# List of top-scoring protein chains for t04-100-30-near-backbone-11-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.soe.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 1mkmA 249 1.93e-24 a.4.5.33,d.110.2.2 79242,79243 1yspA 181 1.73e-23 2ia2A 265 6.78e-23 1td5A 202 1.86e-22 d.110.2.2 106767 1tf1A 198 6.63e-22 d.110.2.2 106826 2o99A 182 7.58e-22 d.110.2.2 138952 1ysqA 193 2.84e-21 2g7uA 257 3.47e-21 3bjnA 165 9.22e-18 2o0yA 260 1.06e-17 2iyeA 263 3.86e-01 2qybA 181 4.70e-01 1ys7A 233 5.10e-01 a.4.6.1,c.23.1.1 123961,123962 1h1yA 228 5.35e-01 c.1.2.2 76506 1qtqA 553 6.88e-01 1gtrA b.53.1.2,c.26.1.1 26940,31579 2uytA 489 7.69e-01 2iutA 574 7.87e-01 2fx0A 201 9.43e-01 a.4.1.9,a.121.1.1 134269,134270 1mc0A 368 9.79e-01 d.110.2.1,d.110.2.1 78937,78938 1ykdA 398 1.14e+00 1wndA 495 1.69e+00 c.82.1.1 114751 2jj7A 186 1.72e+00 2ekcA 262 2.03e+00 2napA 723 2.11e+00 2napA b.52.2.2,c.81.1.1 26926,35334 1qwgA 251 2.21e+00 c.1.27.1 96473 2c0gA 248 2.46e+00 a.71.1.1,c.47.1.7 129590,129591 2v3vA 723 2.53e+00 1ovnA 248 2.73e+00 a.71.1.1,c.47.1.7 93602,93603 2a6aA 218 2.87e+00 c.55.1.9,c.55.1.9 126231,126232 1or3A 165 2.88e+00 1nfn a.24.1.1 16522 2pjhB 193 3.09e+00 1x42A 232 3.39e+00 c.108.1.1 121677 2oqgA 114 3.59e+00 1f5mA 180 3.86e+00 1f5mB d.110.2.1 40895 1iv8A 720 3.94e+00 b.71.1.1,c.1.8.1 76842,76843 2p71A 132 4.19e+00 a.39.2.1 139516 1fmjA 351 4.45e+00 c.37.1.5 59879 1vizA 240 4.85e+00 c.1.4.1 100784 1xfcA 384 4.99e+00 2nvpA 435 5.16e+00 2axpA 173 5.24e+00 c.37.1.1 127497 2hgcA 102 5.54e+00 1yw5A 177 5.88e+00 3bkbA 377 6.26e+00 1svdM 110 6.32e+00 d.73.1.1 119059 1nc5A 373 6.37e+00 a.102.1.6 85548 2v79A 135 6.49e+00 2qxyA 142 6.52e+00 2rc5A 314 6.57e+00 1w7jB 151 6.62e+00 a.39.1.5 120690 1wehA 171 6.63e+00 c.129.1.1 114551 3cblA 377 6.71e+00 2i6xA 211 6.89e+00 2zc2A 78 6.97e+00 1sjiA 350 7.46e+00 1j1nA 492 7.52e+00 c.94.1.1 83978 1j6wA 175 7.57e+00 1j98A d.185.1.2 62663 1m1hA 248 8.09e+00 b.114.1.1,d.58.42.1 78415,78416 2cxcA 144 8.31e+00 2a2lA 145 8.87e+00 d.110.9.1 126035 1nu0A 138 9.20e+00 c.55.3.8 92165 1j8yF 297 9.58e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 2o28A 184 9.66e+00 1r0kA 388 9.71e+00 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 2v0uA 146 1.01e+01 2os0A 188 1.01e+01 1rscI 111 1.03e+01 d.73.1.1 118620 2qv5A 261 1.06e+01 1kgdA 180 1.07e+01 c.37.1.1 68582 1erv 105 1.08e+01 1erv 3rubS 123 1.09e+01 1rboC d.73.1.1 39616 1v5iB 76 1.13e+01 2al6A 375 1.15e+01 a.11.2.1,b.55.1.5,d.15.1.4 126966,126967,126968 1vbuA 328 1.16e+01 c.1.8.3 119963 1y3nA 490 1.20e+01 c.94.1.1 122597 1u55A 188 1.24e+01 d.278.1.1 107677 1uc2A 481 1.29e+01 d.261.1.1 99161 2odiA 