406a017506a37123000113707--------730404670856---------------------------------------------------- >P1;d6y8ya3 ----------------------------------810220000021--0911640684--815000007------4066203600963916-----234156--------------608404a10661600000055-----------9000013--54743b7126601640384-2948677026404962b------------------- Translating the sequences ----------********-***********-***C*HHHHHHHHHH--HHH**H*--*--CCCEEEEECCC******HHHHHHHHH*CCCC-----EEEE*C--------------C*HHHHHHHHH*CCCEEEEECC*CC*--*-****EEEECC--CCCC*----*HHHH*********-----------------------********- -----------------------------------**HHHHHHHHH*****---------CC*EEEE*CCC----**HH*HHHHHHHCCC***---EE**CC-***********--C***HHHHHHH*CCCEEEEECC*CC--------*EEEE*C*CC**---------------------------------------------------- ----------------------------------C*HHHHHHHHHH--HHH***-------CCEEEEEC------***HHHHHHHHHCCC*-----EEEECC--------------C*HHHHHHHHH*CCCEEE**C-----------**EEE*CC*CCCCC******HHHH****-*-**********------------------------ **********************************C**HHHHHHHHH--HH***H****--CC*EEEEECCC******HHHHHHHHHHCCCC-----EEEE*****----------*C*HHHHHHHHH*CCCEEEEECC-CC*********EEEECC*CCCCC******HHHH***************************************** -----------------------------------*HHHHHHHHHH**HHH**H******CCCEEEE*CCC----**HHHHHHH***CCCC-****EE**CC**************C*HHHHHHHH**CCCEEEEECC*CC--------*EEEE****CCC---------------------------------------------------- ----------------------------------C*HHHHHHHHHH--HHH**H****--CCC*EEEEC------****HHHHHHHH*CCC-----EEEECC--------------C*HHHHHHHH**CCCEEEE*C-----------**EEE*C--CCCCC******HHHH****-*****************------------------- 53738.tem _________________________________ ----------------------------------C*HHHHHHHHHH--HHH**H****--CCCEEEEECCC----**HHHHHHHHHHCCCC-----EEEECC-**-----------C*HHHHHHHHH*CCCEEEEECC*CC-------**EEEECC*CCCCC******HHHH****-************------------------------ Structural block scores 0 33 - 4.2 M 28.8 75.0 75.0 4.2 75.0 75.0 36 45 H 4.9 H 1.0 6.2 1.4 0.3 5.7 0.7 46 47 - 4.1 M 75.0 6.5 75.0 75.0 6.0 75.0 48 50 H 4.4 M 0.7 6.5 2.3 0.7 6.5 3.3 51 52 * 1.9 P 1.0 75.0 3.5 4.0 4.0 3.5 54 57 * 3.0 P 40.9 75.0 75.0 5.2 4.5 4.5 58 59 - 4.5 M 75.0 75.0 75.0 75.0 9.8 75.0 60 62 C 4.5 M 3.3 4.7 28.0 3.0 4.0 4.7 63 67 E 4.7 H 0.4 0.0 0.4 0.0 0.4 0.0 68 70 C 4.5 M 2.7 0.7 51.7 2.7 0.3 52.3 71 74 - 4.1 M 4.0 75.0 75.0 2.5 75.0 75.0 75 76 * 1.0 P 3.5 3.5 3.5 2.5 3.0 2.0 77 86 H 4.6 H 2.0 2.8 4.7 0.4 2.5 3.8 87 90 C 4.7 H 0.5 4.0 4.8 1.5 1.8 4.8 91 95 - 4.4 M 75.0 45.2 75.0 75.0 19.4 75.0 96 99 E 4.5 M 2.8 2.2 2.5 0.8 2.5 2.5 100 101 C 4.3 M 3.0 4.0 5.0 1.5 6.0 5.5 103 104 * 3.4 M 75.0 9.0 75.0 2.5 9.8 75.0 105 115 - 4.1 M 75.0 16.6 75.0 68.2 4.5 75.0 118 126 H 4.8 H 4.0 3.3 4.1 4.0 5.1 4.4 128 130 C 5.0 H 5.3 4.8 4.5 4.0 3.3 2.0 131 135 E 4.7 H 0.0 1.0 0.4 0.0 0.8 1.0 136 137 C 4.7 H 0.0 1.0 41.0 1.0 2.0 40.0 139 140 C 4.3 M 5.0 4.0 75.0 5.5 3.5 75.0 141 147 - 4.3 M 35.3 75.0 75.0 4.4 75.0 75.0 148 149 * 1.9 P 0.0 40.0 4.0 0.0 41.0 4.5 150 153 E 4.8 H 1.0 2.2 1.2 0.0 1.8 0.2 154 155 C 4.2 M 1.0 4.5 2.5 3.5 5.0 39.0 157 161 C 4.5 M 18.0 18.4 3.8 2.8 18.8 4.6 162 167 * 3.2 M 52.3 75.0 5.8 5.8 75.0 5.6 168 171 H 4.3 M 3.0 75.0 3.2 2.0 75.0 2.8 172 175 * 2.7 P 3.2 75.0 4.2 3.0 75.0 3.8 177 188 * 3.2 M 51.6 75.0 10.2 2.6 75.0 4.6 189 212 - 4.3 M 52.2 75.0 75.0 4.2 75.0 60.7 >>>>>>