Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ex2a- -----CCCCEEECCCCHHHHHHHHCCC-----C-CCEECCC---CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC-----CCEEEEEEEEEEEC---CEEEC-----CCC----CHHHHHHHHHHHCC-----CEEEEEEEEEEEE-CC--EEEEEEEEEEEEECCCCHHHHHHHHCCCCHHHCCCCCCCC----H-HHHHCEEEEEC----CHHHHHCCCHHHHHHHHCCC----- >P1;d1k7ka1 -------CEEEECCCCHHHHHHHHHHCC--CCC-EEEECCCCCCCCCCCCCC------CHHHHHHHHHHHHHHHHC------CCEEEEEEEEEEHHHCCCC-HHHCCCCCCCCCCHHHHHHHHHHCC-CCCHHHCEEEEEEEEEEECCCCCCCCEEEEEEEEEEECC----CCCCC----CCCCCHHHEECH---HHCCCHHHC----C-CHHHHHCHHHHHC-CHHHHHHC-C---- >P1;d1u14a1 -------CEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEC---CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC-----CCCEEEEEEEEEEC-----------------------------------------CEEEEEEEEECCC----CEEEEECCCEECC---HHHHHHHCCCCCCCCCCCCCCCCCHHHCCHHHHHHC----CCCCCHHHHHHHHHHHHCHHHCCC----- >P1;d1v7ra- -------CEEEEECCCHHHHHHHHHHHHC-CCC-EEEEEC---CCCCCCCCC------CHHHHHHHHHHHHCCCCC------CCEEEEEEEEEEHHHCCCC-HHHHHHHHH-----HCHHHHHHHHCCCC--CCCEEEEEEEEEEEECC---EEEEEEEEEEEEECC----CCCCC----CCCCCHHHEEEC---CCCCCHHHC----CHHHHHCCCHHHHHHHHHHHHHHHHHCC-- >P1;d1vp2a- ------CEEEEECCCCCCCC-CCHHHCC--C-E-EEEECC-----CCCCCCC------CHHHHHHHHHHHHHC-CC------CCEEEEEEEEEEHHHCCCC-HHHCC-CC-CCCCC-CHHHHHHHHCCCCC---CEEEEEEEEEEEECCC-CEEEEEEEEEEEEECC----CCCCC----CCCCCHHHEEEC---CCCCCCCCC----H-HHHHHHCHHHHHHHHHHHHHHHHC---- >P1;d2amha1 ----CCCCEEEECCCCHHHHHHHHHHHCCC-CC-EEEECCC---CCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCC---CEEEEEEEEEEEEC---CEEEC-----CCC----CHHHHHHHHHHHCC-----CEEEEEEEEEEEECCCC-CEEEEEEEEEEEECCCCHHHHHHHHHHCHHHHCHHHCCCC----CHHHHCCEEEEEC----CHHHHHCCCHHHHHHHHHCC----- >P1;d2cara1 CHHHHCCCEEEEECCCHHHHHHHHHHHCCCCCC-EEEEEC---CCCCCCCC-------CHHHHHHHHHHHHHHHHC------CCEEEEEEEEEEHHHCCCEE-CCHHHHHH-----HHHHHHHHHCCCCC--CCCEEEEEEEEEEECCCCCCCCEEEEEEEEEEEC-----CCCCC----CCCCCHHHEEEC---CCCCCCCCC----CHHHHHHHCHHHHHHHHHHHHHCC-CCC-- >P1;d4jhca- -------CCEEEECCCHHHHHHHHHHC-----C-CEEEECC----CCCCCC-CCCHHHHHHHHHHHHHHCCCCCCC-----CCEEEEEEEEEEEC---CEEEC-----CCC----CHHHHHHHHHHHCC-----CEEEEEEEEEEEECCCC-CEEEEEEEEEEEECCCCHHHHHHHHHHHCCCCCCCCCCC-----C-HHHHHEEEEECC---CHHHHHCCCHHHHHHHHHHCCCCCC >P1;d4oo0a- -CCCCCCCCCEECC-CHHHHHHHHHCC-----C--CEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEC---CEECC-----CCC----CHHHHHHHHHHHCC-----CEEEEEEEEEEECCCCC-CCCCEEEEEEEEECCCCHHHHHHHHHCCCCCCCHHHCCCC----C-HHHHCEEEEEC----CHHHHHCCCHHHHHHHHHHCCCCC- PSA >P1;d1ex2a- -----9a15000017284155004519-----5-9173262---a2a1755ab35235103310322043018736-----70000001110008---96209-----609----74750060064002-----4303000000010-67--4541231305010680579503600748302843000205----6-60480056275----34400000017503610680----- >P1;d1k7ka1 -------640000226994184038409--3c1-60210573a0a8193718------515600231043007419------210002131020732b540-3051a51199906575005401746-925895050501000010661807813304010603024----7343a----748200100404---837400040----8-a528730123500-50373276-b---- >P1;d1u14a1 -------45000015240126004500361189a3070330---8090a498115327603600341043047545-----a050000002003a-----------------------------------------6110010001319----5301230841703---870085059755145029529597045660110323----848621161038002600530469----- >P1;d1v7ra- -------2501001646211600451057-4b0-704227---39145392a------60240055006404b405------410000100010342a440-105187046-----4431a3027507c2--a3160202000000196---743314130415008----66419----523300100008---b19400020----6485006500004005501620584283-- >P1;d1vp2a- ------72302001a47511-1055012--3-0-604515-----5084729------615500341034007-28------310000101010320b330-22819-23-79584-40063017408c48---2600000000001077-8322024340404008----6335a----422100100007---a49600021----3-820473000040045005305743---- >P1;d2amha1 ----69162000007492107004840495-06-3155120---828386475b61371024004110910263177b---6100000010002c---b5315-----508----58940471054013-----60030000000013b5a-92213324030406908a9104500836702831000004----1500462157187----65400300105003700865----- >P1;d2cara1 129703a650001146975253057107b5000-604267---1b056295-------834600451042026527------320002220000412a2600-13076427-----736170038307a4--a624020000000010279280500315060501-----60445----696711000207---92a500030----779523610023400750382076-a45-- >P1;d4jhca- -------45000008348156006619-----3-9052151----185747-c1526700310033004403a616-----72100000110007---a8319-----506----65850350044010-----34010100000110456-721230050201039077840660065160273300051-----c-406500752535---07200510005002400460a2098 >P1;d4oo0a- -c784628500002-274126007729-----0--15305349829574a69c2813620440033306302800763a4861000001100007---95409-----608----66930171045014-----54040000000021817-2182300503030383779203700736204834000103----5-70670056255----3510000001a3037106603022- Translating the sequences -----**C*EEECCCCHHHHHHHH***-----C-**EE*CC---CCCCCCCC*******HHHHHHHHHHHHHHH*C-----*C*EEEEEEEEEE*---C****-----CC*----*HHHHHHHHHH*CC-----CEEEEEEEEEEE*-CC--**EEEEEEEEEEECC*************C***C*****CC----*-**HH******C----*HH*HH***HHHHHHHH***----- -------CEEEECCCCHHHHHHHHHH**--**C-*EEE*CC***CCCCCCCC------*HHHHHHHHHHHHHHH*C------CCEEEEEEEEEE****C**-******CC******HHHHHHHHH**-C*****CEEEEEEEEEEE*CCC****EEEEEEEEEEECC----*****----CCCCCHHH**C*---*****HH**----C-****HH*HH****-*HHHHHH*-*---- -------CEEEECCCCHHHHHHHHHH******C***EE**C---CCCCCCCC*******HHHHHHHHHHHHHHH*C-----*CCEEEEEEEEEE*-----------------------------------------*EEEEEEEEE*CC----*EEEEE***EE*C---***********CCCCC*****CC****C***HH***----*****HH*HH***HHHH*HHH***----- -------CEEEE*CCCHHHHHHHHHH***-**C-*EEE*C---*CCCCCCCC------*HHHHHHHHHHHH****C------CCEEEEEEEEEE****C**-*********-----H*HHHHHHHH*CC*--**CEEEEEEEEEEE*CC---**EEEEEEEEEEECC----*****----CCCCCHHH***C---*C***HH**----C********HH***HHHHHHHHH*****-- ------**EEEECCCC****-**HHH**--*-*-*EEE*C-----CCCCCCC------*HHHHHHHHHHHHH*-*C------CCEEEEEEEEEE****C**-*****-CC-*****-*HHHHHHHH*CC**---CEEEEEEEEEEE*CCC-***EEEEEEEEEEECC----*****----CCCCCHHH***C---*C*******----*-****HH*HH***HHHHHHHHH***---- ----***CEEEECCCCHHHHHHHHHH****-*C-*EEE*CC---CCC***CC*******HHHHHHHHHHHHHHH****---***EEEEEEEEEE*---C****-----CC*----*HHHHHHHHHH*CC-----CEEEEEEEEEEE*CCC*-**EEEEEEEEEEECC*****************CHHH**CC----C***H*******C----*HH*HH***HHHHHHHHH**----- *******CEEEE*CCCHHHHHHHHHH******C-*EEE*C---*CCCCCCC-------*HHHHHHHHHHHHHHH*C------CCEEEEEEEEEE****C***-********-----HHHHHHHHH**CC*--**CEEEEEEEEEEE*CCC****EEEEEEEEEEEC-----*****----CCCCCHHH***C---*C*******----C*****HH*HH***HHHHHHHH**-***-- -------C*EEE*CCCHHHHHHHHHH*-----C-*EEE*CC----CCCCCC-*******HHHHHHHHHH******C-----*C*EEEEEEEEEE*---C****-----CC*----*HHHHHHHHHH*CC-----CEEEEEEEEEEE*CCC*-**EEEEEEEEEEECC*************CCCCC*****C-----C-**HH******C*---*HH*HH***HHHHHHHHH******* -******C**EECC-CHHHHHHHHH**-----C--*EE*CC***CCCCCCCC*******HHHHHHHHHHHHHHH********CCEEEEEEEEEE*---C****-----CC*----*HHHHHHHHHH*CC-----CEEEEEEEEEEE*CCC*-****EEEEEEEEECC*************CCCCCHHH**CC----C-**HH******C----*HH*HH***HHHHHHHHH******- 52972.tem _________________________________ -----**CEEEECCCCHHHHHHHHHH***-**C-*EEE*CC--*CCCCCCCC*******HHHHHHHHHHHHHHH*C-----*CCEEEEEEEEEE****C********-CC*----*HHHHHHHHHH*CC*----CEEEEEEEEEEE*CCC*-**EEEEEEEEEEECC*************CCCCCHHH**CC---*C***HH******C*****HH*HH***HHHHHHHHH*****-- Structural block scores 0 4 - 4.4 M 