Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1rl4a- ----------------CCCCCCCHHHHCCCCCCC-----CCCHHHHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEEC-------------------------CEEEEEEEEEECC--CEEEE---EECCCCCC-CCCE-EEEEECCEEEEEECCCCCEEEEEECHHHHHHHHHHHHHHCCCCHHHHCC--------HHHHHHHHHHHHHHHHC-------------- >P1;d1v3ya- ------------CCC-CCCCCCCHHHHCCCCCCC-----CCC-CHHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEEECCC------------CCCC----CEEEEEEEEEEEEE---CCEE---EEEC-CCCC-CCCEEEEEECCEEEEEEECCCCCEEEEEEEHHHHHHHHHHHHHHCCCCHHHHCC--HHH---HHHHHHHCHHHHHHHHHHC------------ >P1;d1ws0a- -----------CCCC-CCCCCCCHHHHCCCCCCC-----CCCHHHHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEEECCC------------C--C----CEEEEEEEEEEEEE---EEEE---EEECCCCCC-CCCE-EEEEEEEEEEEEECCCCCEEEEEEEHHHHHHHHHHHHHHCCCCHHHCEEEECC----------------------------------- >P1;d1xeoa- ------------CCC-CCCCCCCHHHHCCCCCCC-----CCCHHHHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEECCCC--------CCC---------CCEEEEEEEEEEEE---CCCCC---EECCCCCC-CCCE-ECCCCCEEEEEEECCCCCEEEEEECHHHHHHHHHHHHHHCCCCHHHHCC---------------HHHHHHHHHHH--HHHHHHC---- >P1;d2os0a1 -----------CCCHHHCCCCCCHHHHCCCCCCCC----CCCHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEHHHHCCCCCEEEEEEC--------------------CEEEEEEEEEEEEECC--CEEEECC-CCCCCCCCCCCCC-CCCEECEEEEEEECCCCCEEEEEEEHHHHHHHHHHHHHHCCCCHHHHCC--------CCCCCCCC----------------CCCEEEC >P1;d3e3ua- ------------CCC-CEECCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEEECC-----CCCCC------CCC--CEEEEEEEEEEECCCCCCCCCCCCCEEECCCCC-CCEE-ECCCCCEEEEEEECCCCCEEEEEEEHHHHHHHHHHHHHHCCCCHHHHC-C-HHH---HHHHHHHHHHHCCCCCCCEECCCCCCCCCCC >P1;d3g5ka1 ------------C-C-CCCCCCCHHHCCCCCCCC--HHHCCCHHHHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEEEEC-HHHHHCCCHHHHHHHCCCCEEEEEEEEEEEEEEE--EEEEE---EEECCCCCC-CEEE-EEEEEEEEEEEEECCCCCEEEEEEEHHHHHHHHHHHHHHCCCCHHHCC-C-HHHCEECCCCCCCC----------------------- >P1;d3ocaa- ------------CCC-CCCCCCC-CCCCCCCCCC------CCCCCC-CHHHHC-CCCCC-------------CCEEEHHHHCCCCCEEEEEECC--------CCCCCCCCCCCEEEEEEEEEEEEEECC--CEEEE---EECCCCCC-CCCE-EEEEECCEEEEEECCCCCEEEEEECHHHHHHHHHHHHHHCCCCHHHHCC---------------HHHHHHHHHHC--CCC-------- >P1;d4dr8a- CCCCCCCCCCCCCCC-CCCCCCCHHHHCCCCCCC-----CCCHHHHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEECCCC----------------CCCCCCEEEEEEEEEEEEE--EEEEE---EECCCCCC-CCCE-EEEEEEEEEEEEECCCCC--EEEECHHHHHHHHHHHHHHCCCCHHHHCC---------------HHHHHHHHHHC--CCCHHHCCCCC >P1;d4je6a1 ------------CCC-CCCCCCCHHHCCCCCCCC--HHHCCC-CHHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEEEEC-HHHHCCCC-CHHHHHCC-CEEEEEEEEEEEEECC--CCEEE---EEEEECCEE-EEEE-EEEEECEEEEEEECCCCCEEEEEEEHHHHHHHHHHHHHHCCCCHHHCC-C-CCCCEEHHHCCCCCCC----------------CCCCC >P1;d5hgwa1 ------------CCC-CCCCCCCHHHHCCCCCCC-----CCCHHHHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEEEECCCCCCC----------CCCCEEEEEEEEEEEEECC--CCEEE---EEECCCCCC-CEEE-EEEEECEEEEEEECCCCCEEEEEEEHHHHHHHHHHHHHHCCCCHHHCCCC-CCCEEEHHHHCC-----------------------CC >P1;d6jf8a- -----------CCCC-CCCCCCCHHHHCCCCCCCHH--HCCCHHHHHHHHHHHHHHHH------------CCCCEEEHHHHCCCCCEEEECCC----------CCCCCCCCCCCCCEEEEEEEEEECCC--CCC-----EEEECCEE-EEEE-ECCCCC-CEEEEECCCC--CEEECCCCCCC-HHHHHHHHCCCCHHHHCC--------------------------------------- PSA >P1;d1rl4a- ----------------801314471046507508-----81689067206701610593------------91600000006324000007-------------------------700010516843b--84544---51403004-b060-4050134030103216185475616b86001001011004030003402--------a9238806650562578-------------- >P1;d1v3ya- ------------734-814113181035606509-----819-9066204201400173------------63400000000424100000357------------7816----54110010723455---6754---4510-3004-906185010064030513125167652418970010001000003030003405--673---368037726a406605761------------ >P1;d1ws0a- -----------4562-9025574a2065609609-----91499036106001400463------------a240000000443410000107b------------9--3----33110000614457---a624---360102006-8460-2040142030401528183362607661001000002005040027406543b----------------------------------- >P1;d1xeoa- ------------843-900304395035706609-----80666026104300500244------------9240000000421210000021a--------837---------75200030741867---59305---70302002-8172-6070055020503347276242706b42000021011005040002216---------------87526403650--3735779---- >P1;d2os0a1 -----------5041950133b4820457087063----904890461054015005202588428538056120000000544410000205--------------------723200000623753b--5300129-1060000659160-1030305000003226076453706532000001012004040013307--------99736639----------------bb0432a >P1;d3e3ua- ------------833-40300116103760760825b97703a8098206102500530------------5150000000034320000205-----65247------a07--5330002082615b63aa305597251101000-4230-103009203043224906815031694001000100000406001520-5-861---17808822883a1466b33030a749222c6 >P1;d3g5ka1 ------------b-2-81054b482039607508--89304486057106501610585------------7120000000336220000104-691068167a428715084072310020828335--78534---131102007-7340-203042102032222708824161511100000101100602002441-6-7943445786a8be----------------------- >P1;d3ocaa- ------------863-b011074-508770860a------08a903-106302-00a44-------------4500000001324100005068--------309649a26454062000107337419--65261---50102004-8161-5050211000402347277350500040001000002005012006417---------------7a535703950--7bd-------- >P1;d4dr8a- 4937080a265b322-913506493016507709-----80439004102300200103------------815000000022642000012ab----------------8874812000007336345--96564---60101004-4060-405024304041422828--53708a53010000011007020000306---------------98514620774--a164911584c >P1;d4je6a1 ------------b32-a1284a562037608707--4b5075-7036105000600471------------5230000000426110000103-78217816-a4296161-51a2200000817333--96311---01010301a-6430-005032202041122818826160501100000101200406002942-2-8804154a53a6817b----------------c0636 >P1;d5hgwa1 ------------a34-91173b27505770861a-----25588036107102600683------------5000000000136320000019908214----------b057056000020805436--88355---530001005-9200-00502140400042262741434066110100010200030300143094-594246198246-----------------------d2 >P1;d6jf8a- -----------5742-8003595820567066079c--12539504600520320056------------34000000000433210000004----------317216a0552b2220020704754b--96c-----62000005-b533-809113-0405045170--54450673100-00101000403001643e--------------------------------------- Translating