Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1nh8a2 -------CEEEEEEEEE-HH------HHHHHHHHCCCCC---CCEEEEC---------CCC---------CEEEEEEEE-EHHHHHHHHHHHHHC------CCEEEEEECCCCCCC----------------- >P1;d1nzaa- -------CEEEEEEEECCHH------HHHHHHHHHHHCCCCCEEEEEEEEEEEEECC-------CCEEEEEEEEEEEEE-ECCCHHHHHHHHHHHCCCC---CCCEEEEECC----CCCHHHHHHHHHCCC-- >P1;d1o2ca1 ---------CEEEEEEEC-CCCCC-CHHHHHC-CCCCCC--CCCEEEECCCCCC--------------CCCEEEEEEEC-CHHHHHHHC----CCCC-----CCEEEEECCCCCC------------------ >P1;d1ukua- --------CEEEEEEECCHH------HHHHHHHHHHHCCCCCEEEEEE-EEEEEEEC-------CEEEEEEEEEEEEEE-CHHHHHHHHHHHHHHCCCC---CCCCEEEECC----CCCHHHHHHHHHHCCC- >P1;d2cz4a1 ----CEEEEEEEEEEEE-HH------HHHHHHHHHHHCC-CCCCEEEE-ECCC---CCCCCCC--CCCCCCEEEEEEEE-CHHHHHHHHHHHHHHCCCC--CCCEEEEEEE-EEE------CHHHHC------ >P1;d2dcla- -CCCCCCCEEEEEEEEECCCEECCEEHHHHHHHHHHHCC-CCCCEEEECCCCCC--------------CCCEEEEEEEE-EHHHHHHHHHHHCCCCC-----CCEEEEEECCCCCCCCC------------CC >P1;d2hfva1 ---------CEEEEEECCCC------HHHHHHHHHHHCC--CCCEEECC--------CCCCCCC----CCCCCCEEEEE-CCCHHHHHHHHHHHCCCCCCCCCCC---------------------------- >P1;d2nuha- ------CCEEEEEEEECCHH------HHHHHHHHHHHCCCCCEEEEEEEEEEEEECC-------CCEEEEEEEEEEEEE-EHHHHHHHHHHHHHHCCCC---CCCCEEEECC----CCCHHHHHHHHHHHC-- >P1;d2vd3a2 -------CEEEEEEEEE-HH------HHHHHHHHCCCCC---CCEEEEC---------CCC--------CCEEEEEEEE-ECCCHHHHHHHHHCC------CCEEEEEEECCCCCC----------------- >P1;d3opka- -------CCEEEEEEECCHH------HHHHHHHHHHHCCCCCEEEEEEEEEEEEC-C-------CCCEEEEEEEEEEEE-CHHHHHHHHHHHHHHCCCC---CCCEEEEECC----CCCHHHHHHHHHCCC-- >P1;d4affa1 --------CEEEEEEEC-HH------HHHHHHHHHHHCC-CCCCEEEE-EEECC----CCCCCCCCCCCEEEEEEEEEE-CHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCCCCHHHHC------ >P1;d4e98a- CCCCCCCCEEEEEEEECCHH------HHHHHHHHHHHCCCCCEEEEEEEEEEEEEEC-------CEEEEEEEEEEEEEE-EHHHHHHHHHHHHHHCCCC---CCCEEEEECC----CCCHHHHHHHHHHCC-- >P1;d4iyqa1 -------CEEEEEEEECCC-------CHHHHHHHHHHCCCCCEEEEEC-CEEEE-----------CCEEEECEEEEEEE-EHHHHHHHHHHC-CCCCCC---CCCEEEECCC----CCC-CCHHHHHHHHCC- >P1;d6mm2a1 -----CEEEEEEEEEEE-HH------HHHHHHHHHHHCC-CCCCEEEE-EEECCCCCCCCCCCCCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHCCC--CCEEEEEEEE-EEC------------------ >P1;d6t76a- --------CEEEEEEEC-HH------HHHHHHHHHHHCCCCCEEEEEE-EEEEEEEC-------CEEEEEEEEEEEEEE-CHHHHHHHHHHHHHHCCCC---CCCCEEECCCC--CCCCHHHHHHHHHHCCCC PSA >P1;d1nh8a2 -------a312030302-5a------129704610603a---7063673---------b67---------820304010-559619812860582------6077161582993aa----------------- >P1;d1nzaa- -------5113020101579------2054016104846000305256b35265678-------876263a11203010-058024503830562036a---a05051681a----97899416403720a-- >P1;d1o2ca1 ---------220203033-4649a-4016403-31a729--6a162556b8a9a--------------a7320102040-659407703----40a2-----147243584a599------------------ >P1;d1ukua- --------00203010373a------3048007204845000207146-26265757-------a66344600003010-158018503530552033b---a05052762a----a278932640453047- >P1;d2cz4a1 ----4624022000103-27------0484016005616-05536245-167b---b255792--a4876221303020-2781075027307630446--4b07053563-618------706627------ >P1;d2dcla- -aa24484023030402274739873026102440772a-069162657a749b--------------95320101020-41820660184076008-----a5724447252767177------------98 >P1;d2hfva1 ---------4630000855a------116601830593a--26271719--------aa2b7a9----b8a73343010-65a416805830774350804753a---------------------------- >P1;d2nuha- ------37023030002666------0055016104646100404255c3545567a-------a76353900202010-03711a502730461033a---9040716539----958894274046305-- >P1;d2vd3a2 -------6433030301-57------216606920605a---5173663---------a4b--------5800202020-249428504660581------70560634728828a----------------- >P1;d3opka- -------6002020102658------2068017303846000304154b442467-b-------786554700203020-0781385027104740439---8050625729----9689a5175058306-- >P1;d4affa1 --------132010201-47------0386046206819-08917459-35658----856b49887667611202030-46a3195038404810639897226162572a4243a8375555700------ >P1;d4e98a- aa284a0301303000265a------2047018305946000306155935355668-------886355710102010-058136504620473074b---9040626626----9492a4055048305-- >P1;d4iyqa1 -------900304010276-------2065006204744100205166-45357-----------c8866800003010-058218702830-81033b---915162762a----a2a-a3285047307b- >P1;d6mm2a1 -----467122000200-46------0484017006809-0a827269-3555aa393036924ab465181020205074492045027503761397--2207150644-73b------------------ >P1;d6t76a- --------012020102-55------3074005205544000305158-46264836-------c88255801102010-0760172047204610238---71406259175--c53787415502a40649 Translating the sequences -------**EEEEEEE*-HH------HHHHHHHH***CC---**EEEE*---------***---------*EEEEEEEE-*HHHHHHHHHHHHH*------*C**EEEE*CC****----------------- -------**EEEEEEE**HH------HHHHHHHHHHHCC*CC**EEEE*********-------*******EEEEEEEE-****HHHHHHHHHH*CCCC---CC*EEEE*CC----***************-- ---------*EEEEEE**-*****-*HHHHH*-****CC--C**EEEE******--------------***EEEEEEE*-*HHHHHHH*----**CC-----CC*EEEE*CC***------------------ --------*EEEEEEE**HH------HHHHHHHHHHHCC*CC**EEEE-********-------*******EEEEEEEE-*HHHHHHHHHHHHH*CCCC---CC**EEE*CC----****************- ----*****EEEEEEE*-HH------HHHHHHHHHHHCC-CC**EEEE-****---*******--******EEEEEEEE-*HHHHHHHHHHHHH*CCCC--*CC*EEEE**-***------******------ -********EEEEEEE**********HHHHHHHHHHHCC-CC**EEEE******--------------***EEEEEEEE-*HHHHHHHHHHH***CC-----CC*EEEE*CC*******------------** ---------*EEEEEE****------HHHHHHHHHHHCC--C**EEE**--------*******----******EEEEE-***HHHHHHHHHHH*CCCC***CC*---------------------------- ------***EEEEEEE**HH------HHHHHHHHHHHCC*CC**EEEE*********-------*******EEEEEEEE-*HHHHHHHHHHHHH*CCCC---CC**EEE*CC----***************-- -------**EEEEEEE*-HH------HHHHHHHH***CC---**EEEE*---------***--------**EEEEEEEE-****HHHHHHHHH**------*C**EEEE*CC****----------------- -------**EEEEEEE**HH------HHHHHHHHHHHCC*CC**EEEE*******-*-------*******EEEEEEEE-*HHHHHHHHHHHHH*CCCC---CC*EEEE*CC----***************-- --------*EEEEEEE*-HH------HHHHHHHHHHHCC-CC**EEEE-*****----*************EEEEEEEE-*HHHHHHHHHHHHH**CCC***C**EEEE*CC***************------ *********EEEEEEE**HH------HHHHHHHHHHHCC*CC**EEEE*********-------*******EEEEEEEE-*HHHHHHHHHHHHH*CCCC---CC*EEEE*CC----***************-- -------**EEEEEEE***-------*HHHHHHHHHHCC*CC**EEE*-*****-----------*******EEEEEEE-*HHHHHHHHHH*-**CCCC---CC*EEEE*CC----***-************- -----****EEEEEEE*-HH------HHHHHHHHHHHCC-CC**EEEE-**********************EEEEEEEE**HHHHHHHHHHHHH**CCC--*C**EEEE**-***------------------ --------*EEEEEEE*-HH------HHHHHHHHHHHCC*CC**EEEE-********-------*******EEEEEEEE-*HHHHHHHHHHHHH*CCCC---CC**EEE*CC*--****************** 54913.tem _________________________________ ------***EEEEEEE**HH------HHHHHHHHHHHCC*CC**EEEE*********-***---*******EEEEEEEE-*HHHHHHHHHHHHH*CCCC--*CC*EEEE*CC*******************-- Structural block scores 0 5 - 4.5 M 75.0 75.0 75.0 75.0 51.7 17.7 75.0 75.0 75.0 75.0 75.0 7.6 75.0 63.2 75.0 6 8 * 2.8 P 29.5 27.0 75.0 50.0 2.0 4.0 75.0 3.3 28.3 27.0 50.3 1.0 28.0 4.7 50.0 9 15 E 4.9 H 1.3 1.0 1.3 0.9 0.7 1.7 1.9 1.1 1.7 0.7 1.1 1.0 1.1 0.9 0.9 16 17 * 2.0 P 38.5 3.0 3.0 5.0 39.0 2.0 6.5 4.0 38.0 4.0 38.0 4.0 4.5 37.5 38.5 18 19 H 4.3 M 7.8 8.0 39.5 6.8 4.5 5.5 7.8 6.0 6.0 6.5 5.5 7.8 40.5 5.0 5.0 20 25 - 4.6 H 75.0 75.0 18.1 75.0 75.0 6.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 26 36 H 4.8 H 3.3 2.8 10.0 3.3 3.1 3.0 3.6 2.5 3.5 3.5 3.9 3.5 2.9 3.5 2.8 37 38 C 5.0 H 6.8 5.0 5.5 4.5 3.5 6.2 6.8 5.0 7.8 5.0 5.0 5.0 4.0 4.5 4.0 40 41 C 4.6 H 75.0 0.0 40.5 0.0 2.5 3.0 38.5 0.0 75.0 0.0 4.0 0.0 0.0 5.2 0.0 42 43 * 1.0 P 3.5 1.5 5.8 1.0 4.0 5.0 4.0 2.0 3.0 1.5 5.0 1.5 1.0 5.0 1.5 44 47 E 4.9 H 5.5 4.5 4.5 4.5 4.2 4.8 4.0 4.0 5.5 3.5 6.2 4.2 4.5 6.0 4.8 48 56 * 2.7 P 67.0 5.9 31.2 12.8 37.4 30.4 67.7 6.4 67.0 13.9 36.3 5.6 36.0 14.0 12.7 58 60 * 3.8 M 8.2 75.0 75.0 75.0 5.7 75.0 8.0 75.0 8.7 75.0 6.3 75.0 75.0 3.0 75.0 61 63 - 4.3 M 75.0 75.0 75.0 75.0 28.7 75.0 8.8 75.0 75.0 75.0 8.2 75.0 75.0 5.0 75.0 64 70 * 2.2 P 65.4 6.1 45.8 5.6 16.1 45.3 47.1 6.2 55.4 6.0 6.9 6.0 17.6 6.6 6.9 71 78 E 4.9 H 1.2 1.0 1.1 0.5 1.4 0.8 2.6 0.6 0.8 0.9 1.1 0.6 0.5 1.2 0.6 81 93 H 4.7 H 5.2 3.8 26.1 3.7 4.1 3.8 5.0 3.8 4.7 4.1 4.7 3.9 9.8 3.7 3.5 95 98 C 4.5 M 75.0 4.9 40.6 4.4 3.5 39.5 4.0 4.1 75.0 4.0 4.5 5.6 4.4 5.0 3.2 99 100 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 2.0 75.0 75.0 75.0 8.5 75.0 75.0 75.0 75.0 102 103 C 4.6 H 3.5 5.2 2.5 5.2 5.8 7.8 4.0 4.5 2.5 4.0 2.0 4.5 5.0 1.0 4.0 105 108 E 4.7 H 3.2 3.0 3.5 3.5 3.2 3.5 75.0 3.5 3.2 3.2 3.5 3.5 4.0 3.0 3.2 110 111 C 4.5 M 5.5 5.8 7.2 6.2 39.0 3.5 75.0 6.0 5.0 5.5 6.2 4.0 6.2 39.5 4.0 112 130 * 3.3 M 60.9 20.0 64.4 19.3 41.7 49.3 75.0 19.7 60.7 20.1 19.4 19.4 23.6 64.3 12.4 131 132 - 4.4 M 75.0 75.0 75.0 41.0 75.0 8.5 75.0 75.0 75.0 75.0 75.0 75.0 43.2 75.0 6.5 >>>>>>