238 1.31e+01 2hnkA 239 1.32e+01 2i5uA 83 1.34e+01 1wdcB 156 1.34e+01 1wdcB a.39.1.5 17302 1rhcA 330 1.38e+01 c.1.16.3 97468 3bdzA 397 1.41e+01 2tysA 268 1.42e+01 2tysA c.1.2.4 28572 1zunA 325 1.43e+01 c.26.2.2 125676 2z98A 200 1.44e+01 3c19A 186 1.45e+01 2r7hA 177 1.46e+01 1y9uA 323 1.48e+01 c.94.1.1 116594 1vi9A 299 1.49e+01 c.72.1.5 100750 1qazA 351 1.50e+01 1qazA a.102.3.1 18848 1sknP 92 1.51e+01 1sknP a.37.1.1 17127 1lldA 319 1.51e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1avsA 90 1.53e+01 1cll a.39.1.5 17226 1ct9A 553 1.53e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1w4tA 299 1.54e+01 d.3.1.5 120639 1wqgA 185 1.55e+01 2reeA 224 1.56e+01 1rblI 109 1.56e+01 d.73.1.1 118599 2e67A 264 1.58e+01 1tbxA 99 1.59e+01 a.4.5.48 106748 1e6cA 173 1.59e+01 1shkA c.37.1.2 59296 1r59O 505 1.64e+01 c.55.1.4,c.55.1.4 111697,111698 2f3yA 148 1.64e+01 2gruA 368 1.64e+01 1mhyD 521 1.64e+01 1mhyD a.25.1.2 16780 8rucI 123 1.66e+01 1rboC d.73.1.1 39629 1hw1A 239 1.66e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1s6cA 183 1.68e+01 a.39.1.5 98594 1yg2A 179 1.70e+01 a.4.5.61 116681 1khvA 516 1.70e+01 e.8.1.4 68627 1ir21 140 1.71e+01 1a5zA 319 1.72e+01 c.2.1.5,d.162.1.1 30181,42148 1ggzA 148 1.73e+01 a.39.1.5 70176 1eexG 173 1.76e+01 1dioG a.23.2.1 16490 2pr7A 137 1.80e+01 1mgpA 313 1.81e+01 c.119.1.1 79098 2czdA 208 1.83e+01 c.1.2.3 131045 2hszA 243 1.83e+01 c.108.1.6 136726 2i6eA 301 1.84e+01 1td2A 287 1.84e+01 c.72.1.5 106765 2dwcA 433 1.85e+01 3cnhA 200 1.92e+01 2qmoA 220 1.94e+01 1te5A 257 1.94e+01 d.153.1.1 106795 1ctf 74 1.98e+01 1ctf 2aehA 369 1.99e+01 a.11.2.1,b.55.1.5,d.15.1.4 126625,126626,126627 2e7jA 371 1.99e+01 1amy 403 1.99e+01 1jdc 2heuA 401 2.01e+01 1jc4A 148 2.03e+01 1jc4A d.32.1.4 62863 2bgxA 261 2.03e+01 a.20.1.1,d.118.1.1 128504,128505 1fc4A 401 2.03e+01 1bs0A c.67.1.4 59760 3c1oA 321 2.06e+01 1qe3A 489 2.06e+01 2bce c.69.1.1 34630 1ctfA 74 2.07e+01 d.45.1.1 38759 1xtlA 175 2.09e+01 1oxkB 134 2.09e+01 c.23.1.1 93691 1pueE 89 2.09e+01 1awcA a.4.5.21 16165 2qe6A 274 2.09e+01 1ym5A 300 2.09e+01 1yo5C 97 2.13e+01 a.4.5.21 123768 1ji7A 89 2.13e+01 a.60.1.1 71682 1hyeA 313 2.14e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 3bddA 142 2.14e+01 1vpvA 300 2.14e+01 c.119.1.1 113975 2dt8A 280 2.16e+01 2hhcA 330 2.18e+01 1mzhA 225 2.20e+01 c.1.10.1 79698 1ttzA 87 2.22e+01 c.47.1.1 107309 1b0uA 262 2.22e+01 1b0uA c.37.1.12 32370 1gk8I 140 2.27e+01 d.73.1.1 65242 1zp4A 304 2.27e+01 2fcoA 200 2.27e+01 1dceB 331 2.27e+01 1dceB a.102.4.3 18872 2obhA 143 2.27e+01 2b6cA 220 2.34e+01 a.118.1.17 127983 1izcA 339 2.35e+01 c.1.12.5 83838 1xfrA 128 2.37e+01 1rypK 198 