Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1f8ya- -CCCCEEEECCC-C-----CHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCHHHCCCCCCHHHHH-CHHHHHHHHHHHHHHHHCCCEEEEECCHH---HCC--------------------------------------------------HHHHHHHHHHHHCC-CEEEEEECHHHCCC-------------------------------------------CCCHHHHHHC----CEEE---EHHHCCCCCCCCCCCCCCC-CCCC >P1;d1isia- -----CCEECCCC----CHHHHHHHHHHHHHHHCCHHH--C-C--CCHHHHHHHHHHHH-CCCCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCHHHHHHHHCCCCCCEEHHHCHHHHCCCCCCCCCCCCCCCCCCCEECCC-CCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEECCCC-CCCCCCCCHHHHHCHHHCCHHHEEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCHHHHHHHHCCCC--CCHHHCCC >P1;d1s2la- CCCEEEEEECCC-C------CCC-CCCC--CCCCC-CCCEE--EEECCCCCCCCCCCCCCC---CC-CHHHHHHHHHHHHHHHHHCCEEEEEEECC---CCC--------------------------------------------------HHHHHHHHHHHHCC-CCEEEEEECC-----------------------------------------------CCCHHHHCCC----CEECCCCCHHHHHCCCCC-CCCCCCCCCCCC >P1;d1t1ja1 --CCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCC----EEEEHHHHHHHHHCCCCCCC----HHHHHHHHHHHHHHHHHHCCEEEECCCC--CHHHC--------------------------------------------------HHHHHHHHHHHHCC-CEEEE---HHHHHHHC-------------------------------------------------------------------------------------- >P1;d2f62a2 ---CCEEEECHHHH-----CCCCHHHHHHHHHHHHCC-----CCCCCCCCCCCC----------------CHHHHHHHHHC-CCCCCEEEEECCCCCCCCCC--------------------------------------------------HHHHHHHHHHHHCC-C-CEEECCCCCCCCCCCCCCCC-------------------------CCCCCCCCCCCCCC-CCCCC-----CEEC--CHHHHHHHHHHHCCC--------- >P1;d3f6ya- CCCCCCCEECCCC----CHHHHHHHHHHHHHHHC-CCCC---C--CCHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHCCCCCCHHHCCCCCCCC---CHHHH--HHCCCHHHCHHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCC--CCCCCCCHHHHCCHHHCCCCCEEEEEEEEECC-C----CHHHCHHHHHHHHHHHHCCCEEEEEEEC---------------------- >P1;d3i9la- --------CCCCC----CHHHHHHHHHHHHHHHCCCCCCCCCC--CCHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCCCCCCEEEEECCHHHHHHHHCCCCCCCCHHHCHHHHHHCCCCCCCCCCCCCCCCCCCCCH-HHCCHHHHCHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCCCCHHHHHCHHHCC-CCEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHCC--CCHHHCCC >P1;d6evsa- ---CEEEEECCC-C-----CHHHHHHHHHHHHHHHHCCC----EEECHHHCCCC------CCCCC--CHHHHHHHHHHHHHHHHHCCEEEEECCCC---CCC--------------------------------------------------HHHHHHHHHHHHCC-CCEEEECC---CCC-------------------------------------------CCCHHHHCCC----CEEEC--CHHHHHHCCCCCCCCCCCC----- PSA >P1;d1f8ya- -95320000001-6-----4a405601840281066072032970110184046923366567269-4a816730664225004604000000005---322--------------------------------------------------b906510720663a-11000000470144-------------------------------------------5046813620----3100---3076047260262757709-3626 >P1;d1isia- -----16370017----805740292068038307693--4-a--17164005003400-7340260637206600740508055440003141382026004616411010000001001501001469698215920036-712730022002110020004101010100020027-9000367740043103203494054010000150646631115592076027305629080504522740163117857--a375079a >P1;d1s2la- 