Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2gk6a2 -----------------CEEEECEEEEEC--------CCCCEEEEEECCCC-------------CCCEEEEEECCC-----------------CCCCCEEEEEEEECCCC-------------CCCEEEEEEC--CCCCCCCC-------CCCCEEEEECC- >P1;d3jb9x1 CCEECCCCCEECC----CCCCCCEEECCCCC------CCCCCCEEECCCCC---CHHHHHHCCCC-CCCCEECCCCCCCCCCCCCCCCCCC-------CCCEEEEEECCCCCCCCCCCC---CCCCCEEEEECC-CHHHHHHHHCCCCCCCCCCCCEECC-- >P1;d4pj3a1 CEEECCCCCEEECCCCCCEEEEEEEEEEECCCCCCCCCCCCEEEEEEEECCCCHHHHHHHCCCCCCCEEEEEEECCCCCCCCCCCCCCCHHHHHCEEEEEEEEEEECC-CCCCCCCCCCCCCCCEEEEEEEECHHHHHHCCHHHHHCCCCHHHCCCEECCCC PSA >P1;d2gk6a2 -----------------446906060548--------a6852102051727-------------68550003051a-----------------7a16153304052236c-------------7681000107--61a90037-------1584020234b- >P1;d3jb9x1 610337b66024a----34302b07555429------51680301011233---53184378975-76120215a1529495725ba679a-------806051013025a63366a09---867130005063-11725705a7976a2216a012150-- >P1;d4pj3a1 511438aa8242139664040460713342947bb4a3024020201050927a603730250557350402005031776491399686770121324130302210-8786229b43b19b66021203062642471464977a4540081021017a8 Translating the sequences -----------------CEEEECEEEEEC--------CCCCEEEEEECCCC-------------CCCEEEEEECCC-----------------*C***EEEEEEEECCCC-------------CCCEEEEEEC--C***CC**-------CCCC**EE*CC- C*EECCCCCEE*C----C****CEEE**CCC------CCCC**EEE*CCCC---*HHHHH*CCCC-C***EE*CCCCCCCCCCCCCCCC**-------***EEEEE*CCCCCCCCCCCC---CCCC*EEEEEC*-CHHH**HHH**CCCCCCCCCCEECC-- C*EECCCCCEE*C****CEEEE*EEEEE*CC******CCCCEEEEEE**CC****HHHHH*CCCCCCEEEEEE*CCCCCCCCCCCCCCC*****C***EEEEEEEECC-CCCCCCCCCC***CC**EEEEEEC***HHHCCHHH**CCCC***CCCEECCC* 345920.tem _________________________________ C*EECCCCCEE*C----CEEEECEEEEECCC------CCCCEEEEEECCCC---*HHHHH*CCCCCCEEEEEECCCCCCCCCCCCCCCC**--*C***EEEEEEEECCCCCCCCCCCCC---CCCCEEEEEEC*-CHHHCCHHH**CCCCCCCCCCEECCC- Structural block scores 2 3 E 4.0 M 75.0 1.5 2.5 4 8 C 4.0 M 75.0 6.7 8.0 9 10 E 4.0 M 75.0 1.0 3.0 13 16 - 4.0 M 75.0 75.0 6.0 18 21 E 4.0 M 4.8 2.2 2.0 23 27 E 4.6 H 3.0 4.4 2.8 28 30 C 4.0 M 52.7 5.0 5.0 31 36 - 4.0 M 75.0 75.0 8.1 37 40 C 5.0 H 7.4 5.0 2.2 41 46 E 4.5 M 1.7 0.8 0.8 47 50 C 4.5 M 4.2 2.2 3.5 51 53 - 4.0 M 75.0 75.0 6.5 55 59 H 4.0 M 75.0 3.8 2.6 61 66 C 4.3 M 40.7 18.5 4.2 67 72 E 4.3 M 1.3 2.0 1.8 73 88 C 4.1 M 62.0 6.2 4.9 89 90 * 2.7 P 75.0 9.8 6.5 91 92 - 4.0 M 75.0 75.0 3.5 95 97 * 2.7 P 2.7 75.0 2.0 98 105 E 4.6 H 2.8 2.6 1.9 106 118 C 4.2 M 53.7 4.9 10.5 119 121 - 4.0 M 75.0 75.0 7.2 122 125 C 4.2 M 24.0 5.5 5.9 126 131 E 4.8 H 0.3 1.3 1.3 136 138 H 4.0 M 6.8 3.3 4.3 139 140 C 4.0 M 0.0 6.0 2.5 141 143 H 4.0 M 28.3 5.2 6.3 144 145 * 2.7 P 75.0 8.0 7.0 146 155 C 4.1 M 32.0 4.6 3.5 156 157 E 5.0 H 1.0 1.5 0.5 158 160 C 4.3 M 6.2 26.7 6.2 >>>>>>