# List of top-scoring protein chains for t2k-100-30-n_notor2-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1zy9A 564 2.54e-02 1f1uA 323 7.07e-02 d.32.1.3,d.32.1.3 83200,83201 1ktbA 405 8.97e-02 b.71.1.1,c.1.8.1 72960,72961 1u0tA 307 1.36e-01 e.52.1.1 107567 1eiyB 785 3.00e-01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16305,16306,25314,39313,40782,41458 1f1xA 322 3.54e-01 d.32.1.3,d.32.1.3 83208,83209 1wrvA 308 3.67e-01 1fkoA 543 3.85e-01 1rthA c.55.3.1,e.8.1.2 33612,43094 1oxdA 227 4.29e-01 d.22.1.1 93687 1sznA 417 4.49e-01 b.71.1.1,c.1.8.1 106162,106163 1jv1A 505 4.62e-01 c.68.1.5 71892 2f4qA 346 5.49e-01 1z0wA 207 6.15e-01 1dqpA 230 6.85e-01 1dqnA c.61.1.1 34069 1q7fA 286 7.17e-01 b.68.9.1 96036 1qx4A 274 8.00e-01 b.43.4.2,c.25.1.1 104624,104625 1yw5A 177 9.58e-01 1r13A 148 9.79e-01 d.169.1.1,h.1.1.1 96782,96783 1ks2A 219 9.84e-01 c.124.1.4,d.58.40.1 72908,72909 1cb8A 678 1.04e+00 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1kypA 237 1.08e+00 d.22.1.1 73280 1xtlA 175 1.11e+00 1rthA 560 1.25e+00 1rthA c.55.3.1,e.8.1.2 33576,43028 1fecA 490 1.35e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1b7yB 785 1.37e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 2aysA 348 1.37e+00 1hm2A 700 1.43e+00 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 61083,61084,61085 1jeqB 565 1.49e+00 1jeqB b.131.1.2,c.62.1.4 90368,90369 2gkeA 274 1.49e+00 1g1tA 157 1.51e+00 d.169.1.1,g.3.11.1 65104,65105 1xnzA 264 1.52e+00 1vkpA 383 1.55e+00 d.126.1.6 108686 1b0uA 262 1.59e+00 1b0uA c.37.1.12 32370 1vclA 432 1.66e+00 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1esl 162 1.71e+00 1esl d.169.1.1,g.3.11.1 42353,44225 1bn6A 294 1.72e+00 1bn6A c.69.1.8 34678 1pjr 724 1.76e+00 1pjr c.37.1.19,c.37.1.19 32391,32392 2gw2A 198 1.76e+00 1reoA 486 2.21e+00 c.3.1.2,d.16.1.5 97325,97326 1xo7A 166 2.21e+00 1w8oA 601 2.27e+00 1eur 365 2.28e+00 1eut b.68.1.1 27607 1d3vA 323 2.30e+00 1d3vA c.42.1.1 32559 1barA 140 2.48e+00 1bfg b.42.1.1 25504 2blfA 373 2.49e+00 1jclA 260 2.51e+00 c.1.10.1 66501 1eejA 216 2.52e+00 1eejA c.47.1.9,d.17.3.1 33057,38071 1w2wB 191 2.52e+00 2aaa 484 2.66e+00 7taa b.71.1.1,c.1.8.1 27777,28764 1eagA 342 2.71e+00 1eagA b.50.1.2 26826 1ry9A 145 2.72e+00 d.198.1.1 98094 1vb5A 276 2.75e+00 1qhdA 398 2.77e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1czfA 362 2.81e+00 1czfA b.80.1.3 28031 1el6B 219 2.85e+00 1el6B d.182.1.1 42607 1vjfA 180 3.00e+00 d.116.1.1 100809 1e5kA 201 3.01e+00 1fr9A c.68.1.8 34578 1ozhA 566 3.15e+00 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1tp6A 128 3.30e+00 d.17.4.12 107184 1umkA 275 3.38e+00 2avnA 260 3.42e+00 1nrwA 288 