457030000014-8------b61-8208--04208-08103--5230056b3907a15aba---a1-46725733665226006504000000116---853--------------------------------------------------ba046109403849-2300000048-----------------------------------------------a056800860----201040552840281602-167580973c48 >P1;d1t1ja1 --62400000024486a7314701640381153067391----50001024004516829838----5a51996146506620660610000129--51792--------------------------------------------------a507403850678a-35002---16606820-------------------------------------------------------------------------------------- >P1;d2f62a2 ---15000000035-----595067208804730874-----b0130134a44a----------------89963565115-046031000101228a3700--------------------------------------------------a903510920683a-2-00000724554602864429-------------------------69881426610075-13663-----8106--406400840275477--------- >P1;d3f6ya- b858714080049----80373047205610783-7707---7--070640161036002524026062930760073070a0346501010228---5b838--8612202510003003903000378458014a10035861247002200010004300430144010102064a--50015711003000420337406101010217-a----531738205404520683a080306137---------------------- >P1;d3i9la- --------48028----7058303930640465515a20430a--371750182025000537237164810760083010a025530012290482016105607410011000002004902000268a50135970376-96155503100302022100720404000001004694500377040030003303-b6063030000020b584215256b1047027505749040405222860253118966--b174079b >P1;d6evsa- ---340000002-6-----7a604720540060038291----70000253428------53967--48627352673227304305000001061---a42--------------------------------------------------aa04610a205839-13000001---216-------------------------------------------a088810720----30104--6186039060972474428----- Translating the sequences -******EECCC-*-----*HHHHHHHHHHHHH***CCC*******CHHH**********C*****-CHHHHHHHHHHH******CCEEEE*CC**---***--------------------------------------------------HHHHHHHHHHHHCC-**EEEE*****C**-------------------------------------------***HHHH***----C*EE---**HH********CC*****-**** -----**EECCC*----***HHHHHHHHHHHHH*****--*-*--*CHHH*********-C******CHHHHHHHHHHH******CCEEEE*CC************************************************-*********HHHHHHHHHHHHCC***EEEE*****C-***********************************************HHHH*******C*EE*****HH********CC--******** *******EECCC-*------***-****--*****-CCC**--***C*************C---**-CHHHHHHHHHHH******CCEEEE*****---***--------------------------------------------------HHHHHHHHHHHHCC-**EEEE****-----------------------------------------------***HHHH***----C*E******HH*******-CC********** --*****EECCC********HHHHHHHHHHHHH***CCC----****HHH**********C**----*HHHHHHHHHHH******CCEEEE*CC*--*****--------------------------------------------------HHHHHHHHHHHHCC-**EEE---********-------------------------------------------------------------------------------------- ---****EEC****-----****HHHHHHHHHH***C-----****C*******----------------*HHHHHHHH**-***CCEEEE*CC********--------------------------------------------------HHHHHHHHHHHHCC-*-*EEE*****C**********-------------------------**************-*****-----*EE*--**HH********CC*--------- *******EECCC*----***HHHHHHHHHHHHH*