Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1dnpa2 -----CEEEEECCCCCCCCCCHHHHHHCCCC-----CCEEEEEEEECHHHHH----H-CCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHCC--CCEEEEECCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-------------- >P1;d1iqra2 -----CCEEEECCCCCCCCCCHHHHHHHCC------C-CEEEEEEECHHHHCCC--------HHHHHHHHHHHHHHHHHHHHCCCCEEEEEC----CHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHCC---CCEEEECCCCCCCCC-CC-----CCCCCHHHHHCCCC------CCCCCCCCCCCCCCCC-----CCC----------CCCCCCCC--------- >P1;d1np7a2 CCCCCCEEEEEECCCCCCCCCHHHHHHHHC------CCEEEEEEEECHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEC----CHHHHHHHHHHHCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCHHHCCCCHHH-CCCCHHHHHHHHHC--CCCCCCCCCCCCCCCCCCC--------------CCCCCCCCCCHHHCCCCC--C >P1;d1owla2 -----CCEEEECCCCCCCCCCHHHHHHHHH------CCCEEEEEEECHHHHCC-----CCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEC----CHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHH----CCCCCCCCCCCCCCCCC-----HHHHHHHHHHCCCCCCCC-HHHCCCCCCCC >P1;d1u3da2 ------CEEEEECCCCCCCCCHHHHHHHHH-------CCEEEEEEECHHHHC----C-CCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECC---CHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHCCCC-CCCCCCCHHHHHHHHHCC--CCCCCCCCCCCCCCCCCCHHHCCCCCCCC------------------------ >P1;d2wq7a1 -CCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCCEEEEEEEEECCCHHH----CC-CCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEC----CHHHHHHHHHHHCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHCCCCCCCCHHHHHHHHCCC---C-CCCCCCCCCC-----CCCCCCCCCCHHHHHCCCCCCCCCHHHHCCCHHHC >P1;d6ptza1 -CC--EEEEEEECCCCCCCCCHHHHHHHHC---EE---EEEEEEEECHHHHH----HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEC----CHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHHHHCCEEECCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHH---CCCCCCCCCCCC---CHHHHCCCCCCC-----CHHHHCCCCHHHHCCCCCCC PSA >P1;d1dnpa2 -----30000000500418403002300958-----9050000000017105----7-3a1636503400650390053007200302233274193016104600862905300003137a61570075047108--b0705022063603561022c-9966287894359224731678649-8391094099753a3697070808269168877-------------- >P1;d1iqra2 -----32000001b0140730100250287------5-5000000003461837--------587208305302700640472900000176----4017200200650906100002247830660074058405---250512833581447-28-----892a7853437438------869874720a703916-----344----------a0473959--------- >P1;d1np7a2 a89224000000160121730100240263------a31010000013440565a8686305376028237306803730891906002004----401710070076050600000427785225106503750872a06040224768111730116697-41a88762434146--681944973a41a706416--------------b2a0a279138810592a--a >P1;d1owla2 -----5000000150040540400240275------23200000000373185-----aa04446007217206703730771504000044----403720150065090400000215494059109602640991a08032420445014950-33d86771a87954592267----28359739307906306-----8a3283067112a80172-88192a3b695 >P1;d1u3da2 ------100000050142620000210373-------730000001014329----9-843a8863781653089027405824000023438---3005101810450a0730000202484058118505740374a1706320034600473032a-757819889444730670--5693696483197070247852a1390a0------------------------ >P1;d2wq7a1 -5a903000000040120720200240083017357610000010034a507----68-719076038206205701530671513000024----619700330072050500000417598068217704930984a060313214682339604743978509788844710851---a-57984a5086-----06905a1651631687761051074a500435851 >P1;d6ptza1 -77--2300000040121730100120063---04---20000000058118----711a1a486108205304604740482a02000046----514700460093080300000206283166014304700962a070105512381568603741a77508889435601850---9a3696348056---70078060360a-----72870700628509067727 Translating the sequences -----**EEEE*CCCCCCCCCHHHHHH****-----C**EEEEEEECHHHH*----*-CCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEC*****HHHHHHHHHHH*CCCEEEEECCCCHHHHHHHHHHHHH**--CCEEEEECCCCCCC***C***-CCCCCCCHHHHHHHHH*****CCCC-CCCCCCCCCCCC*****CCC*******C**CCC-------------- -----**EEEE*CCCCCCCCCHHHHHHH**------C-*EEEEEEECHHHH***--------HHHHHHHHHHHHHHHHHHHHCCCCEEEEEC----CHHHHHHHHHHH*CCCEEEEECCCCHHHHHHHHHHHHH**---C*EEEECCCCCCC**-C*-----CCCCCHHHHH****------CCCCCCCCCCCCCCCC-----CCC----------CCCCC***--------- *******EEEE*CCCCCCCCCHHHHHHHH*------C**EEEEEEECHHHH*******CCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEC----CHHHHHHHHHHH*C**EEEEECCCCHHHHHHHHHHHHHHH**CCEEEEECCCCCCC***C******-CCCCHHHHHHHHH*--**CCCCCCCCCCCCCCCCC--------------*C**CCCCC*********--* -----**EEEE*CCCCCCCCCHHHHHHHH*------C**EEEEEEECHHHH**-----CCCCHHHHHHHHHHHHHHHHHHHH*CCCEEEEEC----CHHHHHHHHHHH*CCCEEEEECCCCHHHHHHHHHHHHHHH**CCEEEEECCCCCCC***C-***CCCCCCCHHHHHHHHH*----CCCCCCCCCCCCCCCCC-----**********C**CCCCC-*********** ------*EEEE*CCCCCCCCCHHHHHHHH*-------**EEEEEEECHHHH*----*-CCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEC*---CHHHHHHHHHHH*CCCEEEEECCCCHHHHHHHHHHHHHHH**CCEEEEECCCCCCC***C***-CCCCCCCHHHHHHHHH**--*CCCCCCCCCCCCCCCCC*****CCC***------------------------ -******EEEE*CCCCCCCCCHHHHHHHH*******C**EEEEEEEC**HH*----**-CCCHHHHHHHHHHHHHHHHHHHHCCCC*EEEEC----CHHHHHHHHHHH*C**EEEEECCCCHHHHHHHHHHHHHHH**CCEEEEECCCCCCC********CCCCCCCHHHHHHHH***---C-CCCCCCCCCC-----*****CCC*******C**CCCCC************ -**--**EEEE*CCCCCCCCCHHHHHHHH*---**---*EEEEEEECHHHH*----**CCCCHHHHHHHHHHHHHHHHHHHHCCCC*EEEEC----CHHHHHHHHHHH*CCCEEEE*CCCCHHHHHHHHHHHHHHH**CCEEE**CCCCCCC********CCCCCCCHHHHHHHHH**---CCCCCCCCCCCC---C******CCC**-----C****CCC************ 52425.tem _________________________________ -**--**EEEE*CCCCCCCCCHHHHHHHH*------C**EEEEEEECHHHH**---**CCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEC----CHHHHHHHHHHH*CCCEEEEECCCCHHHHHHHHHHHHHHH**CCEEEEECCCCCCC***C****CCCCCCCHHHHHHHHH**--*CCCCCCCCCCCCCCCCC*****CCC*******C**CCCCC************ Structural block scores 1 2 * 3.7 M 75.0 75.0 8.5 75.0 75.0 7.8 7.0 3 4 - 4.2 M 75.0 75.0 2.0 75.0 75.0 4.5 75.0 5 6 * 1.4 P 1.5 2.5 2.0 2.5 38.0 1.5 2.5 7 10 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 12 20 C 5.0 H 2.4 3.1 2.3 2.1 2.2 1.8 2.0 21 28 H 4.9 H 2.1 2.2 1.9 2.4 1.6 2.0 1.2 30 35 - 4.4 M 63.8 75.0 75.0 75.0 75.0 3.8 50.7 37 38 * 1.8 P 2.5 40.0 2.0 2.5 5.0 0.5 38.5 39 45 E 5.0 H 0.0 0.0 0.1 0.0 0.1 0.1 0.0 47 50 H 4.8 H 2.2 3.5 2.8 3.5 2.5 4.9 3.8 51 52 * 2.4 P 40.0 5.5 5.5 6.5 42.0 41.0 41.5 53 55 - 4.5 M 75.0 52.3 7.8 75.0 75.0 75.0 75.0 56 57 * 3.1 M 41.0 75.0 7.0 75.0 42.0 7.0 4.0 58 61 C 4.5 M 5.1 75.0 3.5 6.2 6.4 23.0 5.8 62 81 H 5.0 H 3.0 3.5 4.2 3.6 4.9 3.4 3.7 82 85 C 4.9 H 1.2 2.8 4.0 2.5 1.5 2.5 3.6 86 90 E 4.8 H 2.0 1.6 0.4 0.8 1.8 0.4 0.8 92 95 - 4.5 M 5.2 75.0 75.0 75.0 58.2 75.0 75.0 97 107 H 5.0 H 2.9 2.1 2.6 2.6 2.3 2.9 3.1 109 111 C 4.5 M 4.7 5.0 3.7 4.3 5.8 3.3 3.7 112 116 E 4.9 H 0.6 0.2 0.0 0.0 0.6 0.0 0.0 117 120 C 5.0 H 3.5 3.8 5.0 3.0 2.0 4.2 2.5 121 135 H 4.9 H 4.1 3.7 3.8 4.3 3.9 4.9 3.5 136 137 * 2.5 P 75.0 75.0 4.5 5.0 5.5 6.0 4.0 138 139 C 4.8 H 5.8 38.5 5.2 5.2 5.8 5.2 5.2 140 144 E 4.8 H 2.8 2.6 2.4 3.4 3.6 2.6 2.6 145 151 C 5.0 H 2.9 4.6 4.1 2.3 1.9 3.7 3.6 152 154 * 1.3 P 4.0 28.7 3.7 6.0 4.7 6.0 6.7 156 159 * 2.1 P 22.9 58.2 3.5 23.6 22.6 4.5 3.8 160 166 C 4.7 H 6.7 26.6 16.4 6.8 6.4 6.4 6.5 167 175 H 4.8 H 5.1 5.0 4.3 5.4 5.0 5.3 4.9 176 177 * 2.5 P 5.0 75.0 40.5 41.0 3.5 3.0 2.5 178 179 - 4.4 M 3.5 75.0 40.5 75.0 75.0 75.0 75.0 181 197 C 4.8 H 9.8 9.6 5.1 4.7 4.9 30.8 17.7 198 202 * 3.1 M 6.3 75.0 75.0 75.0 6.5 4.0 4.2 203 205 C 4.3 M 4.7 3.7 75.0 7.2 4.3 5.8 3.0 206 212 * 3.2 M 4.7 75.0 65.9 3.9 44.4 4.3 55.1 214 215 * 2.5 P 7.0 75.0 5.2 6.2 75.0 6.5 5.0 216 220 C 4.4 M 34.4 4.9 5.9 3.6 75.0 1.4 2.8 221 232 * 3.1 M 75.0 58.2 17.2 12.3 75.0 4.4 4.9 >>>>>>