Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1lbua2 ----------------CCCCCCCCCCCCC-----------------C--CCCCCCC------------HH----HHHH---HH---HHHHHHHHHHHHHCC---CCCCCEEECCCCHHHHHHH------------------------------CCCCCCHHHHCCEEEECCC----------------------------------CCCHHHHHHHHHHCCCCEEECCCCCCCC-----------------------CCEEEECCC----CCEEECHHHCC---------------------------- >P1;d1r44a- -------------------------CCCCEEEHHHCCCCCEECCHHH--CCCCCCC------------CC----CCCCCCCCCEEEHHHHHHHHHHHHHCCCC-CEEEEEEECCCCHHHHHHHHHHH-CCCCCCCCHHHHCCCCCCCHHHHCCCCCCCCHHHHCCEEEEEEEECCCCCCCCCCCCCCCCCHHHCCCCCCCC--HHHHHHHHHHHHHHHCCCEEE-----CC-------------------------CCCCEEEECCCCCCCCCCCCCCC------------------------------ >P1;d1tzpa- ---------------------------------CCHHHHCCCCCCCCCEEEEECCEEEEECCEECCCCCCCEEECCHHHC-CCEECHHHHHHHHHHHHHHHH-CCCCCEEECCCCCCCCCCCCC--------------------------------CCCCCCCCCEEEEECCCCC--CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHHHHHHHCCCCCHHHHHEEECCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHCCCC >P1;d1xp2b1 -------------------------C---CCCHHHHHHHHH--HHHC--CC--------------------------------CCCHHHHHHHHHHHHHHHCC-CCCEEEEECCCCHHHHHHHHHCCCCCCCCCCC------CCCCC----------CCHHHHCCEEEEEEECCCCCCEECCCCC----------------------HHHHHHHHHHHHCCCEE-----HHHCC--------------------CCCCCCEEECCCCCCC---CCCCCC------------------------------ >P1;d3k7ib- CCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCHHHHHCEECCCC--CEEECCC------------CC----CCHHHEECH---HHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCC-----------------------------------CCCHHHHCCEEEEEECC-------------------------------CCHHHHHHHHHHHHHCCCCEEEEEEC---------------------------CEEEEEC---------CCCCCCC----------------------------- PSA >P1;d1lbua2 ----------------a30848200604a-----------------7--0660438------------39----5047---20---570072026017518---5470505400205820795------------------------------928ab22003020010245----------------------------------7073440042038290410101438c27-----------------------a2000004b----a65220460a0---------------------------- >P1;d1r44a- -------------------------24a4001015307a07340100--2860001------------82----07005262000054006003603740746-50101010001053008303810-7583677129500280608302747005770100100000000145836860601040010184020a1bb07--b92331063035003704060-----46-------------------------210010104a0234a41241206------------------------------ >P1;d1tzpa- ---------------------------------5440061681087a14000405500001054055a293000052723-120002200600440044039-5a021000220000000509a--------------------------------a650000000020102019--a41896614719445001a73560399305850130022004182031010100003200730bb73b0032010578121300000500a8085075498069b241b94095218b21930541277940 >P1;d1xp2b1 -------------------------a---618493026203--6406--4d--------------------------------50581004201600460175-60001014021468606632231294988442------72504----------5100040000100012880883452454----------------------94065007004829080-----0054a--------------------7944320000130368---5a23a7------------------------------ >P1;d3k7ib- b88365084553149571346a00151365074a3933730350728--4050435------------4a----550021016---302430340074038317c1301011000254629-----------------------------------a5100000000000025-------------------------------645b2012002002408010020346---------------------------7200000---------417559c----------------------------- Translating the sequences ----------------*********CCCC-----------------C--CC**CCC------------**----**HH---**---HHHHHHHHHHHHH**---CCC**EEECCCCHHHHHHH------------------------------***CCCHHHHCCEEEE**C----------------------------------***HHHHHHHHHHCCC*EEE***C****-----------------------CCEEEECCC----CC***C***C*---------------------------- -------------------------CCCC**************C***--CC**CCC------------CC----CC*****C****HHHHHHHHHHHHH***C-C**EEEEECCCCHHHHHHH****-****************************CCCHHHHCCEEEEEE**CC**C**C********************--****HHHHHHHHHHH*CC*EE-----C*-------------------------CCC*EEE*CCCCCCCC*CCCCCC------------------------------ ---------------------------------**HHHH****C**C******CC*************CC****CCHH**-C****HHHHHHHHHHHHHHH*-*CCC*EEE*CCCC********--------------------------------CCC****CCEEEEE*CCCC--C**C**************************HHHHHHHHHHHHCCCEEEE******************************CC*EEEE*CCCCCCCC*CCCCCCC***************************** -------------------------C---******HHHH**--***C--CC--------------------------------***HHHHHHHHHHHHHHH*C-CCCEEEEECCCCHHHHHHH*************------*****----------CCHHHHCCEEEEEE*CCC**C**C****----------------------HHHHHHHHHHHHCCCEE-----*****--------------------**CCC*EEECCCCCCC---CCCCCC------------------------------ *************************CCCC******HHHH****C**C--C***CCC------------CC----CCHH***C*---HHHHHHHHHHHHHHH*C*CCCEEEEECCCC*****-----------------------------------CCCHHHHCCEEEEEECC-------------------------------***HHHHHHHHHHHHCCC*EEE***C---------------------------C*EEEEC---------CCCCCCC----------------------------- 55166.tem _________________________________ -------------------------CCCC******HHHH****C**C--CC**CCC------------CC----CCHH**-C****HHHHHHHHHHHHHHH*C-CCCEEEEECCCCHHHHHHH*--------------------------------CCCHHHHCCEEEEEECCCC--C**C****-------------------***HHHHHHHHHHHHCCCEEEE***C****----------------------CCCEEEECCCCCCCCC*CCCCCCC----------------------------- Structural block scores 0 24 - 4.2 M 49.4 75.0 75.0 75.0 4.7 25 28 C 4.3 M 5.1 5.1 75.0 58.9 3.8 29 34 * 2.7 P 75.0 1.2 51.5 5.2 4.9 35 38 H 4.1 M 75.0 5.1 2.5 2.5 5.5 39 42 * 2.5 P 75.0 3.5 4.0 38.2 2.8 44 45 * 2.1 P 75.0 0.5 7.5 2.0 4.5 47 48 - 4.5 M 75.0 75.0 2.5 75.0 75.0 49 50 C 4.2 M 3.0 5.0 0.0 8.8 2.0 51 52 * 2.1 P 3.0 3.0 2.0 75.0 2.5 53 55 C 4.4 M 5.0 0.3 3.3 75.0 4.0 56 67 - 4.5 M 75.0 75.0 2.5 75.0 75.0 68 69 C 4.1 M 6.0 5.0 5.5 75.0 7.2 70 73 - 4.5 M 75.0 75.0 0.8 75.0 75.0 74 75 C 4.1 M 2.5 3.5 2.5 75.0 5.0 76 77 H 4.1 M 5.5 0.0 4.5 75.0 0.0 78 79 * 3.0 P 75.0 3.5 2.5 75.0 1.5 82 85 * 2.8 P 56.2 0.0 0.5 21.2 57.8 86 100 H 4.8 H 3.4 3.0 1.9 2.2 2.7 104 106 C 4.7 H 5.3 2.0 4.2 2.0 5.5 107 111 E 4.6 H 2.8 0.4 0.6 1.2 0.6 112 115 C 5.0 H 0.5 0.2 0.5 1.8 0.5 116 122 H 3.9 M 5.1 2.7 2.0 5.0 25.1 124 155 - 4.1 M 68.6 6.1 75.0 37.5 75.0 156 158 C 4.8 H 8.0 4.7 7.2 27.0 5.5 159 162 H 4.5 M 1.2 0.5 0.0 1.0 0.0 163 164 C 5.0 H 1.0 0.0 0.0 0.0 0.0 165 170 E 4.7 H 1.2 0.0 0.5 0.2 0.0 171 174 C 4.1 M 57.5 4.5 3.0 4.8 39.2 175 176 - 3.8 M 75.0 4.5 75.0 4.0 75.0 178 179 * 3.0 P 75.0 3.0 2.5 3.5 75.0 181 184 * 3.0 P 75.0 1.2 5.5 3.8 75.0 185 203 - 3.9 M 75.0 11.5 4.6 75.0 75.0 204 206 * 2.7 P 52.3 4.7 2.7 75.0 5.0 207 218 H 4.9 H 2.9 2.6 2.1 3.6 2.0 219 221 C 4.8 H 3.7 1.3 3.7 3.7 2.7 222 225 E 4.3 M 1.5 39.0 1.0 39.5 0.8 226 228 * 3.0 P 1.7 75.0 0.7 75.0 2.3 230 233 * 2.8 P 7.4 57.8 0.8 4.9 75.0 234 255 - 4.4 M 75.0 75.0 3.8 68.9 75.0 256 258 C 4.3 M 29.2 1.0 2.0 3.7 28.0 259 262 E 4.7 H 0.0 0.5 0.0 0.5 0.0 263 271 C 4.2 M 36.9 4.2 4.1 19.0 66.7 273 279 C 4.5 M 3.5 12.9 5.6 16.1 6.2 280 308 - 4.5 M 72.4 75.0 4.9 75.0 75.0 >>>>>>