Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1t95a3 CCCCCCCCCCEEEEC-HHHHHHHHHHHHHH-----CC-CEEEEECC--CCCEEEECCCCC--CCCCCHHHHHHCCCCEEE----------------------------------------------------------- >P1;d1vi7a2 ----C-CEEEEEEEC-CCCHHHHHHHHHHC-----CCEEEEEEECC---CEEEEEEECCCCHHHHHHHHHHHCCCCCCCEECC-------------------------------------------------------- >P1;d2bm1a4 --CCCCCCCCEECCCCCCCCCCCHHHCCCHHHCCCCCEEECC----CCCCCEEEECCCHHHHHCCHHHCCCCC-CCCCCCCC--------------------------------------------------------- >P1;d2cvea2 ----CCEEEEEEEEC-HHHHHHHHHHHHHC-----CCCC-EEEEEC--CEEEEEEEEEHHHHHHHHHHHHHHCCCCCEEC----------------------------------------------------------- >P1;d2dy1a4 --CCCCCEEEEEEECCHHHHHHHHHHHHHHHHHCCCCEEEEC----CCCCCEEEEECCHHHHHHHHHHHHHC--CCCEEEECCCC------------------------------------------------------ >P1;d2dy1a5 CC-EEEEEEEEEEEE-HHHHHHHHHHHHHC-----CCEEEEEEEE--CCEEEEEEEEEHHHCCCHHHHHHHHCCCCCEEEEEEEEEEECC------------------HHHHHHHHHHHHHC----------------C >P1;d3b82a3 CCCCCCCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCEEEEC----C-CCCEEEEECCHHHHHHHHHHHHHCCCCCCEEECCCC------------------------------------------------------- >P1;d3b82a5 ----CEEEEEEEEEE-HHHHHHHHHHHCCC-----CCEEEEEEECCCCCEEEEEEEEEHHHCCCHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCC------------CCHHHHHHHHHHHHCCCCCCCCCHHHHCCCC >P1;d6id0c3 CCC-CCCEEEEEEECCHHHHHHHHHHHHHHHHHCCCCEEEEC----C-CCCEEEEECCHHHHHHHHHHHHHHCCCCCEEECCCC------------------------------------------------------- >P1;d6id0c5 ----CEEEEEEEEEC-HHHHHHHHHHHHCC-----CCCEEECCCCCCCCCEEEEEEEECCCCCCHHHHHHHHCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC-------------- PSA >P1;d1t95a3 b7977b555150402-3720d6018205a3-----74-0583763b--88003015073c--7a8092187007960839----------------------------------------------------------- >P1;d1vi7a2 ----b-444130505-5811a504710760-----7062371655a---504030002693395057305930a67080675c-------------------------------------------------------- >P1;d2bm1a4 --7681647250604879147307500961386563052856----8969430010378a2077025401762-9090574a--------------------------------------------------------- >P1;d2cvea2 ----87714140204-5901b504810874-----91a0-846528--80040405034663780272049309560645----------------------------------------------------------- >P1;d2dy1a4 --78909431004259a607860a600640275362052363----a92812002036a9205504640752--7050515a17b------------------------------------------------------ >P1;d2dy1a5 83-512125050202-6931a502620782-----3072383776--b8411030200263076066405c2086507371640454704------------------79217646679879----------------f >P1;d3b82a3 ba776262403060679b256605500750276383050454----b-866110002698205501550377104050615858------------------------------------------------------- >P1;d3b82a5 ----13023030302-6821a103700871-----50733638468b4631204030035309a059506a30a2507272842474a3c365655------------9381066338315759575722876586879 >P1;d6id0c3 