2.40e+01 d.153.1.4 41879 1fb6A 105 2.41e+01 1thx c.47.1.1 32739 1ynpA 317 2.43e+01 1zu0A 529 2.44e+01 2o5gA 148 2.47e+01 2yvyA 278 2.48e+01 2ri7A 174 2.49e+01 2c4eA 302 2.49e+01 2ahfA 377 2.50e+01 2uv0E 175 2.50e+01 1q7zA 566 2.52e+01 c.1.21.2,c.1.26.1 96090,96091 1mijA 152 2.53e+01 a.4.1.1 79150 1l1qA 186 2.54e+01 c.61.1.1 77653 1k6kA 143 2.54e+01 a.174.1.1 77274 2r6fA 972 2.56e+01 2dgdA 223 2.58e+01 1z6gA 218 2.60e+01 3bofA 566 2.63e+01 1w8sA 263 2.64e+01 c.1.10.1 120744 2fldA 165 2.69e+01 1mvwC 147 2.70e+01 i.15.1.1 79525 2nnwA 376 2.71e+01 1ojxA 263 2.73e+01 c.1.10.1 93164 1t2bA 397 2.75e+01 2hyjA 200 2.75e+01 1uxjA 309 2.76e+01 c.2.1.5,d.162.1.1 108112,108113 1bsgA 266 2.77e+01 e.3.1.1 42729 1ihoA 283 2.78e+01 1ihoA c.26.1.4 62390 1xpxA 163 2.80e+01 a.4.1.1 122230 3b5mA 205 2.80e+01 1jx4A 352 2.84e+01 d.240.1.1,e.8.1.7 90378,90379 1llaA 628 2.84e+01 a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1lla 628 2.85e+01 1lla 1bs0A 384 2.86e+01 1bs0A c.67.1.4 34490 1mtyD 512 2.88e+01 1mhyD a.25.1.2 16742 1mjfA 281 2.90e+01 c.66.1.17 79198 1lfpA 249 2.90e+01 e.39.1.1 73885 1e7uA 961 2.92e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1wddS 128 2.95e+01 d.73.1.1 114532 2zf5O 497 2.95e+01 2yzhA 171 2.95e+01 1p2fA 220 3.00e+01 a.4.6.1,c.23.1.1 87720,87721 1zxxA 319 3.00e+01 1yseA 141 3.01e+01 a.35.1.7 123970 2hj0A 519 3.02e+01 1m6sA 347 3.02e+01 c.67.1.1 78701 1xtmA 175 3.02e+01 2jejA 358 3.03e+01 d.240.1.1,e.8.1.7 138284,138285 2qeeA 437 3.03e+01 3borA 237 3.03e+01 1br1B 150 3.06e+01 1wdcC a.39.1.5 17309 2j13A 247 3.08e+01 c.6.2.3 137934 1y1oA 203 3.09e+01 c.52.1.28 116345 2j66A 428 3.09e+01 1y8aA 332 3.11e+01 1yr0A 175 3.16e+01 d.108.1.1 123905 1jg8A 347 3.18e+01 1jg8A c.67.1.1 62946 1y0vH 146 3.19e+01 2anuA 255 3.24e+01 c.6.3.1 127058 2an9A 207 3.27e+01 c.37.1.1 127037 2hq1A 247 3.27e+01 2apjA 260 3.28e+01 c.23.10.7 127128 1dtdA 303 3.30e+01 1aye c.56.5.1 33823 2bw2A 140 3.31e+01 2do5A 58 3.31e+01 2ifqA 105 3.31e+01 c.47.1.1 137343 2o5cA 659 3.32e+01 1n8vA 112 3.32e+01 a.118.21.1 85457 1im8A 244 3.34e+01 c.66.1.14 66212 1s4iA 175 3.35e+01 2etxA 209 3.35e+01 1b16A 254 3.39e+01 1b16A c.2.1.2 29875 1wwpA 119 3.41e+01 1puzA 82 3.42e+01 a.218.1.1 104320 1ulyA 192 3.44e+01 a.4.5.58 113297 1pztA 286 3.51e+01 c.68.1.2 95470 2ofkA 183 3.52e+01 1uliA 460 3.54e+01 b.33.1.2,d.129.3.3 107921,107922 1mvwB 145 3.54e+01 i.15.1.1 79524 1q7bA 244 3.54e+01 c.2.1.2 96026 2r9qA 370 3.56e+01 1rloA 271 3.56e+01 c.108.1.10 111864 1cqmA 101 3.56e+01 1ris d.58.14.1 39321 2b18A 164 3.57e+01 3boeA 210 3.58e+01 1yslA 402 3.58e+01 2ragA 417 3.60e+01 1gs9A 165 3.61e+01 a.24.1.1 83313 1bg2 325 3.61e+01 