Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1h4xa- ----CEEEEEEE---CCEEEEEEEEEECHHHHHHHHHHHHHHHHCCCC-CEEEEEEEEEEEEC-CHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHCCCHHH-----EECCCHHHHHHHCC-- >P1;d1th8b- --CEEEEEEE-E---CCEEEEEEEEEECHHHHHHHHHHHHHHHHCCCC-CEEEEEEEEEEEECHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHCCHHHCC----EEECCHHHHHHHCCCC >P1;d1vc1a- CCCCEEEEEE-E---CCEEEEEEECCCCCCCHHHHHHHHHHHHHHCCC-CEEEEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCHHHCC----EEECCCCCC------- >P1;d2ooka1 CCCCEEEEEEEEECCEEEEEEEEEEEECHHHHHHHCC-CHHHHCCCCCCCCEEEEEEEEEEEC---CCHHHHC-CCCCCCCEEEEEEECCCCC-CCCC--CHHHHCCEEEEEEECCCCHHHHHHC- >P1;d6m37b- --CEEEEEEE-E---CCEEEEEEEEEECCCCHHHHHHHHHHHHHC--C-CCEEEEEEEEEEECHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHCCCCCCC----EECC------------ PSA >P1;d1h4xa- ----82615413---930000103850468106704570062067760-40000005706704-703900360182067490500002049904940594a0264-----03536286006706-- >P1;d1th8b- --70807141-4---74000020555039910560463027207a6b0-510002038085049301800461174069590500004058905820664304740----4228527500410907 >P1;d1vc1a- 7870705233-5---76000040643015601a6044407710670a2-62000105506603a5019104400630674a050000304a602720664714850----621950960------- >P1;d2ooka1 c693108174663785500104020505682267205-0695068074911000103605006---b230390-6070966072000025b73-6017--5016008096245186570282027- >P1;d6m37b- --90906175-8---994050605550388016505940452055--0-1503010650750384007003303720674b1404025079701530564a24a60----6074------------ Translating the sequences ----*EEEEE*E---CCEEEEEEEEEECHHHHHHHHHHHHHHHHCCCC-CEEEEEEEEEEEEC-*HHHHHHHHHHHHH*CCCEEEEECCCHHHHHHHHHCC*HH*-----EE*CC***HHHH**-- --C*EEEEEE-E---CCEEEEEEEEEECHHHHHHHHHHHHHHHHCCCC-CEEEEEEEEEEEECHHHHHHHHHHHHHHHHCCC*EEEECCCHHHHHHHHHCCHHHCC----EEECC***HHHH**** **C*EEEEEE-E---CCEEEEEEE***C***HHHHHHHHHHHHH*CCC-CEEEEEEEE****CHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCHHHCC----EEECC****------- **C*EEEEEE*E*****EEEEEEEEEECHHHHHHH**-*HHHH*CCCC*C*EEEEEEEEEEEC---**HHHH*-*****CC*EEEEE*CC***-****--CHHH*C****EEE*C***HHHH***- --C*EEEEEE-E---CCEEEEEEEEEEC***HHHHHHHHHHHHHC--C-C*EEEEEEEEEEECHHHHHHHHHHHHHHHHCCC*EEEECCCHHHHHHHHHCC***CC----EE*C------------ 52091.tem _________________________________ --C*EEEEEE-E---CCEEEEEEEEEECHHHHHHHHHHHHHHHHCCCC-CEEEEEEEEEEEECHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCHHHCC----EEECC***HHHH**-- Structural block scores 0 1 - 3.8 M 75.0 75.0 7.5 9.2 75.0 4 9 E 4.9 H 4.3 3.5 3.3 3.5 4.7 12 14 - 4.5 M 75.0 75.0 75.0 6.0 75.0 15 16 C 4.5 M 6.0 5.5 6.5 5.0 9.0 17 26 E 4.8 H 1.7 1.7 1.7 1.2 3.0 28 43 H 4.6 H 3.6 3.8 3.8 8.7 3.9 44 47 C 4.6 H 5.0 7.0 4.9 4.8 38.8 50 61 E 4.7 H 2.1 2.2 2.1 1.3 2.7 63 78 H 4.5 M 7.9 3.7 3.5 21.9 3.1 79 81 C 4.8 H 4.3 4.7 4.8 4.0 5.5 82 86 E 4.8 H 1.0 1.0 1.0 1.8 2.0 87 89 C 4.8 H 2.0 3.0 2.3 2.3 4.0 90 98 H 4.5 M 5.4 4.9 4.4 20.6 4.0 99 100 C 4.8 H 7.2 3.5 5.5 40.0 7.2 101 103 H 4.3 M 2.7 3.7 4.3 2.3 5.5 104 105 C 4.2 M 39.5 2.0 2.5 0.0 3.0 106 109 - 4.5 M 75.0 75.0 75.0 5.8 75.0 110 112 E 4.6 H 2.7 2.7 3.0 3.7 4.3 113 114 C 4.5 M 4.5 6.5 7.0 4.5 39.5 115 117 * 2.1 P 5.3 4.7 5.0 6.0 75.0 118 121 H 4.2 M 3.2 1.2 56.2 3.0 75.0 122 123 * 3.0 P 3.0 4.5 75.0 1.0 75.0 124 125 - 4.2 M 75.0 3.5 75.0 41.0 75.0 >>>>>>