Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1b24a1 ----------------------------------CHHHHHHHHHHHHHCEEEEEEECCC------CC-EEEEEEEEEC--CHHHHHHCCCCCCHHHHHCCCCCCCEEEECC-----CCEEEEEECHHHHH-HHHCC-CCCC--------------------------------------------------------------------- >P1;d1b24a2 --------------------------------CCCCHHHHHHHHHHHHHCC--C-----C----C----C-CCEEEEC--CHHHHH-HHHH--HHHH-CCCCEEEEEEE---CCCC-EEEEEEC-HHHHH-HHHHHHC------------------------------------------------------------------------ >P1;d1dq3a3 ----------------CCCCC------------CCCCHHHHHHHHHHHHEEEEEEECCCCC---CCC-EEEEEEEEEC--CHHHHH-HHHH--HHHHHHC--CCCCCEECC-----CCEEEEECCHHHHH-HHHHHHCCHHH-------------------------------------------------------------------C >P1;d1dq3a4 ------------------CCHHHHC-------CCHHHHHHHHHHHHHHHCEEEC---------------CCEEEEEEC--CHHHHH-HHHH--HHHC-CCCCCEEEEEE---CCCCEEEEEEECCHHHHH-HHHHHCHH---HCCC--HHHHHHHHHHHHCCCC---------------------------------------------- >P1;d1jvaa2 -----------CCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCC------------------CCCEEEEECCCHHHHH-HHHH--HHHH-CCCEEECCC----CCCCCCEEEEEEECCC--CCHHHHHHHHCCCCCC----------------------------------------------------------------- >P1;d1jvaa3 --------------CCCCCCHHHHH-------CCHHHHHHHHHHHHHHHEEEEC-----C----C----CCEEEEEEC--CHHHHH-HHHH--HHHH-CCCEEEEEEEC------CCEEEEEEEC----C-HHHHHHHC---CCCC--CCCCCCCCCC-CCCCC---------------------------------------------- >P1;d1m5xa- --------------------C------------CCHHHHHHHHHHHHHHEEEEEEEEECCCCCCCCEEEEEEEEEEEEHHHHHHHH-HHHH--HC----CCCCEEECCCC-----CCEEEEEEECHHHHH-HHHHHHCC---CCC-CCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCC >P1;d1r7ma1 CCCHHHHCCCCCCCHHHHHHHHHCC-------CCCHHHHHHHHHHHHCCCEEECCCC----------CCCCEEEEEEC--CHHHHHHHHHHCHHHCCC---CCEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHCCCC---------------------------------------------------------------------- >P1;d1r7ma2 ---------------CCCCCCCHHH-------H--HCCHHHHHHHHHHHEEECC-----CCCCCC----CCCEEECCCCCCHHHHH-HHHH--HHHHHHCCCEEEEEEC-------CEEEEEEC-HHHHH-HHHHHHCC---CC-C--HHHHHHCC------------------------------------------------------ >P1;d3eh8a1 -----------------------------------CCHHHHHHHHHHHHEEEEEEEEC-------CE-EEEEEEEEEEHHHHHHHH-HHHH--HH----C-CCEEEEEEECC---EEEEEEEECCHHHHHHCHHHHHHH--CCCCCCCHHHHHHHHHHHHCC-------CCCHHHCCCCCCCCCCC------------------------ >P1;d3eh8a2 --------------CCHHHHH------------CCCCHHHHHHHHHHHHCEEEEEECC----CCCCC-EEEEEEEEEE-CCHHHHH-HHHH--HC----CCCCCCEECC------CCEEEEEECCHHHHH-HHHHHHHHCCCCCCCHHHHHHHHHHHHHHCC-------HHHHCCCC---CCC-CC------------------------ PSA >P1;d1b24a1 ----------------------------------4ab2175029206a6131544767a------c8-3322000236--75640674025255007529092817235ab-----75130204167028-40244-7879--------------------------------------------------------------------- >P1;d1b24a2 --------------------------------b588523730592057703--6-----6----3----8-3030346--748304-5018--1068-28060707234---8865-2100204-69038-5038216------------------------------------------------------------------------ >P1;d1dq3a3 ----------------b6c8b------------797622630192029507256441779c---756-5322030318--545106-6018--2057318--471a14558-----a3200103176005-304731896aa-------------------------------------------------------------------b >P1;d1dq3a4 ------------------0488346-------586b40183009101660603a---------------700030236--756102-2007--2048-28060624579---499842110102648004-50253005---6094--7922550461088177---------------------------------------------- >P1;d1jvaa2 -----------99989869357306835a936a3026005300920596058------------------7600030438579318-4066--0072-070604244----8839665130107459--b120250056053389----------------------------------------------------------------- >P1;d1jvaa3 --------------e98604b7029-------4846510740092027405056-----9----9----a14000306--556126-4016--0063-04080727239------7820003043----9-40032001---3095--99152750b9-b282a---------------------------------------------- >P1;d1m5xa- --------------------a------------16693047009201950403050363892670513010000031657416705-6025--40----86317157339-----653010205758305-50045015---409-814600530260194368026427500600410150312327b83a816127503640484924 >P1;d1r7ma1 b1719503a4999284054028418-------7066702640381077606030728----------47201040419--848504701820540016---7084357749677554122060151800270075228a7---------------------------------------------------------------------- >P1;d1r7ma2 ---------------9851565402-------7--8164640061008301242-----799a39----44000040391767106-2003--0047317030523459-------a6000002-37019-50382035---30-5--78248100------------------------------------------------------ >P1;d3eh8a1 -----------------------------------9844260092029504030656b-------76-020000021439449205-6039--30----8-007055556b8---75300040364a404750051057--250a74112104202700579-------24448517b39449882------------------------ >P1;d3eh8a2 --------------7748611------------84b7024400910364050505555----aa595-3100030247-8275202-0036--30----807771662a------862040403717002-2006104805640988128404700630471-------8302870a---018-b0------------------------ Translating the sequences ----------------------------------***HHHHHHHHHHH**EEE******------**-***EEEEEE*--CHHHHH*******HH****CCC***EEE***-----**EEEEE*CHHHHH-HHH**-****--------------------------------------------------------------------- --------------------------------*C***HHHHHHHHHHHH**--*-----*----*----*-**EEEE*--CHHHHH-HHHH--HH**-*CCC*E*EEE*---****-EEEEEE*-HHHHH-HHHHHH*------------------------------------------------------------------------ ----------------*****------------C***HHHHHHHHHHHH*EEE********---***-***EEEEEE*--CHHHHH-HHHH--HH****C--*****E***-----**EEEEE*CHHHHH-HHHHHH*****-------------------------------------------------------------------* ------------------*******-------*C***HHHHHHHHHHHH*EEE*---------------**EEEEEE*--CHHHHH-HHHH--HH**-*CCC*E*EEE*---*****EEEEEE*CHHHHH-HHHHH***---****--****************---------------------------------------------- -----------**********************C***HHHHHHHHHHHH***------------------***EEEE***CHHHHH-HHHH--HH**-*CC**E***----******EEEEEE*C**--**HHHHHH********----------------------------------------------------------------- --------------***********-------*C***HHHHHHHHHHHH*EEE*-----*----*----**EEEEEE*--CHHHHH-HHHH--HH**-*CC**E*EEE*------**EEEEEE*C----*-HHHHHH**---****--**********-*****---------------------------------------