Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1d2za- CC----CCCCHHHCCHHHHHHHHHHHH----HHCCHHHHHHHC--CCC-----------------------HHHHHHHHHHHHC---CCCHHHHHHHHHHHH----HCCCHHHHHHHHHHCCCHHHHHHHH-HHCCHHHHHHC-------------------------------------- >P1;d1d2zb- CCCCCCCCCCHHHCCHHHHHHHHHHHH----HHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC--------------------------- >P1;d1dgna- ----------CCCHHHHCHHHHHCCCCH-----HHHHHHHHHHHHH---------------------CCCCHHHHHHHHCCC--CCHH-HHHHHHHHHHHHC-C---HHHHHHHHHHHHHH-CCCCHHHHCCC------------------------------------------------ >P1;d1icha- ---------------CHHHHHHHHHCC----CC-CHHHHHHHH--CCC-----------------------HHHHHHHHHHCCC-CHH-HHHHHHHHHHHHH-CCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHC---------------------------------------------- >P1;d1n3ka- -----C------HHHHHHHHHHHHCCC-----HHHHHHHHHHHC-----------------------CCCCHHHHC-----------CCCCHHHHHHHHHHCCCC-CCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC >P1;d1pn5a1 ----------CCCCCCCCHHHHHCCCC-----HHHHHHHHHHHHHHCCCCCCCCCC---------------------------CCCCCCCCHHHHHHHHHHH-HC-CHHHHHCHHHHHHHHCCHHHHHHHHCCCCC--------------------------------------------C >P1;d1ucpa- -----C------HHHHHHHHHHHHHCC-----HHHHHHHHHHCC-CCCCCC--------------CCCCCCHHHHH-----------HC-CHHHHHHHHHHH-CC-HHHHHHHHHHHHHHCCCCHHHHHHHHHHCC--------------------------------------------- >P1;d1wmga- ---------CCCCCCHHHHHHHHHHHHCHHHCCCCHHHHHHHCC-------------------------CC--CHHHHHCCC-------CHHHHHHHHHHHHCCCC-CC-HHHHHHHHHC-CCCCCCCCCCC------------------------------------------------- >P1;d2a5yb2 -----CCCHHHHHHHHHHHHHHHHHCC--------HHHHHHHHHHC---------------------CCCCHHHHHHHHCC---CCHH-HHHHHHHHHHHHH-C---C-CCHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCHHHHCCCC------------------------------ >P1;d2gf5a2 ------------CHHHHHHHHHHHHCC-----CHHHHHHHHHCC-----------------------CCCCHHHHC-----------CCCCCCHHHHHHHHHCCC-CCCCCHHHHHHHHCCCCHHHHHHHHHHC----------------------------------------------- >P1;d2l6aa1 CCCCCC------CCHHHHHHHHHCCCC-----HHHHHHHHHHHH-CCHHHC--------------CC-CCCCCCCC-----------CC-CHHHHHHHHHHH-CC-HHHHHHHHHHHHCCCCCHHHHHCCC--CCCCCCC----------------------------------------C >P1;d2mpca1 -------------CHHHHHHHHHHHCC-----HHHHHHHHHHHC-CCCCCC--------------CCCCCCHHHHH-----------HC-CCCHHHHHHHHH-CC-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHC--------------------------------------------- >P1;d2ygsa- ------CCHHHHHHHHHHHHHHHHHCC--------CHHHHHHHHHH---------------------CCCCHHHHHHHHCC---CCHH-HHHHHHHHHHCCC-C---HHHHHHHHHHHHHCCCHHHHHHHHCCCC---------------------------------------------- >P1;d3crda- ----------CCCCHHHHHHHHHHHHHHCCCCCC---CHHHHHHHH---------------------CCCC-HHHHHHHHHCC---CCHHHHHHHHHHHHHHCC----CCHHHHHHHCC--CHHHHCHHHHHHHHHHCCCCCCC------------------------------------- >P1;d3ezqa1 --------CCHHHHHHHHHHHHHHCCC----HH-HHHHHHHHC--CCC-----------------------HHHHHHHHHHCCC-CHH-HHHHHHHHHHHCC-CCHHHH-HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHCC-------------------------CCCCCHHHHHHHHC >P1;d3qf2a- -------------CHHHHHHHHHHCCC-----HHHHHHHHHHHH-CCCCCC--------------CCCCCCHHHHH-----------HC-CHHHHHHHHHHH-HC-HHHHHHHHHHHHHHCCCHHHHHHHHHCCCCC-------------------------------------------- >P1;d3ygsp1 ------CCHHHHHHHHHCHHHHHHHCC--------CCCCHHHHHHC---------------------CCCCHHHHHHHHCC-CCCCHH-HHHHHHHHHHCCC-C---CCHHHHHHHHHHCCCCHHHHHHHHHHHHCC-------------------------------------------- >P1;d4a2wa3 -------CHHHHHHHHHCHHHHHCCCC--------HHHCCCCCC-----------------------CCCCCCHHHHHHHHHC-CCHH-HHCCCCCHHHHCCCC---CCHHHHHHHHHHHHCCHHHHHHHHCCC----------------------------------------------- >P1;d4a2wa4 -CHHHHHHHHHHHHHHHHHHHHC-CCC--------HHHHCCCCC-----------------------CCCCHHHHHHHHHHHHHCCHH-HHHHHHHHHHHCCCC---CCHHHHHHHHHHHCCCHHHHHCCC-------------------------------------------------- >P1;d4f42a- -------CCCHHHCCHHHHHHHHHHCC----C-CHHHHHHHHH--CCC-----------------------HHHHHHHHHCC-------CHHHHHHHHHCCC----CCCCHHHHHHHHHHCCCHHHHHHHHC------------------------------------------------- >P1;d6ac5a- -----CHHHCCCCCCHHHHHHHHHHCC-----C-CCHHHHHHC--CCC-----------------------HHHHHHHHHHCCCCCHH-HHHHHHHHHHHHH-HHHHHCCHHHHHHHHHHCCCHHHHHHHHHHCC---------------------------------------------- >P1;d6acih- -------------CHHHHHHHHHHHCC-----C-CHHHHHHHC--CCC-----------------------HHHHHHHHHHCCC-CHH-HHHHHHHHHHHHH-HH-HHCCHHHHHHHHHHCCCHHHHHHHHHHHC---------------------------------------------- >P1;d6hj7a- ---CCCCCCCCCCCCHHHHHHHHHHHCCCCCCC-CHHHHHHHHC-------------------------CCHHHHHHHHHCC-------CHHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCCHHHHHHHCCCCCCCCCC----------------------------------------- PSA >P1;d1d2za- 93----a14105604980187008203----846116500821--908-----------------------8a13750231476---a63004100500057----3733014006004717158005203-73069923852-------------------------------------- >P1;d1d2zb- 6b1517162203608980044004301----8a3204600520067070470066b5081751385842079931770144077559a3020320046026229972200000001003414008002100630064a32a23a97820899a9--------------------------- >P1;d1dgna- ----------c65206725830162097-----b108401730383---------------------820778135506663--7926-4206200610393-7---5a025401720484-1790065054b------------------------------------------------ >P1;d1icha- ---------------760060006102----4a-504600460--906-----------------------69106708a7448-665-4102000320596-194a9511620270057292592166068458---------------------------------------------- >P1;d1n3ka- -----8------a30760062018507-----692065016207-----------------------930588318-----------606505200600474d30-6558091025006408267027404705751576565a768576893795386a8899896578878a69799ae >P1;d1pn5a1 ----------8a2b2166114106608-----583054006304a4143aaa5a6a---------------------------7793a29505500410275-16-6b601710040085083a50445074b369--------------------------------------------b >P1;d1ucpa- -----9------960370036006909-----974235005304-62809a--------------c362053b404-----------81-707500440184-07-381006000500730a1b9119b085408a--------------------------------------------- >P1;d1wmga- ---------54360399227711740248b27c50053006208-------------------------59--73b50573b-------4102200550034078a-93-4950440076-b359475976d------------------------------------------------- >P1;d2a5yb2 -----806a623500620584038403--------04501a10394---------------------91069921860353---9335-5107200510353-0---7-606101500562b15600610660262077659417450175------------------------------ >P1;d2gf5a2 ------------880180044007306-----a51065105836-----------------------c40889416-----------619934000410383740-7445057018202827584026403951----------------------------------------------- >P1;d2l6aa1 ab9aa3------a50383018105407-----963063017200-51b72a--------------80-304a6405-----------90-428500620283-03-333005101200250c354045708--3948b69----------------------------------------a >P1;d2mpca1 -------------83263045006607-----881154005302-62838a--------------91670579505-----------90-735500710272-04-385028103600840b39802630660798--------------------------------------------- >P1;d2ygsa- ------066904610482284026607--------07700530285---------------------830768206606a2---6535-5304100500182-6---47004001400362828a1074079124---------------------------------------------- >P1;d3crda- ----------b56623500730485107846592---8009301a5---------------------8005-8705931a628---734411400020015334----91083006006--2357055604513671387a8af------------------------------------- >P1;d3ezqa1 --------b7a7673475068109608----39-302800382--908-----------------------7930780597179-568-4011400230383-1a9961-761076227738-675378537815661773b-------------------------991a6487335826 >P1;d3qf2a- -------------a0444007004508-----b61284005200-603794--------------b0640379605-----------81-834600510272-08-56500600140023092670265049341a2-------------------------------------------- >P1;d3ygsp1 ------086803610471374005406--------08901920384---------------------90087730350361-983634-2103400410271-8---77002300200351718a00640483367f-------------------------------------------- >P1;d4a2wa3 -------68841730585266026501--------02600b606-----------------------7206881165046227-7566-600420061018276---a9015100600531727a007404839----------------------------------------------- >P1;d4a2wa4 -a87478058337206614a306-a03--------045015404-----------------------8005a9227504720777655-200620060007053---550082038005515389009608-------------------------------------------------- >P1;d4f42a- -------d7305705686256018308----b-7003600630--918-----------------------6850561485a-------5214200750086----a9022740220056193670185168------------------------------------------------- >P1;d6ac5a- -----8159395307770061016607-----7-804600530--706-----------------------686067029527a5746-3004200340184-389a3010070061055082670154048307---------------------------------------------- >P1;d6acih- -------------91840061008306-----9-404400830--706-----------------------a851650484359-646-3103000410466-37-a8052860091035080591055056518---------------------------------------------- >P1;d6hj7a- ---baa9b5b43726ab42631261154d7859-8395208618-------------------------2a9a52870495c-------511421277316940a--a1637403220034935800630585664a5ba----------------------------------------- Translating the sequences **----*********HHHHHHHHH***----****HHHHHHH*--***-----------------------HHHHH********---****HHHHHHHHH**----****HHHHHHHHHHCCCHHHHHHHH-***********-------------------------------------- ***************HHHHHHHHH***----****HHHHHHH*****************************HHHHH***************HHHHHHHHH***C******HHHHHHHHHHCCCHHHHHHHH***********************--------------------------- ----------*****HH*HHHHH**CC*-----**HHHHHHH****---------------------****HHHHH******--****-**HHHHHHHHH**-C---***HHHHHHHHHH*-C***HHHH***------------------------------------------------ ---------------*HHHHHHHH*CC----**-*HHHHHHH*--***-----------------------HHHHH********-***-**HHHHHHHHH**-C******HHHHHHHHHHCCCHHHHHHHH****---------------------------------------------- -----*------***HHHHHHHHH*CC-----***HHHHHHH**-----------------------****HHHH*-----------****HHHHHHHHH***C*-*****HHHHHHHHHCCCHHHHHHHH************************************************** ----------********HHHHH**CC-----***HHHHHHH**************---------------------------********HHHHHHHHH**-**-****HH*HHHHHHH*CCHHHHHHHH*****--------------------------------------------* -----*------***HHHHHHHHH*CC-----***HHHHHHH**-******--------------******HHHHH-----------**-*HHHHHHHHH**-C*-****HHHHHHHHHHCCC*HHHHHHH*****--------------------------------------------- ---------******HHHHHHHHH***********HHHHHHH**-------------------------**--*HH******-------**HHHHHHHHH***C**-**-HHHHHHHHH*-CC*********------------------------------------------------- -----**********HHHHHHHHH*CC--------HHHHHHH****---------------------****HHHHH*****---****-**HHHHHHHHH**-C---*-**HHHHHHHHHCCCHHHHHHHH********************------------------------------ ------------***HHHHHHHHH*CC-----***HHHHHHH**-----------------------****HHHH*-----------******HHHHHHH***C*-*****HHHHHHHH*CCCHHHHHHHH***----------------------------------------------- ******------***HHHHHHHH**CC-----***HHHHHHH**-******--------------**-********-----------**-*HHHHHHHHH**-C*-****HHHHHHHH**CCCHHHHH***--*******----------------------------------------* -------------**HHHHHHHHH*CC-----***HHHHHHH**-******--------------******HHHHH-----------**-***HHHHHHH**-C*-****HHHHHHHHHHCCCHHHHHHHH*****--------------------------------------------- ------*********HHHHHHHHH*CC--------*HHHHHH****---------------------****HHHHH*****---****-**HHHHHHHH***-C---***HHHHHHHHHHCCCHHHHHHHH****---------------------------------------------- ----------*****HHHHHHHHH**********---*HHHH****---------------------****-HHHH*******---*****HHHHHHHHH***C----**HHHHHHH**--C*HHH*HHHH*************------------------------------------- --------*******HHHHHHHHH*CC----**-*HHHHHHH*--***-----------------------HHHHH********-***-**HHHHHHHHH**-C*****-HHHHHHHHHH**-HHHHHHHH***********-------------------------************** -------------**HHHHHHHHH*CC-----***HHHHHHH**-******--------------******HHHHH-----------**-*HHHHHHHHH**-**-****HHHHHHHHHHCCCHHHHHHHH******-------------------------------------------- ------*********HH*HHHHHH*CC--------****HHH****---------------------****HHHHH*****-******-**HHHHHHHH***-C---***HHHHHHHHH*CCCHHHHHHHH******-------------------------------------------- -------********HH*HHHHH**CC--------HHH******-----------------------******HHH*******-****-*******HHHH***C---***HHHHHHHHHH*CCHHHHHHHH***----------------------------------------------- -**************HHHHHHH*-*CC--------HHHH*****-----------------------****HHHHH************-**HHHHHHHHH***C---***HHHHHHHHHHCCCHHHHH***-------------------------------------------------- -------********HHHHHHHHH*CC----*-**HHHHHHH*--***-----------------------HHHHH******-------**HHHHHHHH***----****HHHHHHHHHHCCCHHHHHHHH*------------------------------------------------- -----**********HHHHHHHHH