Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1adza- CCCCCCCCCCCHHHHCCCCC-CCCC---CCCCEEEEEHHHCEEEEECCCCCCCC-CCCCCCHHHHHHHCCCCCCCC >P1;d1bunb- -------CCCCCCCCCCCCC-CCCC---CCEEEEEEEHHHCEEEEEEECCCCCC-CCCCCCHHHHHHHHCCCC--- >P1;d1d0da- ---------CCHHHCCCCCCCCCCCHHHCCEEEEEEC-CCCCEEEEEECCCCCCCCCCCCCHHHHHHHHC------ >P1;d1dema- -------CCCCHHHCCCCCC-CCCC---CCEEEEEECCCCCCEEEEEECCCCCC-CCCCCCHHHHHHHHCCC---- >P1;d1g6xa- ---------CCHHHHCCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHHHCC----C >P1;d1ktha- ---------CCHHHHCCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHHHCC----- >P1;d1tocr1 --------CCCHHHCCC-CCC--CCCCCCEEEEEEEE-C-CEEEEEEEEC-----CCCCCCHHHHHHHCC-CCCCC >P1;d1tocr2 -----CCCCCCHHHHCCCCC--CCC---CCEEEEEEECCCCEEEEEEEE-CCCC-CCCCCCHHHHHHHCCCCCCC- >P1;d2kcra- -------CCCCCCCCCCCCCCCCC----CCCCEEEEECCCCEEEEECCCCCCCC-CCCCCCHHHHHHHHHHHC--- >P1;d2odye2 -----CCCCHHHHCCCCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHHHCC----C >P1;d2uuyb1 -------CCCCC--CCCCCCCCCCC---CCEEEEEEEC--CEEEEEEECCC-----CCCCCHHHHHCCCC------ >P1;d3m7qb1 -----------CHHHCCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHHCCC----- >P1;d4ntwb- --------CCCHHHHCCCCCCCCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHC-CCCC----- >P1;d6q61a- ---------CCHHHHCCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHHHCC----C PSA >P1;d1adza- c89b5797a21810557433-0868---7677110125a686055062033902-801078495018404358d93 >P1;d1bunb- -------7932710558126-9757---b1570210439256046181011782-30209549403430339b--- >P1;d1d0da- ---------559304439a0994276a6807401043-b98207303014a41694b0275585057404------ >P1;d1dema- -------b463850644523-4a1a---67550301228493053042127668-40327748504530368---- >P1;d1g6xa- ---------24a20567245-0a49---5745121033a456045130114836-700185575057302c----b >P1;d1ktha- ---------46840537436-1858---9474211023a765056061035a03-8021755850374026----- >P1;d1tocr1 --------b73860714-95a--70ac4755412025-d-9505436015-----820254665058402-a9a9c >P1;d1tocr2 -----b98746710659408--82b---b087101017a4730444770-4438-9031964650063060756f- >P1;d2kcra- -------b916760556429a828----a575121022874306215229930a-063066476036405839--- >P1;d2odye2 -----b02758710539156-195a---7856221124a556044170034a03-8001744850382036----c >P1;d2uuyb1 -------1a06b--b4a41a85a69---3764222205--a4044154109-----824575a3067407------ >P1;d3m7qb1 -----------a33838455-1959---68562211249767036140003b03-7001764860655096----- >P1;d4ntwb- --------814a2046700496657---93660200259664024071041761-70119649603-5046----- >P1;d6q61a- ---------44a20747255-180a---77462010249675027180217803-8001666740123038----a