Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fm0e- --C--CEEEEEECCCCCHHHHHHHHCCCCCCCEEEEEEEECC---------CCCEEEEECHHHHHHHHHHHHHHHHHHC-CEEEEEEEEECEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEEECCEEEECCCCHHHHHHHHCC >P1;d2omda- CCCCCCCCEEEECCCCCHHHHHHHCCCCCCCCEEEEEEECCCCC-HHHCCCEEEEEEEECHHHHHHHHHHHHHHHHHHH-CCCEEEEEEECEEEECCCCCEEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEEEC------------------- >P1;d2q5we1 -----CCCEEEECCCCCCHHHHH-HHCCCCCCEEEEEEEECCCCCC--CCCEEEEEEEECHHHHHHHHHHHHHHHHHHCCCC-EEEEEEECEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEEEC-CEEEECCC---------- >P1;d2wp4a- -----CCCEEEECCCCCHHHHHH-HHCCCCCCEEEEEEEECCC---------CCEEECCCHHHHHHHHHHHHHHHHCCCCCC-EEEEEEECEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCC--------------------- >P1;d5mpoc- CCC--CEEEEEECC-CCHHHHC--CCCCCCCCEEEEEEEECCCC-CC---CCCEEEEEECCCHHHHHHHHHHHHHHHHC-CEEEEEEEEECEEEECCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEECCCCC-------------------- >P1;d6jc0b- --CCEEEEEEEECCCCCHHHHHH-HCC---CCEEEEEEEECCCEEC--CEEEEEEEEEEC-CCHHHHHHHHHHHHHHHCCCEEEEEEEEECEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEEECCCCEEECCC---------- PSA >P1;d1fm0e- --7--8241401577054a815630173b7082122411508---------8211206166a50671056007402931-800100000127605274400000000867610740150012004160105332527a956649b88835631662 >P1;d2omda- 4a2c70320103661011a304851933b709121242340631-8759370610215066970472056026203762-904100001202607284300000000398830750072005106620205563359------------------- >P1;d2q5we1 -----263100177607483047-4056980821214144081635--c650430316064650182044008207952680-300000113506373100000000398740650072016207620105330138-a52743aa---------- >P1;d2wp4a- -----a21050388704596047-304299092222433619a---------851518075540472046008403864a80-4000001172075822100000003887407800730151076404295587--------------------- >P1;d5mpoc- a44--533050289-065a603--40808709221242340776-39---b0511608063750351056007502961-7020000001176033851000000006a880066006401720666010641469-------------------- >P1;d6jc0b- --c07113030278705396037-205---092210324407744c--b56055031614-840461055007500871a8061000001237093731000000005988306610850060066402053101046a64452b7---------- Translating the sequences --C--C**EEEECCCCCHHHHHH*HCCCCCCCEEEEEEEECC---------***EEEEECHHHHHHHHHHHHHHHHHHC-C**EEEEEEECEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEEEC******************* **C**C**EEEECCCCCHHHHHH**CCCCCCCEEEEEEE*CCC*-********EEEEEECHHHHHHHHHHHHHHHHHH*-C**EEEEEEECEEE*CCC**EEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEEEC------------------- -----C**EEEECCCCC*HHHHH-H*CCCCCCEEEEEEEECCC***--*****EEEEEECHHHHHHHHHHHHHHHHHHC*C*-EEEEEEECEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEEEC-********---------- -----C**EEEECCCCCHHHHHH-H*CCCCCCEEEEEEEECCC---------**EEE**CHHHHHHHHHHHHHHHH**C*C*-EEEEEEECEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCC******--------------------- **C--C**EEEECC-CCHHHH*--*CCCCCCCEEEEEEEECCC*-**---***EEEEEEC**HHHHHHHHHHHHHHHHC-C**EEEEEEECEEE*CCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEE*****-------------------- --C*****EEEECCCCCHHHHHH-HCC---CCEEEEEEEECCC***--*****EEEEEEC-**HHHHHHHHHHHHHHHC*C**EEEEEEECEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEEEC*********---------- 54690.tem _________________________________ --C--C**EEEECCCCCHHHHHH-HCCCCCCCEEEEEEEECCC*-*--*****EEEEEECHHHHHHHHHHHHHHHHHHC*C**EEEEEEECEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEEEC-********---------- Structural block scores 0 1 - 4.1 M 75.0 7.2 75.0 75.0 7.2 75.0 3 4 - 4.1 M 75.0 9.8 75.0 75.0 75.0 3.5 6 7 * 1.0 P 3.0 2.5 4.5 1.5 3.0 2.0 8 11 E 5.0 H 1.5 1.0 0.5 2.0 1.8 1.2 12 16 C 4.9 H 4.8 2.8 5.4 5.4 19.6 5.4 17 22 H 4.8 H 5.8 4.4 4.3 5.2 16.6 4.7 25 31 C 4.7 H 5.4 6.1 5.1 4.7 4.6 34.1 32 39 E 4.9 H 2.2 2.4 2.4 3.0 2.5 2.2 40 42 C 4.8 H 27.7 3.0 3.0 6.8 4.7 4.7 46 47 - 4.3 M 75.0 6.0 75.0 75.0 42.0 75.0 48 52 * 2.5 P 47.0 5.0 5.5 61.6 33.3 5.5 53 58 E 4.7 H 1.8 1.5 2.2 3.3 2.7 2.7 60 77 H 4.8 H 4.0 4.0 3.6 3.7 3.6 7.5 81 82 * 1.9 P 0.0 2.0 37.5 37.5 1.0 3.0 83 89 E 5.0 H 0.3 0.6 0.6 0.7 0.1 0.3 91 93 E 5.0 H 4.3 2.7 2.7 3.0 4.3 3.3 94 97 C 4.8 H 4.5 5.2 4.8 5.5 4.8 5.5 98 106 E 4.9 H 0.4 0.3 0.1 0.3 0.1 0.1 107 108 C 5.0 H 7.0 6.0 6.0 5.5 8.2 7.0 109 126 H 5.0 H 2.5 3.3 3.5 3.8 3.7 3.7 127 128 C 5.0 H 0.5 1.0 0.5 2.0 0.5 1.0 129 135 E 4.2 M 2.9 3.9 2.1 15.9 4.3 1.4 138 145 * 3.4 M 7.3 75.0 6.6 75.0 75.0 6.2 146 155 - 4.5 M 4.8 75.0 75.0 75.0 75.0 75.0 >>>>>>