*CC-----*-**HHHHHH*--***-----------------------HHHHH************-**HHHHHHHHH**-*******HHHHHHHHHHCCCHHHHHHHH****---------------------------------------------- -------------**HHHHHHHHH*CC-----*-*HHHHHHH*--***-----------------------HHHHH********-***-**HHHHHHHHH**-**-****HHHHHHHHHHCCCHHHHHHHH****---------------------------------------------- ---************HHHHHHHHH**C******-*HHHHHHH**-------------------------**HHHHH******-------**HHHHHHHHH***C*--****HHHHHHHH*CCCHHHHHHH**********----------------------------------------- 47986.tem _________________________________ -----**********HHHHHHHHH*CC----****HHHHHHH******-------------------****HHHHH***************HHHHHHHHH***C*-****HHHHHHHHHHCCCHHHHHHHH*********----------------------------------------- Structural block scores 0 4 - 4.6 H 47.4 4.9 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 10.4 75.0 75.0 75.0 75.0 75.0 75.0 75.0 20.9 75.0 75.0 75.0 49.4 5 14 * 2.8 P 10.7 3.5 40.0 75.0 47.1 40.9 47.4 32.1 4.0 54.1 46.9 61.1 10.7 40.5 27.7 61.0 10.7 18.7 4.3 19.1 5.0 61.0 7.0 15 23 H 4.8 H 4.6 3.2 4.2 2.8 3.3 2.9 2.8 5.0 4.0 2.7 3.2 2.9 4.0 3.3 4.4 2.6 3.4 4.4 12.4 4.7 3.1 3.0 5.1 25 26 C 4.5 M 1.5 0.5 4.5 1.0 3.5 4.0 4.5 1.0 1.5 3.0 3.5 3.5 3.5 0.5 4.0 4.0 3.0 0.5 1.5 4.0 3.5 3.0 3.0 27 30 - 4.6 H 75.0 75.0 58.0 75.0 75.0 75.0 75.0 6.4 75.0 75.0 75.0 75.0 75.0 6.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 8.1 31 34 * 3.0 P 4.8 5.9 40.6 23.6 23.0 22.8 23.8 6.1 75.0 22.9 23.2 23.0 75.0 22.8 22.5 23.4 75.0 75.0 75.0 23.4 41.2 40.8 24.2 35 41 H 4.8 H 3.1 2.4 3.3 2.9 2.9 2.6 2.6 2.3 3.1 3.6 2.7 2.6 3.1 24.3 3.0 3.0 4.1 3.6 2.7 2.6 2.6 2.7 4.7 42 47 * 2.7 P 28.0 3.3 27.3 27.5 51.2 3.9 15.8 51.3 27.7 51.5 15.4 15.5 27.5 27.8 28.2 14.0 27.5 51.0 50.7 28.0 27.2 27.2 51.5 48 66 - 4.7 H 75.0 4.5 75.0 75.0 75.0 46.9 57.1 75.0 75.0 75.0 56.7 56.9 75.0 75.0 75.0 56.9 75.0 75.0 75.0 75.0 75.0 75.0 75.0 67 70 * 2.8 P 75.0 3.2 4.2 75.0 4.2 75.0 3.2 41.0 4.0 6.1 20.5 4.5 4.5 3.2 75.0 3.2 4.2 3.8 3.2 75.0 75.0 75.0 40.6 71 75 H 4.6 H 5.9 5.8 4.8 4.4 5.6 75.0 4.5 34.3 5.8 5.6 5.1 5.2 4.4 19.0 5.2 5.4 4.0 4.8 6.1 4.8 5.2 6.1 6.9 76 90 * 2.8 P 18.2 4.3 18.7 14.7 56.1 38.5 61.1 37.4 22.9 56.7 60.9 61.1 23.4 18.9 14.6 61.1 13.4 13.7 8.8 37.8 9.5 13.9 37.9 91 99 H 4.9 H 1.1 1.9 2.0 1.3 1.9 1.9 2.3 1.6 2.0 1.7 2.8 2.6 1.2 0.9 1.6 2.3 1.6 1.6 1.6 2.1 1.6 1.3 3.1 100 102 * 2.0 P 29.0 3.3 29.0 30.0 8.2 29.0 29.0 2.3 27.7 6.0 28.7 28.0 28.3 3.7 28.7 28.0 27.7 5.7 4.0 29.7 29.0 29.0 6.3 106 109 * 1.7 P 4.0 1.0 22.6 6.4 6.0 5.9 3.0 40.5 40.8 5.0 2.2 4.0 21.5 40.0 22.8 4.0 22.2 23.6 21.2 5.4 3.6 5.9 23.1 110 119 H 4.8 H 2.2 0.8 3.3 3.0 2.7 2.6 2.1 3.9 2.4 3.3 1.6 3.2 1.8 9.8 4.5 1.6 1.5 2.1 3.1 2.8 2.4 3.4 2.4 120 122 C 4.7 H 3.0 1.7 26.7 4.3 3.3 3.7 3.8 29.8 4.8 4.7 5.2 4.8 4.0 26.7 28.7 3.7 3.0 3.3 3.0 4.3 3.3 2.7 5.3 123 130 H 4.7 H 2.9 1.4 4.0 4.4 3.8 4.4 6.4 6.5 3.0 3.4 4.1 4.2 4.7 4.0 5.5 3.8 4.1 4.1 5.0 4.2 3.4 3.8 3.4 131 139 * 2.9 P 12.7 3.8 60.1 44.4 4.8 37.1 36.4 68.2 4.0 51.7 22.3 36.7 43.4 4.6 5.3 28.3 30.5 52.2 75.0 67.6 43.7 43.9 7.4 140 180 - 4.8 H 69.9 51.8 75.0 75.0 7.5 73.5 75.0 75.0 56.0 75.0 73.4 75.0 75.0 68.9 48.1 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 >>>>>>