Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1lwuc1 CCCHHHHCCCCCCCCCHHHHHCCCCCCCEEEEECCCCCCCCEEEEEEEC-CCCEEEEEEEECCCCCCCCCCHHHHHHCEECCCC-------CCCCCEECCHHHHHHHHCCCCEEEEEEEECCCCCEEEEEEEEEEECCHHHCCCEECCCEEECCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCC-----CCHHHHHCCCCCCCC-CCCEECCCCCCCCCCCCCCCCCCCCCCCCEEHHHCCCCCCCCEEEEEEEECCCCCCCCCCCCC >P1;d1m1jb1 CCCCCCCCCCCCCCCCHHHHHHCCCCCCEEEEECCCCCCCCEEEEEECCHHHCCEEEEEEECCCCCCCCCCHHHHHHCEECCEECCCCCCCCEECCEECCHHHHHHHHCCCCEEEEEEEECCCCCEEEEEEEEEEECCHHHCCCEEEEEE-EECCCCHHHHCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCC-CCCEECCCCCCCCCCCCHHHCCCCCCCCCEEHHHHCCCCCCCEEEEEEEECCCC--------- >P1;d2wnpf- -------CCCCCC-CCHHHHHHCCCCCCEEEEEECCC-CCEEEEEEECCHHHCCEEEEEEECCCCCCCCCCHHHHHHCEECC-----------CCCEECCHHHHHHHHHCCCEEEEEEEECCCCCEEEEEECCEEECCHHHCCCEEECCEEECCCCCCCHHHC--------------CCCCCCCCCCCCCCC-----CCHHHHCCCCCCCCC-CCCEECCCCCCC-EECC------CCCCCCEECCCCCCCEECCEEEEEEEEC------------ >P1;d6euaa1 ------------CCCCHHHHHHCCCCCCEEEEECCC-CCCCEEEEEEEE-CCEEEEEEEEECCCCCCCCCCHHHHHHCEECC-----------CCCEECCHHHHHHHHCCCCEEEEEEEEECCCCEEEEEEE-EEECCHHHCCCEEEE-EEEECCCCCCCCC--------------CCCEEECCCCCCC---------CCHHHCCCCEEECCCCCCCCCCCCCCC-------------CCEEEECCCCC-EEEEEEEEEEEEECC----------- >P1;d6y43a1 -------CCCCCCCCCHHHHHHCCCCCCEEEEEEECC--EEEEEEEECCHHHCCEEEEEEECCCCCCCCCCHHHHHHCEECC-----------CCCEECCHHHHHHHHC-CCEEEEEEEECCCCCEEEEEEEEEEECCHHHCCCEEEEEE-ECCCCCCCHHHC--------------CCCCCCCCCCCCCCC-----CCHHHHHCCCCCCCC-CCCCCCCCCCCCCCCCC------CCCCCCCCCCCCCCCCCCCEEEEEEEECC----------C PSA >P1;d1lwuc1 b987559622834140004016590883200504078099312000204-a710000000024071904350620360108231-------71520000004202200504401020300129645430000504034394103050462270705200404718657407820203512000164330528-----710072030000003-200000005037a621558a7867320000001116212002301000001c34998acab8a >P1;d1m1jb1 a898590631b333500210265817711003040269593150001084690000000002415070433073026001620528a6930241100000053003004366010102010196771302015040473c4403050582-8480500027006438c9637303047140005554103292b478510031040000014-200000005017708057650753320000000135142003401010133a5c--------- >P1;d2wnpf- -------829911-320330164457a4512402039-5451401010934a000000020261718033407203801155-----------93000000410320034c6010001010267782301064050154964020404923516063006a04--------------71400036441070b-----520066140000025-003000003027-071a------6601000013036351004102000236------------ >P1;d6euaa1 ------------525003402767559246230407-a17405030012-a8610000020560829042417501511072-----------9300000052021003a6301010203148688130203-060546864020304-2460603000137--------------4703010534337---------707417000001276153000005056-------------90030308776-31502203000215b----------- >P1;d6y43a1 -------b669020910050392726b2331505078--734302020724b000000010351629031808502411181-----------7400000031024104-c70000020202a4860401033040334954030303a2-528012004305--------------62000037432044a-----620053030000022-10400000402850814------84700000471451700035010002319----------a Translating the sequences *******CCCCCCCCCHHHHH*CCCCCCEEEEECCCCCCCCEEEEEE*C-**C*EEEEEEECCCCCCCCCCHHHHHHCEECC**-------**CCCEECCHHHHHHHHCCCCEEEEEEEECCCCCEEEEEEEEEEECCHHHCCCEE***EEECCCCCCC**CC*************CCCCCCCCCCCCCCCC-----CCHHHH*CCCCCCCC-CCCEECCCCCCCCCCCC******CCCCCCEE***CCCCCCCCEEEEEEEECC*********** *******CCCCCCCCCHHHHHHCCCCCCEEEEECCCCCCCCEEEEEECCHHHCCEEEEEEECCCCCCCCCCHHHHHHCEECC************CCEECCHHHHHHHHCCCCEEEEEEEECCCCCEEEEEEEEEEECCHHHCCCEEEE*E-E*CCCC**HHCC*************CCCCCCCCCCCCCCCC*****CCHHHHCCCCCCCCC-CCCEECCCCCCCCCCCC******CCCCCCEE****CCCCCCCEEEEEEEECC**--------- -------CCCCCC-CCHHHHHHCCCCCCEEEEE*CCC-CC*EEEEEECCHHHCCEEEEEEECCCCCCCCCCHHHHHHCEECC-----------CCCEECCHHHHHHHH*CCCEEEEEEEECCCCCEEEEEE**EEECCHHHCCCEEE**EEECCCCCCCHH*C--------------CCCCCCCCCCCCCCC-----CCHHHHCCCCCCCCC-CCCEECCCCCCC-**CC------CCCCCCEECCCCCCC**CCEEEEEEEEC------------ ------------CCCCHHHHHHCCCCCCEEEEECCC-CCCCEEEEEE**-****EEEEEEECCCCCCCCCCHHHHHHCEECC-----------CCCEECCHHHHHHHHCCCCEEEEEEEE*CCCCEEEEEEE-EEECCHHHCCCEEEE-EEE*CCCCCC**C--------------CCC***CCCCCCC---------C*HHHCCCC***CC*CCC**CCCCCCC-------------CC**EECCCCC-*****EEEEEEEECC----------- -------CCCCCCCCCHHHHHHCCCCCCEEEEE**CC--**EEEEEECCHHHCCEEEEEEECCCCCCCCCCHHHHHHCEECC-----------CCCEECCHHHHHHHHC-CCEEEEEEEECCCCCEEEEEEEEEEECCHHHCCCEEEE*E-ECCCCCCCHH*C--------------CCCCCCCCCCCCCCC-----CCHHHH*CCCCCCCC-CCC**CCCCCCCCCCCC------CCCCCC**CCCCCCCCCCCEEEEEEEECC----------* 56496.tem _________________________________ -------CCCCCCCCCHHHHHHCCCCCCEEEEECCCCCCCCEEEEEECCHHHCCEEEEEEECCCCCCCCCCHHHHHHCEECC-----------CCCEECCHHHHHHHHCCCCEEEEEEEECCCCCEEEEEEEEEEECCHHHCCCEEEE*EEECCCCCCCHHCC-------------CCCCCCCCCCCCCCCC-----CCHHHHCCCCCCCCC-CCCEECCCCCCCCCCCC------CCCCCCEECCCCCCCCCCCEEEEEEEECC----------- Structural block scores 0 6 - 3.8 M 7.8 7.1 75.0 75.0 75.0 7 15 C 4.7 H 3.3 3.9 12.2 43.0 4.9 16 21 H 4.9 H 1.8 1.8 2.2 2.7 2.8 22 27 C 5.0 H 5.5 4.8 5.8 5.7 5.1 28 32 E 5.0 H 1.4 0.8 2.4 3.0 2.4 33 40 C 4.3 M 5.0 4.8 12.9 13.6 22.5 41 46 E 5.0 H 0.8 1.2 1.2 1.3 1.8 47 48 C 4.2 M 2.0 4.0 4.5 1.5 3.5 49 51 H 3.9 M 30.8 6.3 5.8 31.2 5.8 52 53 C 4.2 M 0.5 0.0 0.0 3.5 0.0 54 60 E 5.0 H 0.0 0.0 0.3 0.3 0.1 61 70 C 5.0 H 3.5 2.9 3.5 4.0 3.8 71 76 H 5.0 H 2.8 3.0 3.3 3.2 3.2 78 79 E 5.0 H 0.5 0.5 1.0 0.5 1.0 80 81 C 5.0 H 5.0 4.0 5.0 4.5 4.5 82 92 - 4.2 M 48.8 4.5 75.0 75.0 75.0 93 95 C 4.8 H 2.3 0.7 4.0 4.0 3.7 96 97 E 5.0 H 0.0 0.0 0.0 0.0 0.0 98 99 C 5.0 H 0.0 0.0 0.0 0.0 0.0 100 107 H 5.0 H 1.2 1.4 1.2 1.2 1.4 108 111 C 4.8 H 3.2 4.8 6.4 5.6 24.6 112 119 E 5.0 H 0.8 0.6 0.4 0.9 0.5 120 124 C 4.9 H 4.4 4.6 4.4 5.4 4.9 125 135 E 4.9 H 1.9 2.1 2.6 8.9 1.9 136 137 C 5.0 H 3.5 5.5 3.0 4.5 3.0 138 140 H 5.0 H 5.3 6.5 6.3 6.7 6.0 141 143 C 5.0 H 1.3 2.3 2.0 2.0 2.3 144 147 E 4.6 H 2.2 2.5 2.0 1.8 1.5 149 151 E 4.7 H 3.7 28.3 3.3 4.0 27.3 152 158 C 4.7 H 2.0 2.4 2.3 1.3 1.9 159 160 H 3.8 M 2.0 4.5 8.2 2.0 3.5 161 162 C 4.2 M 5.5 0.0 2.0 41.0 2.5 163 175 - 3.8 M 3.8 5.0 75.0 75.0 75.0 176 191 C 4.8 H 2.7 3.1 7.7 16.6 7.5 192 196 - 4.5 M 75.0 6.5 75.0 75.0 75.0 197 198 C 4.8 H 4.0 3.0 3.5 41.0 4.0 199 202 H 4.9 H 2.2 1.0 3.0 3.0 2.0 203 211 C 4.7 H 0.7 1.0 1.3 1.9 0.8 213 215 C 5.0 H 0.7 0.7 1.0 3.0 1.7 216 217 E 3.8 M 0.0 0.0 0.0 0.0 0.0 218 229 C 4.7 H 3.3 2.8 8.8 32.6 2.7 230 235 - 3.8 M 7.4 5.0 75.0 75.0 75.0 236 241 C 4.7 H 2.0 1.3 2.2 27.0 3.2 242 243 E 4.5 M 0.0 0.0 0.0 1.5 0.0 244 254 C 4.2 M 1.5 1.7 2.4 10.4 2.9 255 262 E 5.0 H 0.5 1.2 1.0 1.0 1.4 263 264 C 4.8 H 6.8 6.8 40.5 8.2 5.0 265 275 - 4.3 M 8.8 63.0 75.0 75.0 69.1 >>>>>>