-*CCC---*--*CHHH**********C******CHHHHHHHHHH**************CC*---*****--***********************************************HHHHHHHHHHHH*C***EEEE*****C--********************************-*----********HHHH*******C*EE*****---------------------- --------*CCC*----***HHHHHHHHHHHHH***CCC****--*CHHH**********C******C****HHHHHHH******CCEEEE*CC************************************************-*********HHHHHHHHHHHH*C***EEEE*****C********************-***************************HHHH*******C*EE*****HH********CC--******** ---****EECCC-*-----*HHHHHHHHHHHHH***CCC----***CHHH****------C****--CHHHHHHHHHHH******CCEEEE*CC**---***--------------------------------------------------HHHHHHHHHHHHCC-**EEEE**---C**-------------------------------------------***HHHH***----C*EE*--**HH********CC*****----- 52309.tem _________________________________ -******EECCC**---***HHHHHHHHHHHHH***CCC**-****CHHH**********C******CHHHHHHHHHHH******CCEEEE*CC*********--*************************************-*********HHHHHHHHHHHHCC***EEEE*****C********************-*************-*************HHHH*******C*EE*****HH********CC********** Structural block scores 1 6 * 2.5 P 3.2 51.2 2.5 14.5 26.0 5.5 75.0 26.2 7 8 E 4.7 H 0.0 5.0 0.0 0.0 0.0 4.0 39.5 0.0 9 11 C 4.8 H 0.3 0.3 1.7 0.7 0.0 1.3 3.3 0.7 12 13 * 2.9 P 40.5 41.0 41.5 4.0 4.0 42.0 41.5 40.5 14 16 - 4.7 H 75.0 75.0 75.0 8.2 75.0 75.0 75.0 75.0 17 19 * 2.8 P 51.3 4.3 75.0 3.7 51.7 3.7 4.0 52.3 20 32 H 4.6 H 3.8 4.0 20.6 3.3 4.5 3.8 3.9 3.4 33 35 * 1.5 P 4.0 4.3 27.7 4.3 5.0 28.3 3.7 3.7 36 38 C 4.5 M 3.0 29.0 3.0 4.3 51.3 4.7 4.2 4.0 39 40 * 3.6 M 1.5 39.5 1.5 75.0 75.0 75.0 3.5 75.0 42 45 * 2.4 P 4.2 40.4 21.2 20.0 3.9 39.2 40.9 20.5 47 49 H 4.3 M 3.0 3.7 3.7 1.0 2.7 3.3 4.3 2.3 50 59 * 1.8 P 4.3 8.7 6.9 3.9 47.9 1.9 1.8 46.7 61 66 * 2.8 P 17.5 2.5 51.9 51.8 75.0 2.3 3.8 29.2 68 78 H 4.8 H 4.9 3.2 4.7 5.1 18.4 3.4 3.4 4.6 79 84 * 1.1 P 2.8 3.8 3.2 4.3 15.2 4.1 3.1 3.2 85 86 C 4.7 H 2.0 4.0 2.0 3.0 1.5 5.5 4.0 2.5 87 90 E 4.7 H 0.0 0.8 0.0 0.2 0.2 0.5 0.8 0.0 92 93 C 4.7 H 0.0 2.5 0.5 1.5 0.5 2.0 4.5 0.5 94 102 * 2.3 P 34.7 2.8 35.9 28.7 11.9 29.8 3.0 35.9 103 104 - 4.3 M 75.0 3.5 75.0 75.0 75.0 75.0 3.0 75.0 105 141 * 3.9 M 75.0 2.5 75.0 75.0 75.0 2.8 2.8 75.0 143 151 * 3.9 M 75.0 2.7 75.0 75.0 75.0 2.7 3.9 75.0 152 163 H 5.0 H 4.5 0.8 4.8 4.6 4.5 1.0 1.4 4.8 164 165 C 4.7 H 6.8 0.5 6.5 9.2 6.8 1.5 1.0 6.0 166 168 * 2.2 P 25.7 0.7 26.7 27.7 50.7 3.0 2.7 26.3 169 172 E 4.8 H 0.0 0.2 0.0 19.2 0.0 0.5 0.0 0.0 173 177 * 1.8 P 2.2 0.8 17.4 32.6 3.6 2.4 1.0 45.2 179 198 * 3.5 M 67.9 6.3 75.0 60.8 39.8 9.1 2.5 67.8 200 212 * 3.9 M 75.0 2.2 75.0 75.0 75.0 2.3 2.4 75.0 214 226 * 3.2 M 58.4 3.8 58.9 75.0 4.5 26.1 4.8 59.1 227 230 H 4.4 M 4.5 3.8 3.5 75.0 21.0 3.2 3.2 4.2 231 237 * 3.0 P 44.0 4.6 44.9 75.0 45.0 4.9 5.3 44.1 240 241 E 4.6 H 0.0 2.5 0.5 75.0 0.5 1.5 2.0 0.5 242 246 * 2.5 P 45.6 2.6 3.2 75.0 32.0 3.4 2.2 32.2 247 248 H 4.5 M 6.5 5.5 6.0 75.0 5.0 75.0 7.0 7.0 249 256 * 2.4 P 3.4 3.4 11.8 75.0 3.2 75.0 3.6 4.2 257 258 C 4.5 M 4.5 6.0 3.5 75.0 5.5 75.0 6.0 3.0 259 268 * 3.3 M 12.0 20.2 6.3 75.0 68.2 75.0 20.1 40.0 >>>>>>