Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2qq4a- ------------------------CCHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCEEEEEEEEECCEEEEEEEEEECCHHHHHHHHHHHHHHCCCC--HHHHHHHHHHHHHHHCCCCCCCH-HHHHHHHHHHHHHCHH-HHHHHHHHHHHHHHHHC------- >P1;d3a7ra2 -------------------------------------------------CCCCEEEEEEEEECCEEEEEEEEEECCEEEEEEEEECCC--CCHHHHHHHHHCCCCCCCHHHHHHHHH-----------------HCCCCCHHH-------HHHHHHHHHHHHHHHC------- >P1;d3g0ma- ---------CCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHH--CCCCCCHHHCCC-CCCCC-CCCCEEEEEEECCCCCEEEEEEEC-CHHHHHHHHHHHHHHCCCC--HHHHHHCC----------------CHHHHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHCCC---- >P1;d4lw4c- CCCCCCCCCCCCC-CHHHHHHHHCCCCCHHHHHHHHHHHHC--CCCCCCHHHHCCCEECCC-CCCCEEEEEEECCCCCEEEEEEEC-CHHHHHHHHHHHHHHCCCC--HHHHHHCC----------------CCHHHHHCCCCCCCHHHHCHHHHHHHHHHHHHHHHC----- >P1;d5idha2 -------------------------------------------------CCCCCCEEEEEEECCEEEEEEEEEECCEEEEEEEEECCC--CCCCCHHHHHHHCCCCCCHHHHHHHHC-----------------CCCHHHHHC-------CCCHHHHHHHHC----------- >P1;d5ij6a2 -------------------------------------------------CCCCCCEEEEEEECCEEEEEEEEEECCEEEEEEEEECCC--CCCCCHHHHHHHCCCCCCHHHHHHHCC-----------------CCCHHHHCC-------CCCHHHHHHHHHC---------- >P1;d5ufta1 ---------------------------CHHHHCCCCC-CCCCCCCCC-CCCCCEEEEEC--CCCCCEEEEEEEECCEEEEEEEEC-CCHHHHHHHHHHHHHCCCCC--HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHC-C-CHHHHCHHHHHHHHHHHHHC---C >P1;d6a6fa1 -----------------------------CCCCHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCEEEEEEEEEECCEEEEEEEECCCCHHHHHHHHHHHHHHCCCC--HHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHCHH-HHHHHHHHHHHHHHHHC------- >P1;d7c8na- ------------------------CCCCCC-CCHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCEEEEEEEEECCEEEEEEEEECCCHHHHHHHHHHHHHHCCCC--HHHHHCCCHHHHH----------------HHHCCCCC--C-HHHHHHHHHHHHHHHHHHHHHHHC PSA >P1;d2qq4a- ------------------------a8a66662641355046713235705805450536189480504000217c7302203032924531200000004303756--29603510610220057539248-50a602005a019578-51500000050026006------- >P1;d3a7ra2 -------------------------------------------------b6964635074719121040304059750460305170a--647007302b40781316063037303-----------------602972591-------5720540071008208------- >P1;d3g0ma- ---------1b702728701750571762951472017007--509a05780359-2309a-071701000553b96205030106-2610200000000004714--18503715----------------174217704058307842360051007304840581a---- >P1;d4lw4c- b924160201780-447404840862876750173024005--605906aa3296074063-aa2500013551988300000005-8542200000000201633--29504848----------------606007505029508204674053018103700683----- >P1;d5idha2 -------------------------------------------------a817274556661921101020325aa10440404361a--185827401630472725692068006-----------------707054006-------806484018004----------- >P1;d5ij6a2 -------------------------------------------------b917383424570813401020016a9504403041709--175919502730472426383048203-----------------a27092004-------6071740040017---------- >P1;d5ufta1 ---------------------------7996133606-119815549-19914030532--a59160102030897405301050-03200300000003203605--18504703630560067828108b30540530420273-9-21700000030013007436---a >P1;d6a6fa1 -----------------------------a14692046207386134609b05442745185380502010318b7504303035812100300000003203445--2850150060032005-96a167b2073034057026488-21500100040027006------- >P1;d7c8na- ------------------------9aa636-45a606504582315640aa2303053408949340100040595506302040903100200000004304842--0740370418415----------------b1097017--8-156105000600240074147559 