Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1i7qa- CCCCEEEEEEEC-CCCC-HHHHHHHHHCCC------CCEEEEEEECCCCCCEEEEEEEEEEEEEEEEECC--EEEEEECCCCHHHHHHHHHHHCCCCCEEEEECCEEEEECCCCCCCCCHHHHHCCCCCHHHHHHHHCCCC-CCC---CCCCCCEEEEEECHHHHHHCCCCCC-CCCCCCCCCEEEEEEEEEEEEECCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHCCCCCEECCEEEEEEEC---CCCHHHHHHHHHHCCCCEEEEEECC-CCEEEEEECCEEEEEECCCCEEEECCEEEEECCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEEEEECCCCCCHHHHHHHHCCCHHHCEECHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCEEEEECCCEEEEECCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC >P1;d1k0ea- --CCCCEEEEEC-CCCCHHHHHHCCCC-CC------CCCEEEECCCCCCCCCCEEEEECCCCEEEEEECC--EEEEEEC-------------------------CEEEEEC---------------CCHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECHHHHHHCCCCCCCCCCCCCCCCEEEEEECEEEEEECCCCEEEEEECC---------CHHHHHHHHHH--CCCCCCCCCEECC-CCEECCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEE--ECCHHHHHHHHHHHHCCCEEEEEECC-CCEEEEEECCCCEEEE--CCEEEECCEEEEEECC--------------------CCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCCCHHHHHHHHCCCHHHCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEECCCCCEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCC------ >P1;d1qdla- ------CEEEEEHHHCCCHHHHHHHHHHHC------CEEEEEECC-------CEEEEEECCCCCEEEC-----------CCHHHHHHCCCC-------------------------------------------------CCCCCCCC-CCCCCEEEEEECHHHHHHCCCCCCCCCCCCCCCCEEEECCCEEEEEEHHHCEEEEECCCC-------------------CCCCCCCCCCEEEEEEEEE--CCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEE--EECCHHHHHHHHHHCCCCEEEEEEEC-CEEEEEEECCEEEEEE--CCEEEECCEEEEEECCCCH------HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCCCHHHHHHHHCCCHHHCEECHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCEEEEEECCEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCC----- >P1;d2fn1a2 -----------------CCCCHHHHHHHC------CCCEEEEEC--------CCEEEEECCCEEEEECCCCCCEEEEECC-------------------------EEEEECCC--------------CHHHHHHHHHHCCCCC--------CC-CEEEEECCCHHHHHHCCCCCCC---CCCCEEEEECCEEEEEC---CCEEEEC-----------------------------------CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCC--CCCHHHHC-CCHHHCCCCEEEEEEEC-CEEEEEEECCEEEEEE--CCEEEECCEEEEEECCCC------CCCC-CHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEEEEEEEEECC-CCCHHHHHHHHCCCHHHCEECHHHHHHHHHHHCCCCCCCCCCEEEEECC--CCEEEECCCEEEECCCCEEEEEEEEECCCCCHHHHHHHHHHHHCCCHHHCC------- >P1;d2g5fa1 -------CCCCCCCCCCCHHHHHHHHHHHHC-CCCCCCEEEEEC--------CCEEEEEEEEEEEEEECC--CEEEECCC-------------------------CCCCCCCC--------------CHHHHHHHHHH-HHCC--------CCCEEEEEECHHHHCHHHCCCCCCC---CCEEEEEEEEEEEEEEC---CCCCCCCCCCCCHHHHCCC--------------------CCCCCCCCCCCCC-CCHHHHHHHHHHHHHCCCCCEEEEEEEE-CCC--CCCHHHHHHHHHCCCCCCEEEEEEEC-CEEEEEEECCEEEEECC-CCEEEECCEEEEEECCCC------HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECCEEEEEEEEEEECCCCCCHHHHHHHCCCCHHHCEECHHHHHHHHHHHC-CCCCCCCCEEEEEECCCCEEEEECCEEEEEECCEEEEEEEEEECCCCCHHHHHHHHC-CHHHCHHHCCCC----- >P1;d3bzna- ---------------CHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCC------------------------------CCCHHHHHHHCCCCCEEEEECCCCCEEEEEEEEEEEEC---------CHHHHHHHHHCCC-------CCC-CCCEEEEECCCCC-----------------CEEEEEEEEEEEEEC--CEEEEEEEEEEC--CCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEEEECCEEEEEEECCEEEEEE--CCEEEEEEEEEEEECCC------CHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCC--CCEEC-CCEEEECCCEEEEEEEEEEECC-CCCHHHHHHHHCCCCCCCEECHHHHHHHHHHHCCCCCCCCCCEEEEECCC-EEEEEECCCEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCC------ PSA >P1;d1i7qa- 418050151905-3145-1020022006a4------50000104043a42753300000100000105a5--40203033700130062039404870725539701304048178a387642032200020021017005-04a---923000000000001003613a05a-17341401000000000000021474604000000078a903640362056037407a2971556636a09081715296017105801610746406000000102040---2121200310167030010000104-30100000001004060b723010100100060045b876329750672276036490037005200710380054006ac226202526003023000000300050296030010000000000000151440021017207110000000011001131020000010000285601000000008707363006103110210030017106082 >P1;d1k0ea- --2a60633819-24650014001100-74------51000100030a0630210000040501010458--5020438-------------------------9667238---------------6200500150066291709258301000000000000001114b03770763080010000001000000174620000008---------71961362067--29559a7905055-9081207296007107402720868405000000103040--60210700250082140010000105-2400000000000104--7240001001007543--------------------a493235005200410490035105b91171464143151210300001030502aa4500200220000000000514300300030031101000000000000800100000100000a730101000000870827801610221062005104a------ >P1;d1qdla- ------a27335288025106001200363------800002033-------8301000058712406-----------71018304a519-------------------------------------------------90a61b02-31030000000001001313a06742630190030000403010000385540105091b-------------------753b2aa187070654320--16481027005500730657607000000010051--85110300410354231420000104-3010000021000105--954011201014264076b------8516812450682a71373062005114700550047a3161364330433984020002020303a724003002000010200004143002000300521010000001000039102000023000006a1000000010286072561155017404401200627----- >P1;d2fn1a2 -----------------66396025206a------573000013--------9110003322000203250660104179-------------------------8555081a--------------4017003502627407--------83-200000101000232b1a1b21---50000000004301106---a631545-----------------------------------a51b071488198028205400510668505000000007067--60601500-40371070210000105-b210000000100207--d54030100100113458------9a42-824750383a10350033007303610660069c2061556150141010000003000402-b351030023000100000050640060027007540000000000019--900000010000009620000000000460638301500401030004202------- >P1;d2g5fa1 -------9541803bc352010000008300-788722000002--------850000002300010015--2014347a-------------------------827781ab--------------80081026106-6008--------3181000000000000318155087---70300100004210404---6004a08153071187825--------------------a05b15a082718-5703720430281056850400000041-071--6020200001015514021000010a-c1200000201001054-650010102033231877------98728724750463942361051006103710681048c21614653504538520102010405127917002002100000100016053002000310-1403000000010237720100002100024ca903010003005807376006301-307401420019----- >P1;d3bzna- ---------------0b9037504640552187055655050141806199------------------------------a0700100010733000000118471000001003509---------1044016104716-------635-4000000011616-----------------703000010001158--a90400000119--820560064038108304946916a090824646241659404800640283086a805000000001010557050000034038407700000001538400000000000203--84703000010014048------78950863066048271052004101600272089307--91715-7371130230000123050505-73102200320020000001316306610883030905100000000024-200000001001056420200000000790417701710530123034002a------ Translating the sequences ************-**CC-HHHHHHHHH***------CCEEEEE***********EEEEE***EEEEE*CC--*EEEE*CC**************************EEEEC****************C*HHHHHHHH**CC-C**---*CCCCCEEEEEECHHHHHH**CCCC-CC***CCCCEEEEEE*EEEEEE***CEEEEE*************************CCCCCCCCC**CC*CCE*CCCHHHHHHHHHHHHHHHHCCCCCEE**EEEEEEE*---CC*HHHHHHHHHHCCCCEEEEEE*C-C*EEEEEECCEEEEEE**CCEEEECCEEEEE*CCCC*******HHHHHHHHHHH*CHHHHHHHHHHHHHHHHHHH**CCCCCCEEEEEEEEEECCC*EEEEEEEEEECCCCCCHHHHHHHHCCCHHHCEECHHHHHHHHHHH*CCCCCCCCCEEEEEECCCCEEEEECCCEEEEECCEEEEEEE***CCCCCHHHHHHHHHHHHHHHHHH********* --**********-**CC*HHHHH****-**------CC*EEEEC********C*EEEE****EEEEE*CC--*EEEE*C-------------------------**EEEEC---------------*C*HHHHHHHHH*CCCC******CCCCCEEEEEECHHHHHH**CCCCCCC***CCCCEEEEEE*EEEEEE***CEEEEE***---------***********--CCCCCCCCC**CC-CCE*CCCHHHHHHHHHHHHHHHHCCCCC*EEEEEEEEEE*--*CCHHHHHHHHHHH*CCCEEEEEE*C-C*EEEEEECC**EEEE--CCEEEECCEEEEEECC--------------------*C*****HHHHHHHHHHHHH*CCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCCCHHHHHHHHCCCHHHC**CHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEE**CCCEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHH*CC------ ------*********CC*HHHHHHHHHH**------C*EEEEEC*-------C*EEEEE*****EEE*-----------C***********-------------------------------------------------CCC*****-CCCCCEEEEEECHHHHHH**CCCCCCC***CCCCEEEE***EEEEEE***CEEEEE****-------------------**CCCCCCCC********E--CCHHHHHHHHHHHHHHHH*CCCCEEEEEEEEEEE*--**C*HHHHHHHHHHCCCCEEEEEEEC-CEEEEEEECCEEEEEE--CCEEEECCEEEEEECCCC*------HHHHHHHHHHH*CHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCCCHHHHHHHHCCCHHHCEECHHHHHHHHHHHCCCCCCCCC*EEEEEECCCCEEEEE*CCEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCC*----- -----------------****HHHHHHH*------*CCEEEEEC--------C*EEEEE***EEEEE*CC***EEEE*CC-------------------------*EEEEC**--------------C*HHHHHHHHH*CCCC--------CC-*EEEEEC**HHHH**CCCCCCC---CCCCEEEEE**