Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1josa- ------CHHHHHHHHHHHHHHHHHHHCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCEEEEEECCC-CCCCC------------ >P1;d1pa4a- -------CCHHHHHHHHHHHHHHHHCCC--CCCHHHCCCCCCEEECCCCEEEECCCCCCC---CCHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCEEECCCCCCCCCC------------- >P1;d2dyja1 ------CHHHHHHHHHHHHHHHHHC-CCCHHHC--CCEEEEEEECCCCCEEEEEEECCC-----CHHHHHHHHHHCHHHHHHHHHCCCCCCCCCEEEEEEHHH-CC--------------- >P1;d2e7ga1 CCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCEEEEEECCCCCCEEEEECCC--CCHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCCCEEEEECCCC---CCCCCCCCCCCCCC >P1;d2kzfa1 CC-CCCCCHHHHHHHHHHHHHHHHH-CCCCCCCHHHEEEEEEEECCCCCEEEEEEEECC--CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCC------------ PSA >P1;d1josa- ------a2a711630363047006532738703--4050350605a7436030203065684a9025601680694276037102830929610606031298-989ba------------ >P1;d1pa4a- -------96766370352045006920a--680040050560614781440203050777---92194027108b05a202810185787782040541155877779------------- >P1;d2dyja1 ------d597217504800452097-2938408--5070430405a8264000006047-----738002600670196005104730828900505031664-14--------------- >P1;d2e7ga1 6a639833840542046103610653810a50582c0704704027817304030606--a58920761170067207602740594c907900505043577a---7ab88b8baa8b9b >P1;d2kzfa1 8d-5aa7177017404810270079-09187073a506067030389384020206094--9887059127105812a403a20374194a80040403352a8975ba------------ Translating the sequences ------CHHHHHHHHHHHHHHHHHH*CCC*CCC--C*EEEEEEECCCCCEEEEEEE*CC**C**HHHHHHHHHHHCHHHHHHHHHHH*CCCCCCEEEEEECCC-CCCCC------------ -------**HHHHHHHHHHHHHHHH*CC--CCCHH*C*****EE*CCCCEEEE***CCC*---**HHHHHHHHHH**HHHHHHHHHHCCCCCCC*EEE**CCCCCCCC------------- ------CHHHHHHHHHHHHHHHHH*-CCC***C--CCEEEEEEECCCCCEEEEEEECCC-----*HHHHHHHHHHCHHHHHHHHH**CCCCCCCEEEEEE***-CC--------------- *******HHHHHHHHHHHHHHH****CCC****HHCC*EEEEEECCCCC*EEEEE*CC--*C**HHHHHHHHHHHCHHHHHHHHH**CCCCCCC*EEEEECCCC---CC************ **-***C*HHHHHHHHHHHHHHHHH-CCC*CCCHH**EEEEEEECCCCCEEEEEEE*CC--C**HHHHHHHHHHH*HHHHHHHHHHHCCCCCCCEEEEE*CCCCCCCCC------------ 89919.tem _________________________________ ------CHHHHHHHHHHHHHHHHHH*CCC*CCCHHCCEEEEEEECCCCCEEEEEEECCC--C**HHHHHHHHHHHCHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCC------------ Structural block scores 0 5 - 3.9 M 75.0 75.0 75.0 7.1 20.4 7 24 H 4.8 H 3.6 4.3 4.2 3.2 3.6 26 28 C 4.8 H 4.0 28.5 4.7 3.0 3.3 30 32 C 4.0 M 3.3 4.7 4.0 3.3 4.7 33 34 H 4.2 M 75.0 2.0 75.0 5.0 6.8 35 36 C 3.8 M 2.0 0.0 2.5 6.2 2.5 37 43 E 4.5 M 2.7 3.3 2.6 3.1 3.1 44 48 C 4.9 H 5.9 4.8 6.3 5.0 6.2 49 55 E 4.6 H 2.0 2.0 1.4 2.3 2.0 56 58 C 4.4 M 3.7 4.7 3.7 27.0 4.3 59 60 - 3.8 M 7.0 41.0 75.0 42.8 75.0 62 63 * 2.5 P 9.8 42.0 75.0 8.5 8.0 64 74 H 4.9 H 3.9 4.1 3.5 3.4 4.1 76 86 H 4.7 H 3.5 3.9 3.3 4.0 4.2 87 93 C 4.9 H 3.9 5.6 3.9 5.4 4.6 94 99 E 4.5 M 2.7 2.5 2.3 2.8 2.3 100 108 C 4.4 M 15.8 14.4 35.7 30.2 7.6 109 120 - 4.5 M 75.0 75.0 75.0 10.0 75.0 >>>>>>