75.0 75.0 75.0 75.0 75.0 61.2 3.8 75.0 21.3 5 6 * 3.4 M 9.8 75.0 75.0 75.0 41.0 5.0 6.8 75.0 4.0 8 11 E 4.7 H 1.2 1.0 1.2 1.5 1.2 0.5 1.2 1.2 1.2 12 15 C 4.7 H 2.5 2.5 2.0 2.8 3.9 2.8 3.0 2.8 19.8 16 25 H 4.7 H 3.3 5.0 2.2 2.6 10.0 3.5 4.4 3.7 3.6 26 28 * 2.4 P 53.0 28.0 3.0 4.0 26.0 4.3 6.2 53.0 53.0 30 31 * 3.2 M 75.0 7.8 4.5 7.8 39.0 37.5 0.0 75.0 75.0 35 37 E 4.7 H 3.7 1.0 2.3 2.0 3.0 3.7 2.0 2.3 3.0 39 40 C 4.6 H 4.0 6.0 1.5 41.0 40.0 1.0 41.0 3.0 4.0 41 42 - 4.4 M 75.0 6.8 75.0 75.0 75.0 75.0 75.0 75.0 6.5 44 51 C 4.8 H 6.4 5.9 6.1 5.4 13.8 5.8 14.2 22.8 6.6 52 58 * 2.9 P 4.4 65.0 3.6 65.1 65.1 4.9 65.4 4.8 4.9 59 73 H 4.8 H 2.5 2.4 2.7 3.0 7.2 2.2 2.8 2.5 2.4 76 80 - 4.6 H 75.0 75.0 75.0 75.0 75.0 48.7 75.0 75.0 6.3 82 83 C 4.3 M 0.0 1.5 2.5 2.5 2.0 0.5 2.5 1.5 0.5 84 93 E 5.0 H 0.3 0.9 0.5 0.2 0.3 0.3 0.6 0.2 0.2 94 97 * 2.9 P 58.2 5.9 58.9 4.9 4.1 59.4 4.4 58.0 58.0 99 106 * 2.9 P 39.6 12.3 75.0 11.8 12.5 39.2 11.5 40.1 39.8 108 109 C 4.2 M 3.0 1.0 75.0 2.0 2.5 2.5 3.0 2.5 3.0 111 114 - 4.4 M 75.0 6.0 75.0 75.0 7.2 75.0 75.0 75.0 75.0 116 125 H 4.6 H 3.2 3.3 75.0 4.0 10.0 4.2 3.8 3.4 3.6 127 128 C 4.6 H 1.0 42.0 75.0 9.8 10.2 2.0 8.8 0.5 2.5 130 133 - 4.3 M 75.0 6.8 75.0 40.9 58.2 75.0 41.6 75.0 75.0 135 145 E 4.9 H 0.6 1.1 7.7 0.9 0.5 0.3 0.5 0.6 0.7 147 149 C 4.7 H 29.3 5.0 28.3 30.0 4.7 6.5 3.0 3.0 3.3 152 153 * 1.3 P 4.5 4.5 40.0 5.5 2.5 5.5 4.0 4.5 1.5 154 164 E 4.8 H 1.8 1.8 2.6 2.3 2.1 2.0 2.3 1.3 2.2 165 166 C 4.8 H 7.0 3.0 39.0 4.0 4.0 7.5 38.0 6.0 5.5 167 179 * 2.4 P 4.2 48.3 15.7 48.2 48.3 4.2 47.6 3.8 4.2 180 184 C 4.6 H 3.4 4.2 3.0 2.6 1.8 4.0 5.8 3.6 3.4 185 187 H 4.0 M 1.0 0.3 5.3 0.3 0.3 0.3 0.3 1.0 1.3 188 189 * 1.0 P 1.0 2.0 5.5 0.0 0.0 0.0 1.0 2.5 0.5 190 191 C 4.2 M 2.5 2.0 7.0 4.0 3.5 2.0 3.5 38.0 1.5 192 194 - 4.7 H 75.0 75.0 3.7 75.0 75.0 75.0 75.0 75.0 75.0 197 199 * 1.6 P 27.0 3.7 2.3 4.3 5.0 1.7 5.2 26.3 27.3 200 201 H 4.2 M 6.0 0.0 0.5 0.0 0.0 5.0 0.0 5.5 6.5 202 207 * 2.7 P 3.3 50.7 38.8 50.3 50.5 4.0 50.5 3.2 3.0 209 213 * 2.8 P 60.6 20.1 5.6 3.4 17.8 61.2 5.2 46.0 60.6 214 215 H 4.7 H 4.0 5.0 1.0 5.5 5.0 4.5 3.5 4.5 3.0 217 218 H 5.0 H 0.0 1.5 0.5 0.0 0.0 1.5 1.0 2.5 0.0 219 221 * 1.0 P 0.0 2.7 3.7 1.3 1.3 0.3 2.3 0.3 0.0 222 230 H 4.8 H 3.2 11.3 2.2 2.7 2.4 2.6 3.6 1.7 3.5 231 235 * 2.6 P 46.6 48.5 48.0 5.0 32.8 47.2 20.1 3.7 2.2 236 237 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 8.5 38.5 >>>>>>