EEEEE*---C*EEEE*-----------------------------------CC*CC**CCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEE***--*CCHHHH*-**HHHCCCCEEEEEEEC-CEEEEEEECCEEEEEE--CCEEEECCEEEEEECCCC------****-*HHHHHH*CHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEE*CCEEEEEEEEEEECC-CCCHHHHHHHHCCCHHHCEECHHHHHHHHHHHCCCCCCCCCCEEEEE*C--C*EEEECCCEEEE*CC*EEEEEEEEECCCCCHHHHHHHHHHHH***HHHCC------- -------********CC*HHHHHHHHHH***-****CCEEEEEC--------C*EEEEE***EEEEE*CC--*EEEE*CC-------------------------*****C**--------------C*HHHHHHHHH-**CC--------CCCEEEEEECHHHH*H**CCCCCCC---CC**EEEEEE*EEEEE*---C******************--------------------C**CC*CC**CCC-**HHHHHHHHHHHHHCCCCCEEEEEEEE-***--*CCHHHHHHHHH**CCCCEEEEEEEC-CEEEEEEECCEEEEE**-CCEEEECCEEEEEECCCC------*HHHHHHHHHHH*CHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEE*CCEEEEEEEEEEECCCCCCHHHHHHH*CCCHHHCEECHHHHHHHHHHHC-CCCCCCCCEEEEEECCCCEEEEECC*EEEEECCEEEEEEEEEECCCCCHHHHHHHH*-*HHH*HHHCCC*----- ---------------C**HHHHHHHHHH********CCEEEEE********------------------------------*************************EEEE*********---------*HHHHHHHHH*CC-------*CC-CC*EEEEEC****-----------------CEEEEEE*EEEEEE*--CEEEEE******--*****************CCCCCCCCC**C****E**CCHHHHHHHHHHHHHHH*CCCCCEEEEEEEEEEE****CCHHHHHHHHHHHCCCCEEEEEEE**CEEEEEEECCEEEEEE--CCEEEE**EEEEEECCC------**HHHHHHHHHHH*CHHHHHHHHHHHHHHHHHHH**CC--CCEE*-**EEEECCCEEEEEEEEEEECC-CCCHHHHHHHHCCC***CEECHHHHHHHHHHHCCCCCCCCCCEEEEE*CC-*EEEEECCCEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHH**CCC------ 56322.tem _________________________________ ------******-**CC*HHHHHHHHHH**-----*CCEEEEEC*******-C*EEEEE***EEEEE*CC--*EEEE*CC-**********-------------**EEEEC**--------------C*HHHHHHHHH*CCCC**---*CCCCCEEEEEECHHHHHH**CCCCCCC***CCCCEEEEEE*EEEEEE***CEEEEE******--*****************CCCCCCCCC**CC*CCE*CCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEE*--*CCHHHHHHHHHHHCCCCEEEEEEEC-CEEEEEEECCEEEEEE--CCEEEECCEEEEEECCCC------*HHHHHHHHHHH*CHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCCCHHHHHHHHCCCHHHCEECHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEECCCEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCC*----- Structural block scores 0 5 - 4.2 M 3.0 28.1 75.0 75.0 75.0 75.0 6 11 * 2.8 P 3.5 5.0 5.1 75.0 17.0 75.0 13 14 * 2.7 P 2.0 3.0 8.0 75.0 7.2 75.0 15 16 C 4.3 M 4.5 5.5 1.0 75.0 7.8 5.8 18 27 H 4.6 H 1.3 8.2 1.3 3.9 1.1 3.4 28 29 * 1.4 P 7.2 5.5 4.5 42.8 1.5 3.5 30 34 - 4.2 M 75.0 75.0 75.0 75.0 19.6 4.2 36 37 C 4.8 H 2.5 3.0 4.0 5.0 2.0 5.5 38 42 E 4.9 H 0.2 0.2 0.4 0.2 0.0 2.2 44 50 * 3.3 M 4.4 3.2 64.7 75.0 75.0 4.9 54 58 E 4.4 M 0.0 0.0 0.2 0.8 0.0 75.0 59 61 * 1.9 P 0.3 3.0 4.3 2.3 1.7 75.0 62 66 E 4.4 M 0.2 0.4 2.8 0.4 0.2 75.0 68 69 C 4.3 M 7.8 6.5 75.0 3.5 3.0 75.0 70 71 - 4.5 M 75.0 75.0 75.0 3.0 75.0 75.0 73 76 E 4.3 M 1.2 1.5 75.0 1.2 2.0 75.0 78 79 C 4.3 M 3.0 41.5 41.0 8.0 8.8 75.0 81 90 * 3.4 M 1.5 75.0 4.2 75.0 75.0 1.9 91 103 - 4.1 M 