6b6-91844030604779137604301640474273040554----b-8641002047a9207502610365308180616a4a------------------------------------------------------- >P1;d6id0c5 ----02133050502-69118307600552-----30914545629c3833103030005308705840475094605073744375a15075839939069a5806671111143256677858-------------- Translating the sequences ****C*****EEEEC-HHHHHHHHHHHHH*-----CC-*EE*****--CC*EEEE*****--*****HHHHH*CCCCEEE----------------------------------------------------------- ----C-*EEEEEEEC-***HHHHHHHHHH*-----CCEEEE*****---C*EEEEE********HHHHHHHHCCCCC**E***-------------------------------------------------------- --**C*****EE**C********HHH*********CCEEE**----**CC*EEEE***HHH****HHH****C-CCC*****--------------------------------------------------------- ----C**EEEEEEEC-HHHHHHHHHHHHH*-----CC**-E*****--C**EEEEE**HHH***HHHHHHHHCCCCCEE*----------------------------------------------------------- --**C**EEEEEEEC*HHHHHHHHHHHHH******CCEEEE*----**CC*EEEEE**HHH***HHHHHHH*--CCCEEE*****------------------------------------------------------ **-****EEEEEEE*-HHHHHHHHHHHHH*-----CCEEEE****--*C**EEEEE**HHH***HHHHHHHHCCCCCEEE**********------------------**************----------------* ****C**EEEEEEEC*HHHHHHHHHHHHH******CCEEEE*----*-CC*EEEEE**HHH***HHHHHHH*CCCCCEEE****------------------------------------------------------- ----C**EEEEEEE*-HHHHHHHHHHH***-----CCEEEE*******C**EEEEE**HHH***HHHHHHHHCCCCC*******************------------******************************* ***-C**EEEEEEEC*HHHHHHHHHHHHH******CCEEEE*----*-CC*EEEEE**HHH***HHHHHHHHCCCCCEEE****------------------------------------------------------- ----C**EEEEEEEC-HHHHHHHHHHHH**-----CC*EEE*******CC*EEEEE********HHHHHHHHCCCCCEEE*********************************************-------------- 54980.tem _________________________________ ****C**EEEEEEEC*HHHHHHHHHHHHH******CCEEEE*******CC*EEEEE**HHH***HHHHHHHHCCCCCEEE*****------------------------------------------------------ Structural block scores 0 3 * 3.6 M 8.6 75.0 40.8 75.0 41.2 22.8 9.0 75.0 24.6 75.0 5 6 * 1.2 P 8.2 39.5 3.5 7.0 4.5 1.5 4.0 1.5 4.5 1.5 7 13 E 4.7 H 2.9 2.4 3.4 1.7 2.0 2.0 2.1 1.6 2.4 2.3 16 28 H 4.7 H 4.5 4.3 4.5 4.6 4.9 4.6 4.7 4.1 3.9 3.9 29 34 * 3.3 M 63.0 62.5 4.8 63.2 3.8 62.8 4.3 62.7 4.0 62.8 35 36 C 5.0 H 5.5 3.5 1.5 5.0 1.0 1.5 1.5 2.5 1.5 1.5 37 40 E 4.5 M 22.0 4.5 5.0 23.4 4.0 5.0 3.5 4.8 3.5 4.8 41 47 * 2.8 P 25.8 25.4 46.1 25.0 46.1 26.4 55.8 6.4 55.8 5.9 48 49 C 4.4 M 8.0 40.0 7.5 4.0 5.0 6.0 7.0 4.5 7.0 5.5 51 55 E 4.9 H 1.8 1.4 0.8 2.6 0.8 1.2 0.4 1.8 0.6 1.4 56 57 * 1.0 P 3.5 1.0 5.0 1.5 4.5 0.0 4.0 0.0 5.5 0.0 58 60 H 4.2 M 30.2 6.0 6.8 5.3 7.2 3.7 6.3 3.7 7.2 2.7 61 63 * 1.2 P 30.8 5.7 4.7 6.0 3.3 4.3 3.3 6.5 4.0 5.0 64 71 H 4.6 H 4.4 4.0 3.1 3.4 3.5 4.4 3.5 4.8 2.9 4.1 72 76 C 4.8 H 4.4 4.7 19.0 4.0 32.4 3.8 2.0 3.5 4.0 3.8 77 79 E 4.1 M 6.7 4.7 4.0 5.0 2.0 5.7 2.3 5.3 2.3 4.0 80 84 * 2.7 P 75.0 34.9 47.9 75.0 7.0 3.0 20.2 4.0 21.2 4.2 85 138 - 4.5 M 75.0 75.0 75.0 75.0 75.0 49.6 75.0 21.0 75.0 23.2 >>>>>>