Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1c44a- -CCCC-CCCHHHHHHHHHHHHHHH-----HHHHHHHHCCEEEEEEEECC--HHH-CCEEEEEEECCCCC-EEEECCCC----------CCCEEEEEEHHHHHHHHCCCCCHHHHHHCCCCEE-EECHHHHH---HHHCCCCCCCCCC------C >P1;d1ikta- --------CCHHHHHHHHHHHHHH-----HHHHHHHHHCEEEEEEEEC----CCCEEEEEEEEECCCCC-EEEECCCCC---------CCCEEEEEEHHHHHHHHCCCCCHHHHHHCCCCEE-EECHHHHH---HHHHHHH--HHCC------C >P1;d1pz4a1 ------CCCCHHHHHHHHHHHHCC-----CCCCC-CCCCCEEEEEEEE----CCEEEEEEEEECC--CC-EEEECCC-----------CCCEEEEEEHHHHHHHHCCCCCHHHHHHCCCEEE-EECHHHHH---HHHHHHHHCC---------- >P1;d2cfua1 CCHHHHHHCCHHHHHHHHHHHCC--------HHHHCCCCEEEEEEECCC-------CEEEEEEEECCEE-EEEECCCCC---------CCCEEEEECHHHHHHHHCCCCCHHHHHHCCCEEE-EECCCHHH---HHHCCCCCCCCCCCCCCCCC >P1;d2cx7a- -------CCCCHHHHHHHHHHHHCC---HHHHHHCCCCEEEEEEEECCCHHHCCCCCEEEEEEEECCEEEEEEEEEC---------CCCCCEEEEECHHHHHHHCCCCCCHHHHCC-CCCEEEECCHHHHHHHHHHHHHHHHHHHCC------C >P1;d2hv2a1 ------------CHHHHHHCCCCCC-----------CCCEEEEEEEECCCCHHHC--EEEEEEECCCCCEEEEE-------------CCCCCCEEEEHHHHHHHHCCCCCHHHHHHCCCCEEC---HHHHH---HHHHHCCC---C-CCCCCCC >P1;d2i00a1 ------------CHHHHHHHCCCCC-----------CCC-CEEEEEECCCCHHHC--EEEEEEECCCCCEEEEC-------------CCCCEEEEEEHHHHHHHHHCCCCHHHHHHCCCCCCC---HHHHH---HHHHHCCC---CCCCCCCCC >P1;d2nsfa2 -----CCHHHHHHHHHHHHHHHHH-----------CCCCCCEEEEECCC-------CEEEECCCCC-----------------------CCEEEEECHHHHHHHHCCCCCC-------CEEECCC------CCCCCCCC--------------- >P1;d2ozga1 ------------CCC-CCCCCCCCC-----------CCCEEEEEEEECCCCHHHC--EEEEEEEE-CCEEEEE---------------CCCCCEEEEHHHHHHHHCCCCCHHHHHHCCCEEEC----CHHH---HHHHHHCC---CCCC-CCCC >P1;d3bkra- -------CCHHHHCHHHHHHHHHH-----CCCCC-CCCCCEEEEEEEE----CCEEEEEEEEECC--CC-EEEEECCCCCCCCCCCHHHCCEEEEEEHHHHHHHHCCCCCHHHHHHCCCCEE-EECHHHHH---HHHHHHCC-C---------- >P1;d4av7a2 CCCCHHHHCCHHHHHHHHHHHCC--------HHHHCCCCEEEEEEECCC-------CEEEEEEEECCEE-EEEECCCCC---------CCCEEEEECHHHHHHHHCCCCCHHHHHHCCCCEE-EECHHHHH---HHHCCCCCCCCCCCCCC--- >P1;d4pdxa2 ---CCCCC-CCC-CCCC-CCCCC--------HHHHCCCEEEEEEEC--C-------CCCEEEEEECCEE-EEEC-CCCC---------CCCEEEECCHHHHHHHHCCCCC-CHHHHCCCCEE-EECCCHHH---HHHCCCCCCCCCCCCCCCC- >P1;d6ovpa- -CCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCEEEEEEEECC--CC--CEEEEEEEECC-CC-CEEECCCCCCC-------CCCEEEEEEHHHHHHHHCCCCCHHHHHHCCCCEE-EECHHHHC---CC------------------ PSA >P1;d1c44a- -9b9b-7a1505600670472076-----10630165040001050470--1b8-65220000046c70-504582b3----------a0402020206203200507150540675a3081-88659005---5026065039165------a >P1;d1ikta- --------1703820442365068-----2045018406010111017----ba944330002058c30-50175607b---------a040102040610122369615138038694170-89747223---4026225--5167------9 >P1;d1pz4a1 ------6a0603600831573188-----16797-1605320103014----ca73122100005--82-5055477-----------a030201040710330035716165028595090-98738103---523633a51a---------- >P1;d2cfua1 a65a7158370270065117106--------7a508c550201040543-------924000406a260-50668423b---------a070303040711132218516577058464172-8856813a---507900686a89838a7999 >P1;d2cx7a- -------920459007501840452---7605800680433000203536a29257000000404405057051373---------a09061112061710430051626136028-650414638896166348034111610470------c >P1;d2hv2a1 ------------5036404807047-----------8872503030518a05604--92020304562709065-------------92a904040438005400516450630185850646---67205---40070048---c-48798aa >P1;d2i00a1 ------------5055504918064-----------407-300030805919604--73000406aa6707039-------------743652050426006100607420340474940806---96017---00350035---9869657a9 >P1;d2nsfa2 -----5767614830460085058-----------58327100020766-------8451500939-----------------------952101460710060017673b-------709055a------914902a3--------------- >P1;d2ozga1 ------------804-50482a038-----------c181501030609869a05--74120404-9180707---------------a2701040338007303515560740477860807----8027---20550077---b828-98ac >P1;d3bkra- -------a0404612a61672168-----37588-2914200001024----a982210000015--60-414618542a23a904894040202050710230024624053039595070-79756003---3126427a-5---------- >P1;d4av7a2 ea679779340361074027202--------5a606a550300020543-------9330003077060-718386358---------9030204032600451368717256049595061-57559205---402a00476889878a8--- >P1;d4pdxa2 ---ba869-702-2086-27203--------89606c370101038--b-------8520003049270-7267-7328---------b030204074910222109338-971486a6072-58618218---304701685789658a696- >P1;d6ovpa- -87053c907006102632981448948a63772197070000120519--7a--73300110033-80-6012556064a-------6210222040620342249728596056375072-88598219---56------------------ Translating the sequences -****-*****HHHHHHHHHH***-----********CCEEEEEEE*CC--***-**EEEEEEE*CC**-EEEE**C*----------CCCEEEEE*HHHHHHHHCCCCCHHHHHHCCCCEE-E*CHHHHH---HHH********C*------* --------***HHHHHHHHHH***-----*********CEEEEEEE*C----*****EEEEEEE*CC**-EEEE**C**---------CCCEEEEE*HHHHHHHHCCCCCHHHHHHCCCCEE-E*CHHHHH---HHH****--**C*------* ------*****HHHHHHHHHH***-----*****-*CCC*EEEEEE**----*****EEEEEE**--**-EEEE**C-----------CCCEEEEE*HHHHHHHHCCCCCHHHHHHCCC*EE-E*CHHHHH---HHH*******---------- ***********HHHHHHHHHH**--------*****CCCEEEEEEE*CC-------*EEEEEEE*CC**-EEEE**C**---------CCCEEEEE*HHHHHHHHCCCCCHHHHHHCCC*EE-E*C**HHH---HHH********C******** -------****HHHHHHHHHH****---********CC*EEEEEEE*CC********EEEEEEE*CC***EEEE**C---------**CCCEEEEE*HHHHHHH*CCCCCHHHH**-CCCEE*E*CHHHHH***HHH********C*------* ------------*HHHHHH******-----------CCCEEEEEEE*CC******--EEEEEEE*CC***EEEE-------------*CCC**EEE*HHHHHHHHCCCCCHHHHHHCCCCEE*---HHHHH---HHH*****---C-******* ------------*HHHHHHH*****-----------CCC-*EEEEE*CC******--EEEEEEE*CC***EEE*-------------*CCCEEEEE*HHHHHHHH*CCCCHHHHHHCCCC***---HHHHH---HHH*****---C******** -----******HHHHHHHHHH***-----------*CCC**EEEEE*CC-------*EEEE****C-----------------------CCEEEEE*HHHHHHHHCCCCC*-------C*EE***------********--------------- ------------***-*********-----------CCCEEEEEEE*CC******--EEEEEEE*-C***EEE---------------CCC**EEE*HHHHHHHHCCCCCHHHHHHCCC*EE*----*HHH---HHH*****---C***-**** -------****HH*HHHHHHH***-----*****-*CCC*EEEEEE**----*****EEEEEE**