Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1jw9b- CCCCHHHHHHCHHHHCCC---------CC--HHHHHHHHHH-CEEEEECCCHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHCCCCCCHHHCCCCHHHHHHHHHHHHCCCCEEEEECCC--CCHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHHH------------HCCCEEEEEEECCEEEEEEECCCCCCCCHHHHHCCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCC--HHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCC----------------------------------------------- >P1;d1ngva- ---CHHHHHHCHHHHHHHH-------------HHHHHHHHH-CEEEECCCCHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHCCCCCHHHCCCCHHHHHHHHHHCCCCCCCCCEECCCHHHHHHCCHHHHHHCCEEEEECCCHHHHHHHHHHHHH------------CCCCEEEEEEECCEEEEEEECC--CEEECCCCCC--CCCCCCCCCCCCHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCEEECCCCHHHHHCCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC-EEEEECCCCEEEEECC--------------------------------------------------------- >P1;d1ngvb- -----CCCCCCHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCEEEEECCCCCHHHHHHHHHCCCCCEEEEECCCCCCHHHHHCCCCCCHHHCCCCHHHHHHHHHHHHCCCCEEEEECCC--HHH-CCHHHHCCCCEEEECCCCHHHHHHHHHHHHHCCCEECCEECHHHCCCEEEEEEECCEEEEEEECCC-CCCCHHHHHHHCCCCCCCC--------HHHHHH----------CCCCHHHHHHHHHHCHHHH------CCCCCC--------------------------------------CCCCCCCC------------------HHHHHHHHHHHHHHHHHCCCC----------------------------------------------------------------------------------------------------------------------------------------------------CCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCEEEEECCCCCCCCCCCCCCCEECCCCCHHHHCCCCCCCCCCCCCCCCCCEECCCCCCCCCEEEE >P1;d1y8xb1 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCEECCCCCCHHHHHHHHHHCC-----CCCCCCEEEEEECCEEEEEEC----CCHHHHH--------HHHHHHHCCCHHHCCCCCCEEEEECCCCCCCEEEEEEC- PSA >P1;d1jw9b- 2a058804840693065a---------80--5591034036-050000203000010035004000130100164506891152080068923842004003620483053070613447--17896067105705000000965820430053037------------35110000405735040000107b910013010255------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------c4a16--3700740044006101110093a92124311213076754665706228a07200----------------------------------------------- >P1;d1ngva- ---9973784039117704-------------950074028-0200001010000000330051002200000067067910930800698048611040026203720930805225440550057647204604000002032901340082037------------3611000010004001000015--1020210339--b3541000252064067118705079297930340000000031185158788680556972157015204730373aa77639070043008207600800613a4057007284057078904410000200330166509810001170290404ac2167014105612760281037006610890a33884059732640041021040040210840166a5045a304720974521000100000002039639320066aa429602a304700490185090b07038810520060126134900340073004100100060220120-0200004576233118--------------------------------------------------------- >P1;d1ngvb- -----66b3017a14560368589226809248731670055140000002500010032006200120200046405891172040056804742004000620485044060332435--014-284a10560600000285230100000000200627a58147920110000217456120000300-6100000207401667726--------571037----------6056130000202332059------521389--------------------------------------a4815273------------------780041026305710884a0a----------------------------------------------------------------------------------------------------------------------------------------------------90549303410345481457005400620050012101304621800140137ab76563440833a7000024962a3b89955550392750207807169b2404055001460507 >P1;d1y8xb1 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------a16607175915055015404719-----9268105030519a8964006----8688516--------8166117450661a061324030519529a44404026- Translating the sequences **********CHHHH***---------**--***HHHHHHH-CEEEE*CCC**HHHHHHHHH**CCCEEEEECCCCCCHHHHH*CCCCCHHHCCCCHHHHHHHHHH**CCCC***EECCC--**H***HHHH**CCEEEE*CCCHHHHHHHHHHHHH------------*CCCEEEEEEECCEEEEEEECC**C***********------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*CCCC--HHHHHHHHHHHHHHHHHHHHCCCCCCCC*EEEEECCCCEEEEE*C***CC*****----------------------------------------------- ---*******CHHHH****-------------**HHHHHHH-CEEEE*CCC**HHHHHHHHH**CCCEEEEECCCCCCHHHHH*CCCCCHHHCCCCHHHHHHHHHH**CCCC***EECCC****H***HHHH**CCEEEE*CCCHHHHHHHHHHHHH------------*CCCEEEEEEECCEEEEEEECC--C*********--********************************************************************************************************************************************************************************************************************************************************************************************************************CCC**HHHHHHHHHHHHHHHHHHHHCCCCCCCC-EEEEECCCCEEEEECC--------------------------------------------------------- -----*****CHHHH*******************HHHHHHH*CEEEE*CCC**HHHHHHHHH**CCCEEEEECCCCCCHHHHH*CCCCCHHHCCCCHHHHHHHHHH**CCCC***EECCC--**H-**HHHH**CCEEEE*CCCHHHHHHHHHHHHH*************CCCEEEEEEECCEEEEEEECC*-C******************--------******----------*******************------******--------------------------------------********------------------*********************----------------------------------------------------------------------------------------------------------------------------------------------------************CCCC**HHHHHHHHHHHHHHHHHHHHCCCCCCCC*EEEE*CCCCEEEEECC***CC**************************************************** --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCC********HHHHHHHHHH**-----CCCCC*EEEEE*CC*EEEEEC----CC*****--------**************************************- 69572.tem _________________________________ ---*******CHHHH****--------**--***HHHHHHH-CEEEE*CCC**HHHHHHHHH**CCCEEEEECCCCCCHHHHH*CCCCCHHHCCCCHHHHHHHHHH**CCCC***EECCC--**H***HHHH**CCEEEE*CCCHHHHHHHHHHHHH------------*CCCEEEEEEECCEEEEEEECC*-C******************--------******----------*******************------******--------------------------------------********------------------*********************----------------------------------------------------------------------------------------------------------------------------------------------------************CCCC**HHHHHHHHHHHHHHHHHHHHCCCCCCCC*EEEEECCCCEEEEECC***CC*****--------**************************************- Structural block scores 0 2 - 4.3 M 4.2 75.0 75.0 75.0 3 9 * 2.6 P 5.3 6.7 25.2 75.0 11 14 H 4.3 M 4.5 3.5 5.6 75.0 15 18 * 2.6 P 24.1 4.5 3.5 75.0 19 26 - 4.3 M 75.0 75.0 5.8 75.0 27 28 * 3.5 M 4.0 75.0 4.0 75.0 29 30 - 4.3 M 75.0 75.0 5.5 75.0 31 33 * 2.7 P 6.3 29.7 6.3 75.0 34 40 H 4.3 M 2.4 3.0 3.1 75.0 43 46 E 4.3 M 1.2 0.5 1.0 75.0 48 50 C 4.3 M 1.7 0.7 0.7 75.0 51 52 * 2.3 P 0.0 0.0 2.5 75.0 53 61 H 4.3 M 1.0 0.7 0.7 75.0 62 63 * 2.3 P 2.0 3.0 4.0 75.0 64 66 C 4.3 M 0.3 0.7 0.3 75.0 67 71 E 4.3 M 0.8 0.4 0.8 75.0 72 77 C 4.3 M 3.7 3.2 3.2 75.0 78 82 H 4.3 M 4.8 5.2 5.2 75.0 84 88 C 4.3 M 2.8 2.8 1.8 75.0 89 91 H 4.3 M 6.3 5.7 4.7 75.0 92 95 C 4.3 M 4.2 4.8 4.2 75.0 96 105 H 4.3 M 1.9 1.8 1.6 75.0 106 107 * 2.3 P 5.5 4.5 6.5 75.0 108 111 C 4.3 M 2.0 3.0 2.0 75.0 112 114 * 2.3 P 4.3 4.3 3.0 75.0 115 116 E 4.3 M 2.0 2.0 2.5 75.0 117 119 C 4.3 M 5.0 4.3 4.0 75.0 120 121 - 4.3 M 75.0 2.5 75.0 75.0 122 123 * 2.3 P 4.0 2.5 0.5 75.0 125 127 * 2.7 P 5.0 6.0 28.3 75.0 128 131 H 4.3 M 3.5 3.2 3.9 75.0 132 133 * 2.3 P 6.0 5.0 5.5 75.0 134 135 C 4.3 M 2.5 2.0 3.0 75.0 136 139 E 4.3 M 0.0 0.0 0.0 75.0 141 143 C 4.3 M 5.0 1.7 5.0 75.0 144 156 H 4.3 M 3.1 3.0 0.6 75.0 157 168 - 4.3 M 75.0 75.0 5.0 75.0 170 172 C 4.3 M 2.3 2.7 0.7 75.0 173 179 E 4.3 M 1.3 0.1 1.4 75.0 180 181 C 4.3 M 5.0 2.0 4.5 75.0 182 188 E 4.3 M 1.3 0.1 1.3 75.0 189 190 C 4.3 M 0.5 3.0 1.5 75.0 194 211 * 2.9 P 30.2 10.8 2.7 75.0 212 219 - 4.3 M 75.0 2.4 75.0 75.0 220 225 * 3.5 M 75.0 5.0 3.8 75.0 226 235 - 4.3 M 75.0 5.1 75.0 75.0 236 254 * 3.5 M 75.0 2.1 2.5 75.0 255 260 - 4.3 M 75.0 6.2 75.0 75.0 261 266 * 3.5 M 75.0 5.7 4.7 75.0 267 304 - 4.3 M 75.0 3.8 75.0 75.0 305 312 * 3.5 M 75.0 3.1 5.1 75.0 313 330 - 4.3 M 75.0 4.3 75.0 75.0 331 351 * 3.5 M 75.0 2.1 4.0 75.0 352 499 - 4.3 M 75.0 3.5 75.0 75.0 500 511 * 3.4 M 69.8 3.3 3.4 75.0 512 515 C 4.8 H 5.4 2.2 5.2 5.9 516 517 * 2.3 P 75.0 2.0 2.5 3.5 518 537 H 4.6 H 1.9 1.8 1.9 10.9 538 545 C 4.7 H 5.1 1.6 3.0 31.4 547 551 E 4.9 H 1.6 0.4 1.8 2.6 552 555 C 4.7 H 5.0 4.0 9.0 7.1 556 560 E 5.0 H 5.2 3.0 4.8 3.8 561 562 C 4.3 M 3.5 4.5 2.0 40.5 563 565 * 3.5 M 3.3 75.0 4.7 75.0 566 567 C 4.3 M 9.2 75.0 8.8 7.0 568 572 * 2.3 P 1.8 75.0 0.4 5.6 573 580 - 4.3 M 75.0 75.0 6.8 75.0 581 618 * 3.5 M 75.0 75.0 4.0 3.9 >>>>>>