Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1tfea- ---CCEEEEEEEECCC-----------CCEEEEEEEEECCHHHHHCHHHHHHHHHHHHHHHHHCCCCCCHHHCCHHHHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHHHHHHHHCHHHCEECCEEEEEHHHHHHHHHHHHCCCCEEEEEEEEECCC------------------ >P1;d1xb2b2 CCCCCEEEEEEEEEC-------------CEEEEEEEEECCHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCC-----------------CCCEEEEEC-----------------HHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEEEEECCC------------------ >P1;d1xb2b3 -----CEEEEEEEECCCCCCCCCCCCCCCEEEEEEEECC----CCHHHCHHHHHHHHHHHHHHCCCCCCCCCCC-----------------------------------CCHHHCCCHHHCCCCCCCCCCHHHHHHHH------CCEEEEEEEEECCCC----------------- >P1;d4pc3c2 --CCCEEEEEEEEEC-------------CEEEEEEEEECCHHHHHCHHHHHHHHHHHHHHHHH-----------------------------CCC-C-----------------HHHHHHH--------HHHHHHHHHHHH-CCCCEEEEEEEEE--C------------------ >P1;d4pc3c3 ------CEEEEEEEC------------CCEEEEEEEE-CCC--------HHHHHHHHHHHHHHCCCCCCHHHCCHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHC------CCEEEEEEEEECCCCCCCCCCCHHHHHHHHCC PSA >P1;d1tfea- ---a530351625295-----------85120600010657a10759504710620020003340521239505a94346235700640386--a3759403720765168134500022030355881305510651287081706046151937b6------------------ >P1;d1xb2b2 e7807504536276c-------------8030501000156910857504501710040006304936759-----------------a56053717-----------------5950080701765a82056107713961912040560204062c------------------ >P1;d1xb2b3 -----862505225957946958b56406240504050a----5887809700430010006240862344a59-----------------------------------52aa9154000010355684100510665------906046151838b5d----------------- >P1;d4pc3c2 --b07401516486b-------------b01050000055691075a7037005600510086-----------------------------615-6-----------------2860386--------05a426713771-91705056060a7--b------------------ >P1;d4pc3c3 ------84645286c------------9611060206-708--------a700520020005260833438506a85367225621850383--a3568603740583087213630012150335582403700965------d0505407083736c9a8a8878967677969 Translating the sequences ---CCEEEEEEEE*C*-----------CCEEEEEEEEECCHHHH*CHHHHHHHHHHHHHHHHHCCCCCC***CC******************--C*C**************HHHHHCHHHC**CC*****HHHHHHHHHHH*CCCCEEEEEEEEECCC------------------ ***CCEEEEEEEEEC-------------CEEEEEEEEECCHHHH*CHHHHHHHHHHHHHHHHH*CCCCC**-----------------********C-----------------HH*HH*CCCCCCCCCCHHHHHHHHHHH*CCC*EEEEEEEEECCC------------------ -----*EEEEEEEEC************CCEEEEEEEE*C----***HH*HHHHHHHHHHHHHHCCCCCC***CC-----------------------------------**HHH**CHHHCCCCCCCCCCHHHHHHHH------CCEEEEEEEEECCC*----------------- --*CCEEEEEEEEEC-------------CEEEEEEEEECCHHHH*CHHHHHHHHHHHHHHHHH-----------------------------**C-C-----------------HH*HHH*--------*HHHHHHHHHHH-CCCCEEEEEEEEE--C------------------ ------*EEEEEEEC------------CCEEEEEEEE-CC*--------HHHHHHHHHHHHHHCCCCCC***CC******************--C*C**************HHHH*C***CCCCCCCCCCHHHHHHH*------CCEEEEEEEEECCC****************** 54713.tem _________________________________ ---CCEEEEEEEEEC------------CCEEEEEEEEECCHHHH*CHHHHHHHHHHHHHHHHHCCCCCC***CC--------------****--C*C------------**HHHHHCHHHCCCCCCCCCCHHHHHHHHHHH-CCCCEEEEEEEEECCC------------------ Structural block scores 0 2 - 4.3 M 75.0 9.8 75.0 53.8 75.0 3 4 C 4.2 M 7.8 3.5 75.0 3.5 75.0 5 13 E 4.8 H 3.0 4.2 3.9 3.9 13.1 15 26 - 4.4 M 69.2 75.0 6.6 75.0 75.0 27 28 C 4.6 H 6.5 41.5 3.0 43.2 7.5 29 37 E 4.9 H 1.1 1.0 2.2 0.7 10.1 38 39 C 4.8 H 5.5 3.0 42.8 5.0 3.5 40 43 H 4.2 M 4.6 4.0 57.5 4.0 58.2 46 62 H 4.9 H 2.5 2.5 2.8 3.4 15.2 63 68 C 4.4 M 2.3 4.8 3.8 75.0 4.0 69 71 * 2.4 P 5.7 29.7 6.2 75.0 5.3 72 73 C 4.2 M 2.5 75.0 7.0 75.0 3.0 74 87 - 3.8 M 4.5 75.0 75.0 75.0 5.0 88 91 * 3.0 P 4.2 5.4 75.0 75.0 3.5 92 93 - 3.8 M 75.0 4.0 75.0 3.5 75.0 97 108 - 3.8 M 4.1 75.0 75.0 75.0 4.2 109 110 * 3.0 P 7.0 75.0 3.5 75.0 7.5 111 115 H 4.2 M 2.6 47.8 7.2 47.0 3.0 117 119 H 4.3 M 1.3 2.7 0.0 3.7 1.0 120 129 C 4.2 M 3.6 4.7 3.3 60.6 3.6 130 140 H 4.7 H 3.6 4.1 22.5 4.9 23.2 142 145 C 4.5 M 4.0 3.0 39.8 4.2 40.9 146 154 E 5.0 H 3.9 2.3 3.8 4.4 3.6 155 157 C 4.7 H 8.2 6.8 8.2 53.8 5.3 158 175 - 4.5 M 75.0 75.0 71.6 75.0 8.2 >>>>>>