Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1x53a1 ---------------CCEEEEEEEEEECCCHHHHHHHHHCHHHHHHHCC----------CCCCCC-CCCCCEEEECC---------CCEEEEEEEEECCCEEEEEEEEC-C--CCCCCCEEEEEECCCC-CCCEEEEEEEEEEEHHH-------HHHHHHHHCCCCHHHHHHHCCCCC------------------- >P1;d1xfsa- ---------------CCCCCCEEEEEECCCHHHHHHHHHCHHHHCCCCCCCCCCCC----EEEEC-CCCCCEEEEECCC-CCC--CCCEEEEEEEEECCCEEEEECCEEHH--HEECCCCCEEEEEEECC-CCEEEEEEECCC-HHHH---HHHHCCHHHHHHH-HHHHHHHHHHHHCCC----------------- >P1;d1z94a1 -----------------CCCEEEEEEECCCHHHHHHHCCCHHHHHHHCCCCCEEEE----EEEEC-CCCCCEEEEEEECCCCC--EECEEEEEEEEECCCEEEECCEECC-------CCCCEEEEEEEEC-CEEEEEEEECCC-CC-----CCCHHHHHHHHHH-HHHHHHHHHCC---C----------------- >P1;d2b79a2 ------------------CEEEEEEEEC-CHHHHHHHHHCHHHHHHCCCCCCCCCCCCCCCCCCEECCC---------------CC-CEEEEEC-CCCCCEEEEEEEECC-------EEEEEEEEEEECCC-CCEEEEEEEECC------CCCCCCCHH-HHHH-HHHHHHHHHCC--------------------- >P1;d2k5ga1 CCCCCCCCCCCCCCCCCCCCEEEEEEEECCCHHHHHHHHCHHHHCCCCCCCCCC-CCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEECCCCC-----CCCEEEEEEEEEECC-EEEEEEEEECCC------CHHHHHHHHCCCHH-HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHC >P1;d2l65a1 ---------------CCCCCEEEEEEEECCHHHHHHHCCC--CCCCCC---CCCCCCCCCCCCCEEECCCCEEECEEC-----CEECCCCEEEEEEEHHHEEEEEECCCCCCCCCCCCCEEEEEEEEEECCCEEEEEEEECCCCCCCCHHHHHHCCCHHHCHHH-HHHHHHHHHHHCCCCC---------------- >P1;d3elia1 ------------------CEEEEEEEECCCHHHHHHHCCCHHHHHHHCCCCCCCCC--CCCCCCCCCCC-EEEEECCCC-CCC--CCCEEEEEEEEECCCEEEEEEEEECC--CCCEEEEEEEEECCCC---CEEEEEEEECC-CCC------CCHHHHHHHHH-HHHHHHHHHC---------------------- >P1;d3ni8a1 ------------------CCEEEEEEECCCHHHHHHHHHCHHHHHHHCC---------CCCCEEC-CCCCCEEEECC---------CCEEEEEEEEECCCEEEEEEEEC-C--CCCCCCEEEEEEEEEEECCEEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHCHHHHHHHCCCCCCC------------------ PSA >P1;d1x53a1 ---------------5634503143304151540250014382044008----------070606-48863604026---------34020204414747102030206-6--03a9220502040574-d9302030406400351-------385048202630053019316107------------------- >P1;d1xfsa- ---------------75a73211635050426100500033910350223774603----50705-2440030301304-866--55673100330584520110653256--5772a96403040662b-910404030066-5a31---6744690994224-0061027204845a9----------------- >P1;d1z94a1 -----------------a330607450605163006001429113702017b3506----13654-2869121211228a867--5521116044056163031226568-------ba4400030674b-620403021570-48-----9453861464143-00720283035---b----------------- >P1;d2b79a2 ------------------4443343509-835700520161940440249060707890667204143c---------------78-6560504-077261010307174-------96032202036398-a30003000206------607930219-7137-10530383039--------------------- >P1;d2k5ga1 7b5447a73a5a855971930435240003062012003438103500001812-9855530705037560108a04384071166475704056174451000319378b-----4541201040455ca-306030305505------73720283000010-01300001000692470473049147225863 >P1;d2l65a1 ---------------8435505472404134950261414--103418---440686454007300047a16140509-----875252305046546344121023365ac2a91a5232151507299a760714242372054387518634a32382436-23a3046201365549---------------- >P1;d3elia1 ------------------460504461a36285003200419302500434b2602--99615020537-57030012c-986--6520206045057561000000315b--a672585030030554---40301020480-979------91661465022-0054057309---------------------- >P1;d3ni8a1 ------------------7505133204131630050004291026007---------8460706-36750802049---------55140203516636402040017-3--05aa3303010205537a800303020480193046975b03740365036710510362092636------------------ Translating the sequences ---------------*****EEEEEEECCCHHHHHHH**CHHHH***CC----------C*****-CCCCCEEE***---------CCEEEEEEEEECCCEEEEEE*EC-*--****CCEEEEEE****-***EEEEEEE*******-------***HHHHH****HHHHHHH*C***------------------- ---------------***C**EEEEEECCCHHHHHHH**CHHHH***CC**C****----*****-CCCCCEEE*****-***--*CCEEEEEEEEECCCEEEEE**E***--****CC**EEEEEEE**-**EEEEEEE*CC-****---******HHHHHHH-HHHHHHHHH******----------------- -----------------*C*EEEEEEECCCHHHHHHH**CHHHH***CC**C****----*****-CCCCCEEE*********--**CEEEEEEEEECCCEEEE***EC*-------CC**EEEEEEE**-**EEEEEEE*CC-**-----******HHHHHHH-HHHHHHHHHC*---*----------------- ------------------C*EEEEEEEC-CHHHHHHH**CHHHH***CC**C*******C******CCC---------------**-CEEEEE*-**CCCEEEEEE*EC*-------**EEEEEEEEE***-**EEEEEE**C*------*******HH-HHHH-HHHHHHHHHC*--------------------- ******************C*EEEEEEE*CC*HHHHHH**CHHHH***CC**C**-****C******CCCCC***************C*EEEE*****CCCEEEEEE**C**-----*CCEEEEEEEEE***-*EEEEEEE*CC*------*******HH***HH-HHHHHHHHHC********************** ---------------***C*EEEEEEE*CCHHHHHHH**C--*****C---C*******C*******CCCCEEE****-----***CC**EEEEEEE***EEEEEE**C********CCEEEEEEEEE*****EEEEEEE*CC**************HHH*HHH-HHHHHHHHH*******---------------- ------------------C*EEEEEEECCCHHHHHHH**CHHHH***CC**C****--*C******CCC-*EEE*****-***--*CCEEEEEEEEECCCEEEEEE*E***--******EEEEEE****---*EEEEEEE*CC-***------****HHHHHHH-HHHHHHHHHC---------------------- ------------------C*EEEEEEECCCHHHHHHH**CHHHH***CC---------*C*****-CCCCCEEE***---------CCEEEEEEEEECCCEEEEEE*EC-*--****CCEEEEEEEEE*****EEEEEEE*CC**************HHHHHHH*HHHHHHH**C****------------------ 55961-3.tem _________________________________ ---------------***C*EEEEEEECCCHHHHHHH**CHHHH***CC**C*******C******CCCCCEEE*****-***-**CCEEEEEEEEECCCEEEEEE*EC**--****CCEEEEEEEEE*****EEEEEEE*CC*****--*******HHHHHHH-HHHHHHHHHC*****----------------- Structural block scores 0 14 - 4.7 H 75.0 75.0 75.0 75.0 6.9 75.0 75.0 75.0 15 17 * 3.2 M 4.7 7.5 53.5 75.0 5.7 5.0 75.0 75.0 20 26 E 5.0 H 2.0 2.6 3.1 3.1 2.6 3.1 2.9 2.0 27 29 C 4.7 H 3.3 3.0 3.7 30.7 1.0 2.7 6.5 2.7 30 36 H 5.0 H 2.4 2.0 2.3 3.1 1.6 3.9 2.9 2.1 37 38 * 1.0 P 0.5 0.0 0.5 0.5 1.5 2.5 0.0 0.0 40 43 H 4.7 H 3.2 3.2 3.2 3.5 3.0 37.8 3.2 3.0 44 46 * 1.0 P 2.7 2.7 3.3 2.7 2.7 2.7 2.3 2.7 47 48 C 4.8 H 4.0 2.0 1.0 3.0 0.0 41.5 2.0 3.5 49 50 * 2.9 P 75.0 5.0 4.0 4.5 0.5 75.0 3.5 75.0 52 58 * 2.9 P 75.0 34.0 34.1 4.4 15.0 4.7 24.1 65.4 60 65 * 1.4 P 15.7 15.3 15.7 3.3 2.5 1.7 2.3 15.7 66 70 C 4.7 H 5.8 2.0 5.2 33.9 4.2 4.5 19.0 4.2 71 73 E 4.4 M 3.3 2.0 1.7 75.0 3.0 3.7 3.3 3.3 74 78 * 2.3 P 31.6 1.6 2.8 75.0 5.1 17.8 3.1 32.6 80 82 * 3.4 M 75.0 6.7 7.0 75.0 2.7 75.0 7.7 75.0 84 85 * 3.1 M 75.0 40.0 40.0 7.5 6.0 6.0 40.5 75.0 86 87 C 4.6 H 3.5 5.5 3.5 40.5 5.5 3.5 3.5 5.0 88 96 E 4.6 H 1.9 2.4 2.4 11.3 3.9 3.2 2.4 2.4 97 99 C 4.7 H 6.0 5.7 4.3 5.0 4.3 4.3 6.0 5.0 100 105 E 4.8 H 1.0 1.7 1.8 0.8 0.8 1.7 0.2 1.7 109 110 * 2.3 P 40.5 5.5 41.5 39.5 9.8 7.8 8.2 39.0 111 112 - 4.7 H 75.0 75.0 75.0 75.0 75.0 7.2 75.0 75.0 113 116 * 2.8 P 5.6 5.2 75.0 75.0 57.2 7.8 6.4 6.5 117 118 C 4.3 M 2.0 9.8 11.0 7.5 4.5 3.5 6.5 3.0 119 127 E 4.6 H 2.6 3.2 2.7 2.0 1.9 2.9 2.3 1.8 128 132 * 2.0 P 20.9 19.7 19.7 21.1 21.2 8.3 46.6 5.7 133 139 E 5.0 H 1.3 1.6 1.4 0.9 1.7 2.9 0.9 1.1 141 142 C 4.5 M 2.0 6.0 3.5 1.0 2.5 4.5 4.0 4.0 143 147 * 2.9 P 16.8 18.9 47.4 61.2 61.0 4.0 35.0 3.4 148 149 - 4.3 M 75.0 75.0 75.0 75.0 75.0 6.0 75.0 7.5 150 156 * 1.8 P 45.1 15.9 15.7 3.9 4.1 5.1 35.3 5.4 157 163 H 4.7 H 3.1 4.3 3.3 14.7 0.6 4.0 2.9 3.3 165 173 H 4.9 H 2.4 2.0 2.4 2.6 0.6 3.4 2.7 2.0 175 179 * 2.9 P 31.6 7.3 48.3 61.8 4.2 4.6 75.0 18.4 180 196 - 4.7 H 75.0 75.0 75.0 75.0 4.2 71.1 75.0 75.0 >>>>>>