Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1uf2a- ---------CCCCC---CCCCCCEEEEHHHCCCCEEEEEEEECCCCCCCCCCEEEEEEEECCCCCHHHHCCC-CCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCEEEEEECCEEEEEECHHHCHHHCHHHHHCCCCCHHHHHHHHHHHHHHCEEEECCCCCCCCCCCCCCCCCCCHHHEEEEEECCCHHHHHHHHHHHHHHHHH-EE-CHHHHHHHHHHCCCC-CEEECHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHCHHHHHHHHHHHHHHC--CCCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHCCCCC-HHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHCHHHHHHHHHHCCCCCHHH----CCHHHHHHHHHHHHHHHHHHCCC------HHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHCCCCCHHHHCCEEECHHHCCCCCCEEHHHCCCCCCCCCHHHCCCCHHHHHHHHHHCCCCCCCCCCCCEE------------CCCEECCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCC----CCCCCCCHHH------CEEEEECHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCEECCEEEECCCCEECCCCC-----CC-EEEECCC----CHHHEEEEEEECCHHHHHHHHCCEEECCCCCEEEHHHHHHHCCCCCCHHHHHCEECCEECCCCCCEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHCC-------CCCCCCCE-EEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCEECCHHHCCCEEECCHHHHHHHCCEEEEEEC--CCCEECCCCCCCEEECC---CCCCCCCCCCCC >P1;d2btva- CCCCCCCCCHHHHHHHHHHHCCCCEEEC-CCCCCCEEECCCC----------CCCEEEEC--CHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCEEEECCCEEEEC----CEEEECHHHCC-CCCCCCCCCC-CHHHHHHHHHHHC-CCCCC---CCCCC--------CCC----EEEEECCCCHHHHHHHHHHHHHHHHHHC-HHHHHHHHHHHHHHHHCCEEECCHHHCC-CHHHHEEECCCCCC-CCCHHHHHHCCCCHHHHHHHHHHHHCCEEEEECCC-HHHHHHHCCCCC---CCCCHH-HHHHCCCCHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEECCCC------------------------CCCCCC--EECC-----------------------CCEEHHHH----CCCCCCCCCCCCCCCC---CEECC-CCCCCC---CCCCEECHHHCCCCCCCCCCCCCC---CCCCCHHHHHHHHHHHHCC-----------------HHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCEECCCCCCHHHHHHCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCHHHHHHHHHHH--CCH-HHHHHHHHHHHHHCCCHHHHHHHHHCC--CCCCCHHHHHHHHHHHHCCCCCCC----CCCCCEEEEEEECCCCCCCCHHHHHCCCCCCCCCCCCCCCHHHEEEEC----HHHHHHHHHC----------CCHHHHHH-------HHHHC-----------CCEEEECCCCCEEEEEEEC-----------CCCCHHHHCCCCEEEEEECCCCCCEEEEEECCEEEEEEECCCCCC------CCCCHHHCC--CCCCEEEEEECCCCCCCEEEC-CCCCHHHHCCEEEEECCCCEEECCHHHHHCEEECCCCCC----------- PSA >P1;d1uf2a- ---------b0814---51005166220560330050410300034773a6160000012158006900217-523761460205102100400462003203802367272cb86140010770c9020351064126975165135404350116906711080a1a1878051548202201000254004007103500110-00-002213622382008-005048923860770a310002212234110500030030054004302831--71914168476048503730936aa6912015008705-39107400400010000000110305907131016000000000000000000----03070011000000000030006------9802620387900542a28740628b4100120055059b29804700530026151850364014297031856022000000020310370541500292068020071100100308------------bb4701260072028005200088048407607935b20530053008104302000110011120200000000----5030802360------05547040220000000040677147045021332030010000012005202920964036319166006102500220053a0504400162185872067202701738654910900420250046017204704811211a1000021003020016-----73-3000000----36a2053244076084016324666747b95721302311690650768200406b1404262a5010030402021315124060a18951b06224085017104736-------94942100-401000000100555596a6475731181032003020000061072541570440051020412113--8607228b19181443b---72a080452c9b >P1;d2btva- 4849479239105603720656208336-3063013022040----------50200001--1002400710540335404400300050022017300000250332748----a6300326000-0306404630-4882675069511-71508---64621--------926----0100500005001300740070044006-7119502610660091020702683273-93573000001110-40416000101302300130020001030414517-882168106388---a39000-612a9a0569802600230020000001000050485894866312100000000000002200002550042004001300333398825166196------------------------c32010--4008-----------------------a3130330----2150660100001417---01342-880008---042100200302065505187307---c370300410160052041-----------------9300500840141000000000100110010002110a30641044246995832624624010300000022001148119102100000000000000000003303604a325-600860746302700363--028-102400620186280649403800736--230400101005200500740200----00043000032602217068287162005220011b7308a9414505----2840572097----------96087317-------81046-----------6210102110000205229-----------86057910554015175876ba75536070424010000015088------a36385344--a92140210010927004404-03500611a250100409150320041036072595477----------- Translating the sequences ---------*****---***CCCEEEEH*HCCCCEEEEEEEE**********EEEEEEEE**C**HHHHCCC-CCCCCCHHHHHHHHHHHHHHHHH**CEEEEECCEEEEE****EEEEECHHHCH*HCHHHHHCCC*CHHHHHHHHHHHH*HCEEE***CCCCC********CCC****EEEEEECCCHHHHHHHHHHHHHHHHH-E*-*HHHHHHHHHH****-CEEECHHHHHH*H*****EEEECCCC*CCCHHHHHHCHHHHHHHHHHHHHH*--*****CCC*HHHHHHHHHHHC***CCCCHH*HH**CCC-HHHHHHHHHHHHH**CCCCCEEEEECCCC**HHH*HHHHHHHHHH***CCHHH----CCHHHHHHHHHHHHHHHHHHCCC------HHH************************CHHHHH****CC***********************EEE*HHH*****CEEHHHCCCCCCCCCH***C**HH*HHHHHH***CCCC**C***EE------------***EECCHHHHHHHHHHHH*CC*****************HHHHHHHHHHHHHHHHHHHHHH**HHHHHCCCCCCC----*******HHH------CEEEEECHHHHHHHHHH******CCCCCCC******HHHHHHHHHHHHHHHHHHHH**CH*HHCCHHHHHHHHHHHHHH**CC***HHHH********CCCHHHHHHHHHCC**CCCCHHHHHHHHHHHHHHHHHHHH****CEECCEEEE***CEECCCCC-----CC-EEEECCC----CHHHEEEEE****HHHHHHHH*C**********EHHHHHHH*******HHHHC***********CEEEEEECCCEEEEEEEEE***********CCCCHHHHHHHH****-------C******E-EEEEEEEEECCCC******CCCHHHHHH**HHHC***EE*CHHHCCCEEEC*HHHHHHH*CEEEEEEC--C**EEC*****CEEECC---C*********** *********HHHHH***HHHCCC*EEE*-*CCCC*EEE****----------***EEEE*--CHHHHHHCCC*CCCCCCHHHHHHHHHHHHHHHHHHHCEEEE*CCEEEE*----*EEEECHHHC*-*C*****CCC-CHHHHHHHHHHH*-*C***---CCCCC--------CCC----EEEEE*CCCHHHHHHHHHHHHHHHHH**-*HHHHHHHHHHHHHHH*CEEEC*HHH**-*HHHHEEE**CCCC-CCCHHHHHHC***HHHHHHHHHHHH**EEEEECCC-HHHHHHH****C---CCCCHH-HHHHCCC*HHHHHHHHHHHHHHHCCCCCEE***CCCCHHH**HHHHHHHHHHHHHHCC*******CCHHHHHHHHHHHHHHH***CCC*********------------------------C*****--EECC-----------------------**EEHHHH----C*****CCCCCCCCC*---CEE**-******---CCCCEECHHH**************---**CC*HHHHHHHHHHHHCC-----------------HHHHHHHH**HHHHHHHHHHHHHHHH***CCCCCCC****HHHHHHHHH*******CEE***C**HHHHHH**EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC*-**CC***HHHHHHHHHHH--CCH-HHHHHHHHHHHHHCCCHHHHHHHHHCC--CCCC*HHHHHHHHHHHH*******----C**CCEEEEEEEC**CCCCC*****CC*****CCC****CHHHEEEE*----HHHHHHHHHC----------**HHHHHH-------HHHHC-----------C*EEEE*CCC*EEEEEEE*-----------CCCCHHHH****EEEE*******CEEEEEE**EEEEEEE**CCCC------CCC*HHH**--***CEEEEEEC***CCCEEEC-****HHHHC*EEEEEC**CEEE*CHHHHHCEEECC***C----------- 56831.tem _________________________________ ---------HHHHH---HHHCCCEEEEH-HCCCCEEEEEEEE----------EEEEEEEE--CHHHHHHCCC-CCCCCCHHHHHHHHHHHHHHHHHHHCEEEEECCEEEEE----EEEEECHHHCH-HCHHHHHCCC-CHHHHHHHHHHHH-HCEEE---CCCCC--------CCC----EEEEEECCCHHHHHHHHHHHHHHHHH-E--HHHHHHHHHHHHHHH-CEEECHHHHHH-HHHHHEEEEECCCC-CCCHHHHHHCHHHHHHHHHHHHHHH--EEEEECCC-HHHHHHHHHHHC---CCCCHH-HHHHCCC-HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHCCHHH----CCHHHHHHHHHHHHHHHHHHCCC------HHH------------------------CHHHHH--EECC-----------------------EEEEHHHH----CEEHHHCCCCCCCCCH---CEEHH-HHHHHH---CCCCEECHHHEE---------------EECCHHHHHHHHHHHHHCC-----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC----HHHHHHHHHH------CEEEEECHHHHHHHHHHEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH-HHCCHHHHHHHHHHHHHH--CCH-HHHHHHHHHHHHHCCCHHHHHHHHHCC--CCCCHHHHHHHHHHHHHHHHHHHH----CEECCEEEEEEECEECCCCC-----CC-EEEECCC----CHHHEEEEE----HHHHHHHHHC----------EHHHHHHH-------HHHHC-----------CEEEEEECCCEEEEEEEEE-----------CCCCHHHHHHHHEEEE-------CEEEEEEE-EEEEEEEEECCCC------CCCHHHHHH--HHHCEEEEEECHHHCCCEEEC-HHHHHHHHCEEEEEEC--CEEEECHHHHHCEEECC---C----------- Structural block scores 0 8 - 3.0 P 75.0 5.6 9 13 H 3.0 P 4.9 4.2 14 16 - 3.0 P 75.0 3.3 17 19 H 3.0 P 2.0 2.7 20 22 C 5.0 H 2.0 4.3 23 26 E 4.5 M 4.0 3.5 30 33 C 5.0 H 1.5 2.2 34 41 E 3.8 M 1.6 1.5 42 51 - 3.0 P 4.2 75.0 52 59 E 4.0 M 1.1 1.0 60 61 - 3.0 P 3.0 75.0 63 68 H 4.3 M 2.5 1.0 69 71 C 5.0 H 3.3 2.7 73 78 C 5.0 H 4.0 3.2 79 97 H 4.8 H 1.9 1.6 99 103 E 4.6 H 3.2 1.4 104 105 C 5.0 H 1.0 1.5 106 110 E 4.6 H 5.0 4.8 111 114 - 3.0 P 8.5 75.0 115 119 E 4.6 H 2.2 3.9 121 123 H 5.0 H 4.7 2.7 129 133 H 3.0 P 1.8 2.8 134 136 C 5.0 H 3.7 3.0 139 150 H 4.8 H 4.2 4.8 154 156 E 3.0 P 2.7 4.3 157 159 - 3.0 P 5.0 75.0 160 164 C 5.0 H 3.4 3.8 165 172 - 3.0 P 5.8 75.0 173 175 C 5.0 H 2.0 5.7 176 179 - 3.0 P 4.8 75.0 180 185 E 4.7 H 0.8 1.0 186 188 C 5.0 H 0.7 0.0 189 205 H 5.0 H 1.8 2.1 208 209 - 3.0 P 37.5 41.0 210 224 H 4.3 M 2.6 3.1 227 229 E 5.0 H 1.7 2.3 231 236 H 4.0 M 6.0 4.8 238 242 H 3.0 P 5.5 5.4 243 247 E 3.8 M 0.6 0.0 248 251 C 5.0 H 1.8 0.8 253 255 C 5.0 H 2.0 2.7 256 261 H 5.0 H 1.3 1.3 263 277 H 4.5 M 2.2 1.0 278 279 - 3.0 P 75.0 0.5 280 284 E 3.0 P 4.4 2.4 285 287 C 