# List of top-scoring protein chains for t04-100-30-alpha-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 1zq9A 285 1.25e-29 1yadA 221 3.36e-02 2astA 159 3.95e-02 1fs1B 141 3.95e-02 1vcbB a.157.1.1,d.42.1.1 19252,38664 1i4wA 353 1.05e-01 c.66.1.24 66028 1mvwC 147 1.47e-01 i.15.1.1 79525 1yf3A 259 2.29e-01 1g8kA 825 2.36e-01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1nxuA 333 3.31e-01 c.122.1.1 86389 1q0sA 259 3.71e-01 c.66.1.28 95509 2f4lA 297 3.74e-01 1i58A 189 4.19e-01 1b3qA d.122.1.3 61773 1fiqC 763 6.64e-01 1fiqC d.41.1.1,d.133.1.1 38588,41418 1lvaA 258 6.97e-01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1b8gA 429 7.88e-01 1b8gA c.67.1.4 34499 2ah5A 210 8.06e-01 1m7yA 435 8.77e-01 c.67.1.4 78761 1cnzA 363 9.09e-01 1cnzA c.77.1.1 35061 1w33A 181 9.29e-01 1a3aA 148 9.42e-01 1a3aA d.112.1.1 40917 1ynuA 473 1.01e+00 2furA 209 1.13e+00 2a0jA 149 1.20e+00 1dk0A 188 1.23e+00 1b2vA d.35.1.1 38530 1y1xA 191 1.46e+00 1w7jB 151 1.48e+00 1oz9A 150 1.51e+00 d.92.1.15 93808 1m65A 245 1.53e+00 c.6.3.1 84847 1v9wA 130 1.68e+00 c.47.1.16 108453 1fo4A 1332 1.74e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 1fnnA 389 1.82e+00 1fnnA a.4.5.11,c.37.1.20 16129,32426 1mwyA 73 1.85e+00 d.58.17.1 79616 1cem 363 1.90e+00 1cem a.102.1.2 18826 1kwfA 363 1.92e+00 a.102.1.2 73078 1ou0A 207 1.92e+00 c.23.17.1 93536 1v97A 1332 1.95e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 2azqA 311 2.33e+00 1gz6A 319 2.38e+00 c.2.1.2 76410 1p57B 255 2.64e+00 b.47.1.2 94126 1qyrA 252 2.77e+00 c.66.1.24 104657 1yovA 537 2.87e+00 1kaeA 434 2.92e+00 c.82.1.2 72247 1zcoA 262 2.92e+00 1oatA 439 2.96e+00 2dkb c.67.1.4 34461 1vqtA 213 3.00e+00 1yarA 233 3.26e+00 2byjA 439 3.35e+00 1h8eD 482 3.38e+00 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1e79D 482 3.58e+00 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1x3sA 195 3.72e+00 1h8dH 260 3.75e+00 5ptp 2ch4A 320 3.75e+00 1dcs 311 3.96e+00 1dcs b.82.2.1 28124 1a79A 171 4.32e+00 1a79A c.52.2.1,d.75.1.1 33340,39739 1pyoB 105 4.36e+00 1sglA 209 4.43e+00 d.124.1.1 105536 1ofdA 1520 4.58e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 2oatA 439 4.79e+00 2dkb c.67.1.4 34452 2bylA 439 4.82e+00 1xiuA 230 4.86e+00 1z7mA 344 4.87e+00 1o1zA 234 5.14e+00 c.1.18.3 86555 1wouA 123 5.38e+00 c.47.1.16 109471 1q5dA 419 5.41e+00 a.104.1.1 95891 1wy6A 172 5.50e+00 1n9dA 199 5.96e+00 a.26.1.1 85464 1p1cA 199 6.14e+00 c.66.1.16 87669 1scuA 288 6.31e+00 2scuA c.2.1.8,c.23.4.1 30307,31135 1pjr 724 6.39e+00 1pjr c.37.1.19,c.37.1.19 32391,32392 1rp4A 389 6.45e+00 a.227.1.1 105027 1s5lA 344 6.85e+00 1mbxC 106 6.87e+00 d.45.1.2 78929 1cy5A 97 6.93e+00 