Translating the sequences *********CCHHH*CCCCC-CCCC---CC**EEEEE***CEEEEE**CCCCCC-CCCCCCHHHHHHH*CC***** -------**CC****CCCCC-CCCC---CCEEEEEEE***CEEEEEEECCCCCC-CCCCCCHHHHHHH*CC**--- ---------CCHHH*CCCCC*CCCC***CCEEEEEE*-CCC*EEEEEECCCCCC*CCCCCCHHHHHHH*C------ -------**CCHHH*CCCCC-CCCC---CCEEEEEE*CCCC*EEEEEECCCCCC-CCCCCCHHHHHHH*CC*---- ---------CCHHH*CCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHH*CC----* ---------CCHHH*CCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHH*CC----- --------*CCHHH*CC-CC*--CC***C*EEEEEEE-C-CEEEEEEE*C-----CCCCCCHHHHHHH*C-***** -----****CCHHH*CCCCC--CCC---CCEEEEEEECCCCEEEEEEE*-CCCC-CCCCCCHHHHHHH*CC****- -------**CC****CCCCC*CCC----CC**EEEEECCCCEEEEE**CCCCCC-CCCCCCHHHHHHH*****--- -----******HH**CCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHH*CC----* -------**CC*--*CCCCC*CCCC---CCEEEEEEEC--CEEEEEEECCC-----CCCCCHHHHH***C------ -----------*HH*CCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHH*CC----- --------*CCHHH*CCCCC*CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHH*-**CC----- ---------CCHHH*CCCCC-CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHH*CC----* 57362.tem _________________________________ -------**CCHHH*CCCCC*CCCC---CCEEEEEEECCCCEEEEEEECCCCCC-CCCCCCHHHHHHH*CC**--* Structural block scores 0 6 - 4.7 H 8.9 75.0 75.0 75.0 75.0 75.0 75.0 56.5 75.0 55.2 75.0 75.0 75.0 75.0 7 8 * 3.1 M 8.8 8.0 75.0 7.8 75.0 75.0 43.2 7.5 10.2 4.5 5.8 75.0 41.5 75.0 9 10 C 4.6 H 1.5 2.5 5.0 4.5 3.0 5.0 5.0 5.0 3.5 6.5 3.0 75.0 2.5 4.0 11 13 H 4.3 M 3.0 2.7 4.0 4.3 4.2 4.0 4.7 2.7 4.3 2.7 53.8 5.5 4.2 4.2 15 19 C 5.0 H 4.4 4.4 5.3 3.6 4.8 4.6 18.8 5.2 5.2 4.8 6.0 5.0 3.4 4.6 21 24 C 4.8 H 5.5 7.0 5.5 6.5 5.9 5.5 39.2 24.1 23.2 6.4 7.6 6.0 6.0 4.9 25 27 - 4.6 H 75.0 75.0 7.5 75.0 75.0 75.0 9.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 28 29 C 4.9 H 6.5 6.2 4.0 6.5 6.0 6.5 6.0 5.8 7.8 7.5 5.0 7.0 6.0 7.0 30 36 E 4.8 H 2.7 2.7 2.7 2.3 2.3 2.4 2.7 2.6 2.6 2.7 2.6 2.7 2.3 2.1 37 40 C 4.6 H 7.4 4.8 25.9 5.8 5.6 6.6 43.1 7.1 5.2 6.1 41.4 6.5 6.5 6.5 41 47 E 4.8 H 3.4 3.7 2.1 2.4 2.7 3.3 3.3 4.1 2.7 3.1 3.1 3.0 2.6 3.3 48 53 C 4.7 H 2.8 3.2 4.4 5.0 3.8 3.6 51.0 15.7 5.6 3.4 39.2 2.9 3.2 3.5 55 60 C 5.0 H 4.0 3.2 4.9 3.8 3.5 3.8 3.5 4.7 3.5 3.3 16.8 3.5 4.0 3.5 61 67 H 4.9 H 4.4 3.9 4.9 4.1 4.6 4.6 4.9 3.4 4.3 4.3 5.1 4.9 14.6 3.3 69 70 C 4.6 H 3.5 3.0 39.5 4.5 7.2 4.0 38.5 3.0 6.5 4.5 41.0 7.5 5.0 5.5 71 72 * 3.8 M 6.5 10.2 75.0 41.5 75.0 75.0 9.8 6.0 6.0 75.0 75.0 75.0 75.0 75.0 73 74 - 4.4 M 11.2 75.0 75.0 75.0 75.0 75.0 9.8 14.2 75.0 75.0 75.0 75.0 75.0 75.0 >>>>>>