3.46e+00 c.108.1.10 86128 1ztcA 221 3.62e+00 1mup 166 3.65e+00 1mup b.60.1.1 27133 2bs3A 656 3.65e+00 1qlaA 656 3.65e+00 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1vr5A 547 3.76e+00 1l0qA 391 3.77e+00 b.1.3.1,b.69.2.3 77644,77645 1mqeA 207 3.88e+00 d.113.1.1 91394 1gw9A 388 3.91e+00 c.1.15.3 70658 1uc8A 280 3.92e+00 c.30.1.6,d.142.1.7 99165,99166 1ydyA 356 3.98e+00 1vcdA 126 4.17e+00 1yaxA 153 4.21e+00 1mtyD 512 4.21e+00 1mhyD a.25.1.2 16742 1kllA 130 4.22e+00 d.32.1.2 72720 3pga1 337 4.29e+00 4pgaA 1nofA 383 4.35e+00 b.71.1.2,c.1.8.3 92020,92021 1jiwI 106 4.36e+00 1smpI b.61.2.1 63078 1j9yA 385 4.56e+00 1j9yA c.1.8.3 62791 1ibsA 317 4.57e+00 c.61.1.2,c.61.1.2 66107,66108 1axcA 261 4.59e+00 1plq d.131.1.2,d.131.1.2 41392,41393 1rm6A 769 4.62e+00 1odzA 386 4.78e+00 c.1.8.3 86889 1q4gA 553 4.84e+00 a.93.1.2,g.3.11.1 95789,95790 1n7vA 555 4.89e+00 b.126.1.1 85377 1bxtA 234 5.09e+00 3seb b.40.2.2,d.15.6.1 25210,37799 1nbaA 264 5.13e+00 1nbaA c.33.1.3 31753 2bjfA 329 5.14e+00 1wyuA 438 5.30e+00 1woyA 500 5.32e+00 1eut 605 5.34e+00 1eut b.1.18.2,b.18.1.1,b.68.1.1 21891,23712,27609 1p32A 209 5.40e+00 1p32A d.25.1.1 38379 1mwsA 646 5.52e+00 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 2b6dA 345 5.60e+00 2dg5A 366 5.65e+00 1u3dA 509 5.69e+00 a.99.1.1,c.28.1.1 107638,107639 1m65A 245 5.77e+00 c.6.3.1 84847 1qh5A 260 5.87e+00 1qh5A d.157.1.2 42057 1gc0A 398 6.04e+00 c.67.1.3 70168 1ec7A 446 6.06e+00 1bqg c.1.11.2,d.54.1.1 29218,38862 1smlA 269 6.15e+00 1smlA d.157.1.1 42053 1iq4A 179 6.19e+00 1iq4A d.77.1.1 62641 1qq2A 199 6.35e+00 1qq2A c.47.1.10 33064 1g6wA 261 6.45e+00 1hqoA a.45.1.1,c.47.1.5 17751,33045 1f3yA 165 6.48e+00 d.113.1.1 59635 1w18A 493 6.56e+00 1sc3A 178 6.62e+00 c.17.1.1 105416 1mnzA 388 6.65e+00 c.1.15.3 79328 1jetA 517 6.75e+00 1jevA c.94.1.1 35718 1s9aA 257 6.86e+00 b.3.6.1 105379 1sqjA 789 6.91e+00 b.69.13.1,b.69.13.1 105918,105919 1ep0A 185 7.08e+00 1dzrA b.82.1.1 28080 1mi3A 322 7.15e+00 c.1.7.1 91274 1mxtA 504 7.28e+00 c.3.1.2,d.16.1.1 79671,79672 1aerA 205 7.38e+00 1aerA d.166.1.1 42249 1bmlC 362 7.57e+00 1bmlC d.15.5.1,d.15.5.1,d.15.5.1 37729,37730,37731 1kxrA 339 7.60e+00 d.3.1.3 73175 1gz6A 319 7.66e+00 c.2.1.2 76410 1pvmA 184 7.83e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 2d1eA 248 7.89e+00 1a12A 413 7.90e+00 1a12A b.69.5.1 27663 1yx1A 264 8.09e+00 1ve5A 311 8.11e+00 1g1sA 162 8.38e+00 d.169.1.1,g.3.11.1 65100,65101 1th7A 81 8.42e+00 1b1yA 500 8.67e+00 1byb c.1.8.1 28796 2b5hA 200 8.92e+00 1qjpA 171 9.16e+00 1bxwA f.4.1.1 43742 1ddlA 188 9.16e+00 1auyA b.121.4.6 23317 1d8iA 311 9.26e+00 1d8iA d.63.1.1 39541 1nrfA 262 9.28e+00 e.3.1.1 92086 