1cy5A a.77.1.3 18430 1wwiA 148 7.04e+00 1afrA 345 7.05e+00 1afrA a.25.1.2 16805 1mgtA 174 7.08e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1eljA 381 7.50e+00 4mbp c.94.1.1 35791 1sqiA 393 7.54e+00 d.32.1.3,d.32.1.3 105914,105915 1xpxA 163 7.65e+00 1wmhB 86 7.72e+00 1q8cA 151 7.78e+00 a.79.1.2 96202 2ax3A 502 8.00e+00 1top 162 8.01e+00 1ncx a.39.1.5 17223 1xclA 235 8.08e+00 1womA 271 8.26e+00 1vljA 407 8.94e+00 e.22.1.2 108832 1r6oC 106 8.96e+00 1gt6A 269 9.03e+00 c.69.1.17 76342 1p80A 753 9.15e+00 c.23.16.3,e.5.1.1 94337,94338 1mijA 152 9.18e+00 a.4.1.1 79150 1o50A 157 9.47e+00 d.37.1.1,d.37.1.1 92478,92479 1o6dA 163 9.51e+00 c.116.1.3 92567 1jy5A 212 9.55e+00 d.124.1.1 71940 1f20A 435 9.63e+00 b.43.4.1,c.25.1.4 64932,64933 1olrA 224 9.92e+00 b.29.1.11 93330 2pgd 482 9.93e+00 2pgd a.100.1.1,c.2.1.6 18778,30190 1cf9A 753 9.98e+00 1cf9A c.23.16.3,e.5.1.1 31441,42815 1vliA 385 1.01e+01 b.85.1.1,c.1.10.6 108830,108831 2bjfA 329 1.04e+01 1xqoA 256 1.04e+01 1hr6B 443 1.05e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1wbpA 397 1.06e+01 2b9lA 394 1.09e+01 2rslA 140 1.09e+01 2rslA c.53.1.1 33345 1j75A 67 1.10e+01 a.4.5.19 62673 1ecrA 309 1.11e+01 1ecrA e.2.1.1 42678 2b61A 377 1.12e+01 1rw6A 210 1.19e+01 a.47.4.1 105113 2f62A 161 1.21e+01 1yzxA 226 1.21e+01 1wy1A 172 1.25e+01 1u04A 771 1.25e+01 b.34.14.1,c.55.3.10 107539,107540 1zbqA 327 1.25e+01 1np8A 159 1.27e+01 a.39.1.8 92022 1hlvA 131 1.29e+01 a.4.1.7,a.4.1.7 65854,65855 1ton 235 1.30e+01 5ptp b.47.1.2 26307 2gsaA 432 1.31e+01 2gsaA c.67.1.4 34446 2g7gA 213 1.31e+01 1lwjA 441 1.32e+01 b.71.1.1,c.1.8.1 74303,74304 1a7s 221 1.33e+01 1a7s b.47.1.2 26284 1iugA 352 1.35e+01 c.67.1.3 90699 2prd 174 1.35e+01 2prd b.40.5.1 25435 1x0vA 354 1.37e+01 1oq9A 363 1.38e+01 a.25.1.2 87257 1paqA 189 1.38e+01 a.118.1.14 94413 3seb 238 1.39e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1psrA 100 1.44e+01 1psrA a.39.1.2 17180 1jmsA 381 1.44e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1pp0A 199 1.50e+01 d.103.1.1 104211 1a4pA 96 1.52e+01 1b4cA a.39.1.2 17176 1tllA 688 1.53e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1pgjA 478 1.57e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1s3aA 102 1.58e+01 1h3lA 87 1.59e+01 a.177.1.1 76639 1zk8A 183 1.59e+01 1u60A 310 1.65e+01 e.3.1.2 107692 1na6A 404 1.67e+01 b.142.1.1,c.52.1.22 91748,91749 1t8qA 336 1.70e+01 c.1.18.3 106669 1jalA 363 1.70e+01 c.37.1.8,d.15.10.2 84138,84139 2a0kA 161 1.71e+01 1qwgA 251 1.74e+01 c.1.27.1 96473 1ydyA 356 1.74e+01 2f2tA 161 1.76e+01 1z8gA 372 1.76e+01 1xizA 159 1.78e+01 1qy6A 274 1.78e+01 b.47.1.1 96574 1sczA 233 1.80e+01 c.43.1.1 98802 