Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1nq4a- ---CCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHH-HCCCCHHHHHHHHHHHHHCCCCCCCCHH-HH-CCCHHHHHHHHHHHHHHCCCCCCCCCCCC >P1;d1t8ka- -----CCHHHHHHHHHHHHHCCC----HHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHH-CC-CCCHHHHHHHHHHCCC------------- >P1;d1vkua1 -------CHHHHHHHHHHHHH--HCCCCCCCCCCCCCCCC-CCCHHHHHHHCCHHHHHC--CCCC---CCC-CCCC-CHHHHHCCCCCC------------ >P1;d2cg5b- ---------CCHHHHHHHHCCCCC-----CCCCCCCCCCC-CCCHHHHHHHC-CCC-CCCCCCCHHHH----CCCCCCCCC-------------------C >P1;d2cgqa1 -------CHHHHHHHHHHHHCCC----C-CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHH-HH-CCCHHHHHHHHHCCC-------------- >P1;d2l4ba1 ----CHHHHHHHHHHHHHHHCCC-HHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHH-CC-CCCHHHHHHHHHHHHHHC----------- >P1;d2mr7a1 CCCCCCHHHHHHHHHHHHHHCCCCC------CCCCCCCCCC-CCCCHHHHHHHHHHHHCCCCCCHHHH-HH-CCCHHHHHHHHHCCC-------------- >P1;d2xz0d- ---CCHHHHHCCHHHHHHCCCCC---CCCCCCCCCCHHH-HCCC-CHHHHHHHHCCCCCCCCCCCCCC-CC-CCCCHHHHHHHHHHCCCCC---------- >P1;d4bpfa1 ------CHHHHHHHHHHHHHCCCHHHH----CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCHHHHHHHHHHHC-------------- >P1;d4h2wc1 -------CHHHHHHHHHHHCC---CCCCHHHCCCCCHHHH-CCCHHHHHHHHHHHHHHC--CCCCCCCCCC-CCCC-CHHHHC------------------ >P1;d4mrtc1 CCCCCCHHHHHHHHHHHHHHCCCCC------CCCCCCCCCC-CCHHHHHHHHHHHHHHHCCCCCHHHH-HH-CCCHHHHCCCCC----------------- >P1;d4pxhb1 -CCCCCHHHHHHHHHHHHHHCCCCC------CCCCCCCCCC-CCHHHHHHHHHHHHHHCCCCCCHHHH-HH-CCCHHHHHHHC------------------ >P1;d6kxfc- ----CCCHHHHHHHHHHHHHCCCCC----------CCCC-CCCC--CCHHHHHHHHHHHCCCCCHHHH-HH-CCCCCHHHHHHHHHHCC------------ >P1;d6yj4t- ----CCCCHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHH-CC-CCCHHHHHHHHCCCCCCC----------- >P1;d7bvgp- -CCCHHHHHHHHHHHHHHHCCCC----CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHH-CC-CCCHHHHHHHHHHHHHCC-CCCHHHCCCC >P1;d7of0w- --CCHHHHHHHHHHHHHHCCCCC----CCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCHHHH-HH-HCCHHHHHHHHHHHC-------------- PSA >P1;d1nq4a- ---4b7073840061036218766316318812754084-080889207600440374150653a824-89-0710530182015008676799c799889 >P1;d1t8ka- -----672564027101630917----984073a0205860a07983285016202930919058a41-78-0730430070059468------------- >P1;d1vkua1 -------64a80272045004--74b4a0b0727340961-807a8416600404a429--108a---519-0740-400620124889------------ >P1;d2cg5b- ---------a6035501310827c-----b2765230281-90698217503-207-72b37166850----61306051c-------------------9 >P1;d2cgqa1 -------26a402600360092b----5-a075a1406850907a73384014302941a07079861-77-073034008204745-------------- >P1;d2l4ba1 ----4a90563036302720807-97459615392302840b0889325702540385281a07a920-96-052034007101835999----------- >P1;d2mr7a1 b899379215201700261093a90------958320771a-06784077016506841876045820-56-333014008226869-------------- >P1;d2xz0d- ---36971266046115841a4b---a68a384815177-1809-a138411630384271a17a941-98-162055007304922776a---------- >P1;d4bpfa1 ------82553005100800a463028----8372301759108691065006303851917046a505595030044008303745-------------- >P1;d4h2wc1 -------54960260055308---0667198096560183-6088a0175015002832--5069a44770-0520-404910------------------ >P1;d4mrtc1 64616792053005002510a4990------005330282a-06793045016205732838043920-47-412063003079----------------- >P1;d4pxhb1 -39077a2044036001600969b0------507340483b-06992187006304840a3b057840-76-50203300931------------------ >P1;d6kxfc- ----95a438403701281194893----------b24a-5a19--8256005302831919075a32-76-036163018002830a1------------ >P1;d6yj4t- ----686028403710481b50a---578316380406939007a9027600540173090806b842-75-062065017205772753----------- >P1;d7bvgp- -3584951074106003601727----3a504492207840a0699215501621274483714aa41-98-074034117234742865-695a448935 >P1;d7of0w- --68785056405600461a509----55406990404810808991053006401742076058841-46-021045017201812-------------- Translating the sequences ---*****HHHHHHHHHHH*CCC********CCCCC***-*CCC*HHHHHHHHHHHHH*CCCCC**HH-**-CCC*HHHHHHH****************** -----***HHHHHHHHHHH*CCC----****CCCCCCCCC*CCC*HHHHHHHHHHHHH*CCCCCHHHH-**-CCC*HHHHHHH*****------------- -------*HHHHHHHHHHH**--********CCCCCCCCC-CCC*HHHHHH**HHHHH*--CCC*---***-CCC*-*HHHHH******------------ ---------**HHHHHHHH*CCC*-----**CCCCCCCCC-CCC*HHHHHH*-***-**CCCCCHHHH----CCC******-------------------* -------*HHHHHHHHHHH*CCC----*-**CCCCCCCCC*CCC*HHHHHHHHHHHHH*CCCCCHHHH-**-CCC*HHHHHHH****-------------- ----****HHHHHHHHHHH*CCC-*******CCCCCCCCC*CCC*HHHHHHHHHHHHH*CCCCCHHHH-**-CCC*HHHHHHH*******----------- ********HHHHHHHHHHH*CCC**------CCCCCCCCC*-CC**HHHHHHHHHHHH*CCCCCHHHH-**-CCC*HHHHHHH****-------------- ---*****HH**HHHHHH**CCC---*****CCCCC***-*CCC-*HHHHHHHH*****CCCCC****-**-CCC*HHHHHHH********---------- ------**HHHHHHHHHHH*CCC****----CCCCCCCCC*CCC*HHHHHHHHHHHHH*CCCCCHHH*****CCC*HHHHHHH****-------------- -------*HHHHHHHHHHH*C---*******CCCCC****-CCC*HHHHHHHHHHHHH*--CCC*******-CCC*-*HHHH*------------------ ********HHHHHHHHHHH*CCC**------CCCCCCCCC*-CC*HHHHHHHHHHHHH*CCCCCHHHH-**-CCC*HHH*****----------------- -*******HHHHHHHHHHH*CCC**------CCCCCCCCC*-CC*HHHHHHHHHHHHH*CCCCCHHHH-**-CCC*HHHHHH*------------------ ----****HHHHHHHHHHH*CCC**----------CCCC-*CCC--**HHHHHHHHHH*CCCCCHHHH-**-CCC**HHHHHH******------------ ----****HHHHHHHHHH**CCC---*****CCCCCCCCC*CCC**HHHHHHHHHH***CCCCCHHHH-**-CCC*HHHHHHH*******----------- -*******HHHHHHHHHHH*CCC----****CCCCCCCCC*CCC*HHHHHHHHHHHHH*CCCCCHHHH-**-CCC*HHHHHHH*******-********** --******HHHHHHHHHH**CCC----****CCCCCCCCC*CCC*HHHHHHHHHHH***CCCCCHHHH-**-*CC*HHHHHHH****-------------- 47336.tem _________________________________ --******HHHHHHHHHHH*CCC********CCCCCCCCC*CCC*HHHHHHHHHHHHH*CCCCCHHHH-**-CCC*HHHHHHH*******----------- Structural block scores 0 1 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 9.8 75.0 75.0 75.0 5.0 39.0 75.0 75.0 39.0 75.0 2 7 * 2.8 P 17.4 40.0 63.5 75.0 62.8 28.9 6.5 16.8 51.7 63.3 5.2 5.9 29.8 28.3 5.3 5.7 8 18 H 4.9 H 3.0 3.2 3.9 10.0 3.4 3.4 2.3 3.9 2.5 3.6 1.9 2.2 3.4 3.5 2.5 3.4 20 22 C 4.7 H 7.0 5.7 51.3 5.7 7.5 5.0 7.5 8.7 6.8 52.7 7.8 8.0 7.0 5.2 5.3 4.7 23 30 * 3.2 M 4.5 40.1 6.1 50.1 48.8 14.5 57.4 32.9 39.1 14.0 57.4 57.7 57.8 31.1 39.8 39.2 31 39 C 4.7 H 11.8 4.6 4.3 3.8 5.2 4.0 4.7 12.9 4.0 4.2 2.6 3.8 44.8 4.3 4.4 4.6 41 43 C 4.9 H 5.3 5.8 5.0 5.0 5.3 6.5 27.0 5.7 3.0 4.7 27.0 27.0 6.8 2.3 5.5 5.3 45 57 H 4.7 H 3.5 3.8 3.8 14.8 3.7 4.1 4.3 4.0 3.5 3.3 3.5 4.0 9.0 3.4 3.5 3.1 59 63 C 4.9 H 3.8 4.8 31.8 5.7 4.9 5.3 5.0 5.3 4.2 32.2 4.6 6.0 5.2 4.6 4.6 3.6 64 67 H 4.4 M 6.1 5.9 58.9 4.8 6.0 5.4 3.8 6.1 5.4 6.9 3.5 4.8 5.1 6.4 6.5 5.2 69 70 * 1.3 P 8.5 7.5 5.0 75.0 7.0 7.5 5.5 8.5 7.0 3.5 5.5 6.5 6.5 6.0 8.5 5.0 72 74 C 4.9 H 2.7 3.3 3.7 3.3 3.3 2.3 3.0 3.0 1.0 2.3 2.3 2.3 3.0 2.7 3.7 1.0 76 82 H 4.6 H 2.7 2.0 12.4 24.9 2.4 2.1 2.4 2.9 2.7 13.3 2.7 2.7 2.6 3.0 3.0 2.7 83 89 * 2.9 P 3.9 26.0 15.3 75.0 35.0 6.3 36.3 5.3 34.9 75.0 65.6 75.0 14.2 5.1 5.1 33.9 90 100 - 4.7 H 8.5 75.0 75.0 69.0 75.0 75.0 75.0 69.1 75.0 75.0 75.0 75.0 75.0 75.0 12.6 75.0 >>>>>>