Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1f13a2 -CCEEEEEEEC-CCCCCCCEEEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEE-EEEECCCCCCEEEEEECHHHHCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEC--- >P1;d1f13a3 -CCCCCEEEEEECCCCCCCEEEEEEEECCCCCCEEEEEEEEEEC------CCE-EEEEEEEE-EECCCCEEEEEEEECCC-----CC--EEEEEEEEEECC-CCEEEEEEEEEEECCC >P1;d1g0da2 --CEEEEEECC-CCCCCCCEEEEEEEEECCCCCEEEEEEEEEEEECCCCCCCCCCCEEEE-EEEECCCEEEEEEEEECHHHHCCCCCCCCEEEEEEEEECC---CEEEEEEEEECC-- >P1;d1g0da3 --CCCCEEECCCCEECCCCEEEEEEEECCCCCCEECCEEEEEEC------CCE-EEEEEECCCEECCCCEEEEEEEECCC-----CC--EEEEEEEEEECC-CCCCEEEEEEEEEECC >P1;d1rlla3 CCCEEEEEEECCCCCCCCCEEEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEE-EEEECCCCEEEEEEEECHHHHHCCCCCCCEEEEEEEEECC-CCCCEEEEEEEECC-C >P1;d1rlla4 ---CCEEEEECCCCCCCCCEEEEEEEECCCCCCCCCEEEEEECC------CCCCCCEEEEEC-CCCCCCEEEEEEEECCC-----CC--EEEEEEEEEECC-CCCCEEEEEEEEECC- >P1;d2q3za2 --CEEEEEECCCCCCCCCCEEEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEEEEEECCCEEEEEEEEECHHHHCCCCCCCCEEEEEEEEEECCCCEEEEEEEEEECC-- >P1;d2q3za3 --CCCCEEEEECCCCCCCCEEEEEEEECCCCCCCCCEEEEEECC------CCCCCCEEEEECCCCCCCCEEEEEEEECCC-----CC--CCEEEEEEEECC-CCCCEEEEEEEC---- PSA >P1;d1f13a2 -7306050706-a08537405020303063965050205030100465985543016441-803063456453405062b304c4128611020504040455644155546070--- >P1;d1f13a3 -a476050616683229550201020602496206304040406------000-86355227-40637532605360605-----52--863305030506-6158061535060789 >P1;d1g0da2 --70404042a-9073563140300030456a5270502020000286577444136443-7060417723524040448303720296310203040623---953632340508-- >P1;d1g0da3 --428050505b60117671204020504273406c02030509------000-9545161aa31747560516261204-----66--861505040405-5068050524150358 >P1;d1rlla3 b51050504247701255403020302032984250507040400386265153017563-52506374626170605585046305a2110303040507-b2952507330608-9 >P1;d1rlla4 ---3805041348050656040101060439520590304061b------001ab3352808-40436651413050606-----82--961604020404-317616163708068- >P1;d2q3za2 --5170603077715454504020104083786250304010300279772565034353570507364642041504376048204b0210103030112977553715540605-- >P1;d2q3za3 --619060424685868780401000603286306b0303052a------600a75342818a40736641315380508-----88--271505030405-516506363500---- Translating the sequences -*C***EEE*C-CCCCCCCEEEEEEEE*CCCCCEE*EEEEEEE*************EEEE-**EECCCC**EEEEEEC*******CC***EEEEEEEEE*C*CCC*EEEEEEEE*--- -*C***EEE***CCCCCCCEEEEEEEE*CCCCCEE*EEEEEEE*------***-**EEEE**-EECCCCEEEEEEEEC**-----CC--*EEEEEEEEECC-CC**EEEEEEEE**** --C***EEE*C-CCCCCCCEEEEEEEE*CCCCCEE*EEEEEEE*************EEEE-**EECCC*EEEEEEEEC*******CC***EEEEEEEEECC---C*EEEEEEEE**-- --C***EEE*C*C**CCCCEEEEEEEE*CCCCCEE**EEEEEE*------***-**EEEE***EECCCCEEEEEEEEC**-----CC--*EEEEEEEEECC-CCC*EEEEEEEE**** **C***EEE*C*CCCCCCCEEEEEEEE*CCCCCEE*EEEEEEE*************EEEE-**EECCCCEEEEEEEEC*******CC***EEEEEEEEECC-CCC*EEEEEEEE**-* ---***EEE*C*CCCCCCCEEEEEEEE*CCCCC***EEEEEE**------******EEEE**-**CCCCEEEEEEEEC**-----CC--*EEEEEEEEECC-CCC*EEEEEEEE***- --C***EEE*C*CCCCCCCEEEEEEEE*CCCCCEE*EEEEEEE*************EEEE***EECCC*EEEEEEEEC*******CC***EEEEEEEEE*C*CC**EEEEEEEE**-- --C***EEE***CCCCCCCEEEEEEEE*CCCCC***EEEEEE**------******EEEE*****CCCCEEEEEEEEC**-----CC--**EEEEEEEECC-CCC*EEEEEEE*---- 49309.tem _________________________________ -*C***EEE*C*CCCCCCCEEEEEEEE*CCCCCEE*EEEEEEE*************EEEE***EECCCCEEEEEEEEC*******CC***EEEEEEEEECC-CCC*EEEEEEEE**** Structural block scores 3 5 * 1.0 P 2.0 4.3 1.3 3.3 1.7 3.7 2.7 3.3 6 8 E 5.0 H 4.0 3.7 2.7 3.3 3.0 3.0 3.0 3.3 12 18 C 4.9 H 5.4 4.9 4.7 4.0 3.4 4.3 4.4 7.1 19 26 E 5.0 H 1.6 1.4 1.4 1.8 1.2 1.5 1.4 1.4 28 32 C 5.0 H 5.8 4.6 6.1 4.0 5.2 4.6 6.4 4.4 33 34 E 4.3 M 2.5 3.0 4.5 3.0 3.5 2.5 3.5 3.0 36 42 E 4.9 H 1.6 1.7 1.3 1.4 2.9 2.0 1.6 1.9 43 55 * 2.2 P 3.8 41.9 3.9 42.2 3.1 37.5 4.1 37.6 56 59 E 5.0 H 3.8 3.8 4.2 4.0 5.2 4.5 3.8 4.2 60 62 * 2.1 P 27.7 28.0 27.3 7.3 27.3 27.7 4.0 6.5 63 64 E 4.3 M 1.5 2.0 3.0 2.0 2.5 2.0 2.5 2.0 65 68 C 4.8 H 4.5 5.2 4.8 5.8 5.0 4.8 5.0 5.5 69 76 E 4.9 H 3.4 3.1 2.5 3.4 3.5 2.4 2.8 3.1 78 84 * 2.7 P 5.3 54.3 3.9 54.1 4.4 54.4 4.3 54.7 85 86 C 5.0 H 1.5 3.5 1.0 6.0 2.5 5.0 2.0 8.0 87 89 * 2.6 P 5.0 52.7 6.0 52.7 4.5 53.0 4.5 50.7 90 98 E 5.0 H 1.8 2.8 1.8 2.8 1.8 2.6 1.0 2.8 99 100 C 4.7 H 2.0 3.0 2.5 2.5 3.5 2.0 1.5 2.5 102 104 C 4.6 H 5.0 4.0 53.0 3.7 7.5 3.7 6.3 4.0 106 113 E 5.0 H 4.1 3.2 3.2 2.8 3.2 4.0 3.9 2.9 114 117 * 3.0 P 56.2 6.0 39.5 4.0 23.0 22.2 38.8 75.0 >>>>>>