Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1o13a- -------CEEEEECCCCHHHCCCCCCCCCCCEEEEEEEECCEEEEEEEEECHHHCCCCCC---CHHHHHHHCCCCEEECCCCCHHHHHHHHC-CCEEECCCC-CCHHHHHHHHHCC-C----------- >P1;d1p90a- CCCCCEEEEEEEECC----CCEECCCCCCCCEEEEEEEECCCEEEEEEEECHHHHHCC-CHHHHHHHHCC--CCCEEEECCCCHHHHHHHHHCCCEEEECCCCEEHHHHHHHHHHHHHCCCCHHHHHHC >P1;d1rdua- -----CCCEEEEECCC-CCCCCCCCCHHHCCEEEEECCC---CCCEEEEECCCCCCCCCC--CCHHHHHHCCCCCEEECCCCCCCCHHHHHCCCCEEEC-CCCCCHHHHHHHHHCC-CCCCCCCCCCCC >P1;d2wfba1 -----CCEEEEEECCC-CCCCCCCCCCCCCCEEEEEECC---CCCEEEEECHHHHCCCCCHHHHHHHHHHHHCCCEEECCCCCHHHHHHHHHCCCEEECCCCCCCHHHHHHHHHCC-CCCCCCCCCC-- >P1;d2yx6a- ------CEEEEEECCCCHHHCCCCCCCCCCCEEEEEEEECCEEEEEEEEECC------CC---HHHHHHHHCCCCEEECCCCCHHHHHHHHHCCCEEECCCC-CCHHHHHHHHHCC-CCCCCC--CCCC PSA >P1;d1o13a- -------20000045568550300570590330000617a871361503805117a9588---60181058470710005709aa1275078-b08055828-520360064416a-7----------- >P1;d1p90a- a25b60020000038----c4403050680620000203299273354260962781a-94362106205--4030000150aa702550681a0414537a12206700650185068a148304831 >P1;d1rdua- -----73400000536-7362501650030410002228---a5b26315271857b9c8--1500930473806200006119702950471905013-0762507601522479-81821570b8ac >P1;d2wfba1 -----67500000546-9279501360130300000306---7372622706804849950144006204827020000040268108206729050007039220560074135a-70821a4336-- >P1;d2yx6a- ------540000054651460601670381530000206c983672533706------b3---a105105838062000110a8733530672b07032004-640380093119b-918239--7188 Translating the sequences -------*EEEEECCC****CCCCCCCCCCCEEEEEEEECC*EEEEEEEECHHH*CCCCC---*HHHHHHHCCCCEEECCCCCHHHHHHHH*-CCEEECCCC-CCHHHHHHHHHCC-C----------- *******EEEEEECC----CC**CCCCCCCCEEEEEEEECC*EEEEEEEECHHH**CC-C***HHHHH**--CCCEEE*CCCCHHHHHHHHHCCCEEE*CCCC**HHHHHHHHH****CCCC******C -----*C*EEEEECCC-**CCCCCCC***CCEEEEE***---***EEEEEC****CCCCC--**HHHHHH*CCCCEEECCCCC***HHHHH*CCCEEEC-CCCCCHHHHHHHHHCC-CCCCCC**CC*C -----*CEEEEEECCC-**CCCCCCCCCCCCEEEEEE**---***EEEEECHHH*CCCCC***HHHHHHHH*CCCEEECCCCCHHHHHHHHHCCCEEECCCCCCCHHHHHHHHHCC-CCCCCC**CC-- ------CEEEEEECCC****CCCCCCCCCCCEEEEEEEECC*EEEEEEEEC*------CC---HHHHHHHHCCCCEEECCCCCHHHHHHHHHCCCEEECCCC-CCHHHHHHHHHCC-CCCCCC--CC*C 53146.tem _________________________________ -----*CEEEEEECCC-**CCCCCCCCCCCCEEEEEEEECC*EEEEEEEECHHH*CCCCC--*HHHHHHHHCCCCEEECCCCCHHHHHHHHHCCCEEECCCCCCCHHHHHHHHHCC-CCCCCC**CC*C Structural block scores 0 4 - 4.5 M 75.0 7.0 75.0 75.0 75.0 7 12 E 4.8 H 0.3 0.3 0.7 0.8 0.7 13 15 C 4.8 H 4.7 28.7 4.7 5.0 5.0 17 18 * 2.1 P 6.5 75.0 5.0 5.5 2.5 19 30 C 4.7 H 3.1 4.0 2.7 3.2 3.6 31 38 E 4.6 H 2.1 0.9 1.9 1.1 1.4 39 40 C 4.2 M 9.2 5.5 75.0 75.0 10.8 42 49 E 4.5 M 3.4 4.0 5.5 4.5 4.5 51 53 H 4.0 M 2.3 5.7 5.3 4.7 52.0 55 59 C 4.5 M 8.1 20.7 9.6 7.0 47.9 60 61 - 3.8 M 75.0 3.5 75.0 0.5 75.0 63 70 H 4.6 H 3.6 11.4 3.5 3.0 3.8 71 74 C 4.8 H 4.5 20.5 4.2 2.8 4.2 75 77 E 5.0 H 0.3 0.0 0.7 0.0 0.7 78 82 C 4.9 H 4.2 3.3 1.6 1.2 2.5 83 91 H 4.7 H 5.7 4.8 4.8 4.2 4.7 92 94 C 4.8 H 28.8 3.8 3.3 3.7 4.5 95 97 E 5.0 H 4.3 3.0 2.0 1.7 3.3 98 104 C 4.6 H 15.0 4.4 14.0 3.3 13.0 105 113 H 5.0 H 2.7 2.8 3.0 2.9 2.8 114 115 C 4.5 M 8.2 6.5 8.0 7.8 10.2 117 122 C 4.4 M 63.7 6.2 4.2 4.8 5.3 123 124 * 3.0 P 75.0 1.5 3.5 3.5 75.0 125 126 C 4.1 M 75.0 6.0 9.8 4.5 4.0 >>>>>>