Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1iqva- CCCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCEEEEEEECCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCC---- >P1;d1rssa- --------------------CCCCCCCCCHHHHHHHHHHCC---CCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHCCCC--CC-CHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHCC--CCCC PSA >P1;d1iqva- 85208406189060638706550318592301620160027182c89777046202500310384195300100040012000711055567ba7552514a0634500200041004002712a73a27014000300120076368040143144117405717---- >P1;d1rssa- --------------------4a4095262620210043019---885776036201300720595296802800450053020520238565c6586735480687113400040026206828--39-63022002001201756--3800651541367068--b879 Translating the sequences ********************HHCCCCCCC*HHHHHHHHHHC***CCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCC*EEEEEEECCEEEEEEE*CCHHHHHHHHHHHHHHHHHHHH**CC*CHHHHHHHHHHHHHCCC**CHHHHHHHHHHHHHHH**---- --------------------**CCCCCCCHHHHHHHHHH*C---CC*HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHH****--CC-CHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHH**--**** 47973.tem _________________________________ --------------------HHCCCCCCCHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHHHHH--CC-CHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHHH------ Structural block scores 0 19 - 3.0 P 4.3 75.0 20 21 H 3.0 P 5.0 7.2 22 28 C 5.0 H 4.0 4.0 29 39 H 4.6 H 1.9 1.7 41 43 - 3.0 P 3.7 75.0 44 45 C 5.0 H 10.2 8.0 46 65 H 4.9 H 3.5 3.5 66 68 C 5.0 H 5.7 7.7 69 80 H 5.0 H 0.7 2.2 81 83 C 5.0 H 2.3 2.3 84 91 E 4.8 H 3.8 3.9 92 93 C 5.0 H 11.0 9.2 94 101 E 4.8 H 4.9 5.8 102 103 C 5.0 H 3.0 3.0 104 123 H 4.6 H 1.8 3.1 124 125 - 3.0 P 8.8 75.0 126 127 C 5.0 H 6.8 6.0 130 142 H 5.0 H 0.8 1.0 143 145 C 5.0 H 5.3 6.0 146 147 - 3.0 P 7.0 75.0 149 163 H 4.7 H 3.1 4.0 164 169 - 3.0 P 51.3 30.9 >>>>>>