1pvmA 184 1.80e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1mzbA 136 1.81e+01 a.4.5.42 91497 1tib 269 1.81e+01 3tgl c.69.1.17 34738 1p9bA 442 1.89e+01 c.37.1.10 94385 1ydwA 362 1.92e+01 1wovA 250 1.98e+01 1nu5A 370 2.00e+01 c.1.11.2,d.54.1.1 92183,92184 1wh8A 111 2.00e+01 1vlwA 217 2.00e+01 c.1.10.1 108868 1b3aA 67 2.00e+01 1b3aA d.9.1.1 37410 1wmaA 276 2.03e+01 1zgzA 122 2.06e+01 2be4A 272 2.07e+01 1zthA 258 2.08e+01 1wiwA 290 2.08e+01 1c02A 166 2.10e+01 1qspA a.24.10.2 16633 1v02A 565 2.10e+01 c.1.8.4 108194 1wyzA 242 2.14e+01 2fdoA 94 2.15e+01 1fseA 74 2.15e+01 1fseA a.4.6.2 60000 1xfjA 261 2.17e+01 d.194.1.2 109585 1eg7A 557 2.19e+01 1eg7A c.37.1.10 32241 1g6hA 257 2.21e+01 1gajA c.37.1.12 60318 1ohvA 472 2.21e+01 c.67.1.4 93031 1rypL 212 2.22e+01 d.153.1.4 41880 1yemA 179 2.25e+01 1mho 88 2.26e+01 1b4cA a.39.1.2 17171 1g2nA 264 2.28e+01 1lbd a.123.1.1 60227 1gln 468 2.31e+01 1gln a.97.1.1,c.26.1.1 18752,31588 2fp3A 316 2.32e+01 1wjxA 122 2.35e+01 2cwyA 94 2.35e+01 2bce 581 2.36e+01 2bce c.69.1.1 34625 1j09A 468 2.42e+01 a.97.1.1,c.26.1.1 77025,77026 1mvcA 240 2.43e+01 a.123.1.1 79499 1ejxA 100 2.45e+01 d.8.1.1 83182 1q0vA 81 2.46e+01 j.105.1.1 95514 1ju2A 536 2.46e+01 c.3.1.2,d.16.1.1 77169,77170 1nnvA 110 2.47e+01 d.17.7.1 92012 1hufA 140 2.48e+01 1hufA d.195.1.1 61272 1s50A 259 2.49e+01 1gxmA 332 2.49e+01 a.102.5.1 76371 1yarH 217 2.50e+01 1p5hA 428 2.54e+01 c.123.1.1 87802 1vzqH 250 2.55e+01 1zrn 232 2.57e+01 1qq5A c.108.1.1 43323 1kpsB 171 2.59e+01 a.118.12.1 68787 1kyqA 274 2.60e+01 c.2.1.11,e.37.1.1 73281,73282 1uhnA 189 2.63e+01 a.39.1.5 99399 2ethA 154 2.63e+01 1js1X 324 2.70e+01 c.78.1.1,c.78.1.1 71834,71835 1j1hA 144 2.71e+01 b.111.1.1 77056 1ri7A 171 2.71e+01 a.4.5.32,d.58.4.2 97504,97505 1sgwA 214 2.74e+01 c.37.1.12 105541 1s9uA 207 2.77e+01 a.184.1.1 105390 1rkqA 282 2.77e+01 c.108.1.10 97621 1g8iA 190 2.80e+01 1rec a.39.1.5 60363 1m2rA 327 2.81e+01 d.144.1.7 84760 1ioj 57 2.85e+01 1ioj j.39.1.1 46293 1wa3A 205 2.87e+01 1zd3A 555 2.93e+01 1y1pA 342 2.93e+01 1tvlA 454 2.96e+01 c.1.16.4 107366 1rlmB 271 2.97e+01 1rloA 271 2.98e+01 2g0wA 296 3.00e+01 1q1vA 70 3.01e+01 a.159.4.1 104479 1rlmA 271 3.03e+01 1pk5A 248 3.04e+01 a.123.1.1 88139 1ujmA 342 3.05e+01 1om1A 332 3.06e+01 d.144.1.7 93347 1elvA 333 3.08e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1ta9A 450 3.09e+01 1fezA 256 3.10e+01 1fezA c.108.1.3 43343 1x31D 99 3.13e+01 1k8kA 418 3.13e+01 c.55.1.1,c.55.1.1 68305,68306 2b33A 140 3.15e+01 1e6cA 173 3.16e+01 1shkA c.37.1.2 59296 1y37A 304 3.16e+01 1jcfA 344 3.24e+01 c.55.1.1,c.55.1.1 62878,62879 1ky3A 182 3.25e+01 c.37.1.8 73193 1aa8A 347 3.29e+01 