Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1iiba- ---CEEEEEEECCHH-HHHHHHHHHHHHHHHCCC-CEEEEEEEHH-----HHHHHHCCCCEEEE-CHHHHHHHHHHHHHCCCCCEEECCHHHHHCCCHH--HHHHHHHHHHHHHHC------- >P1;d1vkra- -CCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCC--------CCCCCCCEEEE-EHH---HHHHHHHHCCCCEEEEECCCCCHH-HHH--HHHHHHHHHHH---C------- >P1;d2kyra- CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHCC-EEEEEEECCCCEECCCCHHHHHHCCEEEEEECCCCC----CHHHHCCCCEEEEECCHHHH-CHH--HHHHHHHHHHHHHH-------C >P1;d2r48a1 ---CEEEEEECCCCCCCCC-CHHHHHHHHHHHCC-CEEEEEEECCEEECCCCHHHHHHCCEEEEEECCCCC-----CHHHCCCCEEEECHHHHHH-CHH--HHHHHHHHCC----CCCC---- >P1;d4tn5a- --CEEEEEEECCCCCCCCC-CHHHHHHHHHHCCC-EEEEEEEECCEEECCCCHHHHHHCCEEEEEECCCCC----CHHHHCCCCEEEECHHHHHH-CCCCCCHHHHHHHCC----CCCEEECC PSA >P1;d1iiba- ---6530000043ba-506600650573096592-6040412528-----30273078040000-0140481356057606913052067930972403--200750471289489------- >P1;d1vkra- -b8464000006508b3066018505820683a29a06064340c--------b0479030000-278---2096059415b1802305a6839b-406--61177047618---a------- >P1;d2kyra- b84000000004811a304601610360078180-613000006682754079910540400000146907----236507a5703528082036-519--40065025526877-------c >P1;d2r48a1 ---6000000049c39504-018304600772a1-70200010b883576058740770600000044b09-----2830671401425053027-414--7007603638----0855---- >P1;d4tn5a- --31000000086638404-01830663067571-9040000067934a8055820860500000033b08----15820781210303050036-62a406006702847----84443717 Translating the sequences ---CEEEEEE*CC**-HHHHHHHHHHHHHHHCCC-CEEEEEEE**-----**HHHH**CCEEEE-***********HHH*CCCCEEE*CHHHHH**CHH--HHHHHHHHHHH***C------- -*CC*EEEE*CCCCC*HHHHHHHHHHHHHHHCCC*C*EEEE**CC--------*****CCEEEE-E**---*****HHH*CCC*EEEEC****HH-*HH--HHHHHHHHHHH---C------- **C*EEEEEECCCC**HHHHHHHHHHHHHHH*CC-*EEEEEE*CC*EECCCCHHHHHHCCEEEEEECCCCC----*HHHHCCCCEEEE***HHHH-CHH--HHHHHHHHHHH***-------* ---CEEEEEECCCCC****-*HHHHHHHHHH*CC-CEEEEEEECC*EECCCCHHHHHHCCEEEEEECCCCC-----*HHHCCCCEEEECHHHHHH-CHH--HHHHHHHH**----C***---- --C*EEEEEECCCCC****-*HHHHHHHHHHCCC-*EEEEEEECC*EECCCCHHHHHHCCEEEEEECCCCC----*HHHHCCCCEEEECHHHHHH-C*****HHHHHHH**----C******* 52794.tem _________________________________ --CCEEEEEECCCCC*HHHHHHHHHHHHHHHCCC-CEEEEEEECC*EECCCCHHHHHHCCEEEEEECCCCC----*HHHHCCCCEEEECHHHHHH-CHH--HHHHHHHHHHH---C------- Structural block scores 0 1 - 4.2 M 75.0 43.2 9.8 75.0 75.0 2 3 C 4.0 M 40.5 6.0 2.0 40.5 2.0 4 9 E 4.8 H 1.3 1.7 0.0 0.0 0.0 10 14 C 4.6 H 5.8 3.8 2.8 5.7 4.6 16 30 H 4.6 H 3.9 3.9 3.0 8.0 8.2 31 33 C 4.6 H 5.3 5.2 3.0 4.5 4.3 36 42 E 4.7 H 2.3 3.3 0.6 0.4 0.6 43 44 C 4.5 M 5.0 6.2 6.0 9.8 6.5 46 47 E 4.2 M 75.0 75.0 4.5 4.0 3.5 48 51 C 4.2 M 38.2 75.0 4.0 4.5 5.9 52 57 H 4.3 M 4.5 17.8 4.7 5.5 4.8 58 59 C 5.0 H 2.0 1.5 2.0 3.0 2.5 60 65 E 4.8 H 12.5 12.8 0.2 0.0 0.0 66 70 C 4.0 M 3.4 48.0 5.2 5.7 5.1 71 74 - 3.8 M 3.8 4.2 75.0 75.0 75.0 76 79 H 4.6 H 4.5 4.8 3.5 3.2 3.8 80 83 C 4.9 H 4.8 6.4 7.4 4.5 4.5 84 87 E 4.9 H 1.8 1.2 2.5 1.8 1.0 89 94 H 4.4 M 5.8 8.0 3.2 2.8 2.3 97 98 H 4.5 M 1.5 3.0 5.0 2.5 6.2 99 100 - 4.5 M 75.0 75.0 75.0 75.0 2.0 101 111 H 4.7 H 3.3 4.4 3.2 10.5 10.5 112 114 - 3.8 M 7.0 75.0 7.3 75.0 75.0 116 122 - 4.1 M 75.0 75.0 66.1 45.4 4.3 >>>>>>