Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3bq9a2 ------------------------CC---C----------CCCCEEEEECCCCCCH--HHHHHHHHHHHHHHHCCCEEEECCCCHHHCHHHHHHHHHHHHCCCCCCCEEEEECCC---CCCCCCCCCCC--CEEEECC----------CHHHHHHHHHHHCCEEEECCCCH-HHHHHHHHHHHHHCCHHHCCCCCCEEEEECHHHHHHHHHHHHHHHH--HCCCCHHHHCEEEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC >P1;d3uqza2 --------CEEECCCCCCCHHHHCCCCCCCEEEEEECHHHHHCCEEEEEECCCCCH--HHHHHHHHHHHCC-CCCCEEEECCCCCHHHHHC-CHHHH----CCC-EEEECCCCCCCCCCHHHHHHHHHHHHHCEEEECCCCCCCCCCCHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHC-CC---------CCEEEECCCCCCCCCC-HHHHHHHHC---------CCEECC-----CHHHHHHHCCC------------------ >P1;d5wq3a- CCCCHHHHH------HHHHHHHHHHHHHHC----------CCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHC----CCC-EEEEEECCCC--------CCCCCC--CEEEEEC----------CHHHHHHHHHHCCCCEEECCCCH-HHHHHHHHHHHHHHCCCCC--CCCEEEECHHHHHHHHHHHHHHCCCCCCCCHHHHHCCEEE-CCHHHHHHHHHHHHC---------C--------C PSA >P1;d3bq9a2 ------------------------57---a----------4602000000167089--722700330023003350000000041002000410460075582ac111000005a---33a71524930--6335426----------437500520023000000001aa-9055003300730367806503020000007706940781296008--43477038206210652630054056208602500570a022530730 >P1;d3uqza2 --------7202395c401920370970084031626250076400000014804a--a037303700560-8460000000072003300-00293----914-000000001622419a1482044007500000213775715980163012001000300000105a3711700540-72---------c041000265895620-600250286---------915407-----40930164074------------------ >P1;d5wq3a- 759688448------633771387048507----------905500001024928783730630250053018280000000360011000200162----a23-0000115498--------b20720--5311605----------174012400151040000000aa-a036004301630456628--700000024a306a21760485228586187610540220-661850173056417---------c--------b Translating the sequences ------------------------CC---C----------CCCCEEEEECCCCCCH--HHHHHHHHHHHHHHHCCCEEEECCCC*HH*HHHHHHHHH****CCC***EEEE*CCC---C****CCCCCC--CEEEE*C----------CHHHHHHHHHHHCCEEEECCCCH-HHHHHHHHHHHHH*C***C**CCCEEEE*CHHHHHHHHHHHHHHHH--*CC**HHH*CEEE*CCHHHHHHHHHHHH**********C********C --------***********HHHH*CC***C************CCEEEEE*CCCCCH--HHHHHHHHHHH**-*CCCEEEECCCCCHHHHH*-*HHHH----CCC-EEEE**CCCC***C**************EEEEC***********HHHHHHHHHHHCCEEEE*CCC**HHHHHHHH*-**---------CC*EEE*CC*******-HHHHHHHHC---------CCEE**-----*HHHHHHH*C*------------------ *********------****HHHH******C----------CCCCEEEEECCCCCC***HHHHHHHHHHHHHHHCCCEEEECCCCC**HHHHHHHHH*----CCC-EEEEEECCCC--------CCCCCC--CEEEEEC----------CHHHHHHHHHH*CC*EEECCCCH-HHHHHHHHHHHHH*C***C--CCCEEEEC*HHHHHHHHHHHHH***C**CC**HHHCCEEE-CCHHHHHHHHHHHHC---------C--------C 102405-1.tem _________________________________ --------*------****HHHH*CC***C----------CCCCEEEEECCCCCCH--HHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHH----CCC-EEEEEECCCC---C****CCCCCC--CEEEEEC----------CHHHHHHHHHHHCCEEEECCCCH-HHHHHHHHHHHHH*C***C--CCCEEEECCHHHHHHHHHHHHHHHHC-*CC**HHHCCEEE*CCHHHHHHHHHHHHC*--------C--------C Structural block scores 0 7 - 4.0 M 75.0 75.0 6.4 9 14 - 4.0 M 75.0 3.5 75.0 15 18 * 2.7 P 75.0 4.4 4.8 19 22 H 4.0 M 75.0 3.5 4.8 24 25 C 4.0 M 6.0 4.5 2.0 26 28 * 2.7 P 75.0 2.3 4.3 30 39 - 4.0 M 75.0 2.9 75.0 40 43 C 4.5 M 3.0 4.2 4.8 44 48 E 5.0 H 0.0 0.0 0.2 49 54 C 4.8 H 3.7 2.8 4.2 56 57 - 4.0 M 75.0 75.0 5.5 58 72 H 4.7 H 2.1 8.5 2.9 73 75 C 5.0 H 2.7 3.3 3.3 76 79 E 5.0 H 0.0 0.0 0.0 80 84 C 4.8 H 1.0 1.8 1.8 85 96 H 4.4 M 1.4 7.9 1.1 97 100 - 4.0 M 4.2 75.0 75.0 101 103 C 5.0 H 6.8 4.7 5.2 105 110 E 4.3 M 0.5 0.0 0.3 111 114 C 4.8 H 3.9 1.8 6.5 115 117 - 4.0 M 75.0 2.7 75.0 119 122 * 2.7 P 5.4 6.1 75.0 123 128 C 4.0 M 3.8 3.0 3.8 129 130 - 4.0 M 75.0 3.5 75.0 132 136 E 4.6 H 3.4 0.0 2.2 138 147 - 4.0 M 75.0 5.3 75.0 149 159 H 4.9 H 2.5 1.3 2.3 160 161 C 5.0 H 0.0 1.5 2.0 162 165 E 4.8 H 0.0 0.0 0.0 166 169 C 4.8 H 2.9 1.5 2.6 172 184 H 4.6 H 2.7 14.2 2.8 187 189 * 2.7 P 5.0 75.0 4.7 191 192 - 4.0 M 2.5 75.0 75.0 193 195 C 4.7 H 1.7 5.5 2.3 196 199 E 4.8 H 0.0 0.2 0.0 200 201 C 4.0 M 0.0 4.0 3.0 202 217 H 4.3 M 4.6 8.3 4.7 221 222 C 4.0 M 3.5 75.0 4.5 223 224 * 2.7 P 7.0 75.0 6.5 225 227 H 4.0 M 3.7 75.0 2.0 228 229 C 4.5 M 1.0 5.0 2.0 230 232 E 4.7 H 3.0 3.0 1.3 234 235 C 4.0 M 5.5 75.0 6.0 236 247 H 4.6 H 2.8 21.0 3.4 250 257 - 4.0 M 2.4 75.0 75.0 259 266 - 4.0 M 2.8 75.0 75.0 >>>>>>