Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1dysa- ----CCCCCCCEECCCHHHHHHHH-HHHHHHHCCCCHHHHHHHHHHHHHCCCCEEECC--CHHH-HHHHHHHHHHHHHHHCC--CCEEEEEEECCCCCCCHHHCCCCCCCCHHHCHHHHHHHHCHHHHHHHHHHCCCCCEEEEECCCHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHCC--CCCEEEEEECCCHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHCCCCC-CEEEEECCCEEC-CCCCCCCCCCCCCCCEECCCCCCCCCC--CCCEEEEECCCCCCCCCCC---------------CCCCCCCCCCCCCHHHHHHHHHCCCCCCC >P1;d1oc7a- CCCCCCCCCCCEECCCHHHHHHHHHCCHHHCC---CHHHHHHHHHHCC-CCCCEEECC--HHHCCCHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCHHHCHHHHHHH-HHHHHHHHHHHCCCCCEEEEECCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCC--CCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHHCCCC-CEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCEEEEECCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCC-CCC >P1;d2bogx- --------CCCCCCCCCCC-HHHH-HHHHC---CCC-CCHHHHHHHCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHH-------CCCCEEEECCCCCCCCCCC-----------CHHHHHH-HHHHHHHCCC---CCCCEEEECCCHHHHHCCCC-----HHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC----CHHHHHHHHHHCCHH----HHCCEEEECCCCCCC--------------HHHHHHHHHHHHHHH---CCCCCEEEEECCCCCCCCCC----CCCCCCCCCCCCCCCCCCCC--CCCEEEEECCCCCCCCCCCCCC--------------------CCCCCHHHHHHHHHCC----- >P1;d5jx5a- --CCCCCCC-CCCCCCHHHHHHHH-HHHCCCC----CHHHHHHHHHCC-CCCCEEECC--HHHHH-CHHHHHHHHC---------CCCEEEEECCCCCCCCCCCCC----CCCCCHHHHHHH-HHHHHHHHHHCCCCCCEEEEECCCHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHHCC-CCCEEEEEECCCHHHHH--HHHHHHHHHHHHHHHCCC-CCCCCEEEECCCCCCCHH--------------HHHHHHHHHHHHHHHCCCCCCEEEEECCCCCC---CCCC-CCCCCCCCCCCCCCCEECCCCCCCCEEEEECCCCCCCCCCCCC-----CCHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCC-CCC PSA >P1;d1dysa- ----d2006c27002056028305-602630485837810610520156000001023--3731-6206500820460586a--4600000001000013058660514031a670264016600420092048076020000000300000030-977306904930050002003302--3b00200000010030038921640050022018406bb0702000000310021529a239209b03000014004200610583912-210000000213-ba00980c5600034000020122a0b--0800000000000010127---------------452cb02567710160011005404b507 >P1;d1oc7a- 961a81006b040100540260047501560a---6892481045005-110001035--58006610360053038207792946200000010002000133214041429980483047-005403600561550200000004000000224a39505a01810370022005303--070000000011002003492165007100501540940700200000031000133a9407007706110034004401530573604-02000000001415050660b2300044000033031a0c--19300000001000101200669295106201370023903428600070011007307-572 >P1;d2bogx- --------a9240021590-4016-11584---5b2-8205205650050000321491249704a503810550485-------9230000010030290306-----------6193027-0054006006---61101000002000400a18-----8831530060015005104830860400000011632----638400500550403----800300000031015--------------396027003400840---7388020000000044012c----977100ab10015502690a--183020100010001003544a--------------------6570325302610435----- >P1;d5jx5a- --b450004-38102035026004-6007619----b83263046016-120002037--6301a-305500740a---------9300000030023193a2708----803763376038-2044027105826b020000000400050034-a396146006102500020022004-0a102000000116205--93074003000301670b-a08020000003102229--------------6006005301500364817c030000000004---9185-b04000480000230616039a162000100000001001307-----5393055b2024b03766500170021005305-670 Translating the sequences ----CCCCCCC**CCCHHHHHHHH-HHHH******C*HHHHHHHHH***CCCCEEECC--*HHH-*HHHHHHHHHHHH****--*C**EEEEECCCCCCC***CCC****C***CHHHHHHH**HHHHHHHHH*CCCCCEEEEECCCHHHHHHHC-CC***HHHHHHHHHHHHHHHHH*C--CCCEEEEEECCC*******HHHHHHHHHHHHHHHH*C*CCCCCEEEECCCCCCC*****************HHHHHHHHHHHHH*CCCC-CEEEEECCC**C-CCCCCC*CCCCCCCC**CCCCCCCCCC--CCCEEEEECCCCCCCCCCC---------------CCCCCCCCCCCCCHHHHHHHHHCCC*CCC ****CCCCCCC**CCCHHHHHHHH***HH***---C*HHHHHHHHHCC-CCCCEEECC--*HH***HHHHHHHHHHHH*******C**EEEEECCCCCCCCCCCCC****C***CHHHHHHH-HHHHHHHHHH*CCCCCEEEEECCC**HHHHHC*CC***HHHHHHHHHHHHHHHHH*C--CCCEEEEEECCC*******HHHHHHHHHHHHHHHH*C*CCC**EEEECCCCCCC*****************HHHHHHHHHHHHH*CCCC-CEEEEECCCCCC*CCCCCC*CCCCCCCCCCCCCCCCCCCC--CCCEEEEECCCCCCCCCCCCC*************CCCCCCCCCCCCCHHHHHHHHHCCC-CCC --------CCC**CCC***-HHHH-HHHH*---**C-**HHHHHHHCC*CCCCEEECC*****H**HHHHHHHHHHHH-------C***EEEECCCCCCCCCCC-----------*HHHHHH-HHHHHHH***---CCC*EEEECCCHHHHH**C*-----HHHHHHHHHHHHHHHHH****CCC*EEEEECCC****----*HHHHHHHHHH**HH----**CCEEEECCCCCCC--------------***HHHHHHHHHHHH---CCC*CEEEEECCCCCC*CCC----CCCCCCCCCCCCCCCCCCCC--CCCEEEEECCCCCCCCCCCCC*--------------------CCCCCHHHHHHHHHCC----- --**CCCCC-C**CCCHHHHHHHH-HHH****----*HHHHHHHHHCC-CCCCEEECC--*HHH*-*HHHHHHHH*---------C**EEEEECCCCCCCCCCCCC----C***CHHHHHHH-HHHHHHHHHH*CCCCCEEEEECCCHHHHHHHC-CC***HHHHHHHHHHHHHHHHH*C*-CCCEEEEEECCC*****--HHHHHHHHHHHHHHH**C-CCCCCEEEECCCCCCC**--------------*HHHHHHHHHHHHH*CCCC*CEEEEECCCCCC---CCCC-CCCCCCCCCCCCCCC**CCC**CCCEEEEECCCCCCCCCCCCC-----********CCCCCCCCCCCCCHHHHHHHHHCCC-CCC 