Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1h3za- -----------------------------CCCCCCCCCEEEEEEECC--EEEEEEEECCCCCCCHHHHCCCCCC-----CCCCEEEEECCCCE----EEEECC--CCEEEC---CHHHHHHHHHCCCC---CCHHHHHHHHHHCCCCCCCCCCCCC----------------------------- >P1;d1khca- -----------------------------CCC-CCCCCCEEEEECCC---CEEEEEEECCCCCCCCCCC------------CEEEEEECCCCC----EEEEEH--HHCEE----CC-CHHHHCCHHHH---CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCC >P1;d1oz2a1 CCCCHHHHHHHHCCCCCCHHHCCHHHHCCCCCCCCCCCCEEEEEECCEEEEEEEEEEEEEE-------------------CCEEEEEECCC--CHHHCEEEECCCCCEEC-----CCHHHH----HCCCEECCC-CC-------------------CCCC------------------------- >P1;d1oz2a2 --CCHHHHHHHHCCCCCCHHHC-CCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEEEEE-------------------CCEEEEEECCC--CHHHCEEECCCCCCEEC-----CCHHHH----HCCCEECCC-CCC------------------CCCC------------------------- >P1;d1wjra1 ------------------------------CCCCCCCCCEEEEECCCCCCEEEEEEEEEEE-------------------CCEEEEEECCCCCCCCCEEEEECCCCCCCC-----CCCCCC----CCCEECCCCCCCCCCC-------------HHHHHHHHHHHHHHHCCCCCCHHHHCCCCCC >P1;d2l89a- -----------------------------CCCCCCCCCEEEEEEECC--EEEEEEEEEEE-EEE------CCCCCCCCCCEEEEEEEECCCCE----EEEECH--HHEEEC---CHHHHHHHHCCCCC---CCHHHHHHHHHHCCCCCCCCCCCCCCC--------------------------- >P1;d4rxja- ----------------------------------CCCCCEEEEEE-C--CEEEEEEECCC--CCCCCCCCCCC--------CEECEEECCCC-----CCCEEH--HHCEECCCCCHHHHHHHCC--CC---HHHHHHHHHHHHHHHHCCCCCC-------------------------------- >P1;d6iipa1 ---------------------------------CCCCCCEEEECCCC--CCCEEEEECCCCCCCCCCCC------------CCEEEEECCCCC----EEEECH--HHEEE----HHHHHHHHCC--CC---CCHHHHHHHHHHHHCCCC------------------------------------ PSA >P1;d1h3za- -----------------------------bb74b06503202043bd--5330000006492028905954198-----ba922100001a46----020042--a20330---76840561266175---729702700640270561b409355----------------------------- >P1;d1khca- -----------------------------305-9175230000545b---420002004460a657058------------720003010458----221140--a7025----00-50571057921---76870160034002403610a391a37ab3657208401700397078456504 >P1;d1oz2a1 c9657864277594a55699648b7632994a09377656000222966731220202427-------------------c2502030173--67760131603185027-----862298----4a4814126-b5-------------------85a5------------------------- >P1;d1oz2a2 --677865266495a5559865-b54784870aa286955000113566a50020103414-------------------17501010273--78931130439174027-----7530a8----5a3833324-958------------------75a8------------------------- >P1;d1wjra1 ------------------------------44a4077600000207955820000102518-------------------805020110205b45731242307172035-----063077----d447120087045429-------------89506720570165085850496018a68ba >P1;d2l89a- -----------------------------999970a30510103389--86310000344-236------746a88c7455120203102887----636233--b30550---75720483192889---3498235005203265a14b5b6389c--------------------------- >P1;d4rxja- ----------------------------------2757230103a-a--95333030153--805a16b647a--------b0100214a57-----730058--b405448ab47a9178559--75---7a88886775637765757989-------------------------------- >P1;d6iipa1 ---------------------------------708394200034ab--533000101827bb39815b------------932101000347----633123--a4025----07743a8217--72---8383045016105453a3------------------------------------ Translating the sequences -----------------------------*CC*CCCCC*EEEEE*CC--**EEEEEE*****************-----**C*EEEEECCCC*----*EEE**--***E**---***HHHH*****CC---CC***********************----------------------------- -----------------------------*CC-CCCCCCEEEEE*CC---*EEEEEE************------------CEEEEEECCCC*----*EEE**--***E*----**-*HHH*******---CC**************************************************** ******************************CC*CCCCCCEEEEE*CC****EEEEEE****-------------------*CEEEEEECCC--*****EEE*******E*-----**HHHH----*CC***CC*-**-------------------****------------------------- --********************-*******CC*CCCCCCEEEEE*CC****EEEEEE****-------------------*CEEEEEECCC--*****EEE*******E*-----**HHHH----*CC***CC*-***------------------****------------------------- ------------------------------CC*CCCCCCEEEEE*CC****EEEEEE****-------------------*CEEEEEECCCC******EEE*********-----******----*CC***CC********-------------******************************* -----------------------------*CC*CCCCC*EEEEE*CC--**EEEEEE***-***------************EEEEEECCCC*----*EEE**--***E**---***HHHH*****CC---CC*************************--------------------------- ----------------------------------CCCCCEEEEE*-C--**EEEEEE***--***********--------CEE*EEECCCC-----***E**--***E********HHHH***--CC---**********************-------------------------------- ---------------------------------CCCCCCEEEE**CC--***EEEEE************------------C*EEEEECCCC*----*EEE**--***E*----***HHHH***--CC---CC****************------------------------------------ 63748-1.tem _________________________________ -----------------------------*CC*CCCCCCEEEEE*CC****EEEEEE************-***-------*CEEEEEECCCC******EEE*******E**---***HHHH*****CC***CC***************************------------------------- Structural block scores 0 28 - 4.3 M 75.0 75.0 6.6 13.4 75.0 75.0 75.0 75.0 30 31 C 4.5 M 9.2 2.5 7.2 3.5 4.0 9.0 75.0 75.0 33 38 C 4.8 H 4.2 4.5 6.2 6.8 4.0 4.2 16.3 5.2 39 43 E 4.9 H 1.6 1.0 1.6 1.2 0.4 1.0 1.4 1.0 45 46 C 4.8 H 12.5 8.2 5.5 4.0 8.0 8.5 42.8 11.0 47 50 * 2.6 P 39.5 57.2 5.5 6.9 5.0 41.0 41.0 39.5 51 56 E 5.0 H 0.5 0.7 1.2 0.5 0.2 0.7 2.0 0.7 57 68 * 2.6 P 4.5 4.6 51.2 51.0 51.3 39.3 16.8 6.5 70 72 * 3.9 M 4.7 75.0 75.0 75.0 75.0 5.7 7.2 75.0 73 79 - 4.6 H 56.4 75.0 75.0 75.0 75.0 7.9 75.0 75.0 82 87 E 4.8 H 0.8 0.8 1.7 1.2 1.5 1.3 0.7 1.2 88 91 C 4.9 H 3.9 2.5 21.5 21.8 1.8 4.5 6.6 1.8 92 97 * 3.2 M 51.0 51.7 16.8 17.2 5.2 52.2 63.7 52.2 98 100 E 4.8 H 0.7 1.3 1.7 1.3 2.7 3.7 1.0 2.3 101 107 * 1.8 P 24.1 24.5 3.3 4.0 2.9 24.4 25.5 24.2 109 110 * 2.5 P 1.5 40.0 41.0 41.0 40.0 2.5 4.0 40.0 111 113 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 10.0 75.0 114 116 * 1.9 P 7.0 25.0 29.7 29.0 27.0 6.3 7.2 4.7 117 120 H 4.6 H 3.8 4.2 5.2 5.4 4.2 3.5 6.2 6.4 121 125 * 3.0 P 3.2 4.4 60.8 61.0 62.7 4.6 33.8 32.0 126 127 C 4.7 H 6.0 1.5 7.2 6.8 4.0 8.5 6.0 4.5 128 130 * 3.9 M 75.0 75.0 4.3 4.7 3.3 75.0 75.0 75.0 131 132 C 4.7 H 4.5 6.5 1.5 2.5 0.0 3.5 8.8 5.5 133 159 * 2.7 P 14.6 4.1 57.4 54.9 38.9 10.4 24.5 32.7 160 184 - 4.3 M 75.0 4.0 75.0 75.0 5.1 75.0 75.0 75.0 >>>>>>