Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1nmoa- ----CHHHHHHHHHHHCCCCCC-CCCCCCEEEECCCC--CCCEEEEEEECCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCC--C-CHHHHHHHHHCCCEEEECCHHHHHCCCCCHHHHHHHHHCEE-CC------------------------------------------------------------------------------------------------------EEECCEEEEEEE-EECHHHHHHHHHHHHCC-CCEEECCCCCC--CEEEEEECCCCCH--HHHHHHHHHCCCEEEECCCCHHHHHHHHHCCCEEEECCHHHHCCHHHHHHHHHHHHHC-----CCEEEECCCCCCC---- >P1;d2fywa1 ----CHHHHHHHHHHHCCHHHC-C-CCCCEEEEC-CCCCCCCEEC-CCCCCHHHHHHHHHCCCCEEEECCCCCCC-CCCCCCCCCHHHHHHHHHHHCCCEEEECCHHHHHCCC-CHHHHHHC-CCCEEEEEEEEEEC------------------------------------------------------------------------------------------------CEEEEEEEEEE-EEEHHHHHHHHHHHCCCCCCCCCCCCCHHHCEEEEEEEECCCCH--HHHHHHHHCCCCEEEECCCCHHHHHCC-CCCCEEECCCHH-HHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCC >P1;d2gx8a1 --CCCHHHHHHHHHHHCCHHHCCC-CCCCEEEEC-CCCCCCCEEEEECCCCHHHHHHHHHHCCCEEEECCCCCCC-CCCCCCCCCHHHHHHHHHHHCCCEEEECCHHHHHCCC-CHHHHHHHHCCCEEEEEEEEEEEEEEEEEEEEECHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEEEEEEEHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEEEEEEEEEEEEEEEEEHHHHHHHHHHHCCCCCCEEECC---CCCEEEEEEEEEEECH--HHHHHHHHCCCCEEEEECCCHHHHHHHHHHCCEEEECCHH-HHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCC >P1;d2nyda1 ---CCHHHHHHHHHHHCCHHHCCC-CCCCEEEEC-CCCCCCCCEEEECCCCHHHHHHHHHHCCCEEEECCCCCCC-CCCCCCC-CCHHHHHHHHHHCCCEEEECCHHHHCCCC-CHHHHHHHHCCCEEEEECCE-EEEEEEEEEC----------------------------------------------------EEECCCHHHHCCCC---------CCCEEEEEEEEEE-EECCEEEEEEEEEEHHHHHHHHHHHCCCCCCEEECC---CCCEEEEEEECCCCCC--CCHHHHHHCCCCEEEECCCCHHHHHHHHHCCCCEEECCHH-HHHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCCCCCCC >P1;d2yyba- ---CCHHHHHHHHHHHCCHHHCCCCCCCCEEEECCCC--CCCCEEEEEECCHHHHHHHHHCCCCEEEEEECCCC-CCCCCCC--HHHHHHHHHHHHCCCEEEECCHHHHHCCCCCHHHHHHHCCCCCCCC------------------------------------------------------------------------------------------------------CCCCCCCCCCCC-CCCCCCHHHHHHHCCCC-CCEEEE-CCCC--CCCCEEEECCCCH--HHHHHC---CCCEEEECCCCHHHHHHHHHCCCEEEECCHHHHCCHHHHHHHHHHHHHH-----CCCEEECCCCCCC---- >P1;d3wsfa1 CCCEEHHHHHHHHHHHCCHHHCCC-CCCCEEEECCCCCCEECEEEEECCCCHHHHHHHHHHCCCEEEECCCCCCC-CCCCCC--HHHHHHHHHHHHCCCEEEECCHHHHHCCC-CHHHHHHHHCCCEEEEECCC----------------------------------------------------------------------------------------------------CCCCEEEEEC--CCHHHHHHHHHHHCC-CCCEEECCCCCC--CCEEEEEEEEECCCHHHHHHHHC-CCCEEEEECCCHHHHHHHHHHCCEEEECCHHHHHHHHHHHHHHHHHHHC-----CCEEEECCC-------- PSA >P1;d1nmoa- ----507602640373090b93-b0705001017146--9063000004044500630462a0100000200337b478758--d-26731720665600000011000318600002200830707-4a------------------------------------------------------------------------------------------------------504820120407-33408601750473093-8052108503a--5054000100301--a304200738020000043498025105844000000021000120040006104852-----b150512337698---- >P1;d2fywa1 ----603600810282024830-a-c23202118-5188808200-00204770081038480300000200267-838466695730500230774a000000330000098-00010006-07079152046328------------------------------------------------------------------------------------------------a200000040a-52305502540494091930812789813757052000001501--821630383903000005079822450-829001000842-0042016400730471376591b0502418061368759 >P1;d2gx8a1 --704065007102620256004b-804102116-6082705200000303380052039390300000200269-81a4565979504103306749000000210000075-0002100730705a181015232250120003025830860272006050065bb8455172569344555aa6565720302010238339601940492016b907351572b7537420001004088523046016302920a1a1061248---7a56052000001502--820830493804000005077722550673a020000431-00230182036202630676828050300837117794b >P1;d2nyda1 ---1404602910572021a104b-604112002-67848060000004034700500382a0100000200249-a4a5476-9a815104306749000000110000027-00020006408058080113-4453113045----------------------------------------------------7705774397349b---------8a46055346609-202000021695330560073048409055072117---4944044000000401--a40460473504000005088842550476a000000231-0020018403820570096591a180400828117793c >P1;d2yyba- ---2214501720372052761760607012016256--50730000030348004502849000000020032-b691758--8525622500772400000012000205600000200560705815------------------------------------------------------------------------------------------------------614500003021-661606006401721a7-605324-1367--5043000100500--c20470---60300000335a7148403844000000420300110042005304752-----80522105165c8---- >P1;d3wsfa1 87514055018302810449403a-b15003013a93625071000004052900550484a0300000210388-839958--a7166116106648000000200000087-0002000810a05846502b----------------------------------------------------------------------------------------------------6320111305--330760173047504-7a072030590a--66050000005104591064008-3030000050877044104734000010425100010055027404740-----804031031-------- Translating the sequences ----CHHHHHHHHHHHCC***C-C*CCCCEEEEC*CC--CCCEEEEE**CCHHHHHHHHH*CCCEEEE**CCCCC*CCCCCC--C-*HHHHHHHHHCCCEEEECCHHHHHCCC*CHHHHHHHH*C*E-**------------------------------------------------------------------------------------------------------**E*C*EEEEEE-EE*HHHHHHHHHHH*CC-CCEEECCCC*C--*EEEEEE*CCCCH--HHHHHHHH*CCCEEEECCCCHHHHHHHHHCCCEEEECCHH*H**HHHHHHHHHHHHH*-----CCEEEECCCCCCC---- ----CHHHHHHHHHHHCCHHHC-C-CCCCEEEEC-CCCCCCCEE*-*CCCCHHHHHHHHH*CCCEEEECCCCCCC-CCCCCC**CHHHHHHHHHHHCCCEEEECCHHHHHCCC-CHHHHHH*-CCCEEEEE******------------------------------------------------------------------------------------------------*E***EEEEEE-EE*HHHHHHHHHHHCCCCCC***CCCC*****EEEEEEECCCCH--HHHHHHHH*CCCEEEECCCCHHHHH**-*CCCEEE*CCHH-HHHHHHHHHHHHHHHHH*****CCEE**CCCCCCC**** --**CHHHHHHHHHHHCCHHHCCC-CCCCEEEEC-CCCCCCCEEEEECCCCHHHHHHHHH*CCCEEEECCCCCCC-CCCCCC**CHHHHHHHHHHHCCCEEEECCHHHHHCCC-CHHHHHHHHCCCEEEEE*******************************************************************************************************E***EEEEEE*EE*HHHHHHHHHHHCCCCCCEEECC---C***EEEEEEE***CH--HHHHHHHH*CCCEEEE*CCCHHHHHHHHH*CCEEEECCHH-HHHHHHHHHHHHHHHHH*****CCEEEECCCCCCC**** ---*CHHHHHHHHHHHCCHHHCCC-CCCCEEEEC-CCCCCCC*EEEECCCCHHHHHHHHH*CCCEEEECCCCCCC-CCCCCC*-C*HHHHHHHHHHCCCEEEECCHHHH*CCC-CHHHHHHHHCCCEEEEE***-**********----------------------------------------------------**************---------*************-E*C*EEEEEE*EE*HHHHHHHHHHHCCCCCCEEECC---C***EEEEEE*CCCC*--**HHHHHH*CCCEEEECCCCHHHHHHHHHCCC*EEECCHH-HHHHHHHHHHHHHHHHH*****CC*EEECCCCCCC**** ---*CHHHHHHHHHHHCCHHHCCC*CCCCEEEEC*CC--CCC*EEEE**CCHHHHHHHHH*CCCEEEE**CCCC-*CCCCCC--*HHHHHHHHHHHCCCEEEECCHHHHHCCC*CHHHHHHH*CCC****------------------------------------