4.8 75.0 75.0 75.0 75.0 1.8 104 105 * 2.6 P 3.5 7.5 75.0 41.5 41.5 5.5 106 109 E 4.2 M 2.0 4.5 75.0 3.8 6.0 0.2 111 112 * 2.7 P 6.0 75.0 75.0 5.8 11.0 0.5 113 126 - 4.3 M 4.5 70.1 75.0 75.0 75.0 44.1 129 137 H 4.5 M 1.4 1.9 75.0 2.7 2.7 2.2 139 142 C 4.4 M 20.0 4.8 23.6 4.5 3.5 39.2 143 144 * 3.4 M 7.2 4.5 3.5 75.0 75.0 75.0 145 147 - 4.1 M 75.0 5.0 4.5 75.0 75.0 75.0 149 153 C 4.5 M 1.0 0.2 1.4 47.2 32.4 17.4 154 159 E 4.9 H 0.0 0.0 0.0 0.3 0.2 0.0 161 166 H 4.3 M 1.7 0.3 0.8 0.5 0.0 27.3 167 168 * 1.9 P 2.0 2.5 2.0 2.5 2.0 75.0 169 175 C 4.5 M 15.6 5.1 5.1 5.5 4.9 75.0 176 178 * 3.4 M 2.7 3.0 1.3 75.0 75.0 75.0 179 182 C 4.4 M 1.2 2.2 3.0 1.2 2.5 58.0 183 188 E 4.8 H 0.0 0.0 0.7 0.0 0.2 0.5 190 195 E 4.9 H 0.3 0.0 0.2 1.8 1.8 1.2 196 198 * 3.2 M 4.0 4.0 5.3 75.0 75.0 52.7 200 204 E 4.4 M 2.0 0.4 2.0 3.8 2.9 2.6 205 210 * 2.4 P 1.2 38.8 28.6 63.3 4.0 1.8 211 212 - 4.1 M 9.2 75.0 75.0 75.0 1.0 75.0 213 229 * 3.4 M 3.4 29.3 66.9 75.0 54.7 3.2 230 238 C 4.3 M 5.8 6.3 5.9 75.0 67.8 5.5 239 240 * 1.9 P 4.5 2.5 3.5 75.0 2.5 4.5 241 242 C 4.3 M 8.2 5.0 5.5 7.8 6.2 5.0 244 245 C 4.1 M 4.5 4.5 2.5 5.8 5.2 5.0 248 250 C 4.7 H 4.3 3.0 27.3 6.7 5.3 3.7 251 266 H 4.9 H 3.4 3.4 3.0 3.2 7.6 3.8 267 271 C 4.9 H 4.0 4.6 5.0 4.8 4.6 5.9 272 282 E 4.7 H 0.6 0.7 0.5 1.2 7.9 0.2 284 285 - 4.5 M 75.0 75.0 75.0 75.0 75.0 5.0 287 288 C 4.8 H 1.5 1.0 3.0 3.0 1.0 2.5 289 299 H 4.6 H 2.1 2.3 1.9 8.7 1.3 2.0 300 303 C 4.9 H 0.8 1.2 2.5 2.2 1.8 3.5 304 310 E 4.9 H 0.3 0.3 0.4 0.3 0.3 0.1 314 320 E 4.9 H 0.1 0.6 0.1 0.4 0.4 0.6 321 322 C 5.0 H 0.0 0.0 1.5 0.0 1.0 0.0 323 328 E 4.8 H 1.8 0.8 1.0 1.7 1.2 0.8 329 330 - 4.3 M 5.8 75.0 75.0 75.0 39.5 75.0 331 332 C 5.0 H 4.5 4.5 7.0 9.2 5.5 6.0 333 336 E 5.0 H 1.0 1.0 1.5 1.8 0.2 2.5 337 338 C 4.5 M 0.5 0.5 1.0 0.5 0.5 0.0 339 344 E 4.9 H 1.2 2.2 2.3 0.5 2.2 1.0 345 348 C 4.7 H 2.2 39.2 4.2 5.0 5.8 21.8 349 354 - 4.4 M 6.2 75.0 64.4 75.0 75.0 63.7 356 366 H 4.4 M 4.1 75.0 4.2 11.0 4.9 4.3 369 387 H 4.8 H 2.6 2.6 3.3 2.7 2.9 2.4 388 395 C 4.7 H 4.6 4.2 3.8 4.4 4.6 22.4 396 405 E 4.8 H 2.6 3.6 3.3 3.4 3.9 11.0 406 408 C 4.7 H 1.7 1.3 6.7 0.7 5.3 1.7 409 419 E 5.0 H 0.7 1.1 1.2 0.6 1.4 1.5 420 425 C 4.9 H 3.3 5.3 4.4 16.1 4.5 15.2 426 433 H 4.9 H 0.1 0.8 0.6 1.1 0.6 1.1 434 436 C 5.0 H 0.0 0.0 0.3 0.3 0.0 0.7 437 439 H 4.5 M 0.0 0.0 0.7 0.0 0.3 0.0 441 442 E 4.5 M 0.5 0.0 0.0 0.0 0.5 0.5 444 454 H 5.0 H 2.0 1.3 1.2 2.3 1.3 3.8 455 464 C 4.8 H 0.9 0.6 0.9 1.6 8.3 1.8 465 470 E 4.9 H 0.3 0.0 0.2 0.2 0.5 0.0 471 474 C 4.6 H 1.5 2.0 3.2 42.0 4.8 20.8 475 479 E 4.7 H 0.4 0.2 0.4 0.0 0.2 0.0 480 482 C 4.7 H 0.3 0.3 1.7 0.3 1.0 0.3 483 487 E 4.9 H 0.4 0.0 0.0 0.0 1.2 1.2 488 489 C 5.0 H 6.5 8.8 8.2 7.5 11.5 5.0 490 499 E 4.8 H 0.7 0.5 0.2 0.2 1.6 0.4 500 504 C 5.0 H 4.4 4.6 4.6 3.2 4.0 4.0 505 522 H 4.8 H 1.7 2.4 2.7 1.9 6.8 2.5 523 525 C 4.3 M 2.7 4.8 2.7 25.7 0.3 4.2 527 531 - 4.5 M 3.2 75.0 75.0 75.0 75.0 75.0 >>>>>>