1an9A 1ve9A 347 3.33e+01 c.4.1.2,d.16.1.3 100571,100572 1k1xA 659 3.34e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1vjqA 79 3.35e+01 k.43.1.1 100830 5ukdA 194 3.41e+01 1zin c.37.1.1 31851 1q0rA 298 3.44e+01 c.69.1.28 95508 1q08A 99 3.45e+01 a.6.1.3 95497 1wywA 230 3.50e+01 1ddjA 247 3.52e+01 5ptp b.47.1.2 26362 1nh1A 330 3.56e+01 e.45.1.1 91871 1u8vA 490 3.57e+01 1k8kG 151 3.62e+01 a.118.13.1 68313 2d0oB 125 3.66e+01 1sf9A 128 3.72e+01 b.34.15.1 98831 1vhwA 253 3.73e+01 c.56.2.1 100706 1q5qA 259 3.75e+01 d.153.1.4 95904 2fz4A 237 3.78e+01 1bqbA 301 3.78e+01 1hyt d.92.1.2 58962 1uwkA 557 3.78e+01 e.51.1.1 108065 2aaoA 166 3.82e+01 1yqtA 538 3.82e+01 2gfgA 193 3.85e+01 1qe3A 489 3.85e+01 2bce c.69.1.1 34630 1swvA 267 3.87e+01 1tn4 159 3.93e+01 1ncx a.39.1.5 17248 1im5A 180 3.95e+01 c.33.1.3 66211 2trcP 217 3.96e+01 1b9yC c.47.1.6 33051 2a9uA 144 3.96e+01 1lwdA 413 3.99e+01 c.77.1.1 78265 2fexA 188 4.01e+01 1whzA 70 4.04e+01 1nteA 82 4.08e+01 b.36.1.1 86163 1t4hA 290 4.11e+01 d.144.1.7 106420 1xfcA 384 4.24e+01 1khbA 625 4.26e+01 c.91.1.1,c.109.1.1 68606,68607 1h2kA 349 4.26e+01 b.82.2.6 76572 1mo7A 213 4.27e+01 d.220.1.1 85028 1ea9C 583 4.28e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1f52A 468 4.28e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 1ytw 306 4.33e+01 1ytw c.45.1.2 32689 1rypC 244 4.35e+01 1rypC d.153.1.4 41934 1ctj 89 4.36e+01 1ctj a.3.1.1 15798 1xo5A 183 4.40e+01 1amf 233 4.43e+01 1wod c.94.1.1 35833 1wdcC 156 4.43e+01 1wdcC a.39.1.5 17317 1vj5A 555 4.44e+01 c.108.1.2,c.69.1.11 100799,100800 1alvA 173 4.45e+01 1alvA a.39.1.8 17370 2f4qA 346 4.52e+01 1vr1H 261 4.56e+01 5ptp 1q7eA 428 4.57e+01 c.123.1.1 96035 1cfzA 162 4.57e+01 1cfzA c.56.1.1 33754 1wrvA 308 4.59e+01 2eutA 294 4.62e+01 1jenB 67 4.62e+01 1jenB d.156.1.1 42029 1dvoA 152 4.63e+01 1dvoA a.136.1.1 19623 2cy5A 140 4.64e+01 1mszA 86 4.65e+01 d.68.7.1 79428 1wod 233 4.65e+01 1wod c.94.1.1 35832 1yrrA 382 4.69e+01 1sh7A 284 4.69e+01 1v74B 87 4.70e+01 a.24.20.1 100443 2a61A 145 4.71e+01 2f06A 144 4.71e+01 1r6jA 82 4.78e+01 b.36.1.1 97151 1ggzA 148 4.85e+01 a.39.1.5 70176 1byrA 155 4.88e+01 1byrA d.136.1.1 41450 1np3A 338 4.90e+01 a.100.1.2,c.2.1.6 85946,85947 1v3rA 116 4.91e+01 1ooeA 236 4.93e+01 c.2.1.2 87196 1vfjA 116 4.93e+01 1sesA 421 4.94e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1yw3A 208 4.95e+01 1uxtA 501 4.98e+01 c.82.1.1 108125 1ivnA 190 4.98e+01 c.23.10.5 83719 2as9A 210 5.01e+01 2bvpA 276 5.02e+01 5eau 548 5.05e+01 5eat a.102.4.1,a.128.1.3 18851,19443 1wf3A 301 5.06e+01 1g8fA 511 5.06e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1xvjA 109 5.12e+01 1itwA 741 