Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1wmia1 CCCEEEECHHHHHHHCCCC---HHHHHHHHHHHHHHCCC-CCC-HHHHCCEEEECCCC-EEEEEEECC-CCEEEEEEECC--CCEEEEEEEECCCC--C >P1;d4ltta1 -CCEEEECHHHHHHHHHHHHCCC-CCHHHHHHHHHHHCC--CCCCHHHCCEECC--HHHCCCEEEEEECCEEEEEEEEC----CEEEEEEEECHHHHC- >P1;d4ml2a- -CCEEEECHHHHHHHHHHHHCCC-CHHHHHHHHHHHHCCC-CCCCHHHCCEECC--HHHCCCEEEEEECCEEEEEEECC----CEEEEEEEECHHHHHC >P1;d6l8gb- CCCCEEECHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCC--CCCEECC--HHHCCCEEEECCCCCEEEEEEEC----CEEEEEECCCCC---- >P1;d6n90a- --CEEEECHHHHHHHHHHHHHCC-CC-CHHHHHHHHHHC-CCCCC--C-EEEC---CCCCCCEEEEEECCEEEEEEEEEECCEEEEEEEEECCCC---- PSA >P1;d1wmia1 a51805269806850a816---85256503604630376-120-7a7070553616c8-614010309-40102010348--55205035135639--a >P1;d4ltta1 -40733448504812751497a0-837507701520246--5905980715417--c9356230020588000001369----820102200389401- >P1;d4ml2a- -b272342d40670275158693-6195067016103766-3905b81714517--ca27913002029600000215a----9202012044595039 >P1;d6l8gb- 8a2a16149805611350575489117305400610476814766--2807429--9b67941104048302020116b----a30404302668---- >P1;d6n90a- --283415a80572144048569-11-305400520366-27774--2-1551---cb37a220050567210003025acb9340203202654---- Translating the sequences *CCEEEECHHHHHHH****---***HHHHHHHHHHH*CC-CCC-*HHHCCEE******-***EEEE**-C*EEEEEEEC*--*CEEEEEEEECCC*--* -CCEEEECHHHHHHHHHHHH*CC-C*HHHHHHHHHHHCC--CCCCHHHCCEECC--HHHCCCEEEEEECCEEEEEEEEC----CEEEEEEEEC*****- -CCEEEECHHHHHHHHHHHH*CC-CHHHHHHHHHHHHCC*-CCCCHHHCCEECC--HHHCCCEEEEEECCEEEEEEE*C----CEEEEEEEEC****** *CC*EEECHHHHHHHHHHHH*C***HHHHHHHHHHHH***CCCCC--*CCEECC--HHHCCCEEEE**CC*EEEEEEEC----CEEEEEE**CCC---- --CEEEECHHHHHHHHHHHH*CC-C*-*HHHHHHHHH*C-CCCCC--*-*EEC---***CCCEEEEEECCEEEEEEEE******EEEEEEE*CCC---- 143011.tem _________________________________ -CCEEEECHHHHHHHHHHHH*CC-CHHHHHHHHHHHHCC-CCCCCHHHCCEECC--HHHCCCEEEEEECCEEEEEEEEC----CEEEEEEEECCC*--- Structural block scores 1 2 C 4.8 H 3.0 2.0 6.8 6.2 38.5 3 6 E 4.9 H 3.8 4.2 4.0 4.6 4.0 8 19 H 4.8 H 11.4 4.5 4.9 4.2 4.5 21 22 C 4.2 M 41.5 5.2 6.0 6.0 7.5 25 36 H 4.8 H 3.4 3.2 3.2 2.6 8.2 37 38 C 4.2 M 6.5 5.0 6.5 6.5 6.0 40 44 C 4.6 H 17.0 18.8 18.4 4.8 5.4 45 47 H 4.1 M 5.8 5.7 6.8 50.7 50.7 48 49 C 4.5 M 3.5 4.0 4.0 4.0 38.0 50 51 E 5.0 H 5.0 4.5 4.5 5.5 5.0 52 53 C 4.3 M 4.5 4.0 4.0 5.5 38.0 54 55 - 4.5 M 3.5 75.0 75.0 75.0 75.0 56 58 H 3.9 M 31.8 8.2 8.3 8.8 9.0 59 61 C 4.5 M 3.7 4.3 5.7 6.7 6.5 62 67 E 4.6 H 2.2 1.7 1.2 1.7 2.0 68 69 C 4.8 H 39.5 8.0 7.5 5.5 6.5 70 77 E 4.8 H 0.9 1.2 1.0 1.5 1.0 79 82 - 4.2 M 40.8 75.0 75.0 75.0 10.9 84 91 E 4.8 H 2.4 0.9 1.4 2.0 1.6 92 94 C 4.2 M 4.7 6.7 6.0 6.7 5.0 96 98 - 3.8 M 53.5 25.3 4.0 75.0 75.0 >>>>>>