Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2xysa- --CHHHHHHHHHHHC---CCCCCCCCCC--CCCEEEEEEEEEEEEEEEECC----CCEEEEEEEEEEEEEE---EEEECCHHHCCCCCEEEEE---HHHCCCCCEEECCCCC-CCEECC----CCEEEEECEEEEEECCEEEEEEECCCCCCCCC-CCEEEEEEEEECCCCCCCEEEECCC--CCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCEEEEEEEEEEEEC- >P1;d4afha- CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEEECHHH---CCCCCCCCCCCEEEEC---HHHCCCCCEEECCCCCCCCEECC----CCCEEEECCCEEEECCEEEEEEEEEEEC-----CEEEEEEEEEECCCCCCCEEEEEHHHCCCCCCCCCC-CC-CCEEEEEEEEEEECCCCCCCCEEEEEEEEEEECC- >P1;d4uxua- --CCHHHHHHHHHHC---CCCCCCCCCCCCCCCEEEEEEEEEEEEEEEECC----CCEEEEEEEEEEEEEE---EEEECCHHHCCCCCEEEEE---HHHCCCCCEEECCCCCCCCCCC-----CCEEEEECEEEEEEEEEEEEEEECEEECCCCCCCEEEEEEEEEECCCCCCCEEEEECC--CCCCCCCCCCCCCEEEEECCEEEEEECCCCCCCCEEEEEEEEEEEECC >P1;d6dw1a- ---CCHHHHHHHHHC---CCCCCCCCCC--C-CEEEEEECCEEEEEEEEC-----CCEEEEEEEEEEEEEC----CCCCC----CCCCCEEEC-CCCCCCCCCCEEECCEEE--ECCCCCCCCCEEEEECCCCEEEEEEECCEEECCCCCCCC--CCEEEEECCEEECCCCCCCEEEEECCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCC--CEEEEEEEEEEEEEC- >P1;d6dw1b- --CCHHHHHHHHHHC---CC-CCCCCCC--CCCEEEEEEEEEEEECCCCC-----CCEEEEEEEEEEEEECC---CCCCC----CCCCCCEECHHHCCCCCCCCEEECCEEE--EEECCCCCCCEEEECCCCCEEEEEEEEEEEEECCC-CCCCCCCCCCEEEEEEECCCCCCCEEEEECCCCCCEECHHHCCCCCCCCCEEEEEEEEEECCC--CEEEEEEEEEECCCC- >P1;d7ndva- ---CCHHHHHHHHHH---HCCCCCCCCCC-CCCEEEEEEEEEEEEEEEECC----CCEEEEEEEEEEEEECHHH---CCCCC--CCCCEEEEE---HHHCCCCCEEECCCCC-CCEECC----CCEEEEECCCEEEECCEEEEEEECCCCCCCCC-CCEEEEEEEEECCCCCCCEEEECCC--C--CCCCCCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEEEEEEEECC PSA >P1;d2xysa- --a954850352118---6796280066--994140002010320240379----6500001040304050---a705052971692630605---1940120403023236-927343----77502034404041411130006060951758-9014040300066200420405056--570539516a609130260305444363b737322000103040255- >P1;d4afha- 38b6237601561072067684a80015ab784030401000240741756ca883030003010101050200---5084675241960404---0640000403052026b208154----a35030419030303030503040636a-----8304040102056211740004118a5440135417-29-071251606254373963b411010304000437- >P1;d4uxua- --9846760374018---a05588000759964060402000330560339----6320103051403060---4504064970773531605---0730030404034524a788a7-----c150304340202142334040708516787064004050200076220640204124--b402387177297040460506264647c874525010102010334b >P1;d6dw1a- ---974762286019---b0458500a6--c-304050103040004044-----8400201040303060----40608----366821518-910840020404020058--464277955324040348050401231204030608489--9070300030007623383020402568800432c446095061563517584673b8--441000103040646- >P1;d6dw1b- --9853871265038---b0-485006a--6821400030304404804a-----84102010502010409---3040a----4178614170810660020503042348--252257865303040238030102130002040a0-5977850407030100076231830505039a8900730a909087060341605666285b8--430010101040427- >P1;d7ndva- ---475850376075---7074a520258-a63080300030220270549----5540001031402060670---10a37--a02830405---2a20030404013142-947244----8450402170403140004050516074057a-a004050300076212740204246--8--4454038808030250616465467a618331200002020334b Translating the sequences --**HHHHHHHHHHC---CCCCCCCCCC--CCCEEEEEEEEEEEEEEEECC----CCEEEEEEEEEEEEE*---****CC****CCCCEEEE*---HHHCCCCCEEECCCCC-CCEECC----CCEEEEEC**EEEE**EEEEEEECCC*CCCCC-C*EEEEEEEEECCCCCCCEEEE*CC--CCCCCCCCCCCCCEEEEEEEEEEEEE*CCCCCC*EEEEEEEEEEEEC- ****HHHHHHHHHH******CCCCCCCC**CCCEEEEEEEEEEEEEEEE*C******EEEEEEEEEEEEEC***---CCC****CCCCEEEE*---HHHCCCCCEEECCCCC*CCEECC----CC*EEEECCCEEEE**EEEEEEE****C-----C*EEEEEEEEECCCCCCCEEEEE****CCCCCCCCC-CC-**EEEEEEEEEEE*CCCCCC*EEEEEEEEEEE*C- --*CHHHHHHHHHHC---CCCCCCCCCC**CCCEEEEEEEEEEEEEEEECC----CCEEEEEEEEEEEEE*---****CC****CCCCEEEE*---HHHCCCCCEEECCCCC*CC**C-----CCEEEEEC**EEEE**EEEEEEEC***CCCCC*C*EEEEEEEEECCCCCCCEEEEECC--CCCCCCCCCCCCCEEEEE**EEEEEE*CCCCCC*EEEEEEEEEEEEC* ---C*HHHHHHHHHC---CCCCCCCCCC--C-CEEEEEE**EEEEEEEEC-----CCEEEEEEEEEEEEEC----**CCC----CCCC*EEE*-*****CCCCCEEECC***--***CC****C*EEEE*CCCEEEE**E**EEE*CCC*CCC--*C*EEEE**EEECCCCCCCEEEEECC**CCCCCCCCCCCCCEEEEEEEEEEEEE*CCC--C*EEEEEEEEEEEEC- --*CHHHHHHHHHHC---CC-CCCCCCC--CCCEEEEEEEEEEEE****C-----CCEEEEEEEEEEEEEC*---**CCC----CCCC**EE*******CCCCCEEECC***--*EECC****C*EEE**CCCEEEE**EEEEEEECCC-CCCCC*C***EEEEEEECCCCCCCEEEEECC**CC**C***CCCCC****EEEEEEEEE*CCC--C*EEEEEEEEE***C- ---C*HHHHHHHHH*---*CCCCCCCCC*-CCCEEEEEEEEEEEEEEEECC----CCEEEEEEEEEEEEEC***---CCC**--CCCCEEEE*---HHHCCCCCEEECCCCC-CCEECC----CCEEEEECCCEEEE**EEEEEEECCC*CCCCC-C*EEEEEEEEECCCCCCCEEEE*CC--C--CCCCCCCCCCEEEEEEEEEEEEE*CCCCCC*EEEEEEEEEEEEC* 