5.12e+01 c.77.1.2 76793 1fs7A 485 5.16e+01 1qdbA a.138.1.3 19691 1qlaC 256 5.21e+01 1qlaC f.21.2.1 43722 1fp2A 352 5.26e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1yucA 255 5.28e+01 1m45A 148 5.31e+01 a.39.1.5 78598 1tu9A 134 5.33e+01 a.1.1.2 107320 1sfe 180 5.34e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1wdkC 390 5.36e+01 c.95.1.1,c.95.1.1 109258,109259 1orrA 347 5.37e+01 c.2.1.2 93460 1ecfA 504 5.38e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1buoA 121 5.40e+01 1buoA d.42.1.1 38631 1xrsA 516 5.41e+01 2pii 112 5.42e+01 2pii d.58.5.1 39071 1gr0A 367 5.48e+01 c.2.1.3,d.81.1.3 70379,70380 1r5zA 323 5.49e+01 f.40.1.1 97135 1nlfA 279 5.50e+01 c.37.1.11 85850 1x93A 55 5.51e+01 1kq3A 376 5.51e+01 e.22.1.2 68790 1pdo 135 5.51e+01 1pdo c.54.1.1 33376 1riqA 465 5.53e+01 a.203.1.1,d.104.1.1 97516,97517 1oa4A 222 5.53e+01 b.29.1.11 86731 1yqfA 203 5.54e+01 1nrfA 262 5.56e+01 e.3.1.1 92086 1rt8A 513 5.57e+01 a.40.1.1 105095 1xocA 520 5.57e+01 1qf9A 194 5.57e+01 1zin c.37.1.1 31848 1rqjA 299 5.59e+01 a.128.1.1 97744 1zu4A 320 5.59e+01 1sseB 86 5.60e+01 2plc 274 5.61e+01 2plc c.1.18.2 29614 1e94F 449 5.66e+01 1do0A c.37.1.20 32443 1g2hA 61 5.69e+01 1g2hA a.4.1.12 60224 1elkA 157 5.75e+01 1dvpA a.118.9.2 19217 1zc3B 113 5.78e+01 2anxA 146 5.79e+01 2esrA 177 5.89e+01 1t9kA 347 5.91e+01 c.124.1.5 106721 1wzaA 488 5.95e+01 2g0qA 173 5.95e+01 1fntc 245 6.04e+01 1yz4A 160 6.05e+01 1wab 232 6.06e+01 1wab c.23.10.3 31341 1go3F 107 6.06e+01 a.60.8.2 65407 1mkrA 294 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7.88e+01 d.264.1.2 97664 1wy5A 317 7.90e+01 1s1hM 132 7.92e+01 i.1.1.1 105165 2ahrA 259 7.97e+01 1ru3A 732 7.99e+01 e.26.1.3 97835 1xpcA 248 8.04e+01 1jv4A 162 8.08e+01 b.60.1.1 67343 1wvfA 520 8.13e+01 1xbbA 291 8.13e+01 2tbs 222 8.15e+01 5ptp b.47.1.2 26009 1dseA 292 8.20e+01 1ryc a.93.1.1 59130 2bs3C 256 8.21e+01 1xk7A 408 8.22e+01 1fjgE 162 8.22e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1twfK 120 8.24e+01 1ym0A 238 8.30e+01 1xkzA 255 8.32e+01 1tzzA 392 8.33e+01 1io0A 185 8.37e+01 c.10.1.1 76753 1poiA 317 8.38e+01 1poiA c.124.1.2 34153 2ew2A 316 8.39e+01 1nni1 174 8.39e+01 4crxA 322 8.40e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1cnoA 87 8.40e+01 a.3.1.1 15814 1h72C 296 8.41e+01 d.14.1.5,d.58.26.1 60712,60713 1wfyA 104 8.43e+01 1zckA 154 8.48e+01 4pah 308 8.53e+01 4pah d.178.1.1 42576 1ni4B 341 8.58e+01 c.36.1.7,c.48.1.2 85729,85730 1va6A 518 8.59e+01 1dp3A 55 8.61e+01 1dp3A a.55.1.2 59128 1avsA 90 8.61e+01 1cll a.39.1.5 17226 1xf1A 926 8.61e+01 2b6nA 278 8.63e+01 1lqpA 135 8.67e+01 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