--**-EEEE**C************CCEEEEE*HHHHHHHHCCCCCHHHHHHCCCCEE-E*CHHHHH---HHH*****-*---------- ***********HHHHHHHHHH**--------*****CCCEEEEEEE*CC-------*EEEEEEE*CC**-EEEE**C**---------CCCEEEEE*HHHHHHHHCCCCCHHHHHHCCCCEE-E*CHHHHH---HHH********C*****--- ---*****-***-****-*****--------*****CC*EEEEEE*--C-------***EEEEE*CC**-EEE*-*C**---------CCCEEEE**HHHHHHHHCCCCC-*HHHHCCCCEE-E*C**HHH---HHH********C*******- -**********HHHHHHHHHH*****************CEEEEEEE*CC--**--**EEEEEEE*C-**-*EEE**C****-------CCCEEEEE*HHHHHHHHCCCCCHHHHHHCCCCEE-E*CHHHH*---**------------------ 55718.tem _________________________________ ---********HHHHHHHHHH****----*******CCCEEEEEEE*CC--******EEEEEEE*CC**-EEEE**C**---------CCCEEEEE*HHHHHHHHCCCCCHHHHHHCCCCEE*E*CHHHHH---HHH********C******** Structural block scores 0 2 - 4.3 M 31.8 75.0 75.0 7.2 75.0 75.0 75.0 75.0 75.0 75.0 10.3 75.0 30.0 3 10 * 3.0 P 14.9 47.9 30.9 5.2 39.4 75.0 75.0 22.8 75.0 39.3 5.8 15.9 4.6 11 20 H 4.5 M 3.7 3.7 3.6 3.0 3.9 10.5 10.9 3.8 18.1 4.5 3.2 17.9 3.7 21 24 * 2.0 P 22.0 22.2 23.0 39.0 2.8 4.5 4.5 22.0 5.4 22.5 38.0 38.2 4.2 25 28 - 4.8 H 75.0 75.0 75.0 75.0 58.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.9 29 35 * 2.9 P 2.4 2.9 15.1 25.8 3.6 75.0 75.0 65.0 75.0 15.4 25.4 25.6 5.0 36 38 C 4.5 M 3.0 3.3 3.7 7.5 4.0 7.7 3.7 4.3 7.2 4.7 6.8 7.5 4.7 39 45 E 4.8 H 0.9 0.6 1.3 1.0 1.1 1.9 11.6 1.4 1.4 0.4 0.7 1.9 0.4 47 48 C 4.5 M 3.5 41.0 39.5 3.5 4.0 4.5 2.5 6.0 4.5 39.5 3.5 43.2 5.0 49 50 - 4.1 M 75.0 75.0 75.0 75.0 8.2 5.2 5.0 75.0 7.0 75.0 75.0 75.0 75.0 51 56 * 3.0 P 17.8 19.0 18.2 64.0 4.2 27.5 28.2 63.8 29.1 17.8 64.0 63.8 29.6 57 63 E 4.8 H 0.6 1.1 0.7 1.4 0.6 2.3 2.0 3.4 2.6 0.3 1.3 1.4 0.7 65 66 C 4.5 M 9.2 10.2 75.0 6.2 2.0 5.5 10.5 42.0 42.0 75.0 3.5 5.5 39.0 67 68 * 1.4 P 3.5 1.5 5.0 3.0 2.5 4.5 6.5 75.0 4.5 3.0 3.0 3.5 4.0 70 73 E 4.6 H 3.5 3.2 3.8 4.2 3.2 5.0 4.8 75.0 22.2 3.8 4.8 5.5 2.2 74 75 * 2.8 P 5.0 5.5 5.5 6.0 5.0 75.0 75.0 75.0 75.0 4.5 7.0 41.0 5.0 77 78 * 3.4 M 39.0 9.2 75.0 7.2 75.0 75.0 75.0 75.0 75.0 3.0 6.5 5.0 3.0 79 87 - 4.7 H 75.0 75.0 75.0 75.0 59.5 67.7 67.4 75.0 75.0 6.2 75.0 75.0 59.9 88 90 C 4.9 H 4.8 4.8 4.5 5.8 5.0 7.2 4.3 29.7 6.5 2.7 4.0 4.8 3.0 91 95 E 4.8 H 0.8 0.6 0.6 1.2 1.0 1.6 2.4 1.6 1.0 0.8 1.2 1.2 1.2 97 104 H 5.0 H 1.6 1.9 1.8 2.1 2.0 2.5 1.9 1.8 3.0 1.6 2.6 2.6 2.4 105 109 C 5.0 H 3.6 5.4 4.4 4.2 4.0 4.2 3.8 4.8 4.4 3.6 5.8 4.6 6.0 110 115 H 4.7 H 3.7 3.8 3.7 5.3 3.3 3.0 3.0 64.4 3.7 3.3 4.3 17.3 5.2 116 119 C 4.6 H 4.6 5.0 4.8 3.8 21.5 4.5 4.2 39.2 5.2 4.8 4.8 5.6 3.8 120 121 E 4.8 H 4.5 3.5 4.5 4.5 2.5 5.0 4.0 4.5 4.0 3.5 3.5 4.5 4.5 126 130 H 4.5 M 3.8 3.6 3.0 5.7 6.0 4.0 4.6 75.0 18.4 2.8 4.2 4.0 5.8 131 133 - 4.6 H 75.0 75.0 75.0 75.0 4.3 75.0 75.0 4.7 75.0 75.0 75.0 75.0 75.0 134 136 H 4.6 H 2.3 2.0 3.3 4.0 3.7 1.3 1.0 3.7 2.3 2.0 2.0 2.3 28.7 137 144 * 2.3 P 3.8 21.4 14.2 5.9 2.2 30.5 29.8 57.9 30.5 23.1 5.4 5.2 75.0 146 153 * 3.5 M 58.2 58.2 75.0 7.9 57.8 16.5 7.6 75.0 16.6 75.0 33.3 15.7 75.0 >>>>>>