Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1i8ua- CCCCEECCCCCCCCCCHHHHHCCEEEC---CEEEECCC-------CCCEEEEEEEECC--------CEEEEEEEEECC----CCCCCCCCHHHCCEEEEEEECCC--CCCC-------CCC-CCEEEEEEECC--CCEEECC-CCC-HHHEEEEEEEE----CCEEEEEEEEECCCCC-------CC---CCCEEEEEEEEEE-----CCCCC-EEEEEEC--CCCCCCCCCCHHHCEEECC----------------------------------------------------- >P1;d1pl3a- --------------------CCEEEECCCCCCEEEEEEEC------CCCEEEEEECCCCCCCCCCCCCEEEEEEEEC--CCCEEEEECCCCCCCCCEEEEEEEC-----------------CEEEEEEEECCCCCCCEECCC-------CCEEEECCCCEECCCEEEEEEEEECCCCCC-CC--CCCCCC-CEEEEEEEEEC-CCCCCCCCCC-CCCC--------------CCC-EEEEEEEE-HHHCCCCCHHHHHC------------------------------------ >P1;d1ug9a3 CCEEEECCC---------------CCC---CCCCCCCCCCCCCCCCCCCCEEEEEEEEEC------CEEEEEEEECC-----CCCCCCCCCCCCCEEEEEEEECCCCCCEECCHHHCEEECCCCCEEEEEECCCCCCEEECCCCCEE---ECCEEEEE---HHHC-EEEEEEEHHHCC-------CCCCCCCEEEEEEEECCC-----HHHCCCCCCCEEEHHHHHHCCCHHHHHHCEEEECCCCCCC--CCCCCCCCCCCCCCEECCCCCCCHHHHCCHHHCCCEEECCEECCC >P1;d4qi3a1 ------------------CCCCEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCCCCC-CCCCEEEEEEEECCCCCCEEEEECCCCCCCCCEEEEEEEC-----------------CEEEEEEEECCCCCCCEECCC-------CCEEE-EEEEEECCCEEEEEEEEECCCEEEECCEEEECCHHHCEEEEEEEEEC-CCCCCCCCHHHCCCC--------------CCCCCEEEEEEECCHHHCCCCHHHHHCCCCCCCC----------------------------- >P1;d6jt6a- --------------------CCEEEECCCCCCEEEEEEEC------CCCEEEEEEEEC-CCCCCCCCEEEEEEEEEC--CCCEEEEECCCCCCCCCEEEEEEEC-----------------CEEEEEEEECCCCCCCEECC--------CCEEEECCCCEECCCEEEEEEEEECCCCCCCCC--CCCCCC-CEEEEEEEEECCCCCCCCCCCC-CCCC--------------CCC-EEEEEEEE-CHHHEECCHHHHHHHHHHCCCCCC-------------------------- PSA >P1;d1i8ua- 8050451608040743a3076052130---62205464-------a201060200007--------730000030506----521373a4242100000000042--6226-------802-b0000000015--4524147-404-69107020453----b800000000404420-------86---9350000000000-----27706-1400001--2045420562043034004----------------------------------------------------- >P1;d1pl3a- --------------------90973508817050002507------72602000001533aaba3541000002026--905001010406217001000014c-----------------98011110107b883185081-------a060530831517a7401000203400606-5a--700704-47650102006-7507637555-0708--------------925-46350604-0360119508701a------------------------------------ >P1;d1ug9a3 410219075---------------a21---30045041052a20382000022030455b------a3110113030-----603223925100000000000608b8627006102010415071000000248200013586735---28040522---5944-30104033a00a-------b15049040000000005-----9820433000004392066275940343000001253358--3612044360000000016bc46067103167a240500015088 >P1;d4qi3a1 ------------------5690833528b060200002296a186065103000002570287-31510001040014b5300010002042160010000049-----------------940101100077793174073-------90601-00518086710200020450050609b36811503943060002003-640762541770708--------------9160456513050595002840981084086519----------------------------- >P1;d6jt6a- --------------------70862608404040021418------606000000001-787799351000002031--a00000000003243001000002c-----------------85120000208776818428--------50715202000229a20000020360060b944--600368-a805000201474304737555-0906--------------814-42651506-05701356086016305828808f-------------------------- Translating the sequences *********************C*EEEC---C*EEE***-------CCC*EEEEEEECC--------CEEEEEEEEEC*----*****CCC***CC*EEEEEE*C*--****-------***-**EEEEEE*CC--CCEE*CC-***-****EEEEEEE----CCEEEEEEEEECCCCC-------CC---*C*EEEEEEEE**-----CCCCC-*******--*********C***CEEE**----------------------------------------------------- --------------------CCEEEECCCCCCEEEEEEEC------CCCEEEEEE*CC*CCCC*CCC*EEEEEEEEC--CCCEEEEECCCCCCCCCEEEEEEEC-----------------CEEEEEEEECCCCCCCEECCC-------CCEEEE****EECCCEEEEEEEEECCCCC*-CC--*CCCCC-CEEEEEEEEEC-CCCCCCCCCC-CCCC--------------CCC-*EEEEEEE-*HH**CCCHHHHHC------------------------------------ *********---------------**C---CC*******C*****CCCC*EEEEEE***C------CEEEEEEEE*C-----*****CCCCCCCC*EEEEEEEC*****************C***EEEEE*CCCCCCEE*CC*****---***EEEEE---****-EEEEEEE***CC-------CCCCC*CEEEEEEEE*C*-----***CC*CCCC******************CEEEE****C**--CCC*****C****C******************************* ------------------**CCEEEECCCCCCEEEEEEEC*****CCCCEEEEEE*CC*CCCC-CCC*EEEEEEEEC**CCCEEEEECCCCCCCCCEEEEEEEC-----------------CEEEEEEEECCCCCCCEECCC-------CCEEE-EEE*EECCCEEEEEEEEECCC****CC****CC***CEEEEEEEEEC-CCCCCCCC***CCCC--------------CCC*CEEEEEEE*CHH**CCCHHHHHC****C**----------------------------- --------------------CCEEEECCCCCCEEEEEEEC------CCCEEEEEEE*C-CCCC*CCCEEEEEEEEEC--CCCEEEEECCCCCCCCCEEEEEEEC-----------------CEEEEEEEECCCCCCCEECC--------CCEEEE****EECCCEEEEEEEEECCCCC**CC--*CCCCC-CEEEEEEEEEC*CCCCCCCCCC-CCCC--------------CCC-*EEEEEEE-CHH***CCHHHHH*****C*****-------------------------- 49344.tem _________________________________ --------------------CCEEEECCCCCCEEEEEEEC-----CCCCEEEEEEECC*CCCC-CCCEEEEEEEEEC--CCCEEEEECCCCCCCCCEEEEEEEC-----------------CEEEEEEEECCCCCCCEECCC-------CCEEEEEEE*EECCCEEEEEEEEECCCCC*-CC--*CCCCC*CEEEEEEEEEC*CCCCCCCCCC-CCCC--------------CCC*CEEEEEEE-CHH**CCCHHHHHC****C**----------------------------- Structural block scores 0 19 - 4.1 M 3.8 75.0 42.7 68.0 75.0 20 21 C 4.3 M 3.0 4.5 75.0 4.5 3.5 22 25 E 4.4 M 2.8 6.0 40.6 4.8 5.5 26 31 C 4.5 M 38.8 4.0 38.2 4.6 2.7 32 38 E 4.1 M 13.7 1.7 2.0 0.9 1.7 40 44 - 3.8 M 75.0 75.0 3.5 6.3 75.0 45 48 C 4.7 H 3.4 22.5 2.5 3.0 21.8 49 55 E 4.8 H 1.1 0.3 1.0 0.4 0.0 56 57 C 4.2 M 3.5 3.0 4.5 3.5 0.5 59 62 C 4.3 M 75.0 8.9 59.1 4.2 7.2 64 66 C 4.5 M 52.3 4.0 53.5 3.0 5.7 67 75 E 4.8 H 1.2 0.6 1.4 0.7 0.7 77 78 - 4.2 M 40.5 75.0 75.0 7.8 75.0 79 81 C 4.2 M 75.0 4.7 75.0 2.7 3.5 82 86 E 3.8 M 3.6 0.4 2.6 0.2 0.0 87 95 C 4.7 H 2.9 2.2 2.2 1.7 1.3 96 102 E 4.9 H 0.0 0.9 0.0 0.7 0.4 104 120 - 4.2 M 41.4 75.0 3.3 75.0 75.0 122 129 E 4.6 H 1.4 1.6 1.6 0.9 1.2 130 136 C 4.7 H 23.6 5.5 2.3 4.9 5.3 137 138 E 5.0 H 3.0 6.5 0.0 5.5 6.0 139 141 C 4.4 M 4.0 3.0 3.0 3.3 28.3 142 148 - 4.2 M 24.7 75.0 25.6 75.0 75.0 149 150 C 3.9 M 0.5 5.2 38.5 4.5 2.5 151 157 E 4.3 M 3.0 3.6 3.0 12.4 2.4 159 160 E 4.2 M 75.0 3.0 75.0 4.0 1.0 161 163 C 4.4 M 31.5 8.2 6.0 7.0 7.2 164 172 E 4.9 H 0.4 1.1 10.0 1.0 0.8 173 177 C 4.5 M 2.0 2.0 4.8 2.0 2.4 180 181 C 4.2 M 75.0 7.8 75.0 10.2 4.0 182 183 - 4.5 M 75.0 75.0 75.0 4.5 75.0 185 189 C 4.4 M 47.8 2.2 4.3 2.0 3.4 192 200 E 4.9 H 0.6 2.3 0.4 1.2 1.8 203 212 C 4.3 M 39.7 5.0 39.8 4.2 4.3 214 217 C 4.5 M 1.2 3.8 0.8 3.8 3.8 218 231 - 3.9 M 12.8 75.0 4.1 75.0 75.0 232 234 C 4.0 M 2.0 5.3 2.3 5.3 4.3 237 243 E 4.5 M 23.0 3.4 1.1 3.6 3.6 246 247 H 4.1 M 75.0 4.5 6.5 7.0 6.0 248 249 * 3.0 P 75.0 0.5 75.0 0.0 0.5 250 252 C 4.4 M 75.0 5.0 3.3 4.7 4.7 253 257 H 4.1 M 75.0 3.2 2.6 3.6 3.0 259 262 * 3.0 P 75.0 75.0 0.0 4.5 4.0 264 265 * 3.0 P 75.0 75.0 0.0 5.0 8.0 266 294 - 4.4 M 75.0 75.0 4.0 75.0 68.3 >>>>>>