Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1pcfa1 ---------------------------------------------------------------------------------------------------------------------------------------CEEEECCEEEEEEEECC--EEEEEEEEEEECCCCCEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHC------ >P1;d2giaa1 CCCHHHHHHHHHHHHCCCEEEEEECCHHHHHHCEEEEEEEEC----------------CEEEEEEEEECCCCCCCC----------CCEE---EEEEEEECCCHHHHHHHHHCC-----------CCC---CEEEECC---CEEEEEEECCCCCCCEEEEEEEEECC--EEEEE--EEEECHHHHHHHHHHHHHHHHHHHCCCC---- >P1;d2giab1 ---------------CCCEEEEEECCC-CHHHCEEEEEEEEC----------------CEEEEEEEECCC------CCCCCCCCCCCCCCHHHC-EEEECCHHHHHHHHHHHCC-----------CCC---EEEEECC---CCEEEEEECC---CEEEEEEEECCCCCCCCEEE--EEEEECHHHHHHHHHHHHHHHHCCCHHHH-HC >P1;d2it9a1 --------------------------------------------------------------CEEEE----CCEEEEECCCCCCCCEEEECC--CCEEEECHHHHHHHHHHC-CHHHHHHHCCCC---CEEEEEEEC----CEEEEEEEECC---EEEEEEEECCC-----CCE--EEEECCCHHHHHHHCCCC-------------- >P1;d2nvna1 ------------------------------------------------------------CEEEEEE----CCEEEEEECCC-CCCEEEECC--CCEEEECCCC-CHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEC---CCEEEEEEEECC---EEEEEEEECCC-----CCC--EEEECCCCHHHHHHHHCCCCC----------- >P1;d3r9za- -----------CCCCCCCCEEEECC-------CEEEEEEEECCCEEECCCCCEEECCCCEEEEEEEEEEEC---------------CEECHHHC-EEEEECHHHHHHHHCCCCC-------------C---CEEEEECCCEEEEEEEEECC-CCCEEEEEEEEEECCCCEEEEE--EEEEEHHHHHHHHHHHHHHHHHHCCHHHC-CC >P1;d4agha- -----------------------------------------------------------------------------------------------------------------------------CCEECCCCCEEEECCCCEEEEEEEECC--EEEEEEEEEEEEC-CEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCC PSA >P1;d1pcfa1 ---------------------------------------------------------------------------------------------------------------------------------------47557834111446489--84200213085287562551a817315585356447659855568789------ >P1;d2giaa1 a967a3798667988437014043233953970110300139----------------630000015013548497----------a215---522204044720760130058-----------939---4040567---50703023398588102060302665--75470--4060777107402610360556450648---- >P1;d2giab1 ---------------b47411154149-7386030020005a----------------540201011056------853969a49661116963-0405063500450030057-----------839---5140649---304000335a---710203560212a3893480--51503874164038105702850548878-88 >P1;d2it9a1 --------------------------------------------------------------84453----a3031235894b730020008--821240268027205501-60075159391c---883515265----30302050237---00205020764-----932--50504371055017064c-------------- >P1;d2nvna1 ------------------------------------------------------------6735466----b5120123684-820130127--9811603670-31016002601750884996b3a951635162---a3030102043a---51303030448-----962--724052a006501700541e5----------- >P1;d3r9za- -----------8bb6877432042c-------8000103437061674ba89163565000201001057a---------------67035974-3401034a10540280966-------------6---524163a473520000613b-8050050100111986768550--30406792045039504802430307448-7c >P1;d4agha- -----------------------------------------------------------------------------------------------------------------------------d45719763404557a65122436789--642134221565d-772443a7272135a634754853684166448696b39a Translating the sequences ---------------------------------------------------------------------------------------------------------------------------------------******CEEEEEEE*CC--*EEEEEEEE**CC****EEE**EEEE**HHHHHHHHHHHHHHHH****------ ******************************************----------------*****EEEE*********----------****---***EEE*C*****HHH*****-----------***---*EEEE**---CEEEEEEE*CC****EEEEEEE**CC--**EEE--EEEE**HHHHHHHHHHHHHHHH******---- ---------------************-**************----------------*****EEEE***------******************-*EEE*C*****HHH*****-----------***---*EEEE**---C*EEEEEE*C---*EEEEEEEE**CC****EEE--EEEE**HHHHHHHHHHHHHHHH*******-** --------------------------------------------------------------*EEEE----*********************--**EEE*C*****HHH***-************---****EEEE*----CEEEEEEE*CC---EEEEEEEE**C-----**E--EEEE***HHHHHHH****-------------- ------------------------------------------------------------***EEEE----***********-*********--**EEE*C***-*HHH***********************EEEE*---*CEEEEEEE*CC---EEEEEEEE**C-----***--EEEE****HHHHHHHH*****----------- -----------**************-------*******************************EEEE****---------------********-*EEE*C*****HHH*****-------------*---*EEEE******EEEEEEE*C-***EEEEEEEE**CC****EEE--EEEE**HHHHHHHHHHHHHHHH*******-** -----------------------------------------------------------------------------------------------------------------------------*********EE*****CEEEEEEE*CC--*EEEEEEEE***C-***EEE**EEEE**HHHHHHHHHHHHHHHH********** 54447.tem _________________________________ ---------------**********-------**********----------------*****EEEE***-***********-*********-***EEE*C*****HHH*****-----------*******EEEE*****CEEEEEEE*CC--*EEEEEEEE**CC****EEE--EEEE**HHHHHHHHHHHHHHHH*******-** Structural block scores 0 14 - 4.5 M 75.0 7.6 75.0 75.0 75.0 57.5 75.0 15 24 * 3.7 M 75.0 2.8 4.0 75.0 75.0 5.0 75.0 25 31 - 4.3 M 75.0 5.6 16.0 75.0 75.0 75.0 75.0 32 41 * 3.7 M 75.0 1.8 2.0 75.0 75.0 2.6 75.0 42 57 - 4.6 H 75.0 75.0 75.0 75.0 75.0 5.6 75.0 58 62 * 3.2 M 75.0 1.8 2.2 61.6 33.2 0.4 75.0 63 66 E 4.4 M 75.0 1.5 0.8 4.0 5.2 0.5 75.0 67 69 * 3.7 M 75.0 1.3 3.7 75.0 75.0 4.0 75.0 71 81 * 3.7 M 75.0 43.8 37.7 4.4 4.0 75.0 75.0 83 91 * 3.0 P 75.0 43.7 4.8 2.2 2.7 28.3 75.0 93 95 * 3.3 M 75.0 3.0 26.0 28.3 30.7 27.3 75.0 96 98 E 4.4 M 75.0 2.0 3.0 2.3 2.7 1.7 75.0 101 105 * 2.6 P 75.0 4.0 2.4 4.6 18.2 4.1 75.0 106 108 H 4.4 M 75.0 2.3 1.7 2.3 0.7 2.0 75.0 109 113 * 2.6 P 75.0 3.2 3.0 17.4 2.8 5.8 75.0 114 124 - 4.2 M 75.0 75.0 75.0 4.8 5.2 75.0 75.0 125 131 * 3.1 M 75.0 35.7 35.7 35.6 6.6 55.1 6.6 132 135 E 4.4 M 57.2 2.2 2.8 3.5 3.8 3.2 3.2 136 140 * 2.8 P 6.4 47.6 47.6 61.0 47.5 5.5 6.3 142 148 E 4.9 H 3.0 2.1 1.4 1.4 0.9 1.3 3.3 150 151 C 4.7 H 8.5 8.5 42.8 5.0 6.8 43.2 8.5 152 153 - 4.2 M 75.0 6.5 75.0 75.0 75.0 4.0 75.0 155 162 E 5.0 H 1.5 1.5 2.1 1.1 1.9 0.9 2.4 163 164 * 1.0 P 6.5 4.0 1.5 6.5 4.0 1.0 5.5 165 166 C 4.5 M 5.0 5.5 6.2 39.5 41.5 8.5 9.2 167 170 * 3.0 P 5.0 40.5 5.8 75.0 75.0 6.8 22.8 171 173 E 4.3 M 3.7 3.7 4.0 4.7 5.7 3.3 3.7 174 175 - 4.2 M 9.2 75.0 75.0 75.0 75.0 75.0 8.8 176 179 E 5.0 H 3.0 2.5 2.8 2.5 3.2 1.8 3.0 180 181 * 1.0 P 5.0 7.0 5.5 3.5 3.5 6.5 4.0 182 197 H 4.6 H 5.7 3.3 3.8 21.8 8.4 3.6 5.4 198 204 * 2.8 P 36.7 14.6 5.7 75.0 75.0 3.7 6.9 206 207 * 3.7 M 75.0 75.0 8.0 75.0 75.0 9.8 9.8 >>>>>>