Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vmga- ------C-CCCC-CCCC-CCC------------CCCCC-HHHHHHHHHHHHHHHHHHHHHCC--------------HHHHHHHHHHHHHHHHHHHHHHC--CCHHHHHHHHCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d1w2ya- ----CCHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCC-----CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------CCCHHHHHHHHHCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCEECCEEHHHHHHHHHCCCCC--HHHHHHHHHHHHCCC--------------- >P1;d1y6xa1 ------C-CCHHHHHHHHHHHHHHCCCCCHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHHCC--------------HHHHHHHHHHHHHHHHHC-CCCC--CCHHHHH-CCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------ >P1;d1yvwa1 ---------CHHHHHHHHHHHHHCCCCCCHHHHHHHHC-HHHHHHHHHHHHHHHHHHHHCCC--------------HHHHHHC-CHHHHHHHHHHHHCC--CCHHHCC-HHHHHHHHC------------------------------------------------------------------------------------------------------------------------------------------------------------------ >P1;d2a7wa1 --------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHC-HHHHHHHHHHHHHHH-CCCCCCC--------------HHHHHHHHHHHHHHC-CHHHHCC--CCHHHHC-CHHHHCC-------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2p06a1 -----CHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHCC-HHHHHHHHHHCC-HHHHHHHCCC--------------HHHHHHHHHHHHHHCCHHHHHHC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2q73a- --------CCHHHHHHHHHHHCC-----------CHHH-HHHHHHHHHHHHHHHHHHHHCCCCCCCC-----HHHCCCCHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHCC------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d3obca1 -----------CHHHHHHHHHHHHC---CCHHHCC----HHHHHHHHHHHHHHHHHHCCCCCCHHH--HHHHC--CCCCCCCHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d4dk2a- ----CCCHHHHHHHHHHHHHHHHHHC--CCCCCC-----HHHHHHHHHHHHHHHHHHCCCCC-----CCCCC-CCCHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCCCHHHCCCCCCCCCEEHHHCCCCCCCCCCC-------------CHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHCCCC---HHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHCCCHHHHC >P1;d5ie9a- -----CC-CCHHHHC-CHHHHHHCC-------CCCCCC-HHHHHHHHHHHHHHHHHHHHHH---------------HCCHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHCCCCCC--------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d6sqwa- CCCCCCCCCCHHHHHHHHHHHHHHC---CCHHHCC----HHHHHHHHHHHHHHHHHHHCCC-CCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHCCHHHC------------------------------------------------------------------------------------------------------------------------------------------------------------ PSA >P1;d1vmga- ------c-6747-3187-489------------40547-39506851651683167068696--------------9a41971673265251120105a--652274449768----------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d1w2ya- ----4752510240052016002521388029361658860302630261065026002339-----5587a670735305000010002000000248c---------------------------a272761058037182085017a49a187b419702520750382047a2061760041004003401010810140010000021002623348970-7440a95601500260186247--383027405742980--------------- >P1;d1y6xa1 ------5-873632284054327653bb1601811589-69707743960584287045758--------------ca4376246425105003-1179--6617364-787------------------------------------------------------------------------------------------------------------------------------------------------------------------------ >P1;d1yvwa1 ---------a687316604833a865792500400853-483058229606643770787a5--------------9943870-642520410210249--5627546-778678b67------------------------------------------------------------------------------------------------------------------------------------------------------------------ >P1;d2a7wa1 --------884574065047339364943500300764-492048227605752-9059886--------------8a4388137427304-022024a--5224656-569869c-------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2p06a1 -----7997848859867712722869c3165037436-485055128507-4285158774--------------5972751510343061186264a------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2q73a- --------464461166048833-----------34a6-474067326605951750674857b908-----99649501220653241150010006b--4723656666578889------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d3obca1 -----------8a626713850574---9557616----6960562176157538602591968a3--48714--748d51717622543510212239--69286996a88bb---------------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d4dk2a- ----b147900500030023126485--b04647-----37411730361056016402338-----55c6b-4075770270014003300001015b7605025289a947d5748959c5b23942108803a40012508-------------62510200050023006--343062001000200521911---00010003000570551802659618378e437108900540826018c6157403400640051050398424708510 >P1;d5ie9a- -----ba-5726730-616961865-------aa5268-5a30683187058317615874---------------7443a81684144040020114a--53157466744967875a87--------------------------------------------------------------------------------------------------------------------------------------------------------------- >P1;d6sqwa- 9687978756362145615650584---8477715----395058417a168527624592-6ba4773a6059a435317716632442400213549--5824746786574368572b86a------------------------------------------------------------------------------------------------------------------------------------------------------------ Translating the sequences ------*-****-****-***------------*****-HHHHHHHHHHHHHHHHHH***CC--------------HHHHHHHHHHHHHHHHHHHHH*C--CC**********----------------------------------------------------------------------------------------------------------------------------------------------------------------------- ----******HHHHHHHHHHHHH*****C*************HHHHHHHHHHHHH****CCC-----*********HHHHHHHHHHHHHHHHHHHHH*C*---------------------------**************************************************************************************************-**********************--***************--------------- ------*-**HHHHHHHHHHHHH*****C*********-HHHHHHHHHHHHHHHHHH***CC--------------HHHHHHHHHHHHHHHHH*-***C--CC*****-***------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ---------*HHHHHHHHHHHHH*****C*********-HHHHHHHHHHHHHHHHHH**CCC--------------HHHHHH*-*HHHHHHHHHHHH*C--CC*****-*********------------------------------------------------------------------------------------------------------------------------------------------------------------------ --------**HHHHHHHHHHHHH*****C*********-HHHHHHHHHHHHHHH-****CCC--------------HHHHHHHHHHHHHH*-*HHHH*C--CC*****-*******-------------------------------------------------------------------------------------------------------------------------------------------------------------------- -----*****HHHHHH************C*********-HHHHHHHHHH**-HHHHH**CCC--------------HHHHHHHHHHHHHH**HHHHH*C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- --------**HHHHHHHHHHH**-----------****-HHHHHHHHHHHHHHHHHH**CCC*****-----*******HHHHHHHHHHHHHHHHHH*C--CC**************------------------------------------------------------------------------------------------------------------------------------------------------------------------- -----------*HHHHHHHHHHH**---C******----HHHHHHHHHHHHHHHHHH**CCC****--*****--*******HHHHHHHHHHHHHHH*C--CC***********---------------------------------------------------------------------------------------------------------------------------------------------------------------------- ----******HHHHHHHHHHHHH***--C*****-----HHHHHHHHHHHHHHHHHH**CCC-----*****-***HHHHHHHHHHHHHHHHHHHH**C***C*****************************************-------------*****************--*********************---******************************************************************************** -----**-**HHHH*-*HHHHHH**-------******-HHHHHHHHHHHHHHHHHH****---------------H**HHHHHHHHHHHHHHHHHH*C--CC******************--------------------------------------------------------------------------------------------------------------------------------------------------------------- **********HHHHHHHHHHHHH**---C******----HHHHHHHHHHHHHHHHHH**CC-**************HHHHHHHHHHHHHHHHHHHHH*C--CC*********************------------------------------------------------------------------------------------------------------------------------------------------------------------ 101386.tem _________________________________ -----*****HHHHHHHHHHHHH*****C*********-HHHHHHHHHHHHHHHHHH**CCC------********HHHHHHHHHHHHHHHHHHHHH*C--CC***************------------------------------------------------------------------------------------------------------------------------------------------------------------------ Structural block scores 0 4 - 4.7 H 75.0 60.8 75.0 75.0 75.0 75.0 75.0 75.0 62.3 75.0 7.8 5 9 * 2.8 P 35.1 4.0 34.0 62.1 48.2 8.0 47.0 75.0 4.2 21.8 6.6 10 22 H 4.5 M 27.0 1.7 3.8 5.0 4.4 5.7 4.2 10.5 1.7 10.0 3.8 23 27 * 2.9 P 75.0 3.8 7.4 7.0 5.2 7.5 75.0 47.2 33.4 47.2 47.4 29 37 * 2.2 P 35.6 4.4 4.3 2.8 2.8 3.9 44.3 28.3 35.7 29.7 28.4 39 56 H 4.9 H 4.4 2.7 5.1 4.4 8.2 8.1 4.3 4.6 3.2 4.6 5.0 57 58 * 1.0 P 7.0 1.0 4.5 7.5 7.0 6.5 6.5 3.5 1.0 6.5 4.5 59 61 C 4.5 M 7.0 5.0 6.7 7.5 7.3 6.0 5.7 6.3 4.7 28.7 28.7 62 67 - 4.2 M 75.0 63.3 75.0 75.0 75.0 75.0 18.4 29.6 63.3 75.0 7.7 68 75 * 3.9 M 75.0 6.3 75.0 75.0 75.0 75.0 41.0 22.6 15.1 75.0 6.0 76 96 H 4.7 H 3.9 1.0 7.2 6.9 7.3 3.9 2.2 3.9 2.0 3.5 3.3 99 100 - 4.7 H 75.0 43.8 75.0 75.0 75.0 75.0 75.0 75.0 6.5 75.0 75.0 101 102 C 4.5 M 5.5 75.0 6.0 5.5 3.5 75.0 5.5 7.5 2.5 4.0 6.5 103 117 * 2.6 P 28.5 75.0 37.9 11.1 20.2 75.0 10.7 26.0 6.3 5.7 5.5 118 279 - 4.6 H 75.0 15.5 75.0 75.0 75.0 75.0 75.0 75.0 11.3 73.8 72.5 >>>>>>