Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ii2a2 --------------------------------------CCEEEECCCHHHHHHHHHH-----HCCC-CCCC--CCCCCCCCC-CCCCCHHHEEEECCCCCC-CCCCC------CCCEECHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCC-CCCEEEEEEECCHHHHHHHHHHCCCCC-CCCCCCCCCCEEEEEECCCCCC-C-----CCCCCCCCCEEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCC---- >P1;d1j3ba2 ----------------------C----CCHHHC--CCCCCCEEECCCHHHHHHHHHH-----CCCCEECCC--CCEECCCCC-CCCCCHHHEEEECCCCCCCCCCCC-----CCCEEECHHHHHHHHHHHHHHHHCC-CEEEEEEEECCCC-CCCEEEEEEECCHHHHHHHHHHCCCHH-HH-CCC-CCCEEEEEECCCCCC-H-----HHHCCCCCCEEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHC---- >P1;d2olra2 ----------------------CCCHHHHHHCC--CCCCCCEEECCCHHHHHHHHHCCCCCHHHCEEECCC--CCEEECCCC-CCCCCHHHEEEECCCCCCCCCCCCC-CCCCCCEEECHHHHHHHHHHHHHHHCCC-CEEEEEEEECCCC-CCCEEEEEEECCHHHHHHHHHHCCCCCHHHHHCC--CCEEEEEECCCCCCCC-----CCCCCCCCCEEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHCHHHC---- >P1;d4gmua1 CCCCCCCCCHHHEEECCHHHCCHHHHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHH--CCCCEECCCCCCCEECCCCCCCCCCCHHHEEEE-CCCHHHHCCCCCCCCCCCCCEECHHHHHHHHHCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEECCHHHHHHHHHHCEECHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCCHHHCEEEEEHHHCEEEEECCCCHHHHCCIIIIIIIHHHHHHHHHHC PSA >P1;d1ii2a2 --------------------------------------8063162174640272037-----3170-45b9--68061614a-376516903000208603-91a1b------92340647004403930571054392000000006957-742130202000010012026413408-932890b804010100032805-4-----9066075400000005441000020131200441051027113555b---- >P1;d1j3ba2 ----------------------a----703a15--0616671225154640262038-----391194498--760627167-266515802100407505b50819-----a512305393047004400720063-1000000115876-731110100000010012008302137-61-aa1-825000000041605-4-----a309053400000005360000000331200440062016233555a---- >P1;d2olra2 ----------------------50548406728--05a0a71214075a30572024992994160844b9--880529208-277414702000329605a507116-eb91412205581067014100720263-3000000024876-931020000000000033015405507aa418a0--1501000003140663-----870a043510000006330000000130100440062016124656a---- >P1;d4gmua1 a299ab6305a4043850880186026101610330404401004048911881065049--6720744a86b6514171065066449631020-18648700653a9c81a7742225860682176104500652100000002463929a0410000001220012026405005601730998800200000021492878346501022740000000763100000003400010043004720383178579 Translating the sequences --------------------------------------CC*EEECCCHHHHHHHHHH-----*CCC-*CCC--CC**CCCCC-CCCCCHHHEEEECCCCCC-CCCCC------CC*EECHHHHHHHHHHHHHHH*CC**EEEEEEEECCCC-CCCEEEEEEECCHHHHHHHHHHCCCC*-****CC*CCCEEEEEECCCCCC-C-----CCCCCCCCCEEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHH*C---- ----------------------*----**HH**--*CCCC*EEECCCHHHHHHHHHH-----*CCCEECCC--CCEECCCCC-CCCCCHHHEEEECCCCCC*CCCCC-----CCC*EECHHHHHHHHHHHHHHH*CC-*EEEEEEEECCCC-CCCEEEEEEECCHHHHHHHHHHCCC**-HH-*CC-CCCEEEEEECCCCCC-*-----***CCCCCCEEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHC---- ----------------------*******HH**--*CCCC*EEECCCHHHHHHHHH********C*EECCC--CCEE*CCCC-CCCCCHHHEEEECCCCCC*CCCCC*-***CCC*EECHHHHHHHHHHHHHHH*CC-*EEEEEEEECCCC-CCCEEEEEEECCHHHHHHHHHHCCCC**HH**CC--CCEEEEEECCCCCC*C-----CCCCCCCCCEEEEECCCCEEEEECCCCCHHHHHHHHHHHHHH*HHHC---- *****************************HH*****CCC**EE*CCCHHHHHHHHHH***--*CCCEECCC**CCEECCCCC*CCCCCHHHEEEE-CCC****CCCC*****CCC*EECHHHHHHHHH*******CC**EEEEEEEECCCC*CCCEEEEEEECCHHHHHHHHHHC**C**HH***C*CCCEEEEEECCCCCC*C*****CCCCC***CEEEEE***CEEEEECCCC*HHH*********HHHHHH***** 68923.tem _________________________________ ----------------------*******HH**--*CCCC*EEECCCHHHHHHHHHH***--*CCCEECCC--CCEECCCCC-CCCCCHHHEEEECCCCCC*CCCCC*-***CCC*EECHHHHHHHHHHHHHHH*CC**EEEEEEEECCCC-CCCEEEEEEECCHHHHHHHHHHCCCC**HH**CC*CCCEEEEEECCCCCC*C-----CCCCCCCCCEEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHC---- Structural block scores 0 21 - 4.3 M 75.0 75.0 75.0 5.4 22 28 * 3.0 P 75.0 45.4 3.7 3.3 29 30 H 4.3 M 75.0 6.8 6.5 3.5 31 32 * 2.3 P 75.0 3.0 5.0 0.5 33 34 - 4.3 M 75.0 75.0 75.0 3.0 36 39 C 4.5 M 39.5 4.8 6.5 3.0 41 43 E 4.8 H 3.3 1.7 1.3 0.3 44 46 C 5.0 H 3.3 3.7 3.7 2.7 47 56 H 4.9 H 3.5 3.5 3.9 4.7 57 59 * 3.5 M 75.0 75.0 6.7 4.3 60 61 - 4.3 M 75.0 75.0 9.0 75.0 63 65 C 4.5 M 2.7 3.7 2.3 3.0 66 67 E 4.3 M 39.5 6.5 6.0 5.5 68 70 C 5.0 H 8.5 7.0 8.2 7.5 71 72 - 4.3 M 75.0 75.0 75.0 8.8 73 74 C 5.0 H 7.0 6.5 8.0 5.5 75 76 E 4.3 M 3.0 3.0 2.5 2.5 77 81 C 4.9 H 4.5 4.6 4.2 3.0 83 87 C 5.0 H 4.4 4.0 4.2 4.0 88 90 H 5.0 H 5.0 4.3 3.7 6.0 91 94 E 5.0 H 0.8 0.8 0.5 0.8 95 100 C 4.7 H 3.2 3.5 4.2 17.0 102 106 C 4.9 H 6.6 4.6 2.8 2.8 109 111 * 3.5 M 75.0 75.0 11.7 7.2 112 114 C 4.8 H 28.7 5.5 2.0 8.2 116 117 E 5.0 H 2.0 1.5 1.0 2.0 119 133 H 4.7 H 3.1 2.9 2.8 3.9 135 136 C 5.0 H 3.5 4.5 4.5 5.5 137 138 * 2.2 P 5.5 38.0 39.0 1.5 139 146 E 5.0 H 0.0 0.2 0.2 0.2 147 150 C 5.0 H 6.8 6.5 6.2 5.5 152 154 C 5.0 H 4.3 3.7 4.3 6.5 155 161 E 5.0 H 1.1 0.4 0.3 0.7 162 163 C 5.0 H 0.0 0.0 0.0 0.5 164 173 H 5.0 H 1.6 1.5 1.6 1.9 174 177 C 4.5 M 2.0 1.5 2.5 1.2 178 179 * 2.2 P 41.5 41.0 8.8 5.5 180 181 H 4.3 M 6.0 3.5 7.2 0.5 182 183 * 1.6 P 5.0 42.8 4.5 5.0 184 185 C 4.7 H 4.5 5.8 5.2 4.5 187 189 C 4.8 H 4.0 5.0 27.0 5.3 190 195 E 5.0 H 0.3 0.0 0.2 0.3 196 201 C 5.0 H 3.0 2.7 2.3 2.7 204 208 - 4.3 M 75.0 75.0 75.0 5.6 209 217 C 4.5 M 4.1 3.8 4.3 2.3 218 222 E 5.0 H 0.0 0.0 0.0 0.0 223 226 C 4.5 M 3.2 3.5 3.0 4.0 227 231 E 5.0 H 0.2 0.0 0.0 0.2 232 236 C 4.9 H 1.4 1.4 0.8 1.4 237 254 H 4.6 H 2.6 2.7 2.7 2.0 256 259 - 4.3 M 75.0 75.0 75.0 7.2 >>>>>>