Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vq8m1 CCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHCC---CCEEEEEEEEEEE---------CCEEEEEEEEECCCCHHHHCCCCCHHHHCHHHCCHHHHCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC-- >P1;d1vq8s1 ---------------------------------------------------------CC-CCEEEECCC------HHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHCCC---EEEEEEEECC-----------CCCEEEEEEECC------------------------CCCHHHHHCCC------------------------- >P1;d1ywxa1 ----------------------------------CEEEEEEEEEECC----------CCEEEEEEEEECCC----------------------CCCCHHHHHHHHHHHHCCCCCCEEEEEEEECC----------CCCEEEEEEEEECCHHHHC------CCCC------------HHHHHHCCCCCCCCCCC------------CCC >P1;d2g1da1 ----------------------------------CCEEEEEEECCCC----------CCEEEEEEEEECCCC---------------------CCCCHHHHHHHHHHHHCCCCCCEECCCCCCCC----------CCCEEEEEEEEECHHHHHH------HHCC-----------------------------CCCCCCCCCCCCCCC >P1;d2j01x1 ---------------------------------------------------------CCCCCCCEECCC------HHHHHHHC-CCCCCEECCCCCCCCCCHHHHCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC------------------------CCCCCCCCCCC------------------------- >P1;d2v94a1 -----------------------------------CEEEEEEEEECC----------CCEEEEEEEEECCCC---------------------CCCCHHHHHHHHHC-CCCCHHHEEEEEEECCC----------CCCEEEEEEEEECCCCC-C------CCCC------------HHHHHHCCC----------------------- PSA >P1;d1vq8m1 b56941636650674a8bb037518521580493860461a70113030471603638001001010329305496287b479764a29a56594511130014006527---7010020060542---------a81300000002083620580a7035016b92470025020600552171899a9907503743a629774-- >P1;d1vq8s1 ---------------------------------------------------------b4-921454384------a8056213763200000056075a5027203871a05---045051683a-----------8b312020401b------------------------92405803754------------------------- >P1;d1ywxa1 ----------------------------------570636577825a----------76054110102169----------------------9727475026203740b38682000282864b----------a761040300106669305------9318------------9823725888998a79c------------99b >P1;d2g1da1 ----------------------------------1506192776869----------54005020003497a---------------------98458852432004407166300418b85279----------b682210503022433037------9578-----------------------------9473b8b8a8a9669 >P1;d2j01x1 ---------------------------------------------------------a88911354055------a9038619-7300002032773557047002623916---056032364396787986837570012203028------------------------a3247349769------------------------- >P1;d2v94a1 -----------------------------------80723526338a----------351220402041587---------------------85272860197018-3a06581000230635b----------b6550501001057664-4------8404------------9701840a2----------------------- Translating the sequences ************************************EEEE*****************CCEEEEEEEEECCC**********************CCC*HHHHHHHHHHH*C---**EEEEEEE****---------CC*EEEEEEEE*C***************C************HHHH**C***********************-- ---------------------------------------------------------CC-**EEEE**C------******************CCCCHHHHHHHHHHH*CCC---EEEEEEE*CC-----------CC*EEEEEEE*C------------------------****HHHH**C------------------------- ----------------------------------**EEEE*******----------CCEEEEEEEEECCC----------------------CCCCHHHHHHHHHHH*CCC***EEEEEEE*CC----------CCCEEEEEEEE*C******------***C------------HHHH**C**********------------*** ----------------------------------**EEEE*******----------CCEEEEEEEEECCC*---------------------CCCCHHHHHHHHHHH*CCC***EE******CC----------CCCEEEEEEEE*C******------***C-----------------------------*************** ---------------------------------------------------------CC*****EE**C------********-*********CCCC****HHHH****CCC---********CC**********CCC*********C------------------------**********C------------------------- -----------------------------------*EEEE*******----------CCEEEEEEEEECCC*---------------------CCCCHHHHHHHHH*-*CCC***EEEEEEE*CC----------CCCEEEEEEEE*C****-*------***C------------HHHH**C**----------------------- 54189.tem _________________________________ ----------------------------------**EEEE*******----------CCEEEEEEEEECCC*---********-*********CCCCHHHHHHHHHHH*CCC***EEEEEEE*CC----------CCCEEEEEEEE*C******------***C--------****HHHH**C**--------------------*-- Structural block scores 0 33 - 4.5 M 5.4 75.0 75.0 75.0 75.0 75.0 34 35 * 3.0 P 7.0 75.0 6.0 3.0 75.0 41.5 36 39 E 4.3 M 2.8 75.0 3.8 4.0 75.0 3.0 40 46 * 2.7 P 3.2 75.0 6.4 6.4 75.0 5.4 47 56 - 4.5 M 3.3 75.0 75.0 75.0 75.0 75.0 57 58 C 5.0 H 4.0 7.8 6.5 4.5 9.2 4.0 59 67 E 4.4 M 0.7 12.3 1.6 1.1 4.0 1.7 68 70 C 4.5 M 4.7 51.3 5.3 6.7 51.7 4.7 72 74 - 4.5 M 6.0 75.0 75.0 75.0 75.0 75.0 75 82 * 3.4 M 6.8 4.4 75.0 75.0 5.8 75.0 84 92 * 3.4 M 6.4 1.2 75.0 75.0 1.7 75.0 93 96 C 4.9 H 4.8 4.5 6.2 6.5 4.8 5.5 97 107 H 4.6 H 1.9 4.5 3.6 3.6 3.5 10.6 109 111 C 4.7 H 52.3 5.2 7.5 4.7 5.3 5.5 112 114 * 2.9 P 27.3 75.0 5.3 3.0 75.0 4.7 115 121 E 4.2 M 1.3 3.0 2.9 5.4 2.7 1.6 123 124 C 4.5 M 4.5 6.8 7.8 8.0 3.5 8.2 125 134 - 4.5 M 67.7 75.0 75.0 75.0 7.1 75.0 135 137 C 4.7 H 6.5 31.5 7.8 8.5 6.3 7.5 138 145 E 4.5 M 0.4 1.5 1.1 1.6 1.0 1.5 148 153 * 2.8 P 4.0 75.0 4.8 3.3 75.0 17.0 154 159 - 4.5 M 4.8 75.0 75.0 75.0 75.0 75.0 160 162 * 2.7 P 2.0 75.0 4.3 7.0 75.0 4.0 164 171 - 4.5 M 4.4 75.0 75.0 75.0 75.0 75.0 172 175 * 3.4 M 1.8 3.8 75.0 75.0 4.9 75.0 176 179 H 4.2 M 2.8 4.0 5.5 75.0 5.8 4.2 180 181 * 1.9 P 3.5 6.0 4.5 75.0 6.5 6.0 183 184 * 3.4 M 4.0 75.0 8.0 75.0 75.0 6.2 185 204 - 4.1 M 6.2 75.0 48.6 35.0 75.0 75.0 206 207 - 4.1 M 75.0 75.0 10.2 7.5 75.0 75.0 >>>>>>