Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ciya2 --CCCC-CCCCCCEEEEC-HHHHCCC-CCCC---CCHHHHHHC-CCCCCCCEEEEEEEEEEEEEC-----------CEEEEEEEEEEEEEHHHCC-CCEECCCEECCCC--CEEEEEEECC---C-CCEEEEEEEE---EEECCCCCCCCCCCCEEEEEEEEEEECCCC-CCCCCEEEC--------CCCCEEHHHC-CCCCCCCCC---HHHHCCEEEEEECCEECCC---------------------CCCCEEEECCEEEEECCCCC >P1;d1dlca2 CCCCCC-CCCCCCEEECC-CCCCCC---CCCCCCCCHHHHHCC-CCCCCCCEEEEEEEEEEEEECCC----CCC-CCEEEEEEEEEEEEECCC-CCCCEECCCEECCC---CCCCEEEECC----CCEEEEEEEEE---EEEEEC------CEEEEEEEEEEEEEEECCCCEEEEEEEECCC-CC--CEEEEEHHHC-CCCCCCCCC---HHHHCCEEEEEEEEEEC------------------------HHHCCEEEEEEEEECCCC- >P1;d1i5pa2 CC---CCCCCCCCCEEEE-CCCCCCCCCCCHHH---HHHHHHHHCCCC--CCCEEEEEEEEEEEEEECCCCCCCEEEEEEEEEEEEEE--HHH-----CCCCCEECCCC---CCCEEEECCCCCCCCCEEEEECCC---EEEEEC------CCEEEEECCCEEEECC-----CCEEECC--------CCCCCE----ECCC--------------CCEEEEEEEEECCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCC-- >P1;d1w99a2 CCCCCCCCCCCCCEEEEEECCC---------CCCCCHHHHHHHHCCCCCCCEEEEEEEEEEECCC------HHH----CCEEEEEEEEEECC--CCCCEECCCEECCC-CCEEEEEEEECC-----CCEEEEEEEE---ECC-----------CCCCEEEEEEEECCC-----CEEEEECCCCCCCCCEEEEE----EECCCCCCCCCCCCCCCCCEEEEEEEEEEEE-------------------------CCEEEEEEEEEECCCCC >P1;d2qkga2 CCCCCC-CCCCCCEEECC-CCCCCCCCCCHHHCCCCHHHHHHHHCCCCCCCEEEEEEEEEEEEEEE-----CCC-EEEEEEEEEEEEEEE-CC-C-CCEEE-EEECCCCCCCCEEEEEECC----CCEEEEEEEEE---EEEECC------CCEEEEEEEEEEEEECCCCCCEEEEEECCCCCCC--EEEEEEHHHH-CCCCCCCCC---HHHHCCEEEEEEEEEC----------------------------CCCEEEEEEEECCCC- >P1;d6ovba2 CCCCCC-CCCCCCEEECC-CCCCCCC-CCCHHHCCCHHHHHHHHCCCCCCCEEEEEEEEEEEEEC-----------CEEEEEEEEEEEEECC-EEEEEEECCCEECCCC--CEEEEEEECC---CCCCEEEEEEEEHHHCC----------CCCEECEEEEEEEECC------CEEEEC--------CCCCEEHHHH-CCCCCCCCC---HHHHCCEEEEEEEEEEECC-----------------------CCEEEEEEEEEEECCCC- PSA >P1;d1ciya2 --b989-69565404311-001640b-7719---c09833772-11893a100022020203525-----------b430000030200347484-944328322541b--2484360515---4-4000301011---12152b7b2a9a431000010010200059-891812303--------562a311185-051558845---421001000000000315b---------------------b2821000000000224072 >P1;d1dlca2 a779b4-88365423307-40302c---928b34059763577-21892a10301303000331404----899-4001100003010315ab-59926507120360---5383351406----81300302010---240635------a142000030401112467762742203085-52--5965120283-161559955---23500111000000030------------------------5b5210000000012407- >P1;d1i5pa2 9a---a688538a14216-07362272a28aa2---540142004004--634030010044565680abb75632123000004030--5bb-----33101000273---c15070406562661001301010---11377a------8231241000002045-----8543001--------a04781----2347--------------912020000203404a5005740782242502039c31940300000001557-- >P1;d1w99a2 