Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1oi0a- --------------------------------CCCCEEEHHHHHHHHHHHHHHCC---CCCEEEEEEC-------CCEECEEEECCCC------------------------CC-----CCEEEEEEEEECCCCCCCCHHHHHHHHH-------CCCEEEEEECCCC--CCCEEEEE----CCCC----------EECCEEE---------------------------------------------------------------- >P1;d2kcqa1 -----------------------------------CCCCHHHHHHHHHHHHHHC---CCCCCEEEEEEEC--CCCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH-----CCEEEEEEEEECCCCCCCCHHHHHCCCCC------CCEEEEEEEE--CCEEEEEEEEEECCCCC-----------------------CEEEECCCCCCCCC------C--------------------------------------- >P1;d2znra1 C------------------------------CCCCEEEECCHHHHHHHHHHHHHCCC-CCCEEEEEEEEEC---CEEEEEEEEECCEEEE-----CCEEEECCHHHHHHHHHHH-----CCEEEEEEEECCCCCCCCCHHHHHHHHHHHH-HCCCC-EEEEEE-HHH--C-EEEEEEEC--HHHHHHHHHCCCCCCCCCCC-CCCCEEECCCEEEEC-CCCEEEECC--------------------------------------- >P1;d4ilgc- CHHHHHHHHHHHHHHHHHHHCEEECCCCCCCCCCEEEEEHHHHHHHHHCCCC----C-CCCEEEEEEEECCCCCCEEEEEEEECCCEEEE-----CCEEEECCCCCCCCCCCCC-----CCEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCCCCEEEEEEEEC-C--EEEEEEEEEC--HHHHHHHHHCCCCCCCCCCCCCHHHEEEE-EEEEECCCCCEEEEECCCCCCCCCCHHHCCCCCCCCEEECCCCCCCCHHHCCCCC >P1;d5w83a- ------------------------------CCCCEEEECHHHHHHHHHHHHHCCCCCCCCCEEEEEEECC--CC-EEEEEEEEECC----EECCCCCCCCEECHHHHHHHHHHHHHHCCCCEEEEEEECCC----CCCCCHHHHHHHHCCCCCCCCEEEEECCCCC---CCCEEEEEEEEECCCC-------------------CCEEEEEEECEEECCC------HHHHHHHHHHHCC--------------------------- >P1;d5w83b- --------------------------------CCEEEECHHHHHHHHHHHHHHC---CCCCEEEEEEEEE--ECCEEEEEEEEECC----CC--------CCCHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCHHHHHHHHHHHHHCC-CCEEEEEECCHHHHCCCEEEEEEEC--------------------------CCEEEEEEECCC---------HHHHHHHHHHHHHHHC------------------------ PSA >P1;d1oi0a- --------------------------------ba511036a00750052058136---6503010004-------9420460563827------------------------bb-----8563000000127750816991372047-------5172000005505--79114002----5706----------6390524---------------------------------------------------------------- >P1;d2kcqa1 -----------------------------------0306571164058333612---87a0501000454--ba842504202238a9a76968954a9719147503630785-----92300010211668606079923680742------c200000005--a3717501012027947-----------------------70654715746795------a--------------------------------------- >P1;d2znra1 b------------------------------92320000640273038107921675-200000000545a---9501021000040601-----6540715458307711964-----a033000000006660303131024007216-91500-000000-274--9-63121202--b4019304729787419079-978024909006457-470421313--------------------------------------- >P1;d4ilgc- 769715743751760541076172567a557843101003500530030002----7-200000000333a9464312040000000104-----6440200410809927809-----a031000000026639303120011005001963470000001037-a--1020100303--87007007616585186379154910630-1071279380600003b320011324b708272a2a0435802500175034a7b >P1;d5w83a- ------------------------------99075000015015305600665b179c40000000050a--75-10405401105----09154657418055a30593266228967913000000005----93281048005103610433000000305ec---b440401003577959-------------------8573205506073608------9834682477869--------------------------- >P1;d5w83b- --------------------------------8110403150164018204813---7540200000602--68610403000405----57--------a268a337732762778a26451000000002430404990082046018859-20000000043067a6330300106--------------------------a73450805448---------aa3697478663777b------------------------ Translating the sequences --------------------------------CC**EE*HHHHHHHHHHHHHHC*---CCCEEEEEE*-------**EE*EEEECC**------------------------**-----CCEEEEEEEE*CCCCCCCCHHHHHHHHH-------CC*EEEEEE****--C**EEEEE----****----------*******---------------------------------------------------------------- -----------------------------------****HHHHHHHHHHHHHHC---*CCC*EEEEEEE*--*CC*EEEEEE**CC*********CC****CCHHHHHHHHHHH-----CCEEEEEEEE*CCCCCCCCHHHHH*****------CCEEEEEEE*--*****EEEEEEEC****-----------------------*EEE******C*CC------*--------------------------------------- *------------------------------*CC*EEE***HHHHHHHHHHHH****-CCCEEEEEEEE**---CEEEEEEEEECC****-----CC****CCHHHHHHHHHHH-----CCEEEEEEEE*CCCCCCCCHHHHHHHHHH**-*C*CC-EEEEEE-***--C-EEEEEEEC--********************-*****EE***E***C-CC*******--------------------------------------- ********************************CC*EEE*HHHHHHHHH****----*-CCCEEEEEEEE****CCEEEEEEEE*CC****-----CC****CC***********-----CCEEEEEEEE*CCCCCCCCHHHHHHHHHH****C*CCEEEEEEE**-*--**EEEEEEEC--**************************EEE-*E***C*CC********************************************** ------------------------------**CC*EEE*HHHHHHHHHHHHH*C****CCCEEEEEEE**--*C-EEEEEEEEECC----*****CC*****CHHHHHHHHHHH*****CCEEEEEEE**C----CCC**HHHHHHHH****C*CCEEEEE*****---C**EEEEEE*******-------------------***EEE**E*****CC------*************--------------------------- --------------------------------CC*EEE*HHHHHHHHHHHHHHC---*CCCEEEEEEEE*--*CCEEEEEEEEECC----**--------*CCHHHHHHHHHHH*****CCEEEEEEEE*CCCCCCCCHHHHHHHHHH****C-CCEEEEEE*******C*EEEEEEEC--------------------------**EEE**E***C---------****************------------------------ 102712.tem _________________________________ -------------------------------*CC*EEE*HHHHHHHHHHHHHHC*-**CCCEEEEEEEE*--*CCEEEEEEEEECC******---CC****CCHHHHHHHHHHH-----CCEEEEEEEE*CCCCCCCCHHHHHHHHHH****C*CCEEEEEEE****--C*EEEEEEEC--****----------******---***EEE**E***C*CC------*************--------------------------- Structural block scores 0 30 - 4.5 M 75.0 75.0 73.0 5.0 72.9 75.0 32 33 C 4.5 M 11.0 75.0 2.5 3.5 3.5 4.5 35 37 E 4.4 M 0.7 1.0 0.0 0.3 0.0 1.3 39 52 H 4.7 H 3.5 3.8 3.7 6.9 3.1 2.9 56 57 * 3.4 M 75.0 41.5 40.0 41.0 10.8 41.0 58 60 C 5.0 H 3.7 5.8 0.7 0.7 1.3 3.0 61 68 E 4.8 H 10.4 1.9 1.1 0.8 0.6 1.0 70 71 - 4.3 M 75.0 75.0 42.8 9.8 75.0 75.0 73 74 C 4.3 M 75.0 9.2 42.0 5.0 40.0 7.0 75 83 E 4.6 H 4.0 2.3 1.0 1.1 1.8 1.3 84 85 C 5.0 H 5.5 5.5 2.0 0.0 2.5 2.5 86 91 * 3.2 M 51.5 8.7 26.2 25.8 51.5 52.0 92 94 - 4.1 M 75.0 7.7 75.0 75.0 3.3 75.0 95 96 C 4.3 M 75.0 4.5 5.5 5.0 5.5 75.0 97 100 * 2.5 P 75.0 6.9 3.0 1.5 5.0 58.9 101 102 C 4.3 M 75.0 5.0 4.5 2.0 2.5 4.0 103 113 H 4.2 M 63.5 4.4 4.6 4.8 4.7 5.3 114 118 - 4.1 M 75.0 75.0 75.0 75.0 6.4 6.9 119 120 C 5.0 H 6.5 5.5 5.2 5.2 5.0 5.0 121 128 E 4.9 H 1.1 0.9 0.8 0.5 0.4 0.8 130 137 C 4.8 H 4.5 4.9 3.0 4.0 39.9 2.1 138 147 H 4.6 H 11.7 5.0 2.0 1.0 2.7 3.8 148 151 * 2.9 P 75.0 75.0 22.8 4.0 2.5 5.5 154 155 C 5.0 H 3.0 7.2 0.0 3.5 1.5 1.0 156 162 E 4.7 H 1.3 0.0 10.7 0.1 0.4 0.0 163 166 * 2.1 P 3.8 41.4 22.0 23.9 26.8 3.2 167 168 - 4.1 M 75.0 5.0 75.0 75.0 75.0 8.8 171 177 E 4.8 H 11.9 1.3 2.1 0.9 1.3 1.0 179 180 - 4.1 M 75.0 8.0 75.0 75.0 6.0 75.0 181 184 * 2.3 P 4.5 40.2 4.1 3.8 7.5 75.0 185 194 - 4.1 M 75.0 75.0 5.6 4.5 75.0 75.0 195 200 * 3.4 M 4.2 75.0 5.0 5.7 75.0 75.0 201 203 - 4.1 M 51.3 75.0 30.3 3.3 75.0 75.0 204 206 * 2.7 P 75.0 52.3 3.3 3.3 6.7 30.8 207 209 E 4.4 M 75.0 3.7 4.3 3.0 1.7 4.0 210 211 * 2.3 P 75.0 5.5 4.5 38.0 5.0 4.0 213 215 * 1.9 P 75.0 5.3 5.0 3.3 4.3 4.3 218 219 C 4.3 M 75.0 7.0 5.5 5.5 4.0 75.0 220 225 - 4.1 M 75.0 75.0 1.8 1.0 75.0 75.0 226 238 * 3.3 M 75.0 70.0 69.5 3.8 6.2 6.7 239 265 - 4.5 M 75.0 75.0 75.0 4.4 75.0 67.6 >>>>>>