5.0 H 5.0 4.3 289 299 H 4.3 M 3.9 4.6 301 303 - 3.0 P 6.5 75.0 304 307 C 5.0 H 6.6 5.6 308 309 H 5.0 H 1.0 0.0 311 314 H 4.0 M 3.2 4.9 315 317 C 5.0 H 4.0 6.5 319 333 H 4.7 H 1.9 2.5 334 338 C 5.0 H 0.0 0.2 339 343 E 3.8 M 1.0 1.0 344 347 C 5.0 H 5.2 4.2 348 366 H 4.2 M 0.6 2.5 367 368 C 5.0 H 0.0 0.0 369 371 H 3.0 P 0.0 0.7 372 375 - 3.0 P 75.0 0.5 376 377 C 5.0 H 1.5 1.0 378 395 H 4.7 H 0.7 1.8 396 398 C 5.0 H 2.0 6.7 399 404 - 3.0 P 75.0 4.7 405 407 H 3.0 P 5.7 5.3 408 431 - 3.0 P 4.6 75.0 433 437 H 3.0 P 0.6 1.2 438 439 - 3.0 P 2.5 75.0 440 441 E 3.0 P 2.5 2.0 442 443 C 5.0 H 7.0 4.0 444 466 - 3.0 P 3.8 75.0 467 470 E 3.5 M 2.2 4.4 471 474 H 4.5 M 4.5 1.5 475 478 - 3.0 P 4.2 75.0 480 481 E 3.0 P 1.0 3.0 482 484 H 3.0 P 0.7 4.0 485 493 C 5.0 H 0.7 0.8 495 497 - 3.0 P 3.3 75.0 499 500 E 3.0 P 2.5 2.0 501 502 H 3.0 P 2.5 3.0 504 509 H 3.0 P 4.5 4.0 510 512 - 3.0 P 0.7 75.0 513 516 C 5.0 H 2.2 1.8 517 518 E 3.0 P 0.0 0.0 520 522 H 3.0 P 1.0 1.0 523 524 E 3.0 P 4.0 1.0 525 539 - 3.0 P 61.8 18.1 540 541 E 3.0 P 3.5 7.8 542 543 C 5.0 H 1.5 3.5 544 556 H 4.7 H 2.5 1.7 557 558 C 5.0 H 0.0 2.5 559 575 - 3.0 P 4.9 75.0 576 604 H 4.5 M 1.5 1.3 605 611 C 5.0 H 0.0 0.7 612 615 - 3.0 P 75.0 3.4 616 625 H 3.4 M 2.7 4.0 626 631 - 3.0 P 75.0 5.5 633 637 E 3.8 M 4.2 3.2 639 648 H 4.2 M 0.4 0.7 649 654 E 3.0 P 4.0 2.3 655 661 C 5.0 H 3.0 2.1 662 689 H 4.4 M 1.9 1.2 693 694 H 3.0 P 4.5 3.0 695 696 C 5.0 H 5.0 4.0 697 710 H 4.6 H 2.2 3.4 711 712 - 3.0 P 0.0 75.0 713 714 C 5.0 H 4.0 1.0 717 729 H 3.6 M 3.4 2.5 730 732 C 5.0 H 3.0 4.7 733 741 H 5.0 H 3.6 3.9 742 743 C 5.0 H 5.5 4.5 744 745 - 3.0 P 5.5 75.0 746 749 C 5.0 H 3.5 2.2 750 769 H 4.2 M 2.6 1.4 770 773 - 3.0 P 3.5 75.0 775 776 E 3.0 P 1.0 0.0 777 778 C 5.0 H 5.8 3.5 779 785 E 4.1 M 0.4 1.6 787 788 E 3.0 P 1.5 2.0 789 793 C 5.0 H 1.8 4.4 794 798 - 3.0 P 75.0 4.8 799 800 C 5.0 H 5.0 1.0 802 805 E 3.0 P 0.8 2.2 806 808 C 5.0 H 0.0 0.7 809 812 - 3.0 P 75.0 5.4 814 816 H 5.0 H 6.2 7.8 817 821 E 4.6 H 2.8 3.0 822 825 - 3.0 P 4.2 75.0 826 834 H 4.8 H 3.1 4.1 836 845 - 3.0 P 6.5 75.0 847 853 H 4.7 H 2.3 4.6 854 860 - 3.0 P 4.7 75.0 861 864 H 5.0 H 2.5 3.2 866 876 - 3.0 P 4.3 75.0 878 883 E 4.3 M 0.7 1.0 884 886 C 5.0 H 2.0 0.7 887 895 E 4.6 H 2.1 2.2 896 906 - 3.0 P 4.7 75.0 907 910 C 5.0 H 3.5 4.8 911 918 H 4.0 M 2.8 3.9 919 922 E 3.0 P 5.0 3.5 923 929 - 3.0 P 75.0 7.9 931 937 E 3.0 P 2.9 3.6 939 947 E 4.6 H 0.6 0.7 948 951 C 5.0 H 1.5 5.2 952 957 - 3.0 P 6.8 75.0 958 960 C 5.0 H 5.7 6.5 961 966 H 4.0 M 4.2 4.5 967 968 - 3.0 P 0.5 75.0 969 971 H 3.0 P 1.7 7.2 973 978 E 3.7 M 0.8 1.2 980 982 H 3.0 P 2.3 3.7 983 985 C 5.0 H 3.0 2.3 986 988 E 5.0 H 3.3 2.7 991 998 H 3.8 M 1.8 2.0 1000 1005 E 4.7 H 1.5 1.3 1007 1008 - 3.0 P 75.0 4.5 1010 1013 E 3.5 M 3.8 2.5 1015 1019 H 3.0 P 6.1 1.6 1021 1023 E 5.0 H 3.0 3.0 1024 1025 C 5.0 H 7.2 7.0 1026 1028 - 3.0 P 75.0 5.3 1030 1040 - 3.0 P 5.9 75.0 >>>>>>