Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ca4a1 -------------------------------CCCEEEEEEE--------CHHHHHHHHHCC-------CCCCEECCCEECCC-CCCEEEEEEECCC--CCCCCCEEEEEEEEECCCCHHHC-CCCCCCEEEEECCCC-----CCEEEEE-CCCCCCHHHCCCCCCCC-CCEEEEEEEECCCCC------------CCCCCCCEEEEEEEECCCCC >P1;d1lb6a- -----------------------------C-CCEEEEEEEC--------CHHHHHHHHHCC-------CCEEEECCCEECCC-CCCEEEEEEEECCCCCCCCCCEEEEEEEEECCCCHHHCCCCCCCEEEEEECCCCCCCCCCCEEEEE-ECCCCCHHHCCCCCCCCCCCEEEEEEEEHHHHH-----------CCCCCCCCCEEEEEEEEC--- >P1;d3ivva1 -----------------------------CCCEEEEEEEEC--------CHHHC-CCC----------CCCCEECCCEEECHHHCEEEEEEEECCCC-CHHHCCEEEEEEEEEECCC-----CEEEEEEEEEEECC---CCCEEEEEECCCCEEEEC----------CCEEEEEEEEEHHHHHC---------HHHCCCHHHCEEEEEEEEECC- >P1;d4ca1a- CCCCCEECCCHHHCCCCEECHHHHHHHHHHCCCCCEECCCCCCCCCCEECHHHHHHHHHHHCCCCEEEECCEEEEEECCCCCCCCEEEEEEEEEC--------CEEEEEEEEEEEC------CEEEEEEEEECCCHHHHCCEEEEEEEEEC----------CEEEEEEECCEECCCCCHHHHHCCCCEEEEHHHHHHHCCCCCEEEEEEEEEC-- PSA >P1;d1ca4a1 -------------------------------4704141505--------507521710457-------75503407102066-7102000301020--4b907720001000050620671-120703010102226-----9215522-70759470045098831-814004500429507------------62024a500302040449b4 >P1;d1lb6a- -----------------------------b-a323330705--------905722730665-------58022206002097-500200020202426399123300020001307209807120733040002013977837433440-805374700540a67406602035400416107-----------635026a52020202055--- >P1;d3ivva1 -----------------------------564713151316--------70481-928----------44642508412006a86030003000404-4770552000100044049-----83240402000036---876454346046125035----------74230234004274035---------a82a00393401010303054- >P1;d4ca1a- ba994460614a380845147a52981187094230700117a92826542940150037627b0723986605050560578973410100212--------c330000020365------a3300000000046940660404010439----------856423634020072519600875500205583045009a520304020676-- Translating the sequences -------------------------------CC*EEEEEE*--------CHHHHHHHHH**-------CCC*EECCCEECCC-CC*EEEEEEE*CC--C***CCEEEEEEEEE*CCC****-C*****EEEEECCC*-----**EEEEE-CC*********C*****-CCEEEEEEEE*****------------*CCCCCC*EEEEEEE**C** -----------------------------*-CC*EEEEEEC--------CHHHHHHHHH**-------CC**EECCCEECCC-CC*EEEEEEE*CC**C***CCEEEEEEEEE*CCC*****C****EEEEEECCC***CC***EEEEE-*C*********C******CCEEEEEEEEHHHHH-----------**CCCCCCCEEEEEEEE*--- -----------------------------**C**EEEEEEC--------CHHH*-***----------CCC*EECCCEE*C***C*EEEEEEE*CC*-C***CCEEEEEEEEE*CCC-----C****EEEEEE*CC---CC***EEEE**CC*****----------*C*EEEEEEEEHHHHH*---------***CCC***CEEEEEEEE*C*- *******************************CC**EE***C********CHHHHHHHHH**********CC*EE*****CCC*CC*EEEEEEE*C--------CEEEEEEEEE**C------C****EEEEE*CC****CC***EEEEE*C----------C*******C*EE*****HHHHH***************CCCCCEEEEEEEE*C-- 49599.tem _________________________________ -----------------------------**CC*EEEEEEC--------CHHHHHHHHH**-------CCC*EECCCEECCC*CC*EEEEEEE*CC*-C***CCEEEEEEEEE*CCC****-C****EEEEEECCC***CC***EEEEE*CC*********C******CCEEEEEEEEHHHHH*---------***CCCCCCCEEEEEEEE*C*- Structural block scores 0 28 - 4.3 M 75.0 75.0 75.0 5.5 29 30 * 2.9 P 75.0 43.2 5.5 3.5 31 32 C 4.7 H 5.5 6.8 5.5 6.5 34 39 E 4.5 M 2.5 2.7 2.3 1.8 41 48 - 4.3 M 75.0 75.0 75.0 6.2 50 58 H 4.5 M 3.0 3.6 20.2 2.7 59 60 * 2.3 P 6.0 5.5 75.0 6.5 61 67 - 4.3 M 75.0 75.0 75.0 4.6 68 70 C 4.5 M 5.7 4.3 4.7 7.7 72 73 E 5.0 H 3.5 2.0 3.5 2.5 74 76 C 4.3 M 2.7 2.0 4.0 1.7 77 78 E 4.3 M 1.0 1.0 1.5 5.5 79 81 C 4.5 M 4.0 5.3 2.0 4.0 83 84 C 4.7 H 4.0 2.5 7.0 8.0 86 92 E 5.0 H 0.9 0.9 0.9 1.1 94 95 C 4.7 H 1.0 3.0 2.0 38.5 99 101 * 2.3 P 6.8 6.3 4.7 75.0 102 103 C 4.7 H 7.0 2.5 5.0 43.8 104 112 E 5.0 H 0.3 0.7 0.8 0.9 114 116 C 4.5 M 2.7 3.0 4.3 28.7 117 120 * 3.5 M 3.5 4.2 75.0 75.0 123 126 * 1.0 P 2.2 3.0 2.2 1.5 127 132 E 4.8 H 0.8 1.2 1.0 0.0 133 135 C 4.5 M 2.0 1.0 3.0 3.3 136 138 * 3.1 M 52.0 6.3 75.0 4.3 139 140 C 4.3 M 75.0 7.5 7.5 6.0 141 143 * 1.4 P 28.7 4.7 5.0 1.3 144 148 E 4.9 H 3.0 2.8 3.4 1.8 150 151 C 4.3 M 3.5 4.0 3.5 42.0 152 160 * 2.8 P 4.6 3.9 35.0 75.0 162 167 * 2.3 P 17.3 5.6 63.7 4.3 168 169 C 4.3 M 4.5 3.0 3.0 3.5 170 177 E 4.5 M 2.1 2.2 2.0 2.1 178 182 H 4.3 M 4.6 3.0 3.2 4.6 184 192 - 4.3 M 75.0 75.0 75.0 3.3 193 195 * 2.3 P 52.0 28.0 6.8 2.3 196 202 C 4.4 M 3.4 4.4 4.2 4.5 203 210 E 4.9 H 1.6 1.4 1.0 1.9 >>>>>>