Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1tt8a- CCHHHHHHHHCCCCCCCCCCCHHHHHHHHCC---CCCHHHHHCC-CC--CEEEEEEEEEEE-C-HHHCCCCHHHCCCCCCEEEEEEEEEECCEEEEEEEEEEEHHHCCHHHHHHHCCCCCCCCHHHCC--CCCEEEEEEEEEEEC---------------CEEEEEEEEEEC--CEEEEEEEEECCCCCCC---------- >P1;d2fa1a1 -----------------------CCCCCEEEECCCCCCCC-----------CCEEEEEEEE-ECCHHHHHHH-CCCCCCEEEEEEEEEEECCEEEEEEEEEECCHHHHHHHCCCC---CCCHHHHHHHHHCCCEEEEEEEEEEEECCCHHHHHHCCCCCCEEEEEEEEEEECCCCCCCEEEEEEEE-CCCEEEECCC---- >P1;d2ikka1 ----------------------------------------------------CEEEEEEEE-ECCHHHHHHH-CCCCCCEEEEEEEEEECCCCEEEEEEEEEECCCCCCHHHHCCC--CCC-CHHHHHHHCCCCCEEEEEEEEEECCHHHHHHHCCCCCCEEEEEEEEEEE-HHHEEEEEEEEECC--CCCCCCCC----- >P1;d2nwia1 --------------------CHHHHHHHHCC---CCHHHHHHHHHCC--CEEEEEEEEEEE-ECCHHHHHHH-CCCCCCEEEEEEEEEEECCEEEEEEEEEEEHHHCCHHHHHHHHCCCCCHHHHHHH-CCCCCEEEEEEEEEEECCHHHHHHHCCC-CCEEEEEEEEEEEC--CEEEEEEEEEEE-HHHC---------- >P1;d2ogga1 --------------------------------------------------CCEEEEEEEEE-CCCHHHHHHH-CCCCCCCEEEEEEEEEECCEEEEEEEEEEECCCCCCCCHHHHC--C-CHHHHHHHHHCCCEEEEEEEEECCCCC-HHHHHHCCCCCCCCCEEEEEEEECC-CCEEEEEEEEEC-HHHCCCCCCCCCCC >P1;d2ooia1 ---------------------------CCEECCCCCCHHHC--------CEEEEEEEEEEECCCCHHHHHHC-CCCCCCCEEEEEEEEEECCEEEEEEEEEEEHHHHCCCCHHHHC---CCHHHHHHHCCCCCEEEEEEEEEEEECCHHHHHHCCCCCCCEEEEEEEEEEECC-CCEEEEEEEEEE-CCCCCEECCC-C-- >P1;d2p19a1 ------------------------------------------CCCCCC--EEEEEEEEEEE-ECCHHHHHHH-CCCCCCEEEEEEEEEEECCEEEEEEEEEECHHHC-CCCHHHHH--HCCHHHHHHHC-CCCCCEEEEEEEEEECCCCHHHHHCCCCCCEEEEEEEEEECCC-CCEEEEEEEEEC-CCCCCCCCCCCCC- >P1;d2pkha1 -------------------------------------------------CEEEEC-CEEEE-ECHHHHHHHH-C-CCCCEEEEEEEEEEECCEEEEEEEEEEECCCCCCHHHCCCC--CCCHHHHHHHH--CCCCEEEEEEEEECCCHHHHHHHCCCCCCCEEEEEEEEEEC--CEEEEEEEEEEE-HHHCCCCCCCC--C >P1;d2ra5a1 -------------------------------------------CEEEEECCEEEEEEEEEE-ECCHHHHHHH-CCCCCCEEEEEEEEEECCCCC-CEEEEEECCCCC-CCCCCHHH--HCCCCC-CCCC-CCCCCEEEEEEEEEECCHHHHHHHCCCCCCEEEE-EEEEECCC-CCEEEEEEEECC-CCCCCCCEEEEECC >P1;d3bwga2 ---------------------------C------------C--------CEEEEEEEEEEE-CCCHHHHHHH-CCC-CCCEEEEEEEEEECCEEEEEEEEEEECCCCCCCCHHHHC---CCHHHHHHHCCCCCEEEEEEEEEEEECCHHHHHHHCCCCCCEEEEEEEEEEECC-CCEEEEEEEEEC-CCCCCCCCCC-C-C >P1;d3cnva1 -------------------------------------CCCCCCCEEE--CCCCEEEEEEEE-CC--CCHHHH-CCC-CCCEEEEEEEECC--CCCEEEEEEEEHHHCCCCCCCCCC--CCCHHHHHHHHHCCC-EEEEEEEEEEECCCCCHHHCCCCCCCEEEEEEEEEEE-CCCCCCEEEEEECC--CCEEECCCCC--- >P1;d3ddva1 -----------------------------------------------CCCEEEEEEEEEEE-CCCHHHHHHH-CCCCCCCEEEEEEEEEECCEEEEEEEEEEEHHHC-------------------------CCCCEEEEEEEEECCHHHHHHCCCCCCCEEEEEEEEEECCC-CCEEEEEEEEEC-CCCCCCCCC----C >P1;d3f8la- ----------------------------CEEECCCCCHHHHHHC-C--CCEEEEEEEEEEE-ECC-CHHHHH-CCCCCCEEEEEEEEEEECCEEEEEEEEEEEHHHCCCHHHHCCC--CCCHHHHHHHC-CCCCCEEEEEEEEECCCHHHHHHHCCCCCCCEEEEEEEEECCC-CCEEEEEEEEEE-CCCCEEECCC-CC- >P1;d3hfia- ---------------------------------------------------CEEEEEEEEE-ECCHHHHHHH-CCCCCCEEEEEEEEEECCCCEEEEEEEEECHHHCCCHHHCCCC--CCCHHHHHHHHHCCCCCEEEEEEEEEECCCCCC-CCC-CCCCEEEEEEEEEEEE-CCEEEEEEEEEEC----CCCCC------ >P1;d3lhea- -----------------------------------------------CCCCCCEEEEEEEE-ECCHHHHHHH-CCCCCCEEEEEEEEEEECCEEEEEEEE--CCCCCCCCC-------------------CCCEEEEEEEEEEECCCHHHHHCCCCC--CCCEEEEEEEEECC-CCEEEEEEECCC-HHHC---------- >P1;d4zsia1 ---------------------------CEEEECCCCCHHHHHHHCC--CCEEEEEEEEEEE-ECCHHHHHHH-CCCCCCEEEEEEEEEEECCEEEEEEEEEEECCCCCCHHHHCCC--CCCHHHHHHHHHCCCEEEEEEEEEEEECCHHHHHHHCCCCCCEEEEEEEEEEECC-CCEEEEEEEEEC-CCCEEEECCC-CCC PSA >P1;d1tt8a- 447108302609067933a277913600336---2000410385-a2--a07062132531-5-5a40530252045284010000101058540000000004700685065027088411043209--809060220101557---------------710001020304--82100000001640103---------- >P1;d2fa1a1 -----------------------c5917242505820036-----------7062340334-6075500920-93876750000100133b850000110102549126104709---431005204752813061472737656068611940507842602003110159b6b81200111002-272031539a---- >P1;d2ikka1 ----------------------------------------------------351054743-6069710920-819771400201104458a303200101101730670273176--a36-5820574172515535573743608a51083081877330222210011-7b740000043012--9139389a----- >P1;d2nwia1 --------------------67317602917---9604720382195--807241441644-6078910620-7086424002001112069510013102001410898026004539321970196-2a1a26254431542909591073090a-55600000010027--860000110100-1400---------- >P1;d2ogga1 --------------------------------------------------77040262737-5089602810-7087a15013000022475320101100004530490668203--8-30882039511b513637462462706-b405820507c37520113111078-850010202010-453284668899bc >P1;d2ooia1 ---------------------------a5121631241251--------51808034054296039902940-708785200102010227a500000302013810660357306---920141047728170250518587480678108308187434013020001159-570000050000-2730426348-9-- >P1;d2p19a1 ------------------------------------------9ca857--66261132542-7089820950-928554600002003133b420001301003812-80566307--75603600572-a1835528383865807c8207208198327021051302297-681000031001-372481988989a- >P1;d2pkha1 -------------------------------------------------656081-42542-4087722930-9-86a35001010011677601200100011810650372604--74705510472--1805733633672608891084070a87260200342011a--a51001030000-4724857999b--9 >P1;d2ra5a1 -------------------------------------------c66567758060432442-6077710820-a2857570230101215aa42-101101015c21-a1746504--735137-1573-91617727473865608871094092a4737022-51103155-870000030011-38356265352859 >P1;d3bwga2 ---------------------------a------------9--------717070141534-6079502820-908-954000010022169611000200003800660588202---750352057627281362646557770796109309192644122020021168-451000011010-4531a59a99-b-c >P1;d3cnva1 -------------------------------------a434113024--592370240543-05--910830-609-844000020104a--a41000202000570790752068--345027004851835-3405172583605870053090757370200303113-8b750010501012--5835164a8f--- >P1;d3ddva1 -----------------------------------------------c5876263145543-706a403820-614684303220404115950110211030593a-------------------------95963755466380487109107197348022123111288-750220111110-146293968----9 >P1;d3f8la- ----------------------------2706494b10044148-c--4804042160373-608-a10b30-a2a871400200000206a540000103002820770487073--65001730872-a141550637468360796008209065926022030201058-650001030000-2630503588-9b- >P1;d3hfia- ---------------------------------------------------7241243532-6089500820-51856350000000317ca842200001001620750482604--769036103820957264571736855089830-308-9683612011310005-7830000011013----a956c------ >P1;d3lhea- -----------------------------------------------88296153143444-4078700930-927575701221413138863012131--039026b3a-------------------e4845737465451507962273c188--a4601313103056-940320112022-2865---------- >P1;d4zsia1 ---------------------------415063612101610772a--2715164061323-707a600a20-81a5846003010001068420001000010930540481097--1a1024003622803047182528675068620a209096636021021304077-552001140100-1430606489-899 Translating the sequences *******************************---**********-**--***EEEEEEEEE-*-*HH****H**CCCCC*EEEEEEEEEECCEEEEEEEEEE****CC***********CC**HHH**--CCC**EEEEEEEEE*---------------*EEEEEEEEEEC--C*EEEEEEEE******C---------- -----------------------*****************-----------**EEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEEECCEEEEEEEEEE*************---*CC**HHHHH**CCC**EEEEEEEEE*CC*HHHHH*CCCCCC*EEEEEEEEEEC**C***EEEEEE**-*******C**---- ----------------------------------------------------*EEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEE*CC*EEEEEEEEE****CCC*******--*CC-*HHHHH**CCC**EEEEEEEEE*CC*HHHHH*CCCCCC*EEEEEEEEEE-****EEEEEEEE**--**C***C*----- --------------------***********---*************--***EEEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEEECCEEEEEEEEEE****CC***********CC**HHHHH-*CCC**EEEEEEEEE*CC*HHHHH*CCC-CC*EEEEEEEEEEC--C*EEEEEEEE**-***C---------- --------------------------------------------------**EEEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEEECCEEEEEEEEEE****CCC*******--*-C**HHHHH**CCC**EEEEEEE***CC-HHHHH*CCCCCC***EEEEEEEEC*-C*EEEEEEEE**-***C***C****** ---------------------------**************--------***EEEEEEEEE**CCHHHHHH*-CCCCCC*EEEEEEEEEECCEEEEEEEEEE*****CC*******---CC**HHHHH**CCC**EEEEEEEEE*CC*HHHHH*CCCCCC*EEEEEEEEEEC*-C*EEEEEEEE**-***C***C**-*-- ------------------------------------------******--**EEEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEEECCEEEEEEEEEE****C-C*******--*CC**HHHHH*-CCC**EEEEEEEEE*CC**HHHH*CCCCCC*EEEEEEEEE*C*-C*EEEEEEEE**-***C***C*****- -------------------------------------------------***EE*-*EEEE-*C*HHHHHHH-C-CCCC*EEEEEEEEEECCEEEEEEEEEE****CCC*******--*CC**HHHHH*--CC**EEEEEEEEE*CC*HHHHH*CCCCCC*EEEEEEEEEEC--C*EEEEEEEE**-***C***C***--* -------------------------------------------*********EEEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEE*CC**-*EEEEEE****C-C*******--*CC***-****-CCC**EEEEEEEEE*CC*HHHHH*CCCCCC*EEE-EEEEE*C*-C*EEEEEEEE**-***C********** ---------------------------*------------*--------***EEEEEEEEE-*CCHHHHHHH-CCC-CC*EEEEEEEEEECCEEEEEEEEEE****CCC*******---CC**HHHHH**CCC**EEEEEEEEE*CC*HHHHH*CCCCCC*EEEEEEEEEEC*-C*EEEEEEEE**-***C***C**-*-* -------------------------------------**********--****EEEEEEEE-*C--**HHHH-CCC-CC*EEEEEEEE**--***EEEEEEE****CCC*******--*CC**HHHHH**CCC-*EEEEEEEEE*CC***HHH*CCCCCC*EEEEEEEEEE-**C***EEEEEE**--******C***--- -----------------------------------------------*****EEEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEEECCEEEEEEEEEE****C-------------------------C***EEEEEEEE*CC*HHHHH*CCCCCC*EEEEEEEEE*C*-C*EEEEEEEE**-***C***C*----* ----------------------------****************-*--****EEEEEEEEE-*CC-*HHHHH-CCCCCC*EEEEEEEEEECCEEEEEEEEEE****CCC*******--*CC**HHHHH*-CCC**EEEEEEEEE*CC*HHHHH*CCCCCC*EEEEEEEEE*C*-C*EEEEEEEE**-***C***C**-**- ---------------------------------------------------*EEEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEE*CC*EEEEEEEEE****CCC*******--*CC**HHHHH**CCC**EEEEEEEEE*CC****-**C-CCCC*EEEEEEEEEE*-*C*EEEEEEEE**----C***C------ -----------------------------------------------******EEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEEECCEEEEEEEE--****CCC**-------------------CCC**EEEEEEEEE*CC*HHHH**CCC--C**EEEEEEEEEC*-C*EEEEEEE***-***C---------- ---------------------------*******************--****EEEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEEECCEEEEEEEEEE****CCC*******--*CC**HHHHH**CCC**EEEEEEEEE*CC*HHHHH*CCCCCC*EEEEEEEEEEC*-C*EEEEEEEE**-*******C**-*** 64288.tem _________________________________ ---------------------------****---*************-****EEEEEEEEE-*CCHHHHHHH-CCCCCC*EEEEEEEEEECCEEEEEEEEEE****CCC*******--*CC**HHHHH**CCC**EEEEEEEEE*CC*HHHHH*CCCCCC*EEEEEEEEEEC*-C*EEEEEEEE**-***C***C****** Structural block scores 0 26 - 