Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1b74a1 -CEEEEEECC--CCHH--HHHHHHHHHCC--------CCEEEEEE---CHH-HCCHHHC----C-HHHHHHHHHHHHHHHHCC-CCCEEEECC-HHHHHHHHHHHHHHC-CCCEEECHHHHHHHHHHHC--C------------------------------------- >P1;d1b74a2 CCEEEEEEC--HHHHHHCHHHHHHHCC----------CCEEEEEE--CCCCCCCCCCCCCCC----CCHHHHHHHHCCCCC--CCCCEEEECCCCCCCC--HHHHHHHHCCCEEECHHHHHHHHCCCCCCCCCCCCCCEEECCCCCCHHHHHHHHHCCCCCEEECCCCC >P1;d1jfla1 CCCEEEEECCCHHHHH--HHHHHHHHCC--CCCCHHHCCCEEEEE---CCC-CCCHHHHHCCCC--CCCHHHHHHHHHHHHHH-CCCEEECCC-CHHHH-HHHHHHHHC-CCCCCCHHHHHHHHHHHCC---------------------------------------- >P1;d1jfla2 CCEEEEECC--HHHHHHCHHHHHHHH-C---------CCEEECCCHHHHHHHHHHHHCCHHHCC-HHHHHHHHHHHHHHHHHC-CCCEEEECC-HHHHH-HCC--HHHC-CCCEECHHHHHHHHHHHHHHCC------------------------------------- >P1;d2zska1 --CEEEEECCCHHHHH--HHHHHHHHHHHHHCC-C-CCCCEEEEE---C-C-C-CCCCCC--CH-HHHHHHHHHHHHHHHHHH-CCCEEEECC-CHHHH-HHHHHHHHC-CCCCCCHHHHHHHHHHHCC---------------------------------------- >P1;d2zska2 CCEEEEECC---CCCCCHHHHHHHHC-C---------CCEEECCCCCCC-CHHHHHHHCHHHCC-CC-CHHHHHHHHHHHHHHCCCCEEEECC-CCHHH-CC---CCCC-CCEEEEHHHHHHHHHHHHHHC-------------------------------------- >P1;d5hqta1 CCCEEEEECCCHHHHH--HHHHHHHHHHHHHHCCC-CCCCEEEEE---C-C-HHHHHHHHHHCC-HHHHHHHHHHHHHHHHHH-CCCEEEECC-CHHHH-HHHHHHHHC-CCCCCCHHHHHHHHHHHCC---------------------------------------- >P1;d5hqta2 CCEEEEECC--HHHHHCCHHHHHHHHHH---------CCEEECCCHHHHHHHHHHHHHCHHHCCCCHHHHHHHHHHHHHHHHC-CCCCEEECC-CCHHH-HCC--HHHC-CCCEEEHHHHHHHHHHHHHC-C------------------------------------- PSA >P1;d1b74a1 -520000114--8a05--8328814a868--------81702121---169-3660674----8-691005001500550484-a04201001-820044029405840-b150603486856677768--9------------------------------------- >P1;d1b74a2 673100003--3852964442672688----------a0701043--00637693859707b----940561067207506--8405301014373004--56202520981814859768686589968a799b84623488348916660458499748035377b7 >P1;d1jfla1 671100000065a507--4246625671--909797432802134---139-026152346865--83036502400540276-704202001-85005-016403830-9160404564775689779---------------------------------------- >P1;d1jfla2 474000002--5a2286462475275-8---------82602206a921720340047005596-6a3046002500520084-804000002-51035-006--6b20-924041277676757776784a------------------------------------- >P1;d2zska1 --43010000358419--63563235607873b-b-633703245---0-9-4-807918--77-370128202700510275-607502001-98007-027303650-9160513785558588789---------------------------------------- >P1;d2zska2 272000002---94063a84276237-7---------936011069a12-30440066003766-47-2472016003505944705001002-73016-00---6b40-405033365585766786779-------------------------------------- >P1;d5hqta1 2812000000377606--536773237267858cb-660603344---0-8-375043026665-2b5007200700391395-904101001-96006-10a404840-9170632676677889a8a---------------------------------------- >P1;d5hqta2 374000002--361026a6337726766---------927021077a126502600562037763369025201800530185-704001001-63016-004--7930-61504224768798668978-9------------------------------------- Translating