the sequences ----------------CCCCCCCHHH*CCCCCCC-----CCC**HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE*-------------------------*EEEEEEEEE***--C*EE*---EECCCCCC-C**E-E**E*C*EEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C*--------*****************-------------- ------------CCC-CCCCCCCHHH*CCCCCCC-----CCC-*HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE**C*------------****----**EEEEEEEEEE**---C*EE---*EEC-CCCC-C**E*E**E*CEEEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C*--***---*******************------------ -----------*CCC-CCCCCCCHHH*CCCCCCC-----CCC**HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE**C*------------*--*----**EEEEEEEEEE**---**EE---*EECCCCCC-C**E-E**E**EEEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*******----------------------------------- ------------CCC-CCCCCCCHHH*CCCCCCC-----CCC**HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE**C*--------***---------**EEEEEEEEEE**---C****---EECCCCCC-C**E-E****CEEEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C*---------------***********--*******---- -----------*CC***CCCCCCHHH*CCCCCCC*----CCC**HHHHHHHHHHHHHH*************CCCEEEHHHHCCCCCEEEE**C--------------------***EEEEEEEEEE***--C*EE***-**CCCCCC*C***-***E*CEEEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C*--------********----------------******* ------------CCC-C**CCCCHHH*CCCCCCC*****CCC**HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE**C-----*****------***--**EEEEEEEEEE*****C*******EE*CCCCC-C**E-E****CEEEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C-*-***---******************************* ------------C-C-CCCCCCCHHH*CCCCCCC--***CCC**HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE**C-**********************EEEEEEEEEE**--***EE---*EECCCCCC-C**E-E**E**EEEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C-*-**************----------------------- ------------CCC-CCCCCCC-***CCCCCCC------CC****-*HHHH*-****C-------------CCEEEHHHHCCCCCEEEE**C*--------**************EEEEEEEEEE***--C*EE*---EECCCCCC-C**E-E**E*C*EEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C*---------------***********--***-------- ************CCC-CCCCCCCHHH*CCCCCCC-----CCC**HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE**C*----------------******EEEEEEEEEE***--**EE*---EECCCCCC-C**E-E**E**EEEEEEECCCCC--EEEE*HHHHHHHHHHHHHHCCCCHHH*C*---------------***********--*********** ------------CCC-CCCCCCCHHH*CCCCCCC--***CCC-*HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE**C-********-********-****EEEEEEEEEE**--*C*EE---*EE**CC**-***E-E**E*CEEEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C-*-****************----------------***** ------------CCC-CCCCCCCHHH*CCCCCCC-----CCC**HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE**C******----------*******EEEEEEEEEE**--*C*EE---*EECCCCCC-C**E-E**E*CEEEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C**-************-----------------------** -----------*CCC-CCCCCCCHHH*CCCCCCC**--*CCC**HHHHHHHHHHHHHH------------*CCCEEEHHHHCCCCCEEEE**C----------*************EEEEEEEEEE***--C**-----EE**CC**-***E-E****C-*EEEEECCCC--*EEE*******-HHHHHHHHCCCCHHH*C*--------------------------------------- 