1bg2 1bg2A 325 3.61e+01 c.37.1.9 32189 1nzjA 298 3.61e+01 c.26.1.1 92377 1zg2A 107 3.65e+01 2qr6A 393 3.65e+01 1rsgA 516 3.65e+01 1g5aA 628 3.67e+01 b.71.1.1,c.1.8.1 65152,65153 3cmgA 667 3.70e+01 1czaN 917 3.70e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1i27A 73 3.70e+01 1i27A a.4.5.30 61555 1w6uA 302 3.73e+01 c.2.1.2 114288 2dr1A 386 3.73e+01 2fsaA 174 3.74e+01 1txuA 273 3.74e+01 a.222.1.1 107439 2fnoA 248 3.76e+01 a.45.1.1,c.47.1.5 133821,133822 1jflA 228 3.79e+01 c.78.2.1,c.78.2.1 71656,71657 1sdjA 310 3.81e+01 d.21.1.2,d.21.1.2 98807,98808 1louA 101 3.81e+01 1ris d.58.14.1 39323 1t1iA 364 3.83e+01 c.41.1.2 106248 1wu7A 434 3.90e+01 c.51.1.1,d.104.1.1 121275,121276 1ro2A 216 3.92e+01 d.264.1.2 97665 1s5jA 847 3.94e+01 c.55.3.5,e.8.1.1 112040,112041 1r1dA 247 3.95e+01 c.69.1.29 96813 1ve3A 227 3.96e+01 c.66.1.43 120010 1xviA 275 3.98e+01 c.108.1.10 116088 2avdA 219 3.99e+01 c.66.1.1 127377 1a8y 367 3.99e+01 1a8y 1a8yA 367 3.99e+01 c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2aheA 267 3.99e+01 1lj9A 144 4.01e+01 a.4.5.28 78035 1fgxA 288 4.03e+01 1fgxA c.68.1.2 34508 2i6tA 303 4.04e+01 1ro0A 216 4.07e+01 d.264.1.2 97664 2iuwA 238 4.09e+01 b.82.2.10 137709 3cmnA 372 4.11e+01 1gegA 256 4.12e+01 1ybvA c.2.1.2 29888 1vd5A 377 4.18e+01 a.102.1.7 108518 1kfcA 268 4.21e+01 c.1.2.4 77371 2kinA 238 4.27e+01 1bg2 c.37.1.9 32190 2fug7 129 4.33e+01 1f60A 458 4.36e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1zh2A 121 4.40e+01 c.23.1.1 125069 1avaA 403 4.42e+01 1jdc b.71.1.1,c.1.8.1 27797,28784 1j09A 468 4.43e+01 a.97.1.1,c.26.1.1 77025,77026 1wdjA 187 4.43e+01 c.52.1.27 114536 1i2sA 282 4.43e+01 e.3.1.1 71104 1exrA 148 4.43e+01 1cll a.39.1.5 17299 1yvoA 172 4.45e+01 d.108.1.1 124106 2yxzA 311 4.45e+01 1aiu 105 4.47e+01 1erv 2gx5A 170 4.49e+01 1hdcA 253 4.50e+01 1e6wA c.2.1.2 29862 1dowA 205 4.52e+01 1dovA a.24.9.1 16626 2c3zA 222 4.53e+01 1wycA 392 4.54e+01 1p0zA 131 4.54e+01 d.110.6.1 93882 2as0A 396 4.55e+01 b.122.1.9,c.66.1.51 127227,127228 2h9aB 310 4.57e+01 2ditA 112 4.58e+01 d.58.7.1 131533 1tqhA 247 4.60e+01 c.69.1.29 107225 1xfxO 149 4.62e+01 a.39.1.5 121955 1erw 105 4.63e+01 1erv 1dqeA 137 4.63e+01 1dqeA a.39.2.1 17388 2p74A 263 4.69e+01 1ae9A 179 4.76e+01 1ae9A d.163.1.1 42153 2d0tA 406 4.77e+01 a.266.1.2 131093 1mwwA 128 4.77e+01 d.80.1.4 91483 2o8lA 274 4.78e+01 b.47.1.1 138932 1yljA 263 4.85e+01 2pmvA 399 4.86e+01 2r25B 133 4.86e+01 1lpjA 133 4.88e+01 b.60.1.2 78123 2ho4A 259 4.91e+01 1rd5A 262 4.95e+01 c.1.2.4 111772 2dulA 378 4.97e+01 1lm6A 215 4.97e+01 d.167.1.1 84628 1mnmA 100 4.97e+01 1mnmA d.88.1.1 40232 2oqzA 223 5.03e+01 b.100.1.1 139255 1gypA 