51989.tem _________________________________ --**CCCCCCC**CCCHHHHHHHH-HHHH***-**C*HHHHHHHHHCC*CCCCEEECC--*HHH**HHHHHHHHHHHH****--*C**EEEEECCCCCCCCCCCCC****C***CHHHHHHH-HHHHHHHHHH*CCCCCEEEEECCCHHHHHHHC*CC***HHHHHHHHHHHHHHHHH*C*-CCCEEEEEECCC*******HHHHHHHHHHHHHHHH*C*CCCCCEEEECCCCCCC*****************HHHHHHHHHHHHH*CCCC*CEEEEECCCCCC*CCCCCC*CCCCCCCCCCCCCCCCCCCC--CCCEEEEECCCCCCCCCCCCC*----********CCCCCCCCCCCCCHHHHHHHHHCCC-CCC Structural block scores 0 1 - 4.3 M 75.0 7.5 75.0 75.0 2 3 * 3.5 M 75.0 5.8 75.0 7.8 4 10 C 4.5 M 5.1 3.8 45.9 12.4 11 12 * 1.0 P 3.5 2.0 2.0 4.5 13 15 C 5.0 H 0.7 0.3 1.0 0.7 16 23 H 4.7 H 3.6 2.6 12.5 2.5 25 28 H 4.5 M 3.5 2.8 3.8 3.2 29 31 * 1.9 P 2.3 5.5 51.3 5.3 33 34 * 3.5 M 6.5 75.0 8.2 75.0 37 45 H 4.8 H 2.6 3.7 3.7 3.6 46 47 C 4.3 M 3.0 2.5 0.0 3.5 49 52 C 5.0 H 0.0 0.5 0.0 0.8 53 55 E 5.0 H 0.3 0.3 2.0 0.7 56 57 C 5.0 H 2.5 4.0 6.5 5.0 58 59 - 4.3 M 75.0 75.0 1.5 75.0 61 63 H 4.3 M 3.7 2.7 5.3 1.3 64 65 * 2.3 P 40.5 6.0 7.2 42.8 66 77 H 4.8 H 2.8 2.6 3.7 15.4 78 81 * 3.5 M 7.4 5.8 75.0 75.0 82 83 - 4.3 M 75.0 5.5 75.0 75.0 86 87 * 1.0 P 0.0 1.0 2.5 1.5 88 92 E 4.9 H 0.0 0.0 0.0 0.0 93 105 C 4.7 H 2.3 1.0 13.4 3.7 106 109 * 3.5 M 2.5 2.2 75.0 75.0 111 113 * 2.3 P 5.8 6.7 75.0 3.3 115 121 H 4.9 H 2.7 3.7 4.0 4.3 123 132 H 4.7 H 2.1 2.3 2.1 2.5 134 138 C 4.7 H 3.0 2.6 31.6 4.3 139 143 E 4.9 H 0.0 0.0 0.2 0.0 144 146 C 5.0 H 1.0 1.3 0.7 1.3 147 153 H 4.6 H 0.4 0.3 2.1 1.1 156 157 C 4.3 M 8.0 6.8 75.0 6.8 158 160 * 2.3 P 3.3 4.7 75.0 5.3 161 177 H 5.0 H 2.6 2.8 2.7 1.8 182 184 C 5.0 H 4.8 2.3 4.7 3.8 185 190 E 4.9 H 0.3 0.0 0.7 0.3 191 193 C 5.0 H 0.3 0.7 0.3 0.3 194 200 * 1.9 P 2.0 1.3 33.9 23.4 201 216 H 4.8 H 2.8 2.9 7.4 2.7 220 224 C 4.3 M 4.1 1.8 17.2 4.1 225 228 E 5.0 H 0.0 0.0 0.0 0.0 229 235 C 5.0 H 0.9 0.6 1.4 1.1 236 252 * 3.1 M 3.9 3.5 62.8 62.8 253 265 H 4.9 H 1.8 2.2 7.9 1.8 267 270 C 4.8 H 3.8 3.2 23.2 5.0 273 277 E 5.0 H 0.2 0.4 0.4 0.6 278 283 C 4.8 H 1.0 0.8 1.3 0.7 285 290 C 4.4 M 6.5 3.7 40.1 28.8 292 311 C 4.9 H 3.0 2.9 4.3 2.4 312 313 - 4.3 M 75.0 75.0 75.0 9.8 314 316 C 5.0 H 2.7 4.3 4.0 3.0 317 321 E 5.0 H 0.0 0.0 0.6 0.2 322 334 C 4.9 H 12.4 0.8 1.4 0.9 336 339 - 4.3 M 75.0 6.2 75.0 75.0 340 347 * 3.5 M 75.0 2.5 75.0 5.2 348 360 C 4.6 H 4.8 2.8 47.8 3.6 361 369 H 5.0 H 1.6 1.8 2.6 1.8 370 372 C 4.8 H 2.7 3.3 27.7 2.7 374 376 C 4.3 M 4.0 4.7 75.0 4.3 >>>>>>