Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2jzka- --C-CHHHHEEEEEEEC--CCCEEEEEEECCCCCEEEEEEEHHHCEECCCCCCEECCCCHHHHEEEEEEC-C----CCCEEEEEECCCCCCCCCCEEEECC-CEEEECCEEEEC- >P1;d2jzla- CCCCC---CCCCCEEEEECCEEEEEEEEECCCCCEEEEEECHHHCCCEECCEECCCCCCHHHCEEEEEEECCCCCCCCCEEEEEEECCCC-CEEEEEECCCCCEEECCCCEEECC >P1;d2l2fa- --CCHHHCCEEEEEEE---CCCEEEEEEECCCCCEEEEEEECCCCEEECCCCEEECCCCCHHHEEEEEEE-EECCCCEEEEEEEECCCCC-CCEEEEEEHHHCEEEECCEEEECC >P1;d2yhha- --CCCHHHHEEEEEEEC--CCCEEEEEEECCCCCEEEEEEEHHHCEEEECCEEEECCCCCHHHEEEEEEE-ECCCCCCEEEEEEEECCCC-CEEEEEECCCCCCCCCCCCCCCC- >P1;d3czza- --CCCHHHCEEEEEEE----CCEEEEEEECCCCCEEEEEEEHHHCCEEECCEEECCCCCHHHCEEEEEEE-C-----CCEEEEEEECCCC-CEEEEEEEHHHCEEEECCEEEEC- PSA >P1;d2jzka- --8-0014406806026--b04004020527848346132400620003b06071a67501700680704-5----9043010302168626386310504-402047060528- >P1;d2jzla- aa958---43550606579940102021539776586140301500007607072528700430760606015995461204010527b5-656634130660054541737356 >P1;d2l2fa- --90900640691505---90330102022a7a7547040304530107606041655802950590807-467b882010403050887-a4680803005401268070513a >P1;d2yhha- --983028407918055--a40304141606647557472300640015505053927702760890714-51c9873040402041794-74471915015b0204539164d- >P1;d3czza- --6050176069070a----81404010447b59535242502710107707041765603820560614-c-----8140203051997-a2581415015201065050433- Translating the sequences --C-CHHH*EEEEEEE*--CCCEEEEEEECCCCCEEEEEEEHHHCEE**CC**EECCCCHHHHEEEEEE*-C----CCCEEEEEE*CCCC*C***EEEECC-CEEEECCEEEEC- **CCC---C****EEE***C**EEEEEEECCCCCEEEEEE*HHHC**EECCEE**CCCCHHH*EEEEEEE*C*CCCCCCEEEEEEECCCC-CEEEEEE*CC*CEEE*CC*EEEC* --CC*HH*CEEEEEEE---CCCEEEEEEECCCCCEEEEEEE***CEEE*CC*EEECCCC*HHHEEEEEEE-**CCCC**EEEEEE*CCCC-C*EEEEEE***CEEEECCEEEEC* --CCCHHH*EEEEEEE*--CCCEEEEEEECCCCCEEEEEEEHHHCEEEECCEEEECCCC*HHHEEEEEEE-**CCCCC*EEEEEEECCCC-CEEEEEE*CC*C****CC****C- --CCCHHHCEEEEEEE----CCEEEEEEECCCCCEEEEEEEHHHC*EEECCEEE*CCCCHHH*EEEEEEE-C-----CCEEEEEEECCCC-CEEEEEEE***CEEEECCEEEEC- 51322.tem _________________________________ --CCCHHHCEEEEEEE*--CCCEEEEEEECCCCCEEEEEEEHHHCEEEECCEEEECCCCHHHHEEEEEEE-C*CCCCCCEEEEEEECCCC-CEEEEEEECC*CEEEECCEEEEC- Structural block scores 0 1 - 4.5 M 75.0 10.5 75.0 75.0 75.0 2 4 C 4.7 H 27.7 7.3 6.0 6.7 3.7 5 7 H 4.4 M 1.7 75.0 2.0 3.3 2.7 9 15 E 4.7 H 3.1 3.6 3.7 4.3 4.6 17 18 - 4.5 M 75.0 8.0 75.0 75.0 75.0 19 21 C 4.5 M 5.2 4.3 4.0 4.8 28.0 22 28 E 5.0 H 1.6 1.6 1.1 2.7 1.9 29 33 C 5.0 H 5.8 6.4 7.4 4.6 7.3 34 40 E 4.9 H 3.3 3.9 3.3 4.7 3.7 41 43 H 4.5 M 2.0 2.0 3.0 2.0 3.0 45 48 E 4.2 M 0.8 1.8 2.0 1.5 2.0 49 50 C 5.0 H 5.8 3.0 3.0 2.5 3.5 51 54 E 4.2 M 3.5 4.0 2.8 3.2 3.0 55 58 C 5.0 H 7.1 5.5 6.0 6.2 6.0 59 62 H 4.4 M 2.0 1.8 4.0 3.8 3.2 63 69 E 4.9 H 3.6 3.6 4.1 4.1 3.1 73 78 C 4.2 M 39.7 5.7 6.1 6.6 51.5 79 85 E 4.8 H 1.3 1.7 1.9 2.0 2.0 86 89 C 5.0 H 5.2 6.4 5.8 5.2 6.5 92 98 E 4.5 M 3.7 4.0 4.1 4.4 3.7 99 100 C 3.8 M 2.0 3.0 0.0 0.5 0.5 103 106 E 4.3 M 1.5 3.5 2.2 1.5 1.8 107 108 C 5.0 H 3.5 2.5 4.0 4.0 2.5 109 112 E 4.3 M 3.2 5.0 3.2 5.0 3.0 >>>>>>