4.7 H 4.4 64.9 75.0 56.7 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 27 30 * 3.9 M 3.0 3.8 75.0 4.8 75.0 4.6 75.0 75.0 75.0 58.9 75.0 75.0 21.0 75.0 75.0 2.5 31 33 - 4.3 M 75.0 3.3 75.0 75.0 75.0 3.3 75.0 75.0 75.0 75.0 75.0 75.0 6.3 75.0 75.0 5.0 34 46 * 3.8 M 8.5 41.8 75.0 4.3 75.0 35.8 49.6 75.0 54.2 69.9 19.8 75.0 15.4 75.0 75.0 8.7 48 51 * 2.5 P 23.1 58.0 75.0 22.5 41.0 22.2 40.5 23.0 6.8 22.5 22.8 6.5 4.0 58.0 6.2 3.8 52 60 E 4.9 H 2.6 2.8 3.6 3.3 3.4 2.9 2.9 11.2 2.8 2.8 3.1 3.7 2.9 2.9 3.2 2.9 63 64 C 4.7 H 40.0 3.5 3.0 3.5 4.0 1.5 4.0 4.0 3.5 3.5 40.0 3.0 4.0 4.0 3.5 3.5 65 71 H 4.8 H 3.5 3.0 4.0 3.7 3.7 4.7 4.7 4.3 3.6 3.7 13.7 3.9 14.4 3.4 3.9 4.1 73 78 C 4.9 H 3.5 6.7 5.5 4.5 5.6 5.8 5.5 18.6 6.2 17.7 17.0 4.8 6.5 4.7 5.8 6.1 80 89 E 4.9 H 0.3 0.8 1.7 0.7 1.2 0.8 0.9 1.0 1.5 0.6 1.8 1.7 0.4 1.1 1.8 0.5 90 91 C 4.8 H 6.5 9.8 9.2 7.5 6.0 8.8 7.2 7.0 10.5 7.5 75.0 7.0 8.2 11.5 8.0 7.0 92 101 E 4.8 H 0.9 0.8 1.1 1.3 0.8 1.0 1.1 1.0 8.5 1.0 1.9 1.4 1.3 1.7 16.7 0.7 102 105 * 1.0 P 2.8 5.0 2.8 1.5 3.0 3.2 3.0 2.8 5.1 2.8 3.0 4.2 3.0 2.2 3.0 3.2 106 108 C 4.5 M 4.7 3.0 4.3 5.7 4.3 4.0 28.3 3.7 28.8 4.0 5.3 53.5 4.7 4.0 6.5 3.0 109 115 * 1.6 P 3.6 13.7 3.7 2.9 3.6 3.4 3.9 3.1 3.9 3.6 4.0 75.0 4.1 3.4 55.5 4.1 116 117 - 4.7 H 4.0 75.0 75.0 4.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 119 120 C 4.7 H 2.5 2.0 4.5 2.5 39.0 5.5 5.5 5.5 4.0 6.0 4.5 75.0 2.5 7.5 75.0 5.8 121 122 * 1.9 P 0.5 0.0 40.0 5.0 4.0 0.5 1.5 2.5 2.0 1.5 1.0 75.0 0.5 1.5 75.0 1.0 123 127 H 4.5 M 3.6 3.6 4.4 4.6 4.4 3.2 3.6 3.4 19.0 3.8 3.8 75.0 5.0 3.6 75.0 2.6 128 129 * 2.7 P 75.0 3.5 2.5 38.5 3.0 4.5 38.5 38.5 39.0 4.0 3.0 75.0 38.5 1.0 75.0 2.0 130 132 C 4.8 H 5.7 4.0 4.7 7.3 5.8 5.3 6.5 28.0 5.3 5.7 5.3 53.0 5.2 7.0 8.8 3.7 133 134 * 1.1 P 3.0 3.0 3.0 4.0 2.0 1.0 4.0 2.5 4.0 2.0 39.0 7.0 3.0 4.0 4.5 2.0 135 143 E 4.9 H 1.8 4.7 4.7 3.3 4.4 4.8 5.3 4.4 5.4 5.3 3.9 5.0 4.7 5.1 4.7 5.1 145 146 C 4.8 H 75.0 3.0 4.0 4.5 3.0 3.0 3.5 4.0 4.0 3.5 2.5 2.0 3.5 4.0 3.5 3.0 148 152 H 4.6 H 75.0 4.2 3.4 4.0 5.7 4.0 3.8 4.4 4.2 3.8 3.0 3.6 3.2 17.8 4.0 4.1 154 159 C 4.7 H 75.0 4.3 5.7 17.4 4.6 5.2 5.2 5.8 5.9 5.2 5.2 5.2 5.2 18.2 29.6 5.5 161 170 E 4.9 H 0.7 1.3 1.1 0.3 1.5 0.8 1.6 1.3 9.0 1.1 1.3 1.5 1.0 0.9 1.8 1.3 176 183 E 4.9 H 0.1 0.8 0.9 0.4 0.6 0.6 0.6 0.6 0.4 0.4 0.9 1.0 0.5 0.2 1.1 1.1 184 185 * 1.0 P 3.5 1.0 1.5 0.0 0.5 0.0 0.5 0.0 1.0 0.5 1.5 0.5 0.0 2.0 2.0 0.0 187 189 * 1.5 P 0.3 3.7 28.3 1.7 4.0 4.0 4.0 4.3 4.7 4.0 29.3 3.7 3.7 75.0 5.3 2.7 191 193 * 2.0 P 75.0 3.0 6.7 75.0 6.0 4.0 6.0 6.7 4.7 8.2 4.0 7.0 2.7 6.7 75.0 4.0 195 200 * 3.5 M 75.0 53.2 64.2 75.0 9.7 41.0 19.9 31.4 5.3 32.0 44.3 52.8 31.1 75.0 75.0 19.7 >>>>>>