Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bdoa- -------CCCCEEEECCCC------EEEECCCCC-------CCCCCCCCCCEECCCCEEEEEEECCEEEEEECCCCEEEEEECCC------CCC-EECCCCEEEEEC------------------------------ >P1;d1dcza- ---CCCCCCCCCEEECCC------CCEEEEE--------------CCCCCCEECCCCEEEEEEECCEEEEEECCCCEEEEEECCC------CCC-CCCCCCEEEEEC------------------------------ >P1;d1ghja- ----------CEEEECCCCCCCCCCEEECC--------------CCCCCCCEECCCCEEEEEECCCCEEEEECCCCEEEEEECCC------CCC-EECCCCEEEEECCCC--------------------------- >P1;d1k8ma1 --------CCCEEEECCCCCCCCCCEEEEEE--------------CCCCCCEECCCCCCEEEECCCCEEECCCCCCEEEEEECCC------CCC-EECCCCEEEEEECCCCCC------------------------ >P1;d2l5ta- ----------CEEEECCCCCCCCCCEEEEEC--------------CCCCCCEECCCCCCCEEECCCCCEECCCCCCEEEEEECCC------CCC-EECCCCEEEEEEC----------------------------- >P1;d2pnrc- -----------CCCCCCC--CCCCEECEEEE--------------CCCCCCEECCCCEEEEEECCCCEEEEECCCCEEEEEECCC------CCCCCEECCCCCEEEECCCCC------------------------- >P1;d3hgba1 CCCCCCCEECCCCEEEEEEEC--CEEEEEECHHHHHHHCCEEEEECCCCCCCCCCCCEEEEEEECCCEEEEECCCCC-CCEECCHHHHCCCHHHHCCCCCCCCEEEECCCCCCCCCCHHHHCCCHHHHHHHCC---- >P1;d3wdna- ----CCCEECCCCEEEEE-EC--CEEEEEECHHHHHHHCCEEEEECCCCCCEECCCCEEEEEEECCCEEEEECCCCEEEEEECHHHCCCCCHHHHCCCCCCCCEEEEEC-----CHHHHHHCEEHHHHHHHHHHHHC PSA >P1;d1bdoa- -------c58431040328------220422368-------a3a02075848096651001013988556050655440340219------456-708663300006------------------------------ >P1;d1dcza- ---c563708a5204034------5150272--------------40759560838610020419a8646070488240560408------595-80635300030c------------------------------ >P1;d1ghja- ----------7541504906b918414016--------------0348176808784200104169776614085606048072b------483-60836230050682c--------------------------- >P1;d1k8ma1 --------d935424072086b673020540--------------6065855056842001052957435260566060640827------594-50428630020316a388------------------------ >P1;d2l5ta- ----------8753605839ab1a3030470--------------3194846065781610011786646362666570663507------793-647255300615b----------------------------- >P1;d2pnrc- -----------2703512--98075010560--------------2186955068644001040967433160787020362217------5747606373600512a8796------------------------- >P1;d3hgba1 28039803015530003548a--51020000231176087045060194a490858540140309944540300020-025208708b6152017501650100005076882650715870362a505940b---- >P1;d3wdna- ----a6230175100031-8a--63020000621177099057050195548091756032040a7654303000225045209608a615102830377010030507-----6680196026675066337746a Translating the sequences -------***C**EECCC*------EEEE*****-------****CCCCCCEECCCCEEEEEE*CC*EEEEECCCCEEEEEECCC------CCC-**CCCC**EEE*------------------------------ ---*******C**EECCC------**EEEE*--------------CCCCCCEECCCCEEEEEE*CC*EEEEECCCCEEEEEECCC------CCC-**CCCC**EEE*------------------------------ ----------C**EECCC**C**C*EEE**--------------*CCCCCCEECCCCEEEEEE*CCCEEEEECCCCEEEEEECCC------CCC-**CCCC**EEE****--------------------------- --------**C**EECCC**C**C*EEEEE*--------------CCCCCCEECCCC**EEEE*CCCEEE**CCCCEEEEEECCC------CCC-**CCCC**EEE*******------------------------ ----------C**EECCC**C**C*EEEEE*--------------CCCCCCEECCCC***EEE*CCC*EE**CCCCEEEEEECCC------CCC-**CCCC**EEE**----------------------------- -----------****CCC--C**C*E*EEE*--------------CCCCCCEECCCCEEEEEE*CCCEEEEECCCCEEEEEECCC------CCC****CCC**EEE******------------------------- **********C**EE*****C--C*EEEEE***************CCCCCC**CCCCEEEEEE*CCCEEEEECCCC*-**EECC*************CCCC**EEE***************************---- ----******C**EE***-*C--C*EEEEE***************CCCCCCEECCCCEEEEEE*CCCEEEEECCCCEEEEEEC**************CCCC**EEE***-----*********************** 51230.tem _________________________________ ----******C**EECCC**C**C*EEEEE****-------****CCCCCCEECCCCEEEEEE*CCCEEEEECCCCEEEEEECCC------CCC***CCCC**EEE******------------------------- Structural block scores 0 3 - 4.6 H 75.0 59.4 75.0 75.0 75.0 75.0 3.2 75.0 4 9 * 3.5 M 41.8 4.8 75.0 53.8 75.0 75.0 3.5 3.8 11 12 * 1.0 P 2.0 3.5 4.5 4.5 6.0 4.5 4.0 3.0 13 14 E 4.7 H 2.0 2.0 3.0 3.0 4.5 1.5 0.0 0.0 15 17 C 4.3 M 1.7 2.3 4.3 3.0 4.3 2.7 2.7 1.3 18 19 * 2.9 P 41.5 75.0 3.0 4.0 6.0 75.0 6.0 41.5 21 22 * 3.4 M 75.0 75.0 5.0 8.8 6.2 4.0 75.0 75.0 25 29 E 4.7 H 2.0 3.0 2.4 2.2 2.8 2.4 0.4 0.4 30 33 * 3.4 M 4.8 56.8 75.0 56.2 56.2 56.2 1.5 2.2 34 40 - 4.3 M 75.0 75.0 75.0 75.0 75.0 75.0 4.1 4.7 41 44 * 3.8 M 6.0 75.0 56.2 75.0 75.0 75.0 3.8 4.2 45 50 C 5.0 H 4.3 5.0 4.8 5.0 4.8 5.2 4.8 4.0 51 52 E 4.7 H 4.0 3.0 4.0 2.5 3.0 2.5 4.5 4.0 53 56 C 5.0 H 6.5 6.2 6.8 5.8 6.5 6.0 6.5 5.5 57 62 E 4.7 H 0.5 1.2 1.2 1.3 1.5 1.5 2.0 2.5 64 66 C 4.8 H 8.3 9.2 7.3 7.0 7.0 7.3 7.3 7.8 67 71 E 4.7 H 4.2 4.6 4.8 4.0 5.0 3.4 3.2 3.0 72 75 C 5.0 H 4.0 5.0 4.8 4.2 5.0 5.5 0.5 0.5 76 81 E 4.8 H 2.5 2.8 3.0 2.7 4.5 2.2 14.0 3.0 82 84 C 4.7 H 4.0 4.0 6.8 5.7 4.0 3.3 5.0 5.0 85 90 - 4.3 M 75.0 75.0 75.0 75.0 75.0 75.0 5.2 5.1 91 93 C 4.3 M 5.0 6.3 5.0 6.0 6.3 5.3 1.0 1.0 94 96 * 2.0 P 27.3 27.7 27.0 26.7 28.3 4.3 4.0 3.7 97 100 C 4.9 H 5.8 4.2 4.8 5.0 4.8 4.8 3.0 4.2 101 102 * 1.0 P 1.5 0.0 1.5 1.5 1.5 3.0 0.5 0.5 103 105 E 5.0 H 0.0 1.0 1.7 0.7 2.3 2.0 0.0 1.0 106 111 * 2.9 P 63.5 64.6 29.8 5.2 52.8 7.1 5.7 39.5 112 136 - 4.4 M 75.0 75.0 75.0 72.3 75.0 75.0 15.9 10.6 >>>>>>