Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1h8pa1 ------------CCCCCCEEECC--------------------------------EEECCCCCCCCC--CCEEECCCCCC--CCEEECCHHHCC >P1;d1l6ja3 CCCCCCCCCCCCCCCCCCEECCC--------------------------------CEECCCCCCCCCCCCCEEECCCCHHHHCCEEECCCC--- >P1;d2fd6a2 ----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHC----CCCCCCCCHHHHCCCCCCCCCCCCCCC-CCEEEEE-EC-CEEEEEECCCCCCC >P1;d2k4ra- -----CCCCCCCCC---CCCCCCCCCCCHHHCCC-----CCCCCCCCC-HHHHCCCCCCCCCCCCC-CCCCEEEEE-CCCCCEEEEECCCCC-C >P1;d3k65a- ----CCCHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCC------CCCCCCC-CCCCCCCCCCCCCEEECC-CC-C--CEEECCCCCC- >P1;d6dcma- CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCC----CCCHHH--CHHHCCCC-CCCCCCCCCCCCCEEECC-CC-CC-CEEECCCCCCC >P1;d6szwd- -CCCCH----HHCCCCCCEEECC--------------------------------EEECCCCCCCCCCCCCEECCCCCHHHHCCCEECC----- PSA >P1;d1h8pa1 ------------7604140517b--------------------------------65175016283a--62000026927--6532508a6044 >P1;d1l6ja3 9916079060b46404160517a--------------------------------86188134553a57520000362238475201063b--- >P1;d2fd6a2 ----404930281486134077728024033a30283----712062b31a71306822300003657-2000003-4c-a916226041834b >P1;d2k4ra- -----90a934462---31007646014066048-----a05592489-179080475350305a6-6c3200015-3b83311101012b6-d >P1;d3k65a- ----4256403618583240597670250949606721794b18------b817247-300000322a50000015-2a-7--4443081914- >P1;d6dcma- 58372087104a020751-066937004085592070----934197--37b32058-220000472870000004-46-a4-5422080551b >P1;d6szwd- -93408----9765041403079--------------------------------861a511678290843000035314847733207----- Translating the sequences ------------CCCCCC***CC--------------------------------***CCCCCCCCC--CCEEECC*CC*--*CEEECC***** ****CCC***CCCCCCCC**CCC--------------------------------C**CCCCCCCCCCCCCEEECC*C*****CEEECCCC--- ----CCC***CCCCCCCC**CCC**************----**************C**CCCCCCCCCC-CCEEE**-*C-****EEECCCC*** -----CC***CCCC---C**CCC***********-----*********-******C**CCCCCCCC-CCCCEEE**-CC*****EEECCCC*-* ----CCC***CCCCCCCC**CCC*********************------*****C*-CCCCCCCCCCCCCEEECC-CC-*--CEEECCCC**- ****CCC***CCCCCCCC-*CCC**************----******--******C*-CCCCCCCCCCCCCEEECC-CC-**-CEEECCCC*** -***C*----**CCCCCC***CC--------------------------------***CCCCCCCCCCCCCEE*CC*C*****C*EECC----- 57440.tem _________________________________ -***CCC***CCCCCCCC**CCC**************----******--******C**CCCCCCCCCCCCCEEECC*CC****CEEECCCC*** Structural block scores 1 3 * 3.7 M 75.0 5.3 75.0 75.0 75.0 6.0 5.3 4 6 C 4.4 M 75.0 5.3 2.7 28.0 3.7 3.3 27.7 7 9 * 2.5 P 75.0 2.0 4.0 7.5 3.3 2.7 75.0 10 17 C 4.7 H 21.5 4.6 4.1 30.5 4.5 3.7 4.5 18 19 * 1.4 P 2.5 2.5 2.0 0.5 2.0 37.5 1.5 20 22 C 4.7 H 6.5 6.2 7.0 4.3 7.0 7.0 5.3 23 36 * 3.2 M 75.0 75.0 3.5 18.9 4.5 3.6 75.0 37 40 - 4.4 M 75.0 75.0 75.0 40.1 5.2 75.0 75.0 41 46 * 3.4 M 75.0 75.0 3.0 5.5 40.9 5.5 75.0 47 48 - 4.4 M 75.0 75.0 7.2 42.0 75.0 75.0 75.0 49 54 * 3.2 M 75.0 75.0 3.8 4.2 17.4 4.4 75.0 56 57 * 1.8 P 3.0 3.5 5.0 6.0 41.0 41.5 3.5 58 70 C 4.9 H 15.4 5.1 7.9 10.1 2.0 2.5 5.0 71 73 E 4.9 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 74 75 C 4.2 M 1.0 1.5 1.5 3.0 3.0 2.0 1.5 77 78 C 4.4 M 5.5 2.0 8.2 7.2 6.2 5.0 2.0 79 82 * 2.5 P 40.8 5.5 23.9 3.8 58.0 41.1 5.8 84 86 E 4.9 H 3.3 1.0 3.3 0.7 3.7 2.7 2.7 87 90 C 4.7 H 6.1 5.1 3.2 3.6 4.5 3.2 39.2 91 93 * 2.9 P 2.7 75.0 6.2 31.5 26.7 5.8 75.0 >>>>>>