b4b989b573555032210228---------91b37a941782020ab38101041000100146------764----1000002001144a--3b74341b32162b-900632251908-----1500100000---058-----------620200301020358-----6422050806761a824342----103074a946750649212000000101418-------------------------60000000000243086 >P1;d2qkga2 9778a4-99565404117-200046982005690389a52684030ca392030050001014132-----6a9-320200000401023-7b-5-a5535-522319ab61454460407----81000202010---000419------a734100030202003397674342404170771--6346331184-150639954---3351011000000003----------------------------80000000002340a- >P1;d6ovba2 9789a5-98655413118-201496a-366994108a9336830419938210031020002249-----------a21000001010046b-75a834618320562b--3594350605---4a40002011200527b----------8140200100100117------764402--------4315620187-151558936---437001110000000234a-----------------------8410000000002340a- Translating the sequences --CCCC-CCCCCCEEE*C-****CCC-CCC*---CCHHHHHH*-CCCCCCCEEEEEEEEEEEEEC-----------*EEEEEEEEEEEEE****C-CCEECCCEECCCC--C*EEEEEECC---*-CCEEEEEEEE---EEE**C******CC*EEEEEEEEEEECCC*-***C*EEEC--------C***EEHHH*-CCCCCCCCC---HHHHCCEEEEEE**EE***---------------------***C**EE**EEEEECCCC* CCCCCC-CCCCCCEEE*C-CCCCCC---CC***CCCHHHHH**-CCCCCCCEEEEEEEEEEEEEC**----***-**EEEEEEEEEEEEE*C*-C*CCEECCCEECCC---C***EEEECC----CC*EEEEEEEE---EEE**C------C**EEEEEEEEEEE**C******EEEE****-**--C***EEHHH*-CCCCCCCCC---HHHHCCEEEEEEEEEE*------------------------***C*EEEEEEEEECCCC- CC---C*CCCCCC*EE**-CCCCCCC*CCC***---HHHHHHHHCCCC--C**EEEEEEEEEEE*************EEEEEEEEEEE--***-----**CCCEECCCC---***EEEECC****CCCEEEEE***---EEE**C------CC*EEEE***EEEECC-----*CEEE*C--------C****E----*CCC--------------C*EEEEEEEEE***************************CC**EEEEEEEECCC-- CCCCCC*CCCCCCEEE***CCC---------**CCCHHHHHHHHCCCCCCCEEEEEEEEEEE**C------***----**EEEEEEEEEE*C--C*CCEECCCEECCC-****EEEEEECC-----CCEEEEEEEE---E**-----------****EEEEEEEECCC-----CEEEE*********C***EE----**CCCCCCCC*******CCEEEEEEEEEE**-------------------------CC*EEEEEEEEECCCC* CCCCCC-CCCCCCEEE*C-CCCCCCC*CC****CCCHHHHHHHHCCCCCCCEEEEEEEEEEEEE**-----***-**EEEEEEEEEEEEE-C*-C-CCEE*-*EECCCC**C*EEEEEECC----CC*EEEEEEEE---EEE**C------CC*EEEEEEEEEEE*CC******EEEEC******--****EEHHH*-CCCCCCCCC---HHHHCCEEEEEEEEE*----------------------------C**EEEEEEEECCCC- CCCCCC-CCCCCCEEE*C-CCCCCCC-CCC***CCCHHHHHHHHCCCCCCCEEEEEEEEEEEEEC-----------*EEEEEEEEEEEEE*C-*****EECCCEECCCC--C*EEEEEECC---*CCCEEEEEEEE*****----------CC*EE*EEEEEEEECC------CEEEEC--------C***EEHHH*-CCCCCCCCC---HHHHCCEEEEEEEEEE***-----------------------*C**EEEEEEEEECCCC- 