Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bxda- CCCCCCCCEECHHHHHHHHHHHCCC-----CCCCEEEECC-CCCCCEEC--CHHHHHHHHHHHHHHHHHCCC----------CCEEEEEEEEC----------CEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCEEEEEEECCCEEEEEEEECCCCCCCCCCCCCC >P1;d1id0a- ------CCEEEHHHHHHHHHHHHHHHCCCC-CCEEEEECC--CCCEEEC--CHHHHHHHHHHHHHHHHHHCC-C---------EEEEEEEECC----------CCEEEEEEECCCCCCHHHCCHHHCCCCCCCCCC--CCCCCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEEECCCC---------- >P1;d1r62a- ------CEEECHHHHHHHHHHHHCCCCCC---CCCEEECC-CCCCCEEE--CHHHHHHHHHHHHHHHHHHHHHH-------CCEEEEEEEEEEEEEECCEEEEEEEEEEEEEECCCC------------------------CHHHHHHHHHHHHCCCEEEEEEEC-CEEEEEEEEEEEC---------- >P1;d1th8a1 CCEEEEEEEECCCCHHHHHHHHHHHHHHHH-CCC---------------HHHHHHHHHHHHHHHHHHHHCCCCCCCC-----CEEEEEEEEEC----------CEEEEEEEECCCCCC--CHHHHCCCC---------CCCCCHHHHHHHHCC----EEEEEEECCCEEEEEEEE-------------- >P1;d1ysra- ----CCCEEEEHHHHHHHHHHHHHHHCC---CCEEEECCC--CCCEEEE--CHHHHHHHHHHHHHHHHHCCCCC---------EEEEEEEEEC----------CEEEEEEEECCCCCCHHHHHHHHCC------------CCCCCHHHHHHHHHCCCEEEEEECCCCCEEEEEEEECCC---------- >P1;d2c2aa2 CCC---CEEEEHHHHHHHHHHHHHHHHHH-CCCEEEEEECCCCCCEEEE--CHHHHHHHHHHHHHHHHHCCC---CCCC--CCEEEEEEEEEC----------CEEEEEEEECCCCCCHHHCCHHHCCCCCCC------C--CCHHHHHHHHHHCCCEEEEEEECCCEEEEEEEEECC----------- >P1;d4e01a2 CEECCEEEEECHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEE--CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEECC----------CEEEEEEECCCCCCCHHHHCCCCCCCCCCC------CCCCHHHHHHHHHHHCCCEEEEEEECCCEEEEEEEEECCC---------C PSA >P1;d1bxda- daaa742632304600570176119-----a968063604-87806050--23610360045003601670d----------54020202068----------56020302041500368657662498687a585bba9b28964615400650b15061528a5050304020423589aaaa899f >P1;d1id0a- ------4561504610781176168518a3-906052905--8701020--65a203500200003003608-5---------505050635a----------6401010101071269852a6207789488583--93143211303500571705030450a36014010100608---------- >P1;d1r62a- ------9564302600440284067414b---60055412-88045060--42830240001004401940496-------044010104017515069661620030000030767------------------------c83264057106515020555549-8210100001065---------- >P1;d1th8a1 a45414251405672265037301720543-a18---------------7941620330022003300342177539-----2502010204a----------740302030915027--637842649---------a58942143059307----405080858701303032-------------- >P1;d1ysra- ----7a1570301500450075049718---a07061490--6515050--24a20250051002002642907---------303020737a----------9103000003081068c62960165------------622001301510750a1705049072902200040413e---------- >P1;d2c2aa2 a0a---467130080065007406a3086-5909051506294505050--039404400320042004413---9718--812010103367----------c001010112050129802a5006592648------b--561220460044090602060766700400020339----------- >P1;d4e01a2 558c641450003610461164027504961a30080606664913150--4151036000300450034003437a447903202020435b----------8202040206040258913a6116571455------c9351102045405946130607052a500212030613a---------b Translating the sequences ******C*EE*HHHHHHHHHHH***-----*CC**EEE*C-*CCC*EE*--CHHHHHHHHHHHHHHHHH*CC----------C*EEEEEEEEC----------CEEEEEEEECCCCCC********CCC**********CCCC*****HHHHHH*CCEEEEEEECCCEEEEEEEE*CCC********** ------C*EE*HHHHHHHHHHHHHHH****-CC**EEE*C--CCC*EE*--CHHHHHHHHHHHHHHHHH*CC-*---------EEEEEEEE*C----------C*EEEEEEECCCCCC********CCC*******--*CCCC*HHHHHHHHHHCCCEEEEEE*CCC*EEEEEEE*CCC---------- ------CEEE*HHHHHHHHHHHH******---C**EEE*C-*CCC*EE*--CHHHHHHHHHHHHHHHHH*****-------*CEEEEEEEEE************EEEEEEEE*CCCC------------------------C**HHHHHHHHHHCCCEEEEEEEC-CEEEEEEEE***C---------- *******EEE****HHHHHHHHHHHH****-CC*---------------***HHHHHHHHHHHHHHHHH*CC*****-----CEEEEEEEEEC----------CEEEEEEEECCCCCC--******CCC---------*CCCC*HHHHHHH**----EEEEEEECCCEEEEEEEE-------------- ----**CEEE*HHHHHHHHHHHHHHH**---CC**EE**C--CCC*EE*--CHHHHHHHHHHHHHHHHH*CC**---------EEEEEEEEEC----------CEEEEEEEECCCCCC********CC------------CCC**HHHHHHHHHCCCEEEEEE*CCC*EEEEEEE*CCC---------- ***---CEEE*HHHHHHHHHHHHHHH***-*CC**EEE*C**CCC*EE*--CHHHHHHHHHHHHHHHHH*CC---****--*CEEEEEEEEEC----------CEEEEEEEECCCCCC********CCC****------C--C*HHHHHHHHHHCCCEEEEEEECCCEEEEEEEE*CC----------- *******EEE*HHHHHHHHHHHHHHH*****CC***EE****CCC*EE*--C*HHHHHHHHHHHHHHHH*************C*EEEEEEE*C----------CEEEEEEE*CCCCCC********CCC****------CCCC*HHHHHHHHHHCCCEEEEEEECCCEEEEEEEE*CCC---------* 55874-1.tem _________________________________ ******CEEE*HHHHHHHHHHHHHHH*****CC**EEE*C-*CCC*EE*--CHHHHHHHHHHHHHHHHH*CC**-**----*CEEEEEEEEEC----------CEEEEEEEECCCCCC********CCC****-----*CCCC*HHHHHHHHHHCCCEEEEEEECCCEEEEEEEE*CCC---------- Structural block scores 0 5 * 3.2 M 9.3 75.0 75.0 4.8 52.9 41.0 6.8 7 9 E 4.7 H 3.7 4.0 5.0 3.3 4.0 4.7 3.0 11 25 H 4.7 H 8.1 4.1 3.1 3.7 3.1 3.3 3.1 26 30 * 2.7 P 62.1 19.5 33.3 17.4 46.8 18.8 4.0 31 32 C 4.8 H 7.5 4.5 40.5 5.8 5.2 4.5 6.8 33 34 * 1.4 P 4.0 3.0 0.0 41.5 3.5 4.5 0.0 35 37 E 4.4 M 5.0 5.3 4.7 75.0 3.7 3.7 4.7 42 44 C 4.6 H 5.0 5.0 4.0 75.0 4.0 3.0 4.7 46 47 E 4.6 H 2.5 1.0 3.0 75.0 2.5 2.5 3.0 49 50 - 4.6 H 75.0 75.0 75.0 8.0 75.0 75.0 75.0 52 68 H 5.0 H 2.6 2.0 2.2 1.6 2.3 2.3 1.8 70 71 C 4.2 M 6.8 4.0 2.0 1.5 5.5 2.0 0.0 72 73 * 2.8 P 75.0 40.0 7.5 7.0 3.5 75.0 3.5 75 76 * 3.7 M 75.0 75.0 75.0 6.0 75.0 8.0 8.8 77 80 - 4.4 M 75.0 75.0 75.0 75.0 75.0 39.8 6.0 83 91 E 4.8 H 1.8 3.2 1.2 1.6 2.8 1.8 2.0 93 102 - 4.6 H 75.0 75.0 4.5 75.0 75.0 75.0 75.0 104 111 E 4.9 H 1.6 0.9 0.4 1.5 0.5 0.5 1.2 112 117 C 4.9 H 2.2 2.8 16.3 4.0 3.0 1.7 2.8 118 125 * 2.0 P 5.8 5.3 75.0 22.5 5.6 4.3 4.9 126 128 C 4.5 M 7.0 7.3 75.0 6.3 28.7 6.7 6.0 129 132 * 3.1 M 7.9 7.2 75.0 75.0 75.0 5.0 3.8 133 137 - 4.4 M 8.2 33.2 75.0 75.0 75.0 75.0 75.0 139 142 C 4.5 M 7.6 2.8 42.6 6.5 21.2 41.6 7.4 144 153 H 4.7 H 3.7 2.5 3.6 10.7 2.3 2.3 3.0 154 156 C 4.5 M 4.2 2.7 2.0 75.0 3.8 3.0 3.7 157 163 E 4.9 H 3.9 2.4 3.7 3.6 3.6 3.0 3.0 164 166 C 4.9 H 5.2 6.5 30.7 6.7 6.0 6.3 5.8 167 174 E 4.9 H 1.8 0.9 0.5 1.5 1.0 0.8 1.0 176 178 C 4.3 M 3.3 4.7 3.7 75.0 6.2 29.0 4.8 179 188 - 4.6 H 10.8 75.0 75.0 75.0 75.0 75.0 68.7 >>>>>>