the sequences -C*EEEE*C*--**HH--HHHHHHHH***--------CC*EE***---C**-***HH*C----C-***HHHHHHHHHHHHH**-CCCEEEECC-**HHH*H****HHHC-CCC****HHHHHHHHHH**--*------------------------------------- CC*EEEE*C--HHHHH**HHHHHHH**----------CC*EE***--*C*********C***----**HHHHHHHH*****--*CCCEEEECC*C****--****HHH**CC****HHHHHHHH********************************************* CC*EEEE*C**HHHHH--HHHHHHHH**--*******CC*EE***---C**-***HH*****CC--***HHHHHHHHHHHHH*-CCCEEE*CC-C*HHH-H****HHHC-CCC***HHHHHHHHHHH**---------------------------------------- CC*EEEE*C--HHHHH**HHHHHHHH-*---------CC*EE*************HH*C***CC-***HHHHHHHHHHHHHH*-CCCEEEECC-**HHH-H**--HHHC-CCC***HHHHHHHHHHH*****------------------------------------- --*EEEE*C**HHHHH--HHHHHHHH*******-*-*CC*EE***---C-*-*-****C*--C*-***HHHHHHHHHHHHHH*-CCCEEEECC-C*HHH-H****HHHC-CCC***HHHHHHHHHHH**---------------------------------------- CC*EEEE*C---******HHHHHHH*-*---------CC*EE******C-*****HH*C***CC-**-*HHHHHHHHHHHHH**CCCEEEECC-C*HHH-**---***C-CC****HHHHHHHHHHH****-------------------------------------- CC*EEEE*C**HHHHH--HHHHHHHH*********-*CC*EE***---C-*-***HH*****CC-***HHHHHHHHHHHHHH*-CCCEEEECC-C*HHH-H****HHHC-CCC***HHHHHHHHHHH**---------------------------------------- CC*EEEE*C--HHHHH**HHHHHHHH**---------CC*EE*************HH*C***CC****HHHHHHHHHHHHHH*-CCC*EEECC-C*HHH-H**--HHHC-CCC***HHHHHHHHHHH***-*------------------------------------- 53681.tem _________________________________ CC*EEEE*C**HHHHH**HHHHHHHH***-***-*-*CC*EE******C******HH*C***CC-***HHHHHHHHHHHHHH*-CCCEEEECC-C*HHH-H****HHHC-CCC***HHHHHHHHHHH*****------------------------------------- Structural block scores 0 1 C 4.6 H 40.0 6.5 6.5 5.5 75.0 4.5 5.0 5.0 3 6 E 5.0 H 0.0 0.2 0.2 0.0 1.0 0.0 0.5 0.0 9 10 * 3.6 M 39.5 75.0 3.0 75.0 1.5 75.0 1.5 75.0 11 15 H 4.5 M 19.7 5.4 5.5 5.5 5.4 18.8 5.2 2.4 16 17 * 3.4 M 75.0 5.0 75.0 5.0 75.0 6.8 75.0 8.2 18 25 H 4.9 H 5.6 4.9 4.4 4.8 4.1 4.9 4.5 5.1 26 28 * 2.6 P 7.3 52.7 27.7 52.7 4.3 52.3 5.0 29.0 30 32 * 3.9 M 75.0 75.0 6.0 75.0 7.2 75.0 7.0 75.0 37 38 C 5.0 H 4.5 5.2 2.5 5.0 3.0 6.0 3.0 5.5 40 41 E 5.0 H 1.0 0.5 1.0 1.0 1.5 0.5 1.5 1.0 42 47 * 2.4 P 38.2 26.2 38.8 4.9 39.3 4.6 39.3 4.4 49 54 * 1.8 P 17.5 5.7 15.8 2.7 41.0 14.3 28.8 3.2 55 56 H 4.3 M 3.0 6.5 3.0 2.0 3.5 3.0 2.0 2.5 59 61 * 2.1 P 75.0 6.2 6.0 3.3 52.7 3.3 4.7 3.3 62 63 C 4.5 M 41.5 75.0 5.5 7.5 7.0 6.0 5.5 6.5 65 67 * 1.7 P 5.3 29.3 28.7 6.5 3.3 28.7 6.2 6.0 68 81 H 4.8 H 2.4 8.6 2.7 2.3 2.6 3.1 2.9 2.5 84 86 C 5.0 H 4.8 3.0 3.7 4.0 4.3 4.0 4.3 3.7 87 90 E 4.8 H 0.8 1.0 1.0 0.0 1.8 0.2 0.5 0.2 91 92 C 5.0 H 0.5 2.5 0.5 1.0 0.5 1.0 0.5 0.5 96 98 H 4.7 H 1.3 1.3 1.7 2.7 2.3 2.3 2.0 2.3 101 104 * 2.1 P 3.8 3.2 2.8 39.0 3.0 56.2 3.6 38.5 105 107 H 4.7 H 5.7 3.0 4.7 6.5 4.7 7.2 5.3 6.3 110 112 C 4.8 H 5.8 5.7 5.3 5.0 5.3 3.0 5.7 4.0 113 115 * 1.0 P 2.0 4.3 1.3 1.7 2.0 2.0 3.0 2.0 116 126 H 4.9 H 6.1 7.0 6.2 6.2 6.3 6.0 7.0 6.5 127 131 * 2.5 P 34.6 8.1 48.2 7.1 48.4 20.8 48.7 21.6 132 168 - 4.7 H 75.0 5.9 75.0 75.0 75.0 75.0 75.0 75.0 >>>>>>