Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1a5ta1 CHHHHHHHHHHHHHHHHH---HC---CCHHHHHHHCCC------CHHHHHHHHHHHHHHHCCC----------CCCC------CCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH----CCCHHHHHHHHHHHHHHHCCCCCCC--------------------------------------------------------------------- >P1;d1iqpa1 --CCCHHHHHHHHHHHHH---C----CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC---------------------------------C-CHHHHHHHHHHHHHHHHHHHCC--C--CHHHHHHHHHHHHHHHHCC------------------------------------------------------------------------- >P1;d1jr3a1 CCC--HHHHHHHHHHHHH----C---CHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHCC----CC--CCCCC--HHHHCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCC--C--CHHHHHHHHHHHHHHCCCCCCCCCC------------------------------------------------------------------- >P1;d1jr3d1 ------CCHHHHHHHHCC----C---CHHHHHHHHCCCCC-CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHC--CCCCHHHHHHHHHHHCCCCCCCC------------------------------------------------------------------------ >P1;d1sxja1 -CCHHHHHHHHHCCHHHCCCCHHHCCCHHHHHHHHCCCC-------CCHHHHHHHHCC----CCEECCCCC-------------------CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCHHHHHCCCEECCC--------------------------------------CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC >P1;d1sxjb1 -------CCHHHHHHHHC---CCC---HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCC---------------------------------CCCHHHHHHHHHHHHHHHHHHHCC--C--CCHHHHHHHHHHHHHHCCC------------------------------------------------------------------------- >P1;d1sxjc1 ---CCHHHHHHHHHHHHC---C----CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCC---------------------------------CCCHHHHHHHHHHHHHHHHHHCCC--C--CHHHHHHHHHHHHHHHCCC------------------------------------------------------------------------- >P1;d1sxjd1 ---CCCHHHHHHHHHHHC---C----CHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHCC---------------------------------CCCHHHHHHHHHHHHHHHHHHCCC--C--CHHHHHHHHHHHHHHC---------------------------------------------------------------------------- >P1;d1sxje1 -CCHHHHHHHHHHHHHHH---CCCHHHHHHHHHHHH-HHHCCCCCHHHHHHHHHHCCCCCC---------------------------------CCCHHHHHHHHHHHHHHHHHHHCC--C--CHHHHHHHHHHHHHHHHC-------------------------------------------------------------------------- >P1;d2qw6a1 -----CCHHHHHHHHHHC-------CCHHHHHHHHHHHHHC-C-CHHHHHHHHHHHHHH------------------------------------CCC---HHHHHHHHHHHHHHHHH--CCCCCHHHHHHHHHHHHHCC--------------------------------------------------------------------------- >P1;d3bgea1 -CHHHHHHHHHHHHHHHC-------CCHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHH------------------------------------CCHHHCCCHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHCCCCC-----CCCCCCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHC >P1;d3ctda1 ----CHHHHHHHHHHHHC-------CCHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHH------------------------------------CCHHHCCCHHHHHHHHHHHHC-C--CCCCCHHHHHHHHHHHHHCCCCCCCCC-----CCCCC-----CCCHHHCCCCCCCCHHHCCCCCCCCC------CCCCC--CHHHHHC------- PSA >P1;d1a5ta1 677a10570073047003---34---405401910449------5012005101100400139----------5608------627c017302a40476207200810570266057----a8a345201400640271178b1b2--------------------------------------------------------------------- >P1;d1iqpa1 --6064720350032006---3----43870471046029638150550060056004607---------------------------------2-977315500820750374066a--3--6647102400420170178------------------------------------------------------------------------- >P1;d1jr3a1 