Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1m1sa1 -----------CEEECC-EEEEECC---CEEEEEEEECCCCCEEEEEEEECCC-------CCEEEECCEEEECCCCEEEEEEEEC------CCCCCEEEEEEEEEEECC-----CCCCCCCCCC----CCCCEEEEEEEEEE--------------- >P1;d1mspa- -----CCCCCCEECCCCCCEEEECCCC----CEEECEECCC-CEEEEC-CCC---------CEEEECCEEEECCC-CCCEEEEEC---CCCCCCCCCCEEEEEEEECCCCCCCC---CCCCCCCC----CCCEEEEEEEEEEC-------------- >P1;d1wica1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCEEEEEEECCC-------CCEEEECCEEEECCCCEEEEEEEECCCCCCCC----CCEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCEEEEEECCCC-------CCCCCCCCCC >P1;d2cria1 CCC----CCCCCEEECCCEEEEECCCCCCEEEEEEEECCCCCCEEEEEEECCC-------CCEEEECCEEEECCCCEEEEEEEEC-CCCCCCCCCCCCCEEEEEEECCCCCC----CHHHHHHHCCCCCCEEEEEEEEEECCCCCCC-------CCC >P1;d2xg5a1 ----------CEEECC-CEEEEECC----CCEEEEEEECCCCCEEEEEEEECCCCCEECCCCEEEECCEEEECCCCEEEEEEEECHHHHHCCC-CCCEEEEEEEEEECCCCCC-----------CCCCCCCEEEEEEEEEC-HHHCCCC-------- >P1;d4ay0a1 ------CCCCCCC-----EEEEECC----CCEEEECCC-----CCEEECCCCCCCCC--CCCEEEECCCEEEC----CEEEEEECCC--CCCC-CCCEEEEEECC-CCC-----------------------CEEEEEEEC-CCC------------ PSA >P1;d1m1sa1 -----------070657-2070619---3383605030649520002051418-------8105064643108354826040304------735557150100205079-----a2a6231096----7544553506030a--------------- >P1;d1mspa- -----9860670809479403062719----445005022b-200020-134---------10708363400338-537030317---711a9472904030200405cc2949---166128ab----85245350506077-------------- >P1;d1wica1 949973360530000015203005b899a421305040419510003060716-------93070624320062b5325020206cb38065----b05010100206b808349930771067147a701315060349-------a9975b4b7d >P1;d2cria1 888----792106043582050604087414170405042a750003050635-------9506064824206365444040205-22b255c8979160203014038c28----72841088176980242706040441e8c98-------aa9 >P1;d2xg5a1 ----------105044-85030304----63210602064a6213010100367576299110305465260738484505031297178245-9731301000406037b89-----------b3848363330502020-573569a-------- >P1;d4ay0a1 ------e999b78-----4130413----90253822b-----83130004267484--c5106054661518----84040323a4--a046-87322110112-763-----------------------b22302040-953------------ Translating the sequences -----------CE**CC-EEEEECC---***EEEEEECCCCC*EEEEEEECCC-------CCEEEECCEEEECCCCEEEEEEEEC------CC*CC**EEEEEEEE*CC-----**********----CC**EEEEEEEE**--------------- -----**CCCC*E**CCC*EEEECC**----*EEE*E*CCC-CEEEE*-*CC---------CEEEECCEEEECCC-***EEEEEC---*CCCC*CCC*EEEEEEEECCCCCC**---*******C----C**EEEEEEEE***-------------- *******CCCCC***CCC*****CC******EEEEEECCCCCCEEEEEEECCC-------CCEEEECCEEEECCCCEEEEEEEEC****CCC----C*EEEEEEEECCCCCC************C***CC**EEEE****-------********** ***----CCCCCE**CCCEEEEECC******EEEEEECCCCCCEEEEEEECCC-------CCEEEECCEEEECCCCEEEEEEEEC-***CCCC*CCC**EEEEEEECCCCCC----********C***CC**EEEEEEEE*******-------*** ----------C*E**C-CEEEEECC----**EEEEEE*CCCCCEEEEEEE*CC*******CCEEEECCEEEECCCCEEEEEEEEC*****CCC-CCC*EEEEEEEE*CCCCC*-----------C***CC**EEEEEEEE*-*******-------- ------*CCCCC*-----EEEEECC----**EEEE**C-----**EEE**CCC****--*CCEEEECC*EEEC----*EEEEEEC**--CCCC-CCC*EEEEE**-CCC-----------------------*EEEEEEE*-***------------ 49354.tem _________________________________ ------*CCCCCE**CCCEEEEECC**-***EEEEEECCCCCCEEEEEEECCC-------CCEEEECCEEEECCCCEEEEEEEEC****CCCC*CCC*EEEEEEEECCCCCC*---********C***CC**EEEEEEEE*****------------ Structural block scores 0 5 - 4.2 M 75.0 64.0 6.8 41.5 75.0 75.0 7 11 C 4.3 M 60.0 3.8 2.8 3.8 45.2 9.1 13 14 * 1.9 P 3.0 4.5 0.0 2.0 2.0 75.0 15 17 C 4.4 M 29.0 6.7 2.0 5.3 29.0 75.0 18 22 E 4.4 M 3.0 2.6 1.0 2.6 2.2 2.4 23 24 C 5.0 H 5.0 4.5 8.2 2.0 2.0 2.0 25 26 * 3.4 M 75.0 5.0 8.5 4.0 75.0 75.0 28 30 * 2.4 P 4.7 75.0 5.5 3.0 28.0 28.0 31 36 E 4.7 H 2.8 3.0 2.2 2.8 1.8 3.7 37 42 C 4.4 M 4.3 15.4 3.3 4.8 4.8 64.4 43 49 E 4.5 M 1.1 11.1 1.3 1.1 0.9 2.1 50 52 C 4.7 H 4.3 27.3 4.7 4.7 3.0 4.0 53 59 - 4.2 M 75.0 75.0 75.0 75.0 6.4 26.5 60 61 C 4.8 H 4.5 38.0 6.0 7.0 1.0 3.0 62 65 E 5.0 H 2.8 3.8 3.2 3.0 2.0 2.8 66 67 C 5.0 H 5.0 4.5 3.0 6.0 5.0 5.0 68 71 E 4.9 H 2.0 1.8 1.2 2.0 3.2 3.2 72 75 C 4.6 H 5.0 22.2 6.1 5.0 5.5 58.2 76 83 E 4.7 H 2.9 2.8 1.8 2.2 3.2 12.0 85 88 * 3.0 P 75.0 58.0 8.8 22.6 6.0 41.1 89 92 C 4.5 M 40.0 5.4 21.5 6.1 4.8 5.1 94 96 C 4.5 M 5.7 6.0 53.8 8.3 6.3 6.0 98 105 E 4.8 H 1.6 1.6 1.1 2.0 1.0 10.4 106 111 C 4.5 M 40.2 6.8 5.6 5.6 5.9 40.2 113 115 - 4.1 M 29.2 53.0 7.3 75.0 75.0 75.0 116 123 * 2.8 P 4.7 13.7 3.9 4.8 75.0 75.0 125 127 * 3.4 M 75.0 75.0 7.2 7.3 5.0 75.0 128 129 C 4.4 M 6.0 41.5 3.5 4.0 5.5 75.0 130 131 * 1.9 P 4.0 3.5 2.0 3.0 4.5 75.0 132 139 E 4.7 H 3.4 3.5 3.5 2.9 1.9 3.1 140 144 * 3.0 P 47.1 32.8 75.0 8.0 18.0 18.4 145 156 - 4.3 M 75.0 75.0 19.8 47.7 52.5 75.0 >>>>>>