1un7A 400 9.39e+00 b.92.1.5,c.1.9.10 99657,99658 1ivnA 190 9.41e+00 c.23.10.5 83719 2aop 497 9.50e+00 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 2atfA 200 9.61e+00 1jmmA 377 9.62e+00 b.30.6.1 71749 1o66A 275 9.76e+00 c.1.12.8 92547 2fh5A 185 9.87e+00 1ep3B 262 9.92e+00 1ep2B b.43.4.2,c.25.1.3 25664,31554 1vr9A 213 9.99e+00 1eqnA 321 1.01e+01 1dd9A e.13.1.1 43256 1nfkA 325 1.02e+01 1a3qA b.1.18.1,b.2.5.3 21929,22444 2liv 344 1.02e+01 2liv c.93.1.1 35708 1nkxA 348 1.03e+01 c.94.1.2 91943 1dciA 275 1.04e+01 1dciA c.14.1.3 30918 1uhgA 385 1.04e+01 e.1.1.1 88491 1bywA 110 1.06e+01 1bywA d.110.3.6 40912 1w7lA 422 1.10e+01 c.67.1.1 109226 1qnnA 191 1.10e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 1y14B 171 1.10e+01 1phk 298 1.10e+01 1cdkA d.144.1.7 41635 1k0wA 231 1.11e+01 c.74.1.1 77220 1wmbA 260 1.11e+01 1q0qA 406 1.11e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1ofzA 312 1.11e+01 b.68.8.1 86978 1y8aA 332 1.12e+01 1jbuH 254 1.16e+01 5ptp b.47.1.2 62856 4matA 278 1.18e+01 1c24A d.127.1.1 41150 1z5bA 469 1.19e+01 1i86A 389 1.19e+01 c.95.1.2,c.95.1.2 66068,66069 1liuA 528 1.20e+01 b.58.1.1,c.1.12.1,c.49.1.1 77970,77971,77972 2cw6A 298 1.21e+01 1lktA 104 1.26e+01 1lktA b.90.1.1 28398 2bjbA 462 1.26e+01 1jdiA 231 1.27e+01 c.74.1.1 66551 1isaA 192 1.27e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1alkA 449 1.28e+01 1b8jA c.76.1.1 34994 1y5iB 512 1.29e+01 1ydnA 295 1.31e+01 1kwgA 645 1.31e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1gm9B 557 1.32e+01 1qh3A 260 1.32e+01 1qh5A d.157.1.2 42059 2ga9D 469 1.33e+01 2a73B 991 1.34e+01 1kwkA 645 1.38e+01 b.71.1.1,c.1.8.1,c.23.16.5 77565,77566,77567 1ajqB 557 1.38e+01 1ajqB 1qw2A 102 1.38e+01 d.249.1.1 96456 1aop 497 1.42e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 2c26A 260 1.42e+01 1r0mA 375 1.43e+01 c.1.11.2,d.54.1.1 104747,104748 1snzA 344 1.46e+01 b.30.5.4 98930 3prn 289 1.47e+01 3prn f.4.3.1 43761 1ga8A 311 1.48e+01 1ga8A c.68.1.4 34516 2c3vA 102 1.48e+01 2acr 315 1.48e+01 1frb c.1.7.1 28674 1fdi 715 1.51e+01 2napA b.52.2.2,c.81.1.1 26918,35326 1rlmB 271 1.51e+01 1kjqA 391 1.51e+01 b.84.2.1,c.30.1.1,d.142.1.2 72616,72617,72618 1zj8A 566 1.52e+01 1bsjA 168 1.52e+01 1bs4A d.167.1.1 42302 1iscA 192 1.53e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1ctt 294 1.55e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1kaeA 434 1.56e+01 c.82.1.2 72247 1m6bA 621 1.57e+01 c.10.2.5,c.10.2.5,g.3.9.1,g.3.9.1 74521,74522,74523,74524 2ar0A 541 1.58e+01 1vi6A 208 1.59e+01 c.23.15.1 100736 1qguA 478 1.59e+01 1qguA c.92.2.3 35625 2cfuA 658 1.61e+01 2cu3A 64 1.61e+01 1b3bA 415 1.62e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 