358 5.04e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1wybA 392 5.08e+01 1yt3A 375 5.09e+01 a.60.8.3,a.60.8.3,c.55.3.5 123992,123993,123994 2ex4A 241 5.09e+01 c.66.1.42 132516 3b9pA 297 5.10e+01 2obpA 96 5.11e+01 2adoA 196 5.14e+01 1nmmB 286 5.16e+01 c.68.1.2 80662 1uedA 406 5.19e+01 a.104.1.1 99256 1xqwA 293 5.20e+01 1hl2A 297 5.21e+01 c.1.10.1 83581 1ra6A 461 5.22e+01 e.8.1.4 104879 2oocA 113 5.23e+01 1t3yA 141 5.23e+01 d.109.1.2 119141 1qwvA 142 5.26e+01 a.39.2.1 96506 2p9jA 162 5.26e+01 1zdsA 336 5.32e+01 b.6.1.3,b.6.1.3 124952,124953 2hjmA 103 5.33e+01 1gln 468 5.34e+01 1gln 2yrrA 353 5.36e+01 3bfxA 296 5.36e+01 2ebbA 101 5.38e+01 1j96A 323 5.39e+01 c.1.7.1 71616 1vemA 516 5.40e+01 b.3.1.1,c.1.8.1 120021,120022 2ou6A 190 5.41e+01 2vluA 122 5.41e+01 2cxxA 190 5.41e+01 c.37.1.8 131013 1ur5A 309 5.43e+01 c.2.1.5,d.162.1.1 99807,99808 2g5gX 268 5.44e+01 2z9wA 392 5.45e+01 2eggA 297 5.45e+01 1kjnA 157 5.46e+01 c.115.1.1 72614 1uwkA 557 5.48e+01 e.51.1.1 108065 1iruK 201 5.50e+01 d.153.1.4 71362 1unkA 87 5.51e+01 1cei a.28.2.1 16935 1kqwA 134 5.51e+01 b.60.1.2 72887 2qs9A 194 5.53e+01 1i7dA 659 5.55e+01 1d6mA e.10.1.1 61886 2jigA 224 5.55e+01 1mtzA 293 5.56e+01 c.69.1.7 79467 2izrA 330 5.58e+01 2qxfA 482 5.58e+01 1iurA 88 5.60e+01 a.2.3.1 90704 2cpmA 94 5.60e+01 1oj6A 151 5.61e+01 a.1.1.2 93088 1sbyA 254 5.61e+01 c.2.1.2 118930 1s1pA 331 5.61e+01 c.1.7.1 98350 3bojA 213 5.62e+01 1id0A 152 5.62e+01 d.122.1.3 66111 1udmA 149 5.63e+01 d.109.1.2 107780 2jikA 101 5.67e+01 2a6hC 1119 5.68e+01 e.29.1.1 126264 2h4tA 626 5.68e+01 1wsuA 124 5.71e+01 a.4.5.35,a.4.5.35 121245,121246 1aj2A 282 5.71e+01 c.1.21.1 29665 1twdA 256 5.71e+01 c.1.30.1 107397 1aj2 282 5.71e+01 1aj2 2dcfA 392 5.73e+01 1el4A 195 5.75e+01 1ej3A a.39.1.5 59453 2ha8A 184 5.76e+01 2bopA 85 5.78e+01 2bopA d.58.8.1 39217 1poiA 317 5.80e+01 1poiA c.124.1.2 34153 1sedA 117 5.82e+01 a.219.1.1 105449 1d3yA 301 5.83e+01 1d3yA e.12.1.1 43252 2bneA 241 5.86e+01 c.73.1.3 128824 2d0iA 333 5.88e+01 1wstA 417 5.93e+01 c.67.1.1 121244 1epxA 370 5.95e+01 1fbaA c.1.10.1 29150 2rhmA 193 5.96e+01 2cjpA 328 5.98e+01 1wr2A 238 6.00e+01 1ej1A 190 6.05e+01 1ejhA d.86.1.1 40144 2nq2C 253 6.06e+01 2hw2A 143 6.06e+01 1uuqA 440 6.10e+01 c.1.8.3 100015 1s94A 180 6.12e+01 a.47.2.1 98738 1e8yA 966 6.13e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 2ciwA 299 6.14e+01 a.39.3.1,a.39.3.1 130502,130503 2veoA 441 6.15e+01 3cklA 298 6.15e+01 1qu5A 182 6.15e+01 1qu5A b.26.1.2 23922 1oe8A 211 6.17e+01 a.45.1.1,c.47.1.5 86905,86906 1qx2A 76 6.18e+01 a.39.1.1 104622 1qopA 268 6.20e+01 2tysA 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