------------------------------------------------------------------****C*******-******HHHHHHH*CCC-CCEEE*-CC*C--****EEEECCCCH--HHHHH*---CCCEEEECCCCHHHHHHHHHCCCEEEECCHH*H**HHHHHHHHHHHHHH-----CC*EEECCCCCCC---- *****HHHHHHHHHHHCCHHHCCC-CCCCEEEEC*CCCC**CEEEEECCCCHHHHHHHHH*CCCEEEECCCCCCC-CCCCCC--*HHHHHHHHHHHCCCEEEECCHHHHHCCC-CHHHHHHHHCCCEEEEE***----------------------------------------------------------------------------------------------------**C*EEEEE*--**HHHHHHHHHHHCC-CCCEEECCCC*C--**EEEEEE***C***HHHHHHH*-CCCEEEE*CCCHHHHHHHHH*CCEEEECCHH*HHHHHHHHHHHHHHHH*-----CCEEEECCC-------- 102705.tem _________________________________ ---*CHHHHHHHHHHHCCHHHCCC-CCCCEEEEC*CCCCCCCEEEEECCCCHHHHHHHHH*CCCEEEECCCCCCC-CCCCCC*-CHHHHHHHHHHHCCCEEEECCHHHHHCCC-CHHHHHHHHCCCEEEEE***-**-----------------------------------------------------------------------------------------------**E*C*EEEEEE-EE*HHHHHHHHHHHCCCCCCEEECCCC*C***EEEEEEECCCCH--HHHHHHHH*CCCEEEECCCCHHHHHHHHHCCCEEEECCHH*HHHHHHHHHHHHHHHHH*****CCEEEECCCCCCC**** Structural block scores 0 2 - 4.4 M 75.0 75.0 52.3 75.0 75.0 6.7 5 15 H 5.0 H 3.5 2.7 2.6 3.3 2.9 3.0 16 17 C 5.0 H 4.5 1.0 1.0 1.0 2.5 2.0 18 20 H 4.5 M 6.8 5.0 3.7 4.2 5.0 5.7 21 23 C 4.8 H 29.8 28.5 5.2 5.2 4.7 4.5 25 28 C 5.0 H 3.0 4.9 3.2 2.8 3.2 4.4 29 32 E 5.0 H 0.5 1.0 1.0 0.8 1.0 1.0 35 41 C 4.7 H 25.0 5.4 4.0 5.6 24.7 4.6 42 46 E 4.5 M 0.6 15.4 0.4 0.0 0.6 0.2 47 50 C 4.5 M 2.0 1.5 1.5 1.8 1.5 2.2 51 59 H 5.0 H 3.1 3.8 3.3 3.0 3.4 3.7 61 63 C 5.0 H 3.8 3.7 4.0 3.8 3.0 4.5 64 67 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 68 74 C 4.7 H 2.1 2.4 2.7 2.4 11.7 3.1 76 81 C 5.0 H 6.5 5.8 5.8 6.8 6.0 7.0 85 95 H 4.9 H 10.5 3.1 3.5 4.1 3.7 3.7 96 98 C 5.0 H 3.7 4.8 4.3 4.3 2.0 4.0 99 102 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 103 104 C 5.0 H 0.5 1.5 1.0 0.5 0.5 1.0 105 109 H 4.9 H 0.8 0.6 0.2 0.2 0.8 0.0 110 112 C 5.0 H 5.0 5.7 4.0 3.0 3.7 5.0 115 122 H 4.8 H 1.9 10.2 1.6 1.5 1.6 1.4 123 125 C 4.7 H 2.3 2.3 2.3 2.7 2.3 3.5 126 130 E 4.2 M 34.3 4.8 5.1 4.2 18.8 5.6 131 133 * 2.7 P 75.0 3.3 2.0 1.7 75.0 4.5 135 136 * 3.4 M 75.0 5.0 2.5 4.0 75.0 75.0 137 231 - 4.4 M 75.0 75.0 4.0 49.9 75.0 75.0 232 233 * 2.7 P 2.5 42.8 5.5 42.0 3.5 75.0 238 243 E 4.4 M 2.3 2.4 2.2 1.5 1.0 1.8 245 246 E 4.2 M 3.0 3.5 3.5 4.0 6.0 39.0 248 258 H 4.8 H 3.7 3.5 3.0 3.4 2.9 3.6 259 264 C 4.7 H 15.8 3.7 3.8 3.2 16.6 16.1 265 267 E 4.5 M 2.7 3.7 3.0 3.3 3.3 3.0 268 271 C 4.4 M 3.2 8.0 40.5 39.5 20.8 4.2 274 276 * 2.6 P 51.7 6.3 7.2 5.7 51.7 52.0 277 283 E 4.6 H 1.4 1.0 1.0 1.1 1.1 1.6 284 287 C 4.3 M 0.8 1.5 1.5 1.0 1.2 1.5 289 290 - 4.5 M 75.0 75.0 75.0 75.0 75.0 4.5 291 298 H 4.7 H 3.3 3.9 4.2 4.4 21.9 3.5 300 302 C 5.0 H 3.3 4.0 4.0 3.0 3.0 2.0 303 306 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 307 310 C 4.8 H 2.8 3.0 3.0 3.2 2.8 3.2 311 319 H 4.8 H 4.2 12.6 4.6 4.8 5.1 3.8 320 322 C 4.7 H 2.7 3.7 4.5 5.5 2.7 2.3 323 326 E 4.8 H 0.0 0.2 0.5 0.0 0.0 0.2 327 328 C 5.0 H 0.0 4.0 2.0 1.0 2.0 2.0 329 330 H 5.0 H 1.5 3.0 2.0 2.0 1.0 3.5 332 348 H 4.8 H 1.9 2.5 2.2 2.4 2.0 2.3 349 353 * 3.4 M 75.0 5.6 5.8 6.0 75.0 75.0 354 355 C 5.0 H 6.2 5.8 4.0 5.8 4.0 4.0 356 359 E 4.5 M 2.8 2.8 2.0 3.0 2.5 2.0 360 366 C 4.7 H 5.4 3.6 3.9 3.9 5.4 43.4 367 370 * 3.4 M 75.0 7.2 7.9 7.9 75.0 75.0 >>>>>>