Translating the sequences ------------------------*******************CCCC*CCCCC**EEEE***CC*EEEEEEEEECCEEEEEEEEE*CCHHHHHHHHHHHHHHCCCC--HHHHHHH****************-**H**HHHH*******-*HHHHHHHHHHHHHHH*------- -------------------------------------------------CCCC**EEEE***CC*EEEEEEEEECCEEEEEEEEECCC--**HHHHHHHHH*CCCC**HHHHHHH**-----------------H*****H**-------HHHHHHHHHHHHHHH*------- ---------********************************--CCCC*C***C**-*****-CC**EEEEEEE*CC**EEEEEEEC-CHHHHHHHHHHHHHHCCCC--HHHHHH**----------------**H**HHH**********HHHHHHHHHHHHHHH****---- *************-***************************--CCCC*C*******EE***-CC**EEEEEEE*CC**EEEEEEEC-CHHHHHHHHHHHHHHCCCC--HHHHHH**----------------**H**HH************HHHHHHHHHHHHHH***----- -------------------------------------------------CCCC**EEEE***CC*EEEEEEEEECCEEEEEEEEECCC--*****HHHHHHHCCCC**HHHHHHH**-----------------***HHHH**-------***HHHHHHHH*----------- -------------------------------------------------CCCC**EEEE***CC*EEEEEEEEECCEEEEEEEEECCC--*****HHHHHHHCCCC**HHHHHHH**-----------------***HHHH**-------***HHHHHHHHH*---------- ---------------------------**********-*****CCCC-CCCCC**EEE*--*CC**EEEEEEEECCEEEEEEEE*-CCHHHHHHHHHHHHH*CCCC--HHHHHHH*******************H**HHHH*****-*-*HHHH*HHHHHHHHHH****---* -----------------------------**************CCCC*CCCCC**EEEE***CC*EEEEEEEEECCEEEEEEEE*CCCHHHHHHHHHHHHHHCCCC--HHHHHHH*********-*********H**HHHH*******-*HHHHHHHHHHHHHHH*------- ------------------------******-************CCCC*CCCCC**EEEE***CC*EEEEEEEEECCEEEEEEEEECCCHHHHHHHHHHHHHHCCCC--HHHHH********----------------HHH*****--*-*HHHHHHHHHHHHHHH******** 82649.tem _________________________________ ------------------------*******************CCCC*CCCCC**EEEE***CC*EEEEEEEEECCEEEEEEEEECCCHHHHHHHHHHHHHHCCCC--HHHHHHH******-----------**H**HHHH*******-*HHHHHHHHHHHHHHH***----- Structural block scores 0 23 - 4.5 M 75.0 75.0 30.8 7.1 75.0 75.0 75.0 75.0 75.0 24 42 * 3.0 P 5.1 75.0 11.4 11.2 75.0 75.0 19.5 23.0 9.2 43 46 C 4.4 M 3.2 75.0 6.1 5.0 75.0 75.0 5.8 3.5 3.8 48 52 C 4.5 M 3.6 21.5 4.6 6.4 20.3 20.7 4.8 5.1 5.2 53 54 * 1.0 P 4.5 5.0 7.0 7.5 4.5 5.5 1.5 4.0 1.5 55 58 E 4.5 M 3.5 3.8 20.0 2.8 5.0 3.2 2.5 4.5 3.0 59 61 * 1.8 P 6.0 4.0 31.5 28.0 4.3 4.0 53.5 4.7 5.7 62 63 C 5.0 H 6.0 5.0 3.5 10.5 5.5 4.5 7.0 5.5 6.5 65 73 E 4.8 H 2.1 1.9 2.3 2.2 1.6 1.6 2.2 2.2 1.6 74 75 C 5.0 H 9.8 8.0 10.2 8.5 10.5 9.8 8.0 9.2 7.0 76 84 E 4.8 H 1.7 2.7 1.9 1.2 2.2 2.3 2.0 2.6 2.2 85 87 C 4.7 H 5.0 5.8 27.7 29.3 5.8 5.3 26.0 3.7 4.0 88 101 H 4.6 H 1.3 13.9 0.6 1.1 13.9 14.2 0.7 0.6 0.7 102 105 C 5.0 H 5.2 4.8 4.0 3.2 5.0 4.2 3.5 4.0 4.5 106 107 - 4.0 M 75.0 3.5 75.0 75.0 3.5 4.0 75.0 75.0 75.0 108 114 H 4.8 H 3.7 3.1 3.6 4.6 4.4 4.0 3.6 3.0 3.0 115 120 * 2.9 P 1.8 50.5 63.3 63.8 51.0 50.5 3.8 1.8 3.8 121 131 - 4.1 M 10.7 75.0 75.0 75.0 75.0 75.0 4.7 11.9 75.0 132 133 * 3.2 M 2.5 75.0 4.0 3.0 75.0 75.0 1.5 1.0 75.0 135 136 * 1.6 P 3.0 1.0 1.5 0.0 3.5 4.5 2.0 1.5 75.0 137 140 H 4.5 M 1.8 5.8 4.5 4.2 2.2 2.8 3.0 3.0 5.4 141 147 * 2.4 P 5.8 55.0 4.4 3.7 54.4 54.1 14.0 5.0 24.7 150 164 H 4.7 H 1.3 2.7 2.7 3.0 17.9 12.5 1.0 1.3 1.9 165 167 * 3.1 M 52.0 52.7 4.7 5.7 75.0 75.0 4.7 52.0 4.0 168 172 - 4.5 M 75.0 75.0 62.1 75.0 75.0 75.0 48.3 75.0 6.0 >>>>>>