56420.tem _________________________________ -----------*CCC-CCCCCCCHHH*CCCCCCC----*CCC**HHHHHHHHHHHHHHC------------CCCEEEHHHHCCCCCEEEE**C*----*---**************EEEEEEEEEE***-*C*EE*--*EECCCCCC-C**E-E**E*CEEEEEEECCCCCEEEEEE*HHHHHHHHHHHHHHCCCCHHH*C**-***---******************--***-******* Structural block scores 0 10 - 4.8 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 5.0 75.0 75.0 75.0 12 14 C 4.7 H 75.0 4.7 4.3 5.0 1.7 4.7 29.5 5.7 2.3 5.5 5.8 4.3 16 22 C 4.9 H 3.0 2.7 4.6 2.7 3.9 1.3 4.8 3.5 4.0 5.9 4.9 4.3 23 25 H 4.8 H 2.7 3.0 4.2 4.7 3.3 2.3 3.3 26.7 4.0 2.7 4.0 3.3 27 33 C 5.0 H 4.4 4.4 5.0 4.7 4.7 4.9 5.0 5.5 4.9 5.0 5.6 4.6 34 37 - 4.4 M 75.0 75.0 75.0 75.0 57.0 6.9 41.8 75.0 75.0 41.4 75.0 42.9 39 41 C 4.9 H 5.0 6.0 4.7 4.7 4.3 3.3 2.7 27.7 4.0 4.0 4.0 3.3 42 43 * 1.4 P 8.5 42.0 9.0 6.0 8.5 9.2 7.0 9.8 6.0 41.0 8.0 7.0 44 57 H 4.9 H 3.6 2.4 2.2 1.9 2.4 2.9 3.2 12.8 0.9 2.3 2.9 2.4 59 70 - 4.8 H 75.0 75.0 75.0 75.0 4.8 75.0 75.0 75.0 75.0 75.0 75.0 69.0 71 73 C 4.9 H 5.3 4.3 5.5 5.0 3.0 3.7 3.3 28.0 4.7 3.3 1.7 1.3 74 76 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 77 80 H 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 81 85 C 5.0 H 3.0 2.2 3.2 2.0 3.6 2.4 3.2 2.2 3.2 2.8 3.0 2.6 86 89 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 90 91 * 1.2 P 41.0 1.5 0.5 1.0 1.0 1.0 0.5 2.5 1.5 0.5 0.5 0.0 94 97 - 4.3 M 75.0 75.0 75.0 75.0 75.0 75.0 4.0 75.0 75.0 4.5 2.8 75.0 99 101 - 4.3 M 75.0 75.0 75.0 75.0 75.0 3.7 5.0 75.0 75.0 5.0 75.0 75.0 102 115 * 3.2 M 75.0 45.1 54.9 50.4 59.8 45.2 4.7 4.9 45.4 14.9 40.0 9.4 116 125 E 5.0 H 2.8 1.9 1.7 2.5 2.0 2.2 2.7 2.3 2.1 2.1 1.9 2.4 126 128 * 1.8 P 6.2 28.3 29.0 29.3 6.5 7.5 27.7 4.7 4.0 27.0 28.0 6.8 133 134 E 4.3 M 4.5 4.5 3.0 1.5 0.0 2.5 3.5 4.0 5.5 1.0 5.0 43.8 136 137 - 4.6 H 75.0 75.0 75.0 75.0 5.5 8.0 75.0 75.0 75.0 75.0 75.0 75.0 139 140 E 4.8 H 3.0 3.0 3.0 3.5 0.5 3.0 2.0 2.5 3.0 0.5 1.5 4.0 141 146 C 4.6 H 1.8 13.7 1.5 1.2 2.0 0.3 1.7 1.2 1.0 2.6 1.0 0.8 149 150 * 1.0 P 3.0 3.0 5.0 4.0 3.5 2.5 3.5 3.5 3.0 3.5 1.0 4.0 154 155 * 1.0 P 2.5 0.5 2.0 3.5 1.5 1.5 1.5 2.5 2.5 2.5 2.5 4.5 159 165 E 4.9 H 1.6 2.3 1.4 2.1 1.1 2.0 1.4 1.0 2.3 1.4 1.7 12.6 166 170 C 5.0 H 3.6 3.0 4.8 4.6 3.4 4.2 3.8 4.6 4.4 4.2 3.8 17.6 171 176 E 4.8 H 4.7 4.2 3.3 3.5 4.2 3.0 3.7 3.3 27.5 3.8 2.7 15.5 178 191 H 4.9 H 2.1 1.3 1.1 1.6 1.0 1.1 0.4 0.5 1.5 0.4 0.9 6.3 192 195 C 5.0 H 1.8 1.5 2.2 2.2 2.0 2.5 2.0 2.0 2.2 2.5 1.5 1.8 196 198 H 5.0 H 1.0 1.0 3.0 0.7 1.3 2.0 2.0 2.0 0.0 3.7 1.7 2.3 201 202 * 3.0 P 38.5 40.0 5.5 40.5 41.0 40.0 40.5 41.0 40.5 38.5 6.5 44.8 204 206 * 3.5 M 75.0 5.3 29.8 75.0 75.0 5.0 6.7 75.0 75.0 5.3 6.0 75.0 207 209 - 4.3 M 75.0 75.0 75.0 75.0 75.0 75.0 3.7 75.0 75.0 3.3 4.0 75.0 210 227 * 3.2 M 9.2 4.8 75.0 31.7 44.6 5.4 45.6 32.2 32.1 37.0 51.7 75.0 228 229 - 4.7 H 75.0 38.0 75.0 75.0 75.0 1.5 75.0 75.0 75.0 75.0 75.0 75.0 230 232 * 4.0 M 75.0 75.0 75.0 4.3 75.0 4.5 75.0 10.7 5.8 75.0 75.0 75.0 234 240 * 3.9 M 75.0 75.0 75.0 46.1 6.1 5.4 75.0 75.0 5.8 25.4 55.8 75.0 >>>>>>