Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1cxya- -------CCCCCCHHHHCCCEEC--C-EEEEEEC--------CEEEECCCCHHHCCCCCCCCHHHCCCCCHHHHHHCC---------------C-CCCCHHHHHHH-C-C-EEEEC-------------- >P1;d1kbia2 C----CCCCCCCCCCHHHHCEEC--C-EEEEEEC--------CEEEECCCCHHHCCCCHHHHHCCCCCCCHHHHHHH-------------------CCCCHHHHHCCHHH-EEEECCCCCCCCCCCCCC- >P1;d1mj4a- -------CCCCCCCC-CCCCEEC--CCEEEEEEC--------CEEEECCCCHHHCCCCC-CHHHHCCCCCHHHHCCC-----------------HHHCCHHHHHHH-HCC-EEEEC-------------- >P1;d1sv7a- CCCCCCCCCCCEEHHHHHCCCCCCCCCCCEEEEC--------CEEEECHHHHHHHCCC-CCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEE-----------C- >P1;d1x3xa- ------CCCCEECHHHHHCCEEC--C-EEEEEEC--------CEEEECHHHHHHCC-CHHHHHHHCCCCCHHHHHHCH---------------HHHHCHHHHHHHH-HHH-EEEEEC------------- >P1;d2keoa- ------CCCCEECHHHHHHH---HHCCCCEEEEC--------CEEEECHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHH-------------------CCCCHHHH-HHH-EEEEECCHHHCCCCCCCCC >P1;d3lf5a- ------CCCEEECHHHHHHCEEC--C-EEEEEEC--------CEEEECHHHCCCCCCCHHHHHCCCCEECHHHHHHH-------------------HCCCCHHHHC--CC-EEEEECCCCCC-------- >P1;d3x34a- ------C-CCEECHHHHCCCEEC--C-EEEEEEC--------CEEEECCCHHHCCCCCCHHHHCCCCCCCHHHHHHH-------------------CCCHHHHHHH-HCC-EEEEECHHHCCCCCC---- >P1;d7bwha- ------C-CCEECHHHHCCCEEC--C-EEEEEEECCCCCCCCEEEEECHHHCCCCCCCHHHHHHCCCCCCHHHHHHC-------------------CCCHHHHHHH-HHH-EEEEECCC----------- PSA >P1;d1cxya- -------b457164950482645--9-5010005--------7400303611672778b4413730054039115435---------------8-78178725751-7-3-23041-------------- >P1;d1kbia2 a----29186a352950272474--9-5010007--------70002028204918894721282003212412655-------------------25952027704882-121309b90388240776- >P1;d1mj4a- -------c3752889-0682446--a2201002a--------64003029218718c44-61370004505541775-----------------77165a714740-463-33132-------------- >P1;d1sv7a- 599a896a6742339503513085b933010003--------2400205635860066-7951310020002000363574a0042716c069813730573186036606230603-----------f- >P1;d1x3xa- ------1aa65147940571565--9-4010016--------7200303b119617-798612840056029415769---------------6169559614730-852-030406------------- >P1;d2keoa- ------b7663076651593---698a1511227--------630020540564095ae2302615b45137005601b-------------------59606730-860-34351355a5799777b9f >P1;d3lf5a- ------b9747068930761574--a-5010004--------43004015206717884a51251005602931366-------------------3684815741--b2-31051259b77-------- >P1;d3x34a- ------b-464251830562667--8-3000004--------14003029105818883861372005201a81396-------------------a288a24551-572-2312034803a61a8---- >P1;d7bwha- ------a-475043950582566--a-400000328929c420100302a11a817886851463006312932887-------------------a27a726931-661-43020599----------- Translating the sequences -------CCC**CHHHH*CCEEC--C-EEEEEEC--------CEEEEC***HHHCCCC****H**CCCCCHHHHHH**---------------*-**CCHHHHHHH-*-*-EEEE*-------------- *----*CCCC**C**HH**CEEC--C-EEEEEEC--------CEEEEC***HHHCCCC**HHH**CCCCCHHHHHH*-------------------*CC*HHHHH**H**-EEEE*C************- -------CCC**C**-**CCEEC--C*EEEEEEC--------CEEEEC***HHHCCCC*-*HH**CCCCCHHHH***-----------------***CCHHHHHHH-H**-EEEE*-------------- ******CCCC*E*HHHH*CC**C**C***EEEEC--------CEEEEC**HHHH*CCC-******CCCCCHHHHHH***********************HHHHHHH*H***EEEEE*-----------*- ------CCCC*ECHHHH*CCEEC--C-EEEEEEC--------CEEEEC**HHHHCC-C**HHH**CCCCCHHHHHH**---------------****C*HHHHHHH-H**-EEEEEC------------- ------CCCC*ECHHHH***---**C***EEEEC--------CEEEEC**HHHHCCCC**HHH**CCCC*HHHHHH***-------------------C***HHHH-H**-EEEEEC************* ------CCC**ECHHHH**CEEC--C-EEEEEEC--------CEEEEC**H***CCCC**HHH**CC**CHHHHHH*-------------------*CC**HHHH*--**-EEEEEC*****-------- ------C-CC*ECHHHH*CCEEC--C-EEEEEEC--------CEEEEC**HHH*CCCC**HHH**CCCCCHHHHHH*-------------------*CCHHHHHHH-H**-EEEEEC*********---- ------C-CC*ECHHHH*CCEEC--C-EEEEEE**********EEEEC**H***CCCC**HHH**CCCCCHHHHHH*-------------------*CCHHHHHHH-H**-EEEEEC**----------- 55856.tem _________________________________ ------CCCC*ECHHHH*CCEEC--C-EEEEEEC--------CEEEEC**HHHHCCCC**HHH**CCCCCHHHHHH**-----------------**CCHHHHHHH-H**-EEEEEC*****-------- Structural block scores 0 5 - 4.6 H 75.0 52.1 75.0 8.4 75.0 75.0 75.0 75.0 75.0 6 9 C 4.7 H 23.9 6.0 24.4 7.4 7.0 7.6 7.9 24.1 24.1 13 16 H 4.5 M 4.5 4.0 23.0 4.2 5.0 4.5 5.0 3.0 4.2 18 19 C 4.3 M 5.0 4.5 5.0 3.0 4.0 6.0 3.5 4.0 5.0 20 21 E 4.5 M 5.0 5.5 4.0 1.5 5.5 75.0 6.0 6.0 5.5 23 24 - 4.4 M 75.0 75.0 75.0 8.2 75.0 7.5 75.0 75.0 75.0 27 32 E 4.8 H 1.0 1.0 0.8 0.7 1.0 2.0 1.0 0.5 0.7 34 41 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 6.1 43 46 E 5.0 H 1.8 0.5 1.8 1.5 1.2 1.2 1.8 1.8 1.0 48 49 * 1.0 P 4.5 5.0 5.5 5.5 7.2 4.5 3.0 5.5 6.2 50 53 H 4.2 M 3.8 3.8 4.5 5.5 4.2 3.8 3.8 3.5 5.1 54 57 C 4.8 H 6.0 6.5 6.4 3.0 22.5 6.1 6.0 6.2 6.0 58 59 * 1.6 P 7.8 5.5 39.5 41.0 8.5 8.2 7.2 5.5 7.0 60 62 H 4.4 M 2.7 1.7 3.3 5.0 3.0 1.7 2.7 3.3 3.3 63 64 * 1.0 P 5.0 5.0 3.5 2.0 6.0 3.5 3.0 4.5 4.5 65 69 C 4.8 H 1.8 1.2 1.8 0.4 2.2 5.3 2.2 1.4 2.0 70 75 H 4.9 H 3.8 3.3 4.8 0.8 4.7 3.5 4.0 5.4 5.3 76 77 * 2.3 P 4.0 40.0 40.0 4.5 7.5 0.5 40.5 40.5 41.0 78 94 - 4.6 H 71.1 75.0 71.0 4.9 66.6 71.3 75.0 75.0 75.0 95 96 * 2.6 P 7.5 38.5 4.0 5.0 7.5 75.0 39.0 42.8 42.8 97 98 C 4.5 M 4.0 7.0 5.5 1.5 5.0 40.0 7.0 5.0 4.5 99 105 H 4.6 H 5.0 3.3 4.8 4.3 4.3 4.4 4.3 5.1 5.5 108 109 * 1.3 P 39.0 5.0 4.5 3.0 3.5 3.0 6.8 4.5 3.5 111 115 E 4.8 H 2.0 1.4 2.4 2.2 1.4 3.2 2.0 1.6 1.8 117 121 * 3.4 M 75.0 6.3 75.0 75.0 75.0 6.5 7.9 5.1 48.6 122 129 - 4.2 M 75.0 13.6 75.0 68.4 75.0 10.2 75.0 40.7 75.0 >>>>>>