Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2a29a- CEEEEEEEECC-----------------------------------CCC-HHHHHHHHHHHHHCCC----------------CHHHHHHHHHHHHHHCCCCC------------CCCCC-----CCEEEEEECCCCEEEEEEC------------CEEEEEECHHHHHHHHHHHCCCCC---------HHHHHHHHHHHHC------CCEEEEEEECC--------------------------EEEEEEEEEECCCC >P1;d2b8ea2 --CEEEEEECC-----------------------------------C-C-HHHHHHHHHHHCCCC------------------CCC-CCC-CCHHH-CCCCC------------CCC----------CEEEECC-CEEEEC----------------CEEEEC---CCCC----CCCCC---------HHHHHHHHHHHCC------CCEEEEEEECC--------------------------EEEEEEEEC----- >P1;d2zxea1 -CEEEEEEECC---------EEEECC-CCCCCCCC-------CCCCCCHHHHHHHHHHHHCCCCEECCCCCCCCHHHCCEECCHHHHHHHHHHHHHHC----------------CHHHHHHHCCEEEEECCCCCCCEEEEEEECCCC----CCCCEEEEEEECHHHHHC----CEEEECCCCCCCCCCHHHHHHHHHHHHHHHH--CCCEEEEEEEEECC--CCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEC---- >P1;d3ar4a4 -CCCCEEEEEEEEECCEEEEEEEEECCCCCCCCCCEEECCEECCHHHCHHHHHHHHHHHHCCCCEEEEECCCCE---EEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHEEEEEEEEEECCCCEEEEEEEECCCCCCC--CCCEEEEEECHHHHHH----CEEEEEECCEEEECCHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCHHHCCCC---CHHHHHHHCCCEEEEEEEEE------ PSA >P1;d2a29a- b5304604107-----------------------------------c27-6660020000000009----------------383071015004551a4854------------80b65-----807416169b461000217------------a66020022900672058483802---------7205720560588------91411000273--------------------------7000001074497f >P1;d2b8ea2 --903303222-----------------------------------b-6-453003000100616------------------920-304-20673-a0819------------808----------80633ac-340104----------------601005---6073----c1a16---------a802830470474------a1701100577--------------------------711000015----- >P1;d2zxea1 -1300200015---------621811-45893779-------9128917007000200000050615ba29b46216070567610200011013329----------------609611750422221444a9340000003136a----825100000001055018----3053013739538059804730570286059--5a050100013503--5b7097a2804398730416800000000049---- >P1;d3ar4a4 -3205200004606c99050140404496200725013a98525005350022001000000703061379657---04368731100000000002036461873755610310053038517321207549906000000224939a5a--a633000014197005----10630127773370584027403711870376a47060100001190284860439---56930650044000000000------ Translating the sequences ***EEEEEECC-----------------------------------CC*-HHHHHHHHHH***C**----------------CHHHHHHHHHHHHH*CCCCC------------C****-----**EEEEEECCCCEEEEEE*------------*EEEEEECHHHHH**********C---------HHHHHHHHHHHH*------CCEEEEEEE*C--------------------------EEEEEEEE****** --*EEEEEECC-----------------------------------C-*-HHHHHHHHHH*CCC*------------------***-***-**HHH-CCCCC------------C**----------*EEEECC-CEEEE*----------------*EEEEC---****----****C---------HHHHHHHHHHH**------CCEEEEEEE*C--------------------------EEEEEEEE*----- -**EEEEEECC---------******-********-------****CC**HHHHHHHHHH*CCC******************CHHHHHHHHHHHHH*C----------------C***********EEE***CCCCEEEEEE*****----*****EEEEEECHHHHH*----*****C*********HHHHHHHHHHHH****--*CCEEEEEEE****--**********************EEEEEEEE**---- -****EEEE**************************************C**HHHHHHHHHH*CCC**********---*****CHHHHHHHHHHHHH*CCCCC************************EEEEEECCCCEEEEEE*********--***EEEEEECHHHHH*----***************HHHHHHHHHHHH*******CCEEEEEEE*C***********---************EEEEEEEE------ 81660.tem _________________________________ -**EEEEEECC---------******-********-------****CC**HHHHHHHHHH*CCC**********---*****CHHHHHHHHHHHHH*CCCCC------------C***********EEEEEECCCCEEEEEE*****------***EEEEEECHHHHH**---*****C*********HHHHHHHHHHHH****--*CCEEEEEEE*C**--*******---************EEEEEEEE**---- Structural block scores 1 2 * 1.6 P 4.0 42.0 2.0 2.5 3 8 E 4.8 H 2.5 1.8 0.3 1.2 9 10 C 4.3 M 3.5 2.0 3.0 2.0 11 19 - 4.3 M 75.0 75.0 75.0 5.3 20 25 * 3.5 M 75.0 75.0 3.2 2.2 27 34 * 3.5 M 75.0 75.0 6.5 3.9 35 41 - 4.3 M 75.0 75.0 75.0 5.2 42 45 * 3.5 M 75.0 75.0 5.0 1.8 46 47 C 4.3 M 7.2 43.2 5.0 4.0 48 49 * 2.2 P 41.0 40.5 3.5 2.5 50 59 H 5.0 H 2.0 1.6 0.9 0.5 61 63 C 4.5 M 0.0 2.3 1.7 2.3 64 73 * 3.1 M 60.9 68.1 6.7 4.7 74 76 - 4.3 M 75.0 75.0 3.0 75.0 77 81 * 3.5 M 75.0 75.0 3.6 4.2 83 95 H 4.5 M 3.0 14.3 1.4 0.4 97 101 C 4.4 M 6.3 5.7 61.8 3.8 102 113 - 4.3 M 75.0 75.0 75.0 3.9 115 125 * 2.6 P 36.9 62.1 3.4 3.4 126 131 E 4.4 M 4.2 15.8 2.8 3.2 132 135 C 4.8 H 7.6 25.2 6.6 6.0 136 141 E 4.8 H 0.7 14.0 0.0 0.0 142 146 * 3.3 M 61.4 75.0 4.7 4.0 147 152 - 4.3 M 75.0 75.0 51.7 30.8 153 155 * 3.1 M 53.5 75.0 2.0 6.5 156 161 E 4.8 H 2.3 13.7 0.0 0.7 163 167 H 4.3 M 3.4 46.2 2.2 3.4 168 169 * 2.2 P 4.5 5.0 41.5 40.0 170 172 - 4.3 M 4.3 75.0 75.0 75.0 173 177 * 1.3 P 4.6 20.0 2.2 2.0 179 187 * 3.5 M 75.0 75.0 4.8 4.6 188 199 H 4.9 H 3.9 4.5 4.4 3.8 200 203 * 2.9 P 58.2 57.2 5.0 4.2 204 205 - 4.3 M 75.0 75.0 75.0 8.2 207 208 C 5.0 H 5.0 5.8 5.2 3.5 209 215 E 5.0 H 1.1 2.0 1.0 1.0 218 219 * 3.5 M 75.0 75.0 1.5 4.5 220 221 - 4.3 M 75.0 75.0 75.0 5.0 222 228 * 3.5 M 75.0 75.0 7.1 4.9 229 231 - 4.3 M 75.0 75.0 3.3 75.0 232 243 * 3.5 M 75.0 75.0 4.4 3.5 244 251 E 5.0 H 1.0 1.2 0.0 0.0 252 253 * 2.9 P 5.5 40.0 6.5 75.0 254 257 - 4.3 M 10.6 75.0 75.0 75.0 >>>>>>