Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bdfa1 --------CCCCCCCCCCEEEEEEC--CCCEEEEEEEEEECCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCC----------------------------------------------------------CEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHC------------------- >P1;d1twfc1 -------------CCCCCCCCCCCCC---CEECCEECCCC----HHHHHHHHHHHHH--CCCCCEEEEECCCCCCCCCCCCCCCCHHHHCCCCHHHCCCCCCCCCCCCCC----------------------CCCCC--CEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHH---------CCC >P1;d1twfk- CCCCCCHHHCCCCCCCCCCCEEECCCCC-CEEEEEEECCC----HHHHHHHHHHHCC-CCCEEEEEEECCCC----------------------------------------------------------------CCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC------- >P1;d1xppa- --------------CCCEEEEEEEC---CCEEEEEEECCC----HHHHHHHHHHHCC-CCCEEEEEEECCCC----------------------------------------------------------------CCCCCEEEEEECCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----- >P1;d4c2mc1 -------CCHHHHHHHCEEEEEECCC---CEEEEEEECCC----HHHHHHHHHHHHH--CCCCCEEEEEEEEEEEC--CCCCCHHHHHHHCCCCC-CCEEECCCCCCEEECCHHHCCCCCHHHHCHHHHCCEEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC------------- >P1;d7d59k- ---------------CCCEEEEECCCCCCCEEEEEEECCC----HHHHHHHHHHHHH-CCCEEEEEEEECCC----------------------------------------------------------------CCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC PSA >P1;d1bdfa1 --------ea979626281472654--6a320301022014a40673053037104740610570506165082a548----------------------------------------------------------700301030405471704500640542375756876------------------- >P1;d1twfc1 -------------ba6556851757a---74100113708----3960440370047--4103807142102231655a48569459835873800942a549bc79478----------------------85916--30001040689260730164055228747677876-6787---------88b >P1;d1twfk- 9a86695456639bc374362681a928-40130100127----6930740261067-39705405162647----------------------------------------------------------------8613030202069b25155017704740896688778976677775aa------- >P1;d1xppa- --------------99345854758---831011203528----a850840161055-1b404305252866----------------------------------------------------------------9733320203067a-70430274058524677754968685677779886----- >P1;d4c2mc1 -------7688738862748557368---65020002406----6840420360047--40076061411050614--56066830450390039-500015ab643052551360816540365a4039207072475100040306183404402740462376586989838a9c------------- >P1;d7d59k- ---------------876444732bc49631010013927----6940740461046-28605705182368----------------------------------------------------------------865404040206a944045017614752776776876777885887877667898 Translating the sequences --------******CCCCEEEEE*C--**CEEEEEEE*******HHHHHHHHHHH***CCCEEEEEEE*CCC******----------------------------------------------------------C**EEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH*------------------- -------------*CCCC*****CCC---CEE**EE*CCC----HHHHHHHHHHH**--CC***EEEE*CCC**************************************----------------------****C--*EEEEEE*CCCCCHHHHHHHHHHHHHHHHHHHHHH-HHH*---------*** **************CCCC**EEECCC**-CEEEEEEECCC----HHHHHHHHHHH**-CCCEEEEEEE*CCC----------------------------------------------------------------C**EEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH*HHH******------- --------------CCC*EEEEE*C---*CEEEEEEECCC----HHHHHHHHHHH**-CCCEEEEEEE*CCC----------------------------------------------------------------C****EEEEEECCC-CHHHHHHHHHHHHHHHHHHHHHH*HHH********----- -------*********C*EEEEECCC---CEEEEEEECCC----HHHHHHHHHHH**--CC***EEEE********--*****************-*******************************************EEEEEEE*CCCCCHHHHHHHHHHHHHHHHHHHH******------------- ---------------CCCEEEEECCC***CEEEEEEECCC----HHHHHHHHHHH**-CCCEEEEEEE*CCC----------------------------------------------------------------C**EEEEEEEECCCCC*HHHHHHHHHHHHHHHHHHHHH*HHH************* 55257.tem _________________________________ --------******CCCCEEEEECCC-**CEEEEEEECCC----HHHHHHHHHHH**-CCCEEEEEEE*CCC****------------------------------------------------------------C**EEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH*HHH******------- Structural block scores 0 7 - 4.5 M 75.0 75.0 7.2 75.0 66.5 75.0 8 13 * 3.3 M 9.3 64.4 6.8 75.0 6.7 75.0 14 17 C 4.4 M 4.5 6.6 6.6 6.2 5.8 24.0 18 22 E 4.3 M 4.0 5.4 5.0 5.8 5.8 4.4 23 25 C 4.5 M 28.0 7.5 6.8 29.3 5.7 8.7 27 28 * 3.4 M 8.2 75.0 41.5 41.5 75.0 7.5 30 36 E 4.8 H 1.1 1.4 0.7 1.1 1.3 0.9 37 39 C 4.5 M 1.0 5.0 3.3 5.0 3.3 6.0 40 43 - 4.5 M 4.6 75.0 75.0 75.0 75.0 75.0 44 54 H 5.0 H 3.2 3.3 3.5 4.0 3.0 3.7 55 56 * 1.0 P 5.5 5.5 6.5 5.0 5.5 5.0 58 60 C 4.8 H 2.3 26.7 6.3 5.5 26.3 5.3 61 67 E 4.6 H 3.3 3.3 3.0 2.7 3.4 3.7 69 71 C 4.5 M 3.7 1.0 5.7 6.7 2.0 5.7 72 75 * 3.4 M 6.4 3.0 75.0 75.0 2.8 75.0 76 135 - 4.3 M 72.7 31.5 75.0 75.0 7.5 75.0 137 138 * 1.9 P 0.0 75.0 3.5 5.0 6.0 5.5 139 146 E 4.7 H 1.4 1.0 1.2 1.6 1.0 1.8 147 151 C 4.9 H 4.8 6.2 6.7 21.1 4.4 6.7 152 173 H 4.9 H 10.6 4.6 5.3 4.7 4.8 5.0 175 177 H 4.2 M 75.0 7.0 6.3 6.3 10.7 7.7 178 183 * 3.3 M 75.0 63.7 7.8 7.5 75.0 7.2 184 190 - 4.2 M 75.0 46.8 75.0 55.6 75.0 7.3 >>>>>>