308--4630010010016----1---64a40362086018-490813200430080064035019----67--9106c--b16903a3035107404690073047104404740591--7--6535102500430047015656899------------------------------------------------------------------- >P1;d1jr3d1 ------553450032001----9---51770271064065-4a282460051048005103602828a748486005738448b14b3007008805870062036206703521357--893903740470042007918a9------------------------------------------------------------------------ >P1;d1sxja1 -976126006400208207a72377257a4016003425-------630120051005----408061279-------------------c164960175048127507712971764982863255004200040031000815a--------------------------------------90750864a654765688868666578789a >P1;d1sxjb1 -------06584047003---2a7---3950371047202669461450041046105809---------------------------------91889316602820560374057a--5--16281024004401824a9------------------------------------------------------------------------- >P1;d1sxjc1 ---277730560071017---5----95b5057106412774a04065008503830684a---------------------------------18696036506650771576177a--7--68a8103300500261284------------------------------------------------------------------------- >P1;d1sxjd1 ---048920660173078---5----86830571056018846834-5018205830483a---------------------------------8198a227606710620555178c--3--6637102300140172---------------------------------------------------------------------------- >P1;d1sxje1 -85833420450062028---6359a0276057206-80187a05163006400710192a---------------------------------908a62362057218516750875--a--721720250045008207-------------------------------------------------------------------------- >P1;d2qw6a1 -----8632410171049-------662a303610741187-5-628300730340066------------------------------------304---87006504810650584--62760561048004400707--------------------------------------------------------------------------- >P1;d3bgea1 -da827811530261049-------452a503630630284-a1712200530270073------------------------------------00240046067305703542676--7584027103800430060410604451755356287636a29602233c966-----c490948317627925227037635067337737768 >P1;d3ctda1 ----67a20330061049-------5539304730750187-a1628200720340066------------------------------------001403280563067028407-5--648705830370033006052070337-----a359a-----b629125aa1a46449971a08653a------55426--5507957------- Translating the sequences ******HHHHHHHHHHH*---**---C*HHHHHHH***------CHHHHHHHHHHHHH*****----------****------************CCHHHHHHHHHHHHHHHHHH**----**CHHHHHHHHHHHHHH*CC*****--------------------------------------------------------------------- --****HHHHHHHHHHH*---*----CHHHHHHHHH******CCCHHHHHHHHHHHHH***---------------------------------*-CHHHHHHHHHHHHHHHHHH**C--C--CHHHHHHHHHHHHHH**C*------------------------------------------------------------------------- ***--*HHHHHHHHHHH*----*---CHHHHHHHHH****-*CCCHHHHHHHHHHHHH*******----**--*****--***************CCHHHHHHHHHHHHHHHHH***C--C--CHHHHHHHHHHHHHH*CC*******------------------------------------------------------------------- ------**HHHHHHHH**----*---CHHHHHHHH*****-*CCCHHHHHHHHHHHHH*************************************CCHHHHHHHHHHHHHHHHHH**C--C**CHHHHHHHHHHH****CC**------------------------------------------------------------------------ -*****HHHHHH**HHH*********CHHHHHHHH****-------**HHHHHHHH**----*********-------------------*******HHHHHHHHHHHHHHHHHH**C**C***HHHHHHHH*HHHHH*CC*****--------------------------------------******************************* -------**HHHHHHHH*---***---HHHHHHHHH******CCCHHHHHHHHHHHHH***---------------------------------*CCHHHHHHHHHHHHHHHHHH**C--C--C*HHHHHHHHHHHHH*CC*------------------------------------------------------------------------- ---***HHHHHHHHHHH*---*----CHHHHHHHHH******CCCHHHHHHHHHHHH****---------------------------------*CCHHHHHHHHHHHHHHHHHH**C--C--CHHHHHHHHHHHHHH*CC*------------------------------------------------------------------------- ---***HHHHHHHHHHH*---*----CHHHHHHHHH******CCC*-*HHHHHHHHHH***---------------------------------*CCHHHHHHHHHHHHHHHHHH**C--C--CHHHHHHHHHHHHHH*---------------------------------------------------------------------------- -*****HHHHHHHHHHH*---******HHHHHHHHH-*****CCCHHHHHHHHHH******---------------------------------*CCHHHHHHHHHHHHHHHHHH**C--C--CHHHHHHHHHHHHHH**C-------------------------------------------------------------------------- -----**HHHHHHHHHH*-------*CHHHHHHHHH*****-C-CHHHHHHHHHHHHH*------------------------------------CC*---HHHHHHHHHHHHHH***--C**C*HHHHHHHHHHHHH*C--------------------------------------------------------------------------- -*****HHHHHHHHHHH*-------*CHHHHHHHHH*****-CCCHHHHHHHHHHHHH*------------------------------------CCHHH***HHHHHHHHHHHH**C--C***HHHHHHHHHHHHHH*CC********************************-----************************************* ----**HHHHHHHHHHH*-------*CHHHHHHHHH*****-CCCHHHHHHHHHHHHH*------------------------------------CCHHH***HHHHHHHHHHHH*-C--C**C*HHHHHHHHHHHHH*CC******-----*****-----**************************------*****--*******------- 48019.tem _________________________________ -*****HHHHHHHHHHH*---**--*CHHHHHHHHH******CCCHHHHHHHHHHHHH***-*---------------------------*****CCHHHHHHHHHHHHHHHHHH**C--C**CHHHHHHHHHHHHHH*CC*****--------------------------------------------------------------------- Structural block scores 1 5 * 3.0 P 5.1 18.2 32.4 75.0 5.0 75.0 33.2 32.4 5.4 61.6 8.2 47.6 6 16 H 4.8 H 3.0 2.0 1.1 2.5 2.5 9.9 2.7 3.7 2.3 2.6 2.8 2.7 18 20 - 4.8 H 75.0 75.0 75.0 75.0 8.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 21 22 * 3.2 M 3.5 39.0 38.0 42.0 2.5 6.2 40.0 40.0 4.5 75.0 75.0 75.0 23 24 - 4.4 M 75.0 75.0 75.0 75.0 7.0 41.0 75.0 75.0 7.0 75.0 75.0 75.0 27 35 H 4.9 H 2.7 3.8 4.2 3.4 3.5 3.6 4.5 3.9 3.9 3.6 3.9 4.0 36 41 * 2.0 P 52.2 4.3 15.7 15.7 39.3 3.8 4.2 4.5 16.5 16.0 15.3 16.0 42 44 C 4.6 H 51.7 4.7 5.7 6.8 75.0 6.3 4.8 5.7 5.2 28.7 6.2 5.8 45 57 H 4.8 H 1.2 2.4 2.1 2.7 7.5 2.4 3.4 8.8 2.2 2.8 2.2 2.6 58 60 * 2.3 P 0.3 4.3 2.3 1.3 75.0 5.7 7.5 7.2 7.2 52.0 51.0 52.0 63 89 - 4.5 M 46.5 75.0 25.9 5.1 54.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 90 94 * 3.7 M 3.9 60.4 3.4 4.6 6.5 61.8 60.2 61.6 61.8 75.0 75.0 75.0 95 96 C 4.7 H 2.0 42.0 2.0 2.5 3.0 4.5 7.0 5.0 4.0 1.5 0.0 0.0 97 114 H 4.9 H 3.3 3.6 3.3 3.2 4.1 3.9 4.4 4.1 4.2 15.5 3.2 3.3 115 116 * 1.2 P 6.0 6.0 7.0 4.0 6.5 6.0 7.0 7.5 7.5 6.5 6.5 41.0 118 119 - 4.8 H 75.0 75.0 75.0 75.0 8.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 121 122 * 3.4 M 9.2 75.0 75.0 6.0 7.0 75.0 75.0 75.0 75.0 4.5 6.5 6.0 124 137 H 4.9 H 2.7 2.7 2.3 2.7 1.8 2.9 3.3 2.5 2.6 2.8 2.4 2.7 139 140 C 4.5 M 4.0 4.0 0.5 4.5 0.0 7.2 5.0 75.0 3.5 41.0 2.5 3.5 141 145 * 3.4 M 6.8 61.6 6.0 48.9 4.9 61.8 60.8 75.0 75.0 75.0 2.8 2.6 146 214 - 4.6 H 75.0 75.0 73.1 75.0 44.2 75.0 75.0 75.0 75.0 75.0 10.2 31.0 >>>>>>