Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1m65a- ------CCEECCCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEEEECCCCC---------CCCCC----HHHHHHHHCC--CEECCEEEEEEEEEECCCCCCCCCCCHHHHHHC--CEEEEECCCCCCCCCCHHHHHHHHHHHHHCCCCCEECCCCCC-CCCCCHHHHHHHHHHHCCEEEEECCC----------CHHHHHHHHHHH----CCCEEEECCCCCHHHCCCCHHHHHHHHH--CCCCHHHCHHHCHHHHHHHHHHCCCCCCHHHCCC >P1;d2anua1 ---CEEEEEEEEECCCC--CCCCCHHHHHHHHHHCCCCEEEEEEEEECCHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHC-CCCCEEEEEEEEECC---------------CCEEEEEECCC---CCCCCCCCCC-CCCCCCCCCEEEECCCCC-------CCHHHHCCCCCCCEEEEEECC--EEC-------HHHHHC--------CCCEEEECCCCCHHHHCCC---------EEEEEECCC----HHHHHHHHHHCCCEEEECCC--- >P1;d2czva- CCCCCCCCEEEEECC----------HHHHHHHHHH-CCEEEEEEEECC------------CCCH----HHHHHHHH-------HHCCEEEEEECCC------HHHHHHHHHHCCCCEEEEECCC-----------HHHHHHHHHCC-CCEEECCCCCCCCCCCCHHHHHHHHHHCCEEEEECHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHCCCHHHHHHHHHH--CCCCHHHHHHCCCHHHHHHHHC------------ PSA >P1;d1m65a- ------21000000052094060528501610673a05000000001518---------40164----7301606615--133690000100000034470600069803900--000000015301627749301600330033760100010047-50705073006101736000000255----------527600320371----8110000010230860040870482095--1a03673000340330070036091960a608b2 >P1;d2anua1 ---48402000000060--5072406600320173a02000000100070385377ca520137a70771056046139306-625100000000034---------------64020000104---7105053606-014048160000001146-------924015526920000010027--651-------960576--------9243000000236710301---------003030637----26100610370840525288--- >P1;d2czva- 764cb7520000013----------6701520373-014000005067------------9067----76058048-------6194000001706------4810640176078110002044-----------58104200434-0000000039194100665007104838000000122025178955731361056006203748020000000453700440570060046--0508573042000720540174------------ Translating the sequences ------CCEE***CCCC**CCCCCHHHHHHHHHHHCCCEEEEEEE*CCC*---------CCCCC----HHHHHHHH**--***CC**EEEEEEEECCC********HHHHHHC--CEEEEECCC***CCCC****HHHHHHHHHCCCCCEECCCCCC-CCCCC*HHHHHHHHHHCCEEEEECCC----------*HHHHHHHHHHH----CCCEEEECCCCCHHHCCCCHHHHHHHHH--CCCCHHH*HH*CHHHHHHHHH*CC********** ---C****EEEEECCCC--CCCCCHHHHHHHHHH*CCCEEEEEEEE*CC**********CCCCC****HHHHHHHH******-CCCCEEEEEEEE*CC---------------CC*EEEEECCC---CCCC******-******CCC**EECCCCC-------C*HHHH*****CCEEEEE*CC--**C-------