------- --------------------*------------C***HHHHHHHHHHHH*EEE******************EEEEEE****HHHHH-HHHH--H*----CCC*E*E****-----**EEEEEE*CHHHHH-HHHHHH**---***-**************************************************************** *************************-------*C***HHHHHHHHHH***EEE****----------****EEEEEE*--CHHHHH*HHHH**HH***---C*E*EEE*********EEEEE**C*HHHH*HHHHH****---------------------------------------------------------------------- ---------------**********-------*--***HHHHHHHHHHH*EE**-----******----***EEE*****CHHHHH-HHHH--HH****CCC*E*EEE*-------*EEEEEE*-HHHHH-HHHHHH**---**-*--********------------------------------------------------------ -----------------------------------**HHHHHHHHHHHH*EEE*****-------**-***EEEEEE****HHHHH-HHHH--HH----C-C*E*EEE****---**EEEEEE*CHHHHH**HHHHH**--*********************-------*****************------------------------ --------------*******------------C***HHHHHHHHHHHH*EEE*****----*****-***EEEEEE*-*CHHHHH-HHHH--H*----CCC***EE**------**EEEEEE*CHHHHH-HHHHHH*************************-------********---***-**------------------------ 55608.tem _________________________________ --------------***********-------*C***HHHHHHHHHHHH*EEE*****-*----***-***EEEEEE***CHHHHH-HHHH--HH****CCC*E*EEE***-*****EEEEEE*CHHHHH-HHHHHH*********--**************------------------------------------------------ Structural block scores 0 13 - 4.7 H 75.0 75.0 75.0 75.0 60.9 75.0 75.0 5.8 75.0 75.0 75.0 14 24 * 3.3 M 75.0 75.0 45.4 30.3 5.8 6.5 69.1 4.0 10.9 75.0 30.4 25 31 - 4.8 H 75.0 75.0 75.0 75.0 6.4 75.0 75.0 75.0 75.0 75.0 75.0 34 36 * 1.3 P 8.7 7.0 7.3 7.2 2.7 5.0 7.0 6.3 28.0 30.7 7.5 37 48 H 4.9 H 4.2 4.2 3.4 2.9 3.2 3.0 3.3 3.7 3.2 3.6 2.8 50 52 E 4.5 M 3.0 51.0 4.7 3.0 29.3 3.3 2.3 3.0 2.3 2.3 3.3 53 57 * 2.9 P 5.6 61.2 4.4 62.1 75.0 61.2 2.8 18.4 60.4 5.7 4.0 60 63 - 4.3 M 75.0 75.0 59.4 75.0 75.0 75.0 6.0 75.0 7.9 75.0 42.8 64 66 * 3.5 M 31.8 51.0 6.0 75.0 75.0 53.0 2.0 75.0 53.0 29.3 6.3 68 70 * 2.1 P 2.7 52.7 3.3 27.3 52.3 28.8 0.3 3.0 27.7 0.7 1.3 71 76 E 4.7 H 1.2 2.2 1.5 1.3 1.5 1.2 0.7 1.7 0.7 0.5 1.5 77 79 * 2.8 P 52.0 52.0 52.7 52.0 5.0 52.0 6.0 53.0 4.3 5.3 30.0 81 85 H 5.0 H 4.2 3.8 3.2 2.8 5.6 4.0 3.8 4.2 4.0 4.0 3.2 87 90 H 4.8 H 2.8 3.5 3.8 2.2 4.0 2.8 3.2 2.8 1.2 4.5 2.2 91 92 - 4.5 M 3.5 75.0 75.0 75.0 75.0 75.0 75.0 2.5 75.0 75.0 75.0 93 94 H 4.8 H 2.5 0.5 1.0 1.0 0.0 0.0 2.0 2.0 0.0 1.5 1.5 95 98 * 2.9 P 3.5 22.8 4.0 22.2 21.0 21.0 75.0 20.5 3.8 75.0 75.0 99 101 C 4.5 M 6.0 4.7 52.7 4.7 4.3 4.0 5.7 52.3 3.3 27.7 5.0 105 107 E 4.3 M 4.0 4.0 5.2 5.3 27.7 4.0 5.0 5.0 4.0 5.0 4.7 108 110 * 3.0 P 9.0 51.3 6.0 53.0 75.0 53.0 29.0 6.7 53.0 7.5 53.5 112 116 * 3.1 M 61.4 20.4 62.1 6.8 6.4 48.0 47.2 5.6 62.1 47.4 47.8 117 122 E 4.9 H 1.8 0.8 1.0 0.8 1.7 0.8 1.0 1.8 1.0 1.2 1.7 125 129 H 4.5 M 4.6 5.2 3.6 3.2 35.1 61.8 4.2 2.2 4.0 4.5 2.0 131 136 H 4.8 H 14.8 3.2 3.0 2.5 1.5 1.5 2.3 2.7 3.0 1.8 1.5 137 145 * 2.9 P 45.1 67.3 38.2 27.7 12.7 27.0 35.4 52.8 35.1 20.7 4.9 146 147 - 4.2 M 75.0 75.0 75.0 75.0 75.0 75.0 4.5 75.0 75.0 2.5 4.5 148 161 * 3.4 M 75.0 75.0 75.0 4.1 75.0 11.1 3.1 75.0 34.3 2.9 3.3 162 209 - 4.6 H 75.0 75.0 73.7 72.2 75.0 72.1 3.8 75.0 75.0 50.4 55.9 >>>>>>