2akaB 299 1.63e+01 5gcnA 166 1.64e+01 1yghA d.108.1.1 40807 1eg7A 557 1.64e+01 1eg7A c.37.1.10 32241 1okjA 251 1.65e+01 c.55.1.9,c.55.1.9 103998,103999 1x8qA 184 1.66e+01 1jdrA 294 1.66e+01 1ryc a.93.1.1 62908 2b8mA 117 1.66e+01 1ar71 302 1.67e+01 1pov1 1p3dA 475 1.69e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1f00I 282 1.70e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1qh8A 478 1.71e+01 1qguA c.92.2.3 35633 1gkfB 557 1.72e+01 2matA 264 1.73e+01 1c24A d.127.1.1 41146 2bcqA 335 1.73e+01 1wnfA 328 1.73e+01 1g9rA 311 1.74e+01 1ga8A c.68.1.4 34517 1mp4A 292 1.75e+01 c.68.1.6 79376 1gjjA 168 1.77e+01 a.140.1.1,a.140.1.1 83291,83292 1j31A 262 1.78e+01 d.160.1.2 90808 1n7hA 381 1.78e+01 c.2.1.2 80250 1s0aA 429 1.82e+01 c.67.1.4 98263 2bdvA 231 1.83e+01 1erxA 184 1.88e+01 1np1A b.60.1.1 27164 1o7jA 327 1.90e+01 c.88.1.1 81140 1gk9B 557 1.91e+01 1gm7B 557 1.91e+01 1b63A 333 1.93e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 3cln 148 1.93e+01 1cll a.39.1.5 17286 1inp 400 1.94e+01 1inp e.7.1.1 42972 1sjyA 159 1.96e+01 d.113.1.1 98900 1kh5A 449 1.97e+01 c.76.1.1 72475 1qwgA 251 1.97e+01 c.1.27.1 96473 1vzyA 291 1.97e+01 1vjlA 164 1.98e+01 d.257.1.1 100822 1mu5A 471 1.98e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1ebuA 358 1.98e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1c3oB 382 2.00e+01 1c3oB c.8.3.1,c.23.16.1 30744,31421 1bucA 383 2.02e+01 3mdeA a.29.3.1,e.6.1.1 16590,42851 1y7bA 542 2.02e+01 1apa 266 2.06e+01 1qi7A d.165.1.1 42205 1ne9A 335 2.08e+01 d.108.1.4,d.108.1.4 91839,91840 2admA 421 2.09e+01 2admA c.66.1.27 34238 1qavB 115 2.10e+01 1qauA b.36.1.1 24780 1w3fA 315 2.11e+01 1bxwA 172 2.11e+01 1bxwA f.4.1.1 43743 1hw7A 255 2.13e+01 1i7fA d.193.1.1 61297 1izcA 339 2.14e+01 c.1.12.5 83838 1ald 363 2.14e+01 1fbaA c.1.10.1 29100 1p1jA 533 2.18e+01 c.2.1.3,d.81.1.3 87687,87688 1dik 874 2.20e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1ytvA 366 2.22e+01 2c0hA 353 2.22e+01 1d1vA 444 2.23e+01 1nseA d.174.1.1 59101 1ylhA 560 2.24e+01 1d8hA 311 2.25e+01 1d8iA d.63.1.1 39544 1ia6A 441 2.25e+01 a.102.1.2 76738 1adqL 213 2.29e+01 8fabA b.1.1.1,b.1.1.2 20272,21272 2gupA 292 2.31e+01 1cs0B 382 2.31e+01 1c3oB c.8.3.1,c.23.16.1 30740,31417 1uesA 191 2.31e+01 a.2.11.1,d.44.1.1 107798,107799 1ex0A 731 2.33e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 2ex0A 399 2.33e+01 1a7aA 432 2.34e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 1a23 189 2.34e+01 1fvkA c.47.1.13 90319 1gqyA 475 2.35e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1fts 295 2.36e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1d4fA 431 