Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ejfa- -----------------CCCCCEEEEEC-CCEEEEEECCC--CEE---EEEEEEE-CCEEEEEEEECCC-----------------CEEEEEEEECCCCEE---EEEEEEEECC-CCEEEEEEECCCCCCCCCCCCCCCCCCCEEECCCCCCCCC >P1;d1rl1a- ------------------CCCCEEEEEC-CCEEEEEEECC--CCCHHH-EEEEEC-CCCEEEEEECC-C-----------------CCEEEEEECCCCCCCHHH---EEEEECC-CEEEEEEECCCC-CCCCCCCCCC----------------- >P1;d1wgva1 --------CCCCCCCCCCCCCCCCCCCC-CCCEEEEEECCCCCCCCCC-EEEEEC-CCEEEEEEECC------------C------CEEEEEEEECCCCCCCCC---CEEEECCCCEEEEEECCCC-CCCCCCCCC-----CCCCCCCC------ >P1;d1wh0a1 --------CCCHHHCEECCCCCEEEEEECCCEEEEEEECC--CCCCC-CCEEEEC-CCEEEEEECCCCHHHHHHCCCCCC------CCCEEEEEECCCCCCCC---CCEEEECC-CEEEEEEECCC-CCCCCCCCCCCCC-----------CCCC >P1;d2xcmc- ------------------CCCEEEEEEE-CCEEEEEEECC--CCCHHH-EEEEEC-CCCEEEEECCC-C-----------------CCCEEECCCCCCCCCHHH---CEEEECC-CCEEEEEECCCC-CCCCCCCCCC----------------- >P1;d3aaba- --------CCHHHHH--HHCCCEEEEEE-CCEEEEEEECC--CCCHHH-CEEEEECCCEEEEEEECCC---------CCCCCCCC--CEEEEEEECCCEECCCC---CEEEEE-CCEEEEEEE-HH----------------HEECCCCC----- >P1;d3glaa- --------CC--------CCCCEEEEEC-CCEEEEEEECC--CCCHHH-CEEEEEC-CEEEEEEEECCHHHCC--HHHCCCCCCCC-EEEEEEEECCCCCCCCC---CEEEEE-CCEEEEEEE-CC----------------------------- >P1;d3qora1 --------CCCCCCCCCCCCCCCEEEEC-CCEEEEEEECCCCCCCHHH-EEEEEE-CCEEEEEEC---------------------CCCCCEEEECCCCCCHHH---CEEEEECCCEEEEEEECCCCCCCCCCCCC-----CCCCCCHHHCCCCC >P1;d3w1zd- ---------C--------CCCCEEEEEC-CCEEEEEEECC--CCCHHH-EEEEEEC-CEEEEEEEECCCCCCCCCCCCCCCCCCCC-EEEEEEEECCCCCCCCC---CEEEEE-CCEEEEEEE-CC--------------C-CCCCCCCCCCC-- >P1;d4elda- CCCCCEEEEE--------CCCCEEEEEC-CCEEEEEEECC--CCCHHH-EEEEEEC-CEEEEEEECCCC--CCCCCCCCCCCCCCCCCEEEEEEECCCCCCHHH---CEEEEE-CCEEEEEEE-CC--------------HHHCC----CCCCCC >P1;d4feia- ------CCEE--------CCCCEEEEEE-CCEEEEEEECC--CCCHHH-CEEEEEC-CEEEEEEEECCCC-------CCCCCCCEE-EEEEEEEECCCCCCCCC---CEEEEE-CCEEEEEEE-CC--------------C-CCCCCCC------ >P1;d5ds2a- -------------------CCCEEEEEC-CCEEEEEEECC--CCCHHH-CEEEEC--CEEEEEEEECCC-CCC--CCCCCCCCCCC-EEEEEEEECCCCCCHHH---CEEEEE-CCEEEEEEE-C------------------------------ >P1;d5zs3a- -----CEEEE--------EEECCCEECC-CC-CEEEEECC--CCC--C-CCCC-----EEEEEEEECCCCCCCC-----CCCCCCE-EEEEEEEECCCCCCHHH---CEEEEE-CCEEEEECC-CC--------------CC----CCCCCCCCC PSA >P1;d1ejfa- -----------------56307030103-53302020307--705---8080605-85302030205a8-----------------556130407024604---2b50736377-810301040386417052015883a3a118208a536815 >P1;d1rl1a- ------------------4619273705-82402020417--808591-050416-65200040435-8-----------------b83310507024606393---0525057-730102030384-6606502398----------------- >P1;d1wgva1 --------b877a24d242678030226-9730305060294067582-050617-33305000559------------d------8474103480046053a5---0626044462020304039-a55030008-----b2951b59------ >P1;d1wh0a1 --------ba829a15607805171555881100020504--50379-6060606-7420000020518b018728c113------8110205070654032a---7073803a-44030203049-6480a81427a69-----------ba89 >P1;d2xcmc- ------------------b316363615-76200010308--915882-090815-83503030627-b-----------------6b20714080326042a6---073703b-530302020278-58082046a6----------------- >P1;d3aaba- --------672a432--86205082557-b8300020607--807785-052514a41300010612b---------c8986360--44042316041006b1a---273617-b13010402-3a----------------2049764b----- >P1;d3glaa- --------57--------1608082444-a8200030604--808497-0606089-5301063508080586--5973a737573-1502262704b402394---182809-924030404-15----------------------------- >P1;d3qora1 --------54701a30006087050306-44205040502b5805682-030506-544040016---------------------c68120525033403486---073624bc230304010365932003004-----915303395075a5 >P1;d3w1zd- ---------a--------1607073757-46403030607--905782-0517199-35030315023676639889868867562-770544260738035a6---183716-b24020401-14--------------8-54a498a889a-- >P1;d4elda- ca4b484815--------2503061545-97403020605--a08783-0526188-440304051855--947ba6849828649466041405011503476---182817-b23030402-02--------------79219----6cabad >P1;d4feia- ------8079--------0708081562-46300020605--a066b3-07182bc-9403010407659-------a2aa1a632-76052716044606891---182839-c33030503-05--------------8-448aa8a------ >P1;d5ds2a- -------------------818093643-79101050606--807584-071435--31010246197a-a77--c58688778a4-78153417049605196---171709-a14020202-2------------------------------ >P1;d5zs3a- -----85167--------a317794456-ca-20020606--808--4-1136-----4040505076479a79-----9889642-111256270b9413277---172627-a13030504-06--------------57----89787a9a9 Translating the sequences -----------------*CCCCEEEEEC-CCEEEEEE*CC--C**---**EEEE*-*CEEEEEEE*CC*-----------------**EEEEEEECCCC**---****EEEE**-C*EEEEEE*CC***************************** ------------------CCCCEEEEEC-CCEEEEEEECC--CCCHHH-*EEEE*-*C*EEEEEE*C-*-----------------**EEEEEE*CCCCCC***---*EEEE**-CEEEEEEE*CC*-**********----------------- --------**********CCCC*****C-CC*EEEEEECC**CCC***-*EEEE*-*CEEEEEEE*C------------C------**EEEEEEECCCCCC***---CEEEE**CCEEEEEE**CC-*********-----********------ --------**********CCCCEEEEE**CCEEEEEEECC--CCC**-**EEEE*-*CEEEEEE**CC***********C------***EEEEEECCCCCC**---*CEEEE**-CEEEEEEE*CC-*************-----------**** ------------------CCC*EEEEE*-CCEEEEEEECC--CCCHHH-*EEEE*-*C*EEEEE**C-*-----------------***EEE***CCCCCC***---CEEEE**-C*EEEEEE*CC*-**********----------------- --------*******--**CCCEEEEE*-CCEEEEEEECC--CCCHHH-*EEEE***CEEEEEEE*CC---------**C*****--*EEEEEEECCC**C***---CEEEE*-CCEEEEEEE-**----------------********----- --------**--------CCCCEEEEEC-CCEEEEEEECC--CCCHHH-*EEEE**-CEEEEEEE*CC*****--****C******-*EEEEEEECCCCCC***---CEEEE*-CCEEEEEEE-CC----------------------------- --------**********CCCC*EEEEC-CCEEEEEEECC**CCCHHH-*EEEE*-*CEEEEEE*---------------------*****EEEECCCCCC***---CEEEE**CCEEEEEEE*CC**********-----************** ---------*--------CCCCEEEEEC-CCEEEEEEECC--CCCHHH-*EEEE**-CEEEEEEE*CC***********C******-*EEEEEEECCCCCC***---CEEEE*-CCEEEEEEE-CC--------------*-***********-- **********--------CCCCEEEEEC-CCEEEEEEECC--CCCHHH-*EEEE**-CEEEEEEE*CC*--********C********EEEEEEECCCCCC***---CEEEE*-CCEEEEEEE-CC--------------*****----****** ------****--------CCCCEEEEE*-CCEEEEEEECC--CCCHHH-*EEEE**-CEEEEEEE*CC**-------**C******-*EEEEEEECCCCCC***---CEEEE*-CCEEEEEEE-CC--------------*-*******------ -------------------CCCEEEEEC-CCEEEEEEECC--CCCHHH-*EEEE*--CEEEEEEE*CC*-***--****C******-*EEEEEEECCCCCC***---CEEEE*-CCEEEEEEE-C------------------------------ -----*****--------***C**EE*C-CC-*EEEEECC--CCC--*-****-----EEEEEEE*CC******-----C******-*EEEEEEECCCCCC***---CEEEE*-CCEEEEE**-CC--------------**----********* 49764.tem _________________________________ --------**-------*CCCCEEEEEC-CCEEEEEEECC--CCCHHH-*EEEE***CEEEEEEE*CC*****--****C********EEEEEEECCCCCC***---CEEEE**CCEEEEEEE*CC--********----*************** Structural block scores 0 7 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.8 57.2 75.0 48.6 8 9 * 2.8 P 75.0 75.0 9.8 11.0 75.0 6.5 6.0 4.5 42.8 3.0 8.0 75.0 6.5 10 16 - 4.2 M 75.0 75.0 6.6 5.9 75.0 24.5 75.0 3.1 75.0 75.0 75.0 75.0 75.0 18 21 C 4.7 H 4.0 5.0 5.8 5.0 5.4 3.2 3.8 5.2 3.5 2.5 3.8 23.0 5.4 22 26 E 4.6 H 0.8 3.8 1.4 3.8 3.8 4.0 3.6 1.6 4.4 3.2 4.0 4.4 5.8 29 30 C 5.0 H 4.0 5.0 8.0 4.5 6.5 9.8 9.2 4.0 5.0 8.0 5.0 8.0 11.5 31 37 E 4.9 H 1.4 1.7 2.4 1.1 0.9 1.6 1.6 2.3 2.3 2.1 1.6 1.9 12.1 38 39 C 5.0 H 3.5 4.0 1.0 2.0 4.0 3.5 2.0 1.0 3.5 2.5 2.5 3.0 3.0 40 41 - 4.6 H 75.0 75.0 6.5 75.0 75.0 75.0 75.0 8.2 75.0 75.0 75.0 75.0 75.0 42 44 C 4.9 H 4.0 5.3 4.3 2.7 5.0 5.0 5.3 4.3 4.7 6.2 5.5 5.0 5.3 45 47 H 4.3 M 75.0 5.0 5.0 30.3 6.0 6.7 6.7 5.3 5.7 6.0 6.8 5.7 51.3 50 53 E 4.8 H 3.5 2.5 3.0 3.0 4.5 3.2 3.0 2.0 3.5 3.5 4.5 3.8 21.2 54 56 * 2.8 P 29.3 29.0 28.3 29.3 29.3 6.2 30.7 28.7 31.0 30.3 33.0 51.7 75.0 58 64 E 4.9 H 1.4 1.4 1.9 0.6 2.4 1.4 2.6 2.1 2.4 2.3 1.7 2.0 2.6 66 67 C 4.6 H 7.8 40.0 42.0 3.0 41.0 6.8 4.0 75.0 2.5 6.5 6.5 8.0 6.5 68 72 * 3.4 M 61.6 61.6 75.0 5.7 62.3 75.0 5.4 75.0 5.6 33.6 47.8 22.0 7.5 73 74 - 4.2 M 75.0 75.0 75.0 4.5 75.0 75.0 75.0 75.0 8.5 9.2 75.0 75.0 42.0 75 78 * 3.5 M 75.0 75.0 75.0 5.6 75.0 42.6 6.0 75.0 7.8 7.1 40.6 7.9 75.0 80 87 * 3.0 P 57.5 58.7 57.8 57.4 58.4 22.1 13.5 58.6 14.5 5.9 14.4 15.8 14.1 88 94 E 4.7 H 3.0 2.7 3.9 2.1 3.1 2.9 3.4 3.3 4.0 2.9 3.9 4.1 3.4 95 100 C 4.9 H 2.7 3.0 2.5 3.0 2.5 1.8 3.6 2.2 3.5 1.7 3.3 4.0 4.8 101 103 * 1.5 P 75.0 5.0 6.2 29.2 6.2 7.7 5.3 6.0 7.2 5.7 6.0 5.3 5.3 104 106 - 4.7 H 6.2 75.0 75.0 52.3 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 108 111 E 5.0 H 4.8 3.0 3.5 4.5 4.2 4.2 4.5 4.5 4.8 4.8 5.2 3.8 4.2 112 113 * 2.3 P 7.0 6.0 4.0 6.8 7.2 41.0 42.0 7.8 40.5 41.0 42.0 42.0 41.0 114 115 C 4.7 H 41.5 41.0 5.0 39.5 40.0 6.2 5.5 7.2 6.8 6.8 7.8 5.8 5.8 116 122 E 4.9 H 1.3 1.3 1.6 1.7 1.4 1.4 2.1 1.6 1.6 1.7 2.0 1.4 2.1 124 125 C 4.7 H 5.5 5.5 6.0 6.5 4.5 6.8 3.0 4.5 2.5 1.0 2.5 38.5 3.0 126 127 - 4.1 M 5.0 39.5 42.8 40.5 41.5 75.0 75.0 7.0 75.0 75.0 75.0 75.0 75.0 128 135 * 3.6 M 2.6 3.5 2.6 4.7 4.1 75.0 75.0 1.5 75.0 75.0 75.0 75.0 75.0 136 139 - 4.3 M 7.4 41.8 75.0 8.1 41.6 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 140 154 * 3.5 M 4.8 75.0 38.6 57.6 75.0 37.9 75.0 9.4 21.3 26.2 39.2 75.0 26.0 >>>>>>