HHHHH*--------CCCEEEECCCCCHHH*CCC---------*********----*HHHHHHHHHCCC*******--- ***C**CCEEEEECC----------HHHHHHHHHH-CCEEEEEEEECC------------CCC*----HHHHHHHH-------**CCEEEEEE**C------****HHHHHHCCCCEEEEECCC-----------HHHHHHHHHCC-CCEE*CCCCC*CCCCCCHHHHHHHHHHCCEEEEEC******C******HHHHHHHHHHH****CCCEEEECCCCCHHHCCC*HHHHHHHHH--CCCCHHH*HH*C*HHHHHHHHC------------ 89550.tem _________________________________ ---C**CCEEEEECCCC--CCCCCHHHHHHHHHHHCCCEEEEEEEECCC*---------CCCCC----HHHHHHHH**--**-CCCCEEEEEEEECCC----****HHHHHHCCCCEEEEECCC---CCCC****HHHHHHHHHCCCCCEECCCCCC-CCCCCCHHHHHHHHHHCCEEEEECCC--**C-----*HHHHHHHHHHH----CCCEEEECCCCCHHHCCCCHHHHHHHHH--CCCCHHH*HH*CHHHHHHHHHCCC*******--- Structural block scores 0 2 - 4.0 M 75.0 75.0 5.7 4 5 * 2.7 P 75.0 6.0 9.2 6 7 C 4.0 M 1.5 1.0 3.5 8 12 E 4.4 M 0.0 0.0 0.0 13 16 C 4.5 M 1.8 1.5 38.5 17 18 - 4.0 M 4.5 75.0 75.0 19 23 C 4.0 M 3.0 3.6 75.0 24 34 H 4.8 H 3.5 2.5 9.9 35 37 C 4.7 H 5.2 4.2 25.3 38 45 E 4.9 H 0.0 0.1 1.1 46 48 C 4.3 M 2.3 2.3 29.3 50 58 - 4.0 M 75.0 6.8 75.0 59 63 C 4.6 H 3.0 2.6 19.4 64 67 - 4.0 M 75.0 6.1 75.0 68 75 H 5.0 H 3.6 3.6 4.8 76 77 * 2.7 P 3.0 2.0 75.0 78 79 - 4.0 M 75.0 6.0 75.0 80 81 * 2.7 P 2.0 3.0 75.0 83 86 C 4.0 M 3.8 3.5 5.0 87 94 E 4.8 H 0.1 0.0 1.0 95 97 C 4.0 M 2.3 2.3 52.0 98 101 - 4.0 M 4.2 75.0 75.0 102 105 * 2.7 P 1.5 75.0 3.2 106 111 H 4.0 M 4.8 75.0 4.0 112 115 C 4.0 M 37.5 21.2 4.0 116 120 E 5.0 H 0.0 0.4 0.6 121 123 C 5.0 H 2.0 1.7 2.7 124 126 - 4.0 M 1.3 75.0 75.0 127 130 C 4.0 M 5.5 3.2 75.0 131 134 * 2.7 P 4.0 3.5 75.0 135 143 H 4.0 M 1.8 10.9 2.7 144 148 C 4.4 M 3.4 1.4 16.4 149 150 E 5.0 H 0.0 0.0 0.0 151 156 C 4.7 H 2.0 14.5 2.0 158 163 C 4.0 M 2.8 64.0 3.3 164 173 H 4.4 M 2.8 3.6 3.4 174 175 C 5.0 H 3.0 0.0 4.0 176 180 E 5.0 H 0.0 0.2 0.0 181 183 C 4.0 M 4.0 3.0 1.7 184 185 - 4.0 M 75.0 75.0 1.0 186 187 * 2.7 P 75.0 5.5 3.0 189 193 - 4.0 M 75.0 75.0 6.8 195 205 H 4.5 M 2.8 37.1 2.7 206 209 - 4.0 M 75.0 75.0 3.5 210 212 C 5.0 H 3.3 5.0 3.3 213 216 E 5.0 H 0.0 0.8 0.0 217 221 C 5.0 H 1.2 1.0 1.8 222 224 H 5.0 H 4.7 4.7 3.3 225 228 C 4.5 M 1.0 1.0 2.0 229 237 H 4.0 M 4.8 75.0 3.1 238 239 - 4.0 M 75.0 0.0 75.0 240 243 C 4.0 M 3.6 1.5 3.2 244 246 H 4.0 M 5.3 5.3 5.0 248 249 H 4.0 M 0.0 75.0 3.0 252 260 H 4.9 H 1.8 2.7 2.9 261 263 C 4.0 M 5.0 4.0 51.3 264 270 * 2.7 P 4.6 4.3 75.0 271 273 - 4.0 M 7.2 75.0 75.0 >>>>>>