2.37e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 1a4iA 301 2.38e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1euu 605 2.39e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21892,23713,27610 2apsA 162 2.40e+01 1yaiA b.1.8.1 22298 1xeoA 168 2.40e+01 1pjxA 314 2.41e+01 b.68.6.1 104167 2gfpA 375 2.42e+01 1ej6B 1275 2.44e+01 i.7.1.1 45968 1l9gA 192 2.45e+01 c.18.1.2 84568 1m7vA 363 2.46e+01 d.174.1.1 78748 1z3eB 73 2.46e+01 1ppjD 241 2.50e+01 a.3.1.3,f.23.11.1 104258,104259 2al2A 436 2.53e+01 1tf1A 198 2.54e+01 d.110.2.2 106826 1xqaA 113 2.55e+01 1svcP 365 2.57e+01 1a3qA b.1.18.1,b.2.5.3 21924,22443 1i7fA 292 2.59e+01 1i7fA d.193.1.1 61888 1i88A 389 2.60e+01 c.95.1.2,c.95.1.2 66070,66071 1m3sA 186 2.63e+01 c.80.1.3 78573 1ed5A 444 2.64e+01 1nseA d.174.1.1 42530 1xesA 413 2.66e+01 1m2oA 768 2.67e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1lrzA 426 2.69e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1h0pA 182 2.73e+01 b.62.1.1 76450 1rypB 250 2.77e+01 1rypB d.153.1.4 41933 2fhxA 246 2.78e+01 2sns 149 2.78e+01 1snc b.40.1.1 24860 1c30B 382 2.87e+01 c.8.3.1,c.23.16.1 30736,31413 1cs0C 1073 2.88e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1fwrA 213 2.89e+01 1fwrA c.1.10.1 29164 1jc9A 269 2.90e+01 d.171.1.1 66490 2gu3A 136 2.93e+01 1gqzA 274 2.93e+01 d.21.1.1,d.21.1.1 83311,83312 1o1zA 234 2.95e+01 c.1.18.3 86555 1ykdA 398 2.98e+01 1ezm 301 2.98e+01 1hyt d.92.1.2 58980 1id0A 152 3.01e+01 d.122.1.3 66111 1e9iA 431 3.03e+01 c.1.11.1,d.54.1.1 64818,64819 1l9fA 389 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560 7.36e+01 1ajqB 1ecpA 238 7.39e+01 1ecpA c.56.2.1 33775 1usuA 260 7.44e+01 d.14.1.8 99885 1xtoA 311 7.44e+01 1smrA 335 7.45e+01 1smrA b.50.1.2 26878 1uaqA 158 7.50e+01 c.97.1.2 88386 2al3A 90 7.51e+01 1vns 609 7.52e+01 1vns a.111.1.3 19061 1ysqA 193 7.55e+01 1xvsA 126 7.56e+01 1tsp 559 7.58e+01 1tyv b.80.1.6 28044 1mngA 203 7.59e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1v0jA 399 7.59e+01 1q1lA 401 7.60e+01 d.258.1.1 95591 1dquA 538 7.62e+01 1dquA c.1.12.7 29314 2azqA 311 7.67e+01 1vhsA 175 7.68e+01 d.108.1.1 100698 1q1uA 144 7.68e+01 b.42.1.1 95608 1fl2A 310 7.68e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1ie7C 570 7.70e+01 1ubpC b.92.1.1,c.1.9.2 62315,62316 1ut8A 291 7.73e+01 a.60.7.1,c.120.1.2 99908,99909 1ws6A 171 7.73e+01 1sg6A 393 7.75e+01 e.22.1.1 105522 1kpuA 274 7.78e+01 b.1.1.2,d.19.1.1 84456,84457 1q0sA 259 7.78e+01 c.66.1.28 95509 1rlr 761 7.81e+01 1rlr a.98.1.1,c.7.1.2 18753,30679 1gvjA 146 7.82e+01 a.4.5.21 90525 1zq4A 693 7.82e+01 1yc5A 246 7.83e+01 1q25A 432 7.86e+01 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