Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1knca- ------------------CHHHHHHHCC---HHHHHHHH----HHHHHC------C--CCCCCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC---------------------CCCCCCCCCCCCHHHH-----------------------CCCCCHHHHHHHHHHHHHHHCCHHHH--HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC---------- >P1;d1vkea- ----------------CCCCCCCCCCCCH-HHHHHCCCCCCCCHHHHHHHHHHHHHHC----CCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH--CHHHCCCCCHHHHHHHHHHHCCCCCCC-------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2af7a1 ----------------CHHHHCC--CCCC-CCHHHHHHCCCHHHHHHHHHIIIIIIICC-CCCCHHHHHHHHHHHHHCCC--HHHHHHHHHHHHHC--C--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC------------------------------------------------------------------------------------------------------------------------------------ >P1;d2cwqa1 ------------CCCCHHHHHCCCCCHHHCCCHHHHHHHHCHHHHHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHHCC--HHHHHC-CHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHCCHHHHCCC-------------------------------------------------------------------------------------------------------------------------------------- >P1;d2gmya1 ---------------------------CCCCCHHHH----CHHHHHHHHHHHHHHHC--CCCCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHC-C--CCHHHHHHHHHHHHCCCCC-------------------------------------------------------------------------HHHHHHHHHHHHHHCHHHHCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCC--CCCC----CCC >P1;d2ouwa1 -CCCCCCCHHHHHCCCCHHHHHHHHHCCCCCHHHHHHCC-CCCC-CCCCCCCC--CCCC-CCCHHHHC-CHHHHHHHCCC--HHHHHHHHHHHHHC--C-CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC------------------------------------------------------------------------------------------------------------------------------------ >P1;d2oyoa1 CCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCCHHHHHHH-CHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH--CCHHHHHHHHHHHHHHHC--CHHHHHHHHHCHHHCC-CC-------------------------------------------------------------------------CHHHHHHHHHHHHHCHH--HCCHHHHHHHHHCCCCCCCC-CHHHHHC-CHHHHHHHHHCC--CCCCHHHCCCC >P1;d2q0ta1 --------CCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHCHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCHHHHHCCHHHHHCCCCCCHHHH--HHHHHHHHHCCCCC-CCCCHHHHHH-HHHHHHHHHHHHHHHHHHHHCCCCC >P1;d3c1la- CCCCC-----CCCHHHHHHHHHHHC-CCCCCHHHHHHCC-CHHHHHHHHHHHHHCC-CCCCCCHHHHC-CHHHHHHHC--CCHHHHHHHHHHHHHHHC--CHHHHCCC--CHHHHC-CC-------------------------------------------------------------------------HHHHCCHHHHHHHHCHH--HCCHHHHHHHHHCCCCHHHHHHHHHHHH-HHCCHHHHHHHC---CCCHHHHCCC PSA >P1;d1knca- ------------------1187018501---97169335----502700------8--1a307733000000000100--6186047201720782078503800330081024007313827838---------------------47558693b3827328-----------------------a0919542010000000112709503--8513740454a277720700440071045008105437877---------- >P1;d1vkea- ----------------3a576879b5784-9867362668a57233201600361028----4427503300120032906484057107702972--8860651250491077028358a7818-------------------------------------------------------------------------------------------------------------------------------------------- >P1;d2af7a1 ----------------a468406--1077-18245735843788145311742034136-88467520263057126752--58604320320271--a--0855048367178268701731360077018a------------------------------------------------------------------------------------------------------------------------------------ >P1;d2cwqa1 ------------4a6368326658521901297145207744a6035536567975a91-a5845420155136022694--a66361-5220853--90789225605770875676688a827776878-------------------------------------------------------------------------------------------------------------------------------------- >P1;d2gmya1 ---------------------------a45572486----55973772474195048--0a06630010000100212--a072032402340595-a--1767008304706909207-------------------------------------------------------------------------8302000300011046a83914a92476056-3079840810440090014106204735--1637----87b >P1;d2ouwa1 -5b57306693079509208403824a790265011203-6584-07308349--85ba-a6753510-66146048894--95348222732784--9-69963774676297577587767887867877a------------------------------------------------------------------------------------------------------------------------------------ >P1;d2oyoa1 306492176960376047008716774800011030104-719802812961261056b3508431000000000322--906004101203006419--439205404931470b-08-------------------------------------------------------------------------3262005101420545a--72797238505838077721-0045008-026106406737--05017515426 >P1;d2q0ta1 --------ba9897064740485053079618103000625245017007605307--4740753010001010000631719402811410683a0675115005400500a1191076137617624766728846916a4267127604982831681030001340750571365024035825064220000000000832618622--7223430574a068-5110053106-11c11a3087037636458778569 >P1;d3c1la- 3067b-----f45860574067168-6a10113032207-4495077117635826-5a080753211-000000222--80610111101300731a--54920613--70582a-15-------------------------------------------------------------------------9455205001220545a--7177824560391907761181042006-202206628725---5009724925 Translating the sequences ------------------*HH*****CC---*HHHHH**----HHHHH*------*--C*CCCHHHHHHHHHHHHHHC--C*HHHHHHHHHHH********HHHHHHHHHHHHHH*HH********---------------------****************-----------------------**************************--*****************************************---------- ----------------**********CC*-**HHH*****C**HHHHHHHHHH****C----C*HHHHHHHHHHHHHC**C*HHHHHHHHHHHHH*--***H*****HHHHHHHH*HH*******-------------------------------------------------------------------------------------------------------------------------------------------- ----------------*HHHH**--*CCC-C*HHHHH***CHHHHHHHHH*******CC-CCC*HHHHHHHHHHHHHC**--HHHHHHHHHHHHH*--*--***************HH***************------------------------------------------------------------------------------------------------------------------------------------ ------------*****HHHH********CC*HHHHH***CHHHHHHHHHHHH****CC-CCCHHHHHHHHHHHHHH***--HHHHH*-*HHHHH*--***HHHHHHHHHHHHHH*HH*************-------------------------------------------------------------------------------------------------------------------------------------- ---------------------------CCCC*HHHH----CHHHHHHHHHHHH****--*CCCHHHHHHHHHHHHHHC--C*HHHHHHHHHHHHH*-*--**HHHHHHHHHHHH*****-------------------------------------------------------------------------*******************************-****************************--****----*** -****************HHHH*****CCCCC*HHHHH**-C***-********--**CC-CCCHHHH*-*HHHHHHHC**--HHHHHHHHHHHHH*--*-*HHHHHHHHHHHHHH*HH***************------------------------------------------------------------------------------------------------------------------------------------ *****************HHHH******CCCC*HHHHH**-CHHHHHHHHHHHH****CC*CCCHHHHHHHHHHHHHH*--C*HHHHHHHHHHHHH***--*HHHHHHHHH*HHH**-**-------------------------------------------------------------------------*****************--********************-*******-************--*********** --------*********HHHH*****CCCCC*HHHHH***CHHHHHHHHHHHH***--C*CCCHHHHHHHHHHHHH*C**C*HHHHHHH***HHH******HHHHHHHHHHHHHH*HH**********************************************************************************************--**************-**********-************************* *****-----*******HHHH****-CCCCC*HHHHH**-CHHHHHHHHHHHH***-CC*CCCHHHH*-*HHHHHHHC--C*HHHHHHHHHHHHH***--*HHHH***--*HHHH*-**-------------------------------------------------------------------------*****************--****************************-************---********** 69118.tem _________________________________ ----------*******HHHH*****CCCCC*HHHHH***CHHHHHHHHHHHH****CC*CCCHHHHHHHHHHHHHHC**C*HHHHHHHHHHHHH******HHHHHHHHHHHHHH*HH*************-------------------------------------------------------------*****************--*--*************************-************--****----*** Structural block scores 0 9 - 4.2 M 75.0 75.0 75.0 75.0 75.0 12.8 4.7 62.2 40.2 10 16 * 3.2 M 75.0 64.7 65.8 25.6 75.0 4.7 3.7 6.1 7.2 17 20 H 4.4 M 21.2 7.1 5.5 4.8 75.0 3.5 3.8 3.8 4.2 21 25 * 2.0 P 4.2 8.1 31.4 5.2 75.0 3.4 5.6 4.2 19.4 26 30 C 4.4 M 45.2 20.6 18.0 2.6 19.9 5.7 2.4 4.6 3.7 32 36 H 4.8 H 5.2 4.8 4.2 3.8 19.0 1.8 1.0 0.8 2.0 37 39 * 2.3 P 27.7 6.7 5.7 4.7 75.0 26.0 26.3 2.7 27.3 41 52 H 4.5 M 38.7 2.7 4.2 5.0 5.4 10.5 4.1 3.1 4.6 53 56 * 2.0 P 58.2 2.2 2.0 7.9 4.2 40.8 3.0 21.2 22.8 57 58 C 4.5 M 38.0 41.5 4.5 5.0 75.0 11.0 8.8 39.5 7.8 60 62 C 4.8 H 3.3 51.3 6.7 7.8 5.5 7.8 4.3 3.7 5.0 63 76 H 4.8 H 1.0 2.1 3.7 2.9 1.0 8.9 0.9 0.8 6.5 78 79 * 3.2 M 75.0 4.5 3.5 6.5 75.0 6.5 75.0 2.0 75.0 82 94 H 4.8 H 4.0 4.4 3.2 10.0 3.2 4.8 1.8 3.6 1.7 95 100 * 2.6 P 3.7 29.0 51.9 28.2 40.2 40.7 28.0 4.9 28.2 101 114 H 4.4 M 2.3 3.4 4.6 5.1 4.1 6.2 3.6 2.3 14.1 116 117 H 4.2 M 5.0 5.5 7.5 6.5 1.0 6.0 37.5 0.5 38.0 118 130 * 3.0 P 31.9 38.3 2.8 7.1 69.8 7.2 69.8 4.8 69.6 131 191 - 4.6 H 50.0 75.0 72.8 75.0 75.0 72.8 75.0 4.0 75.0 192 208 * 3.2 M 1.6 75.0 75.0 75.0 2.3 75.0 3.0 1.8 3.5 209 210 - 4.0 M 2.5 75.0 75.0 75.0 5.5 75.0 75.0 4.0 75.0 212 213 - 4.0 M 75.0 75.0 75.0 75.0 2.5 75.0 4.5 75.0 4.0 214 238 * 3.2 M 3.9 75.0 75.0 75.0 7.3 75.0 7.0 6.3 3.9 240 251 * 3.2 M 3.1 75.0 75.0 75.0 2.8 75.0 3.5 4.0 3.5 252 253 - 4.4 M 7.5 75.0 75.0 75.0 75.0 75.0 75.0 6.5 75.0 254 257 * 3.6 M 58.0 75.0 75.0 75.0 4.2 75.0 1.5 4.5 20.0 258 261 - 4.0 M 75.0 75.0 75.0 75.0 75.0 75.0 4.5 7.5 5.5 262 264 * 3.6 M 75.0 75.0 75.0 75.0 8.8 75.0 4.0 6.7 5.3 >>>>>>