63712.tem _________________________________ --*CHHHHHHHHHHC---CCCCCCCCCC*-CCCEEEEEEEEEEEEEEEECC----CCEEEEEEEEEEEEEC*---**CCC****CCCCEEEE*---HHHCCCCCEEECCCCC-CCEECC----CCEEEEECCCEEEE**EEEEEEECCC*CCCCC*C*EEEEEEEEECCCCCCCEEEEECC**CCCCCCCCCCCCCEEEEEEEEEEEEE*CCCCCC*EEEEEEEEEEEEC- Structural block scores 0 1 - 4.5 M 75.0 5.5 75.0 75.0 75.0 75.0 4 13 H 4.9 H 3.4 3.1 3.8 4.3 4.0 4.8 15 17 - 4.5 M 75.0 2.7 75.0 75.0 75.0 75.0 18 27 C 4.8 H 5.0 5.0 4.3 5.0 12.0 4.2 30 32 C 4.8 H 7.3 6.3 6.3 30.2 5.3 6.5 33 48 E 4.8 H 1.4 2.1 2.0 1.6 2.2 2.0 49 50 C 4.4 M 8.0 5.5 6.0 39.5 42.8 6.5 51 54 - 4.5 M 75.0 9.8 75.0 75.0 75.0 75.0 55 56 C 4.5 M 5.5 1.5 4.5 6.0 6.0 5.0 57 69 E 5.0 H 1.3 1.1 1.9 1.5 1.2 1.6 72 74 - 4.1 M 53.5 25.0 51.3 75.0 75.0 27.3 75 76 * 2.7 P 3.5 75.0 2.5 2.0 1.5 75.0 77 79 C 4.7 H 3.3 4.3 3.3 4.7 4.8 3.8 80 83 * 3.1 M 4.8 5.5 5.0 75.0 75.0 40.0 84 87 C 5.0 H 5.8 4.0 5.5 5.8 5.0 5.1 88 91 E 4.7 H 2.2 2.5 2.5 2.2 3.0 1.8 93 95 - 4.2 M 75.0 75.0 75.0 28.3 3.0 75.0 96 98 H 4.1 M 4.7 3.3 3.3 4.0 4.0 4.8 99 103 C 5.0 H 1.4 0.8 1.4 1.2 1.4 1.4 104 106 E 5.0 H 1.0 1.0 1.3 1.3 1.0 1.3 107 111 C 4.5 M 3.2 3.0 3.6 3.0 4.2 2.2 113 114 C 4.2 M 5.5 1.0 7.5 39.5 38.5 6.5 115 116 E 4.1 M 5.0 4.5 9.2 5.0 3.5 4.5 117 118 C 4.8 H 3.5 4.5 41.0 4.5 3.5 4.0 119 122 - 4.1 M 75.0 75.0 75.0 6.5 6.5 75.0 123 124 C 4.5 M 7.0 6.8 6.8 2.5 1.5 6.0 125 129 E 4.6 H 2.0 2.4 2.4 2.2 1.8 2.2 130 132 C 4.4 M 2.7 3.3 2.3 4.0 3.7 2.7 133 136 E 5.0 H 2.2 1.5 1.2 2.2 1.0 2.0 137 138 * 1.0 P 2.5 1.5 3.0 1.5 1.5 2.0 139 145 E 4.8 H 1.6 2.1 3.0 1.9 1.3 2.0 146 148 C 4.2 M 2.0 3.0 4.3 2.0 3.5 2.3 150 154 C 4.5 M 5.2 62.1 5.6 34.2 7.2 5.3 158 166 E 4.8 H 1.3 1.2 1.2 0.7 1.2 1.3 167 173 C 5.0 H 2.9 3.7 3.9 4.6 4.3 4.1 174 178 E 4.8 H 1.8 1.0 1.4 1.2 2.0 1.6 179 180 C 4.5 M 5.5 4.5 3.0 3.5 6.0 5.0 181 182 * 3.4 M 75.0 7.8 75.0 7.0 9.2 75.0 183 195 C 4.7 H 5.1 14.6 5.3 4.4 4.8 15.5 196 208 E 4.7 H 2.7 3.2 3.3 4.4 3.5 3.2 210 215 C 4.8 H 5.8 6.1 7.2 29.4 29.8 5.9 217 228 E 4.8 H 1.4 1.3 1.3 1.6 1.1 1.1 >>>>>>