Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ln1a- ----------CCHHHHHHCCHHHHCCCCCCCCCEEEEEEC-CEEEEEEECCCCCCEEEEEEEEECCCCHHHHHHHHHCHH-HHHHHCCCEEEEEEEEEC--CEEEEEEEECCC--CCCCCEEEEEEEEEEEECCCCCCEEEEEEEECCCCCCCCCCCCEEECCEEEEEEEEECC--CCCEEEEEEEEECCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHCC-------------- >P1;d2moua- -----CHHHHHHHHHHHHHHHHCC-CCC---CCEEEEECC-CCEEEECCCCCCCCCCEEEEEEEC-CCHHHHHHHCCCCC-CHHHHCCCEEEEEECCCCCCCEEEEEEEECCCHHHCCCCEEEEEEEEEEEEC---CCEEEEEEEECCCCCCCCCCCCEEECEECEEEEEEECCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCC >P1;d2psoa1 ---------CCCCHHHHHCCCC------CCCCCEEECCC-CCCEEEEECCCCCCCCEEEEEEEEC-CCHHHHHHHHHH---CHHHCCCCC--CCCCEEEECCEEEEEECCCCCCC---CCCCEEEEEECCCCC----CCEEEEEEECCCCCC----CCCCCCEEEEEEEEEECCC--CCEEEEEEEEECCC-CCCCCCHHHHHHHHHHHHHHCCCC------------------- >P1;d2r55a1 -------CHHHHHHHHHHHHHHHH-CC-C--CCEEEECCC-CEEEEEEECCCCCCEEEEEEEEEC-CCHHHHHHHHCCCC-CHHHHCCCCCEEEEEEECCCCEEEEEEECCCCCCCCCCCEEEEEEEEEEECC---CCCEEEEEEECCCCCCCCCCCCEEEEECCEEEEEEECC--CCCEEEEEEECEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC------------ >P1;d5i9ja- CCHHHHHHHHHHHHHHHHHHHHHH-HHH---HCEEEEECCCCCEEEEEEEC-CCEEEEEEEEEEC-CCHHHHHHHHCCCHHHHHHHCCCEEEEEEEEEEC-CEEEEEEEECCCCCCCCCCEEEEEEEEEEC------CEEEEEEEECCCCCCCCCCCCEECEECCEEEEEEECCCCCCCEEEEEEECEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----------- >P1;d6l1ma- ----CCCHHHHHHHHHHHHHHHHC-CCHH--HCEEEEECC-CEEEEEEECCCCCCEEEEEEEEEC-CCHHHHHHHHCCCH-HHHHHCCCEEEEEEEEEEECCEEEEEEEECCCC--CCCCEEEEEEEEEEEEC---C-EEEEEEEECCCC--CCCCCCEECEECCEEEEEEEECCEEEEEEEEEEECEECCCCCCHHHHHHHHHHHHHHHHHHHHHHC----------------- PSA >P1;d1ln1a- ----------077750470081078382ad5807321736-b02122235995822331214215804173005012319-11471073054053463a--b53000203414--97142000001042351729a3801000051290971a55bc1300660512000150a--8800500222204177b23a6028430760416218515600853-------------- >P1;d2moua- -----6a23640560056012205-377---a18545449-403000230713335000020304-12082025003054-201200300460820550495000101005411b420630010000013629---6822010120170844726b94300324102000103a76764010000020302380568205300151012105002600501758529b3b77a9b >P1;d2psoa1 ---------9786669966886------96952382b0a-7a0700133d4c3843103000505-041650051003---314500505--64315647832010311363869---551100030413b49----920204151392808----a3440402413040444aa--83030101001335-94a577106600610040152159------------------- >P1;d2r55a1 -------58a50460075027026-49-a--7066146ac-703013260921932001031507-07282005004135-4259006206616216635b5010001123423986053000000001362b---77000001032a19806649c33104110140001239--7940100002013033a167a1258201500150062037107544a------------ >P1;d5i9ja- 477625501620570072047008-548---90752672959020200707-a473000020706-0505301400045255027104015305214605-5000002043318a9606300000021134------721000022091b52566a42510520010000242ba57740100101006037a3556312810172014005101610751987----------- >P1;d6l1ma- ----1a729530680262047017-2879--608524649-701012170932c22000022308-37085006202159-51390082054053058279401000201533b--c1740000001102718---9-010001201b2b--6938824203010101001219956a3030000100315aa1748313800133017006202821----------------- Translating the sequences ----------**HHHHHH**HHH**CC****CCEEEEE*C-C*EEEEEECCCCCCEEEEEEEEEC*CCHHHHHHHH*C**-*HHHHCCCEEEEEEEEE*--CEEEEEEEECCC--*CCCCEEEEEEEEEEE*C***CCEEEEEEEECCCCCCCCCCCCEE*****EEEEEEECC--CCCEEEEEEE*E*CCCCCCHHHHHHHHH*HHHHHHHHHHHHHH**-------------- -----***HHHHHHHHHHHHHH**-CC*---CCEEEEECC-C*EEEE**CCCCCC**EEEEEEEC-CCHHHHHHH*CCC*-*HHHHCCCEEEEEE*****CCEEEEEEEECCC***CCCCEEEEEEEEEEE*C---CCEEEEEEEECCCCCCCCCCCCEE**E*CEEEEEEECCC*CCCEEEEEEE*E*CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH**************** ---------****HHHHH****------***CCEEE**C-*C*EEEEE*CCCCCC*EEEEEEEEC-CCHHHHHHHH**---*HHH*CCC*--****EE**CCEEEEEE**CCCC*---CC**EEEEEE****C----C*EEEEEEECCCCCC----CC****E**EEEEEEECCC--CCEEEEEEE*E*CC-CCC***HHHHHHHHHHHHHH****------------------- -------*HHHHHHHHHHHHHHH*-CC-*--CCEEEE*CC-C*EEEEEECCCCCCEEEEEEEEEC-CCHHHHHHHHCCC*-*HHHHCCC**EEEEEEE**CCEEEEEEE*CCCC**CCCCEEEEEEEEEEE*C---CC*EEEEEEECCCCCCCCCCCCEE**E*CEEEEEEECC--CCCEEEEEEE*E*CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH****------------ ********HHHHHHHHHHHHHHH*-***---*CEEEEECC*C*EEEEEE*C-CC*EEEEEEEEEC-CCHHHHHHHHCCC***HHHHCCCEEEEEEEEE**-CEEEEEEEECCCC**CCCCEEEEEEEEEE*------CEEEEEEEECCCCCCCCCCCCEE**E*CEEEEEEECCC*CCCEEEEEEE*E*CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH*****----------- ----****HHHHHHHHHHHHHHH*-CC**--*CEEEEECC-C*EEEEEECCCCCCEEEEEEEEEC-CCHHHHHHHHCCC*-*HHHHCCCEEEEEEEEE**CCEEEEEEEECCCC--CCCCEEEEEEEEEEE*C---C-EEEEEEEECCCC--CCCCCCEE**E*CEEEEEEE*CC****EEEEEEE*E*CCCCCCHHHHHHHHHHHHHHHHHHHHHH*----------------- 55961-4.tem _________________________________ -----***HHHHHHHHHHHHHHH*-CC**--CCEEEEECC-C*EEEEEECCCCCCEEEEEEEEEC-CCHHHHHHHHCCC*-*HHHHCCCEEEEEEEEE**CCEEEEEEEECCCC**CCCCEEEEEEEEEEE*C---CCEEEEEEEECCCCCCCCCCCCEE**E*CEEEEEEECCC*CCCEEEEEEE*E*CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH****------------ Structural block scores 0 4 - 4.4 M 75.0 75.0 75.0 75.0 5.2 60.2 5 7 * 3.2 M 75.0 6.2 75.0 51.7 3.3 6.5 8 22 H 4.5 M 13.1 2.7 16.3 3.8 2.7 3.5 25 26 C 4.2 M 5.5 5.0 75.0 6.5 4.5 5.0 27 28 * 2.7 P 6.2 41.0 42.0 42.8 41.5 8.0 29 30 - 4.1 M 9.2 75.0 7.5 75.0 75.0 75.0 31 32 C 4.5 M 4.0 5.8 3.5 3.5 4.5 3.0 33 37 E 4.7 H 4.0 5.2 4.9 4.6 5.4 5.0 38 39 C 4.5 M 4.5 6.5 42.8 11.5 5.5 6.5 43 48 E 4.8 H 2.0 1.3 2.3 2.5 1.8 2.0 49 54 C 4.8 H 6.3 2.8 7.5 4.0 17.2 4.8 55 63 E 4.8 H 2.1 1.1 1.3 1.3 1.3 1.0 66 67 C 5.0 H 2.0 1.5 2.0 3.5 2.5 5.0 68 75 H 4.9 H 2.1 2.1 2.2 2.1 1.6 2.6 76 78 C 4.3 M 2.0 2.7 26.0 2.7 3.0 2.7 82 85 H 4.9 H 3.2 0.8 2.5 4.0 2.5 3.2 86 88 C 5.0 H 3.3 1.0 1.7 2.7 1.3 3.3 89 97 E 4.4 M 3.3 3.3 20.0 3.8 3.0 3.3 98 99 * 1.4 P 42.8 2.0 5.5 4.0 2.5 4.5 100 101 C 4.7 H 43.2 7.0 5.5 8.2 40.0 6.5 102 109 E 4.8 H 1.6 0.2 1.4 0.6 0.8 0.5 110 113 C 4.8 H 21.0 2.8 5.8 3.0 3.8 5.6 114 115 * 2.7 P 42.0 7.8 42.0 8.5 9.8 75.0 116 119 C 4.8 H 3.5 2.8 40.0 3.5 3.8 6.1 120 130 E 4.7 H 1.4 1.0 2.2 0.9 1.0 1.0 133 135 - 4.5 M 7.2 75.0 75.0 75.0 75.0 75.0 136 137 C 4.4 M 5.5 7.0 42.0 7.0 41.0 42.0 138 145 E 4.9 H 0.9 1.0 1.9 0.5 0.9 0.5 146 157 C 4.8 H 6.1 5.3 28.6 5.9 5.2 17.7 158 159 E 4.5 M 1.5 1.5 4.0 2.0 3.0 3.0 160 161 * 1.0 P 3.0 1.5 2.0 2.0 2.5 1.5 165 171 E 5.0 H 1.3 0.4 2.3 1.1 1.0 0.7 172 174 C 4.6 H 28.5 6.8 8.3 29.0 8.0 6.3 176 178 C 4.4 M 5.3 5.7 28.7 6.7 6.0 6.5 179 185 E 5.0 H 1.6 0.1 0.7 0.4 0.4 0.6 189 194 C 4.9 H 5.2 3.0 17.8 3.9 4.8 5.8 195 218 H 4.8 H 3.9 2.2 12.1 3.1 2.6 5.8 219 222 * 3.1 M 39.5 3.2 75.0 5.9 5.8 75.0 223 234 - 4.5 M 75.0 7.9 75.0 75.0 69.3 75.0 >>>>>>