Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1coja1 ---------CCCCCCHHHCCCC-CC--CCCHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCC-CHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC---- >P1;d1ix9a1 ----------CCCCCCCCCCCCCCCC-CCCHHHHHHHHHCHHHHHHHHHHHHHCCCHHHHCCCHHHHCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCC---- >P1;d1my6a1 ----------CCCCCCCCCCCCCCHHHCCCHHHHHHHHHCHHHHHHHHHHHHHCCC-HHHHCCHHHHHHHHCC-CCCC-HHHHHHHHHHHHHHHHHHCCCC---- >P1;d2cw3a1 ---------CCCCCCCCCCCCCCCCC-CCCHHHHHHHHHCHHHHHHHHHHHHHC--CCHHHCCHHHHHHHC---HHHHCHHHHHHHHHHHHHHHHHHCCCC---- >P1;d3ak2a1 -----CCCCCCCCCCCCCCCCCCCCC-CCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHC--CCC-----CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC >P1;d3ceia1 ----------CCCCCCCCCCCCCCCC-CCCHHHHHHHCCCHHHHHHHHHHHHHCCC-CCCCCCHHHHHHHCC-------HHHHHHHHHHHHHHHHHHCCCCC--C >P1;d4f2na1 CCCCCCCCCCCCCCCCCCCCCCCCCC-CCCHHHHHHHHHCHHHHHHHHHCCCCC----CCCCCHHHHHHHHCCC----CCCHHHHHHHHHHHHHHHHCCCC---- >P1;d4f6ea1 -----------CCCCCC-CCHHHHCC-CCCHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHH--HHCCCCHHHHCCHHHHHHC-CHHHHHHHHHHHHHCCCC---- >P1;d6gsca1 ---------------------------------CHHHHHCHHHHHHHHHHHHHCCC-CCCCCCHHHHHHHHHHCC----HHHHHHHHHHHHHHHHHHCCCCC--C PSA >P1;d1coja1 ---------8528156821059-0a--b474a606430376027207602401641867a50-24974699604344145628714530362175038284---- >P1;d1ix9a1 ----------70813a0418364046-657676054313760363066036108707712a2606402732960489258407710310081194087185---- >P1;d1my6a1 ----------41816803185430666b25574074326660562056028503a3-902956154027607a-5a84-6712610130351274066283---- >P1;d2cw3a1 ---------45b0419031b474048-825476047214760392066017318--465970705512943---4a70887137002402710540362a4---- >P1;d3ak2a1 -----6a529428238041a262047-7365860552046604610640250244214464--a54-----a075750675377145314714640572143b94 >P1;d3ceia1 ----------92913a02174830cb-62657405631466036206402940785-a24928282025709-------c6248101305612740651539--b >P1;d4f2na1 791315a14060922a0b19680068-82667505421367027208503730c----36a50014026405c6----c4714810130161054075283---- >P1;d4f6ea1 -----------3912a1-1a363057-934297058215-704720732460584468337--5387739825818815953-711822681274088274---- >P1;d6gsca1 ---------------------------------798465760673476078217a3-70592627702742a707----96068104124715541754689--a Translating the sequences ---------*CCCCC***CCCC-CC--CCCHHHHHHHHHCHHHHHHHHHHHHH*******CC-*HHH************HHHHHHHHHHHHHHHHHHCCCC---- ----------CCCCCCCCCCCCCCCC-CCCHHHHHHHHHCHHHHHHHHHHHHHC******CCCHHHH************HHHHHHHHHHHHHHHHHHCCCC---- ----------CCCCCCCCCCCCCC***CCCHHHHHHHHHCHHHHHHHHHHHHHC**-****CCHHHH**H***-****-HHHHHHHHHHHHHHHHHHCCCC---- ---------*CCCCCCCCCCCCCCCC-CCCHHHHHHHHHCHHHHHHHHHHHHHC--*****CCHHHH**H*---*****HHHHHHHHHHHHHHHHHHCCCC---- -----*****CCCCCCCCCCCCCCCC-CCCHHHHHHHHHCHHHHHHHHHHHHH*******C--***-----********HHHHHHHHHHHHHHHH**CCCC**** ----------CCCCCCCCCCCCCCCC-CCCHHHHHHH**CHHHHHHHHHHHHHC**-***CCCHHHH**H**-------HHHHHHHHHHHHHHHHHHCCCC*--* **********CCCCCCCCCCCCCCCC-CCCHHHHHHHHHCHHHHHHHHH****C----**CCCHHHH**H****----***HHHHHHHHHHHHHHHHCCCC---- -----------CCCCCC-CC****CC-CCCHHHHHHHH*-*HHHHHHHHHHHH********--HH****H*********HH*-*HHHHHHHHHHHHHCCCC---- ---------------------------------*HHHHHCHHHHHHHHHHHHHC**-***CCCHHHH**H*****----HHHHHHHHHHHHHHHHHHCCCC*--* 46609.tem _________________________________ ---------*CCCCCCCCCCCCCCCC-CCCHHHHHHHHHCHHHHHHHHHHHHHC******CCCHHHH**H*********HHHHHHHHHHHHHHHHHHCCCC---- Structural block scores 0 8 - 4.6 H 75.0 75.0 75.0 75.0 44.3 75.0 4.6 75.0 75.0 10 25 C 4.5 M 13.3 4.1 4.0 4.6 4.0 5.2 4.9 13.2 75.0 27 29 C 4.7 H 7.5 6.0 6.2 5.0 5.3 4.7 5.3 5.3 75.0 30 38 H 4.8 H 4.1 3.9 4.2 3.9 3.9 3.9 3.7 4.3 29.3 40 52 H 4.9 H 2.8 3.1 3.5 3.4 2.8 3.2 3.4 3.6 4.4 54 59 * 1.9 P 6.1 4.0 16.6 29.0 3.5 17.4 51.5 4.7 16.8 60 62 C 4.3 M 26.7 6.2 6.7 4.7 51.3 6.3 5.2 52.3 5.7 63 66 H 4.5 M 5.5 2.5 2.5 2.8 23.6 3.0 1.2 5.8 4.0 67 68 * 1.6 P 5.0 4.5 4.5 5.5 75.0 3.5 4.0 5.0 4.5 70 78 * 2.3 P 3.9 5.0 21.7 28.6 12.8 59.3 37.3 5.1 36.3 79 96 H 4.9 H 3.8 3.4 3.1 3.0 4.1 3.8 2.9 8.3 3.9 97 100 C 5.0 H 5.5 5.2 4.8 5.6 3.5 3.5 4.5 5.2 5.8 101 104 - 4.3 M 75.0 75.0 75.0 75.0 6.9 42.6 75.0 75.0 42.4 >>>>>>