51096.tem _________________________________ CCCCCC-CCCCCCEEE*C-CCCCCCC-CCC***CCCHHHHHHHHCCCCCCCEEEEEEEEEEEEEC*-----***-**EEEEEEEEEEEEE*C*-C*CCEECCCEECCCC--C*EEEEEECC---*CCCEEEEEEEE---EEE**C------CC*EEEEEEEEEEECCC*-***CEEEEC***-**--C***EEHHH*-CCCCCCCCC---HHHHCCEEEEEEEEEE***----------------------**CC*EEEEEEEEECCCC- Structural block scores 0 5 C 4.6 H 31.2 8.2 42.5 8.8 7.6 8.1 7 12 C 5.0 H 5.8 5.7 7.1 5.0 6.3 6.2 13 15 E 4.8 H 2.3 2.7 2.3 1.7 1.7 1.7 19 25 C 4.4 M 3.2 13.8 3.9 44.6 3.0 4.6 27 29 C 4.3 M 5.0 28.7 6.8 75.0 0.7 5.0 30 32 * 1.9 P 53.0 7.5 7.7 28.3 6.7 7.3 33 35 C 4.4 M 29.2 3.0 75.0 7.2 3.7 3.0 36 43 H 4.7 H 14.2 14.9 2.0 5.2 5.6 5.3 44 50 C 4.9 H 4.8 4.8 23.4 5.1 5.7 5.1 51 63 E 4.8 H 1.4 1.3 2.3 0.9 1.2 1.2 66 70 - 4.4 M 75.0 60.8 8.3 75.0 75.0 75.0 71 73 * 2.7 P 75.0 8.7 6.0 5.7 8.5 75.0 75 76 * 2.6 P 43.2 2.0 1.5 75.0 2.5 42.8 77 89 E 4.8 H 1.2 0.8 12.5 6.5 0.9 0.7 96 97 C 4.2 M 6.5 5.5 75.0 5.5 7.8 5.5 98 99 E 4.5 M 3.5 5.5 3.0 3.5 4.0 5.0 100 102 C 4.5 M 4.3 2.7 0.7 5.2 28.3 4.0 103 104 E 5.0 H 2.0 1.0 0.0 1.5 2.0 1.0 105 108 C 4.8 H 5.4 21.0 3.0 23.6 5.9 6.1 109 110 - 4.1 M 75.0 75.0 75.0 4.5 8.8 75.0 113 118 E 4.7 H 4.3 4.0 2.8 3.7 3.8 4.5 119 120 C 5.0 H 3.0 3.0 3.0 4.0 3.5 2.5 121 123 - 4.5 M 75.0 75.0 4.3 75.0 75.0 75.0 125 127 C 4.5 M 26.3 4.0 2.3 27.0 3.0 4.8 128 135 E 4.8 H 0.8 0.8 0.8 0.1 0.6 0.8 136 138 - 4.5 M 75.0 75.0 75.0 75.0 75.0 2.3 139 141 E 4.3 M 1.3 2.0 1.7 4.3 0.0 31.2 142 143 * 2.7 P 3.5 4.5 7.0 75.0 2.5 75.0 145 150 - 4.5 M 8.4 75.0 75.0 75.0 75.0 75.0 151 152 C 4.3 M 3.5 5.8 5.0 75.0 8.8 4.5 154 164 E 4.7 H 0.4 1.0 0.9 0.9 1.1 0.5 165 167 C 4.3 M 1.7 2.3 28.0 5.3 2.0 27.7 170 172 * 3.2 M 6.0 5.0 52.7 75.0 5.7 75.0 174 177 E 4.8 H 1.5 2.0 1.8 2.0 2.5 3.5 179 181 * 3.4 M 75.0 4.3 75.0 2.7 2.7 75.0 183 184 * 3.4 M 75.0 3.5 75.0 6.5 4.0 75.0 185 186 - 4.5 M 75.0 75.0 75.0 5.8 75.0 75.0 188 190 * 1.0 P 6.2 6.7 3.7 3.0 4.3 3.0 191 192 E 4.8 H 2.0 1.5 4.5 3.0 3.0 4.0 193 195 H 4.3 M 3.3 3.3 75.0 75.0 3.3 3.0 198 206 C 4.6 H 4.6 5.1 51.6 4.8 4.7 4.8 207 209 - 4.5 M 75.0 75.0 75.0 4.0 75.0 75.0 210 213 H 4.2 M 1.8 2.5 75.0 5.2 3.0 3.5 214 215 C 4.8 H 0.5 0.5 42.0 1.5 0.5 0.5 216 225 E 4.8 H 0.3 0.5 0.7 0.6 0.4 0.4 226 228 * 2.7 P 5.8 50.0 2.3 28.0 75.0 5.8 229 250 - 4.5 M 72.1 75.0 4.2 75.0 75.0 75.0 251 252 * 3.0 P 5.0 8.2 2.0 75.0 75.0 41.5 253 254 C 4.2 M 1.5 3.5 6.5 3.0 41.5 2.5 256 264 E 4.8 H 0.2 0.1 0.4 0.2 0.2 0.2 265 268 C 4.9 H 3.2 3.2 23.0 3.8 4.4 4.4 >>>>>>