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comparison orthologs/ucsb_hamster/lib/wisecfg/pb.gf @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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-1:000000000000 0:5b9a38ec4a39
1 # Splice sites and intron regions information for GeneWise-21 May 1500
2 # Created by Mor Amitai (mor@compugen.co.il)
3 # dataset : ~/ftp/pub/PomBase/temp/cds_cdna ~/ftp/pub/PomBase/temp/cds_ex
4 # Consensi are read from top down. The value, for a sequence,
5 # is the number in the line of the first consensus that
6 # matches the sequence.
7 # Note: the set of sequences that are represented by a consensus
8 # are all the sequences that match this consensus and none of the
9 # previous consensi
10 #
11 # the numbers in types 5SS, 3SS, CDS, and the emissions are the number of
12 # occurrences of each sequence in the database.
13 # In case of a consensus this is the number of occurrences of sequences
14 # that are represented by the consensus in the database divided by the
15 # number of sequences that are represented by the consensus.
16 # *stay_prob is the probability of the transition from the state to itself.
17 # No_Spacer_Prob is the probability of transition from Pyrimidine directly
18 # to 3SS (no spacer).
19 type 5SS
20 center 3
21 phase all
22 begin consensus
23 ---GTA-GT- 8.69141
24 ---GT----- 0.0821553
25 end consensus
26 type 5SS
27 center 3
28 phase 0
29 begin consensus
30 ---GTA-GT- 3.71094
31 ---GT----- 0.0356523
32 end consensus
33 type 5SS
34 center 3
35 phase 1
36 begin consensus
37 ---GTA-GT- 2.92969
38 ---GT----- 0.0294519
39 end consensus
40 type 5SS
41 center 3
42 phase 2
43 begin consensus
44 ---GT----- 0.0488281
45 end consensus
46 type 3SS
47 center 3
48 phase all
49 begin consensus
50 TAG--- 1.64062
51 -AG--- 22.9167
52 end consensus
53 type 3SS
54 center 3
55 phase 0
56 begin consensus
57 TAG--- 0.765625
58 -AG--- 9.375
59 end consensus
60 type 3SS
61 center 3
62 phase 1
63 begin consensus
64 TAG--- 0.515625
65 -AG--- 8.85417
66 end consensus
67 type 3SS
68 center 3
69 phase 2
70 begin consensus
71 -AG--- 12.5
72 end consensus
73 type CDS
74 phase all
75 begin consensus
76 AAA 238.6335
77 AAC 105.316
78 AAG 156.4912
79 AAT 168.6987
80 ACA 98.7639
81 ACC 64.5552
82 ACG 58.8997
83 ACT 105.1091
84 AGA 126.4206
85 AGC 83.1769
86 AGG 72.7625
87 AGT 86.5564
88 ATA 99.3847
89 ATC 104.0746
90 ATG 139.4558
91 ATT 185.1134
92 CAA 149.8701
93 CAC 57.5203
94 CAG 70.8314
95 CAT 95.1086
96 CCA 79.5215
97 CCC 49.1751
98 CCG 45.5887
99 CCT 83.2459
100 CGA 70.6935
101 CGC 36.8985
102 CGG 35.4502
103 CGT 74.1419
104 CTA 83.6597
105 CTC 86.1426
106 CTG 91.798
107 CTT 143.6629
108 GAA 168.216
109 GAC 64.1414
110 GAG 82.3493
111 GAT 125.593
112 GCA 79.3146
113 GCC 51.589
114 GCG 36.4847
115 GCT 96.488
116 GGA 94.6258
117 GGC 47.037
118 GGG 35.2433
119 GGT 84.6942
120 GTA 73.7281
121 GTC 68.8313
122 GTG 72.4867
123 GTT 127.5931
124 TAA 113.0406
125 TAC 99.9364
126 TAG 59.1066
127 TAT 138.5592
128 TCA 115.9373
129 TCC 92.1429
130 TCG 76.4179
131 TCT 120.5582
132 TGA 148.7666
133 TGC 96.7638
134 TGG 118.0064
135 TGT 96.6949
136 TTA 153.8704
137 TTC 145.5251
138 TTG 156.6981
139 TTT 212.8391
140 end consensus
141 type CDS
142 phase 0
143 begin consensus
144 AAA 248.8005
145 AAC 103.9424
146 AAG 172.7552
147 AAT 217.5971
148 ACA 87.4108
149 ACC 69.0194
150 ACG 38.6426
151 ACT 163.0428
152 AGA 70.2593
153 AGC 51.4546
154 AGG 27.6904
155 AGT 88.0307
156 ATA 74.1855
157 ATC 72.1191
158 ATG 126.4667
159 ATT 251.6935
160 CAA 170.2754
161 CAC 39.4692
162 CAG 70.2593
163 CAT 104.5623
164 CCA 77.4918
165 CCC 56.6207
166 CCG 25.8306
167 CCT 144.4448
168 CGA 48.1483
169 CGC 42.1556
170 CGG 17.1515
171 CGT 131.8395
172 CTA 50.628
173 CTC 47.735
174 CTG 34.3031
175 CTT 165.7292
176 GAA 288.4763
177 GAC 103.9424
178 GAG 150.4375
179 GAT 257.6862
180 GCA 100.4294
181 GCC 74.5988
182 GCG 29.1369
183 GCT 190.5266
184 GGA 104.9756
185 GGC 59.927
186 GGG 26.4506
187 GGT 158.29
188 GTA 76.252
189 GTC 75.0121
190 GTG 49.5948
191 GTT 200.6522
192 TAA 0
193 TAC 77.0786
194 TAG 0
195 TAT 147.7511
196 TCA 102.4959
197 TCC 77.2852
198 TCG 41.5356
199 TCT 182.6741
200 TGA 0
201 TGC 32.2366
202 TGG 58.8938
203 TGT 48.5616
204 TTA 163.0428
205 TTC 90.7171
206 TTG 145.0647
207 TTT 196.5193
208 end consensus
209 type CDS
210 phase 1
211 begin consensus
212 AAA 234.9249
213 AAC 117.7724
214 AAG 221.908
215 AAT 133.0621
216 ACA 116.7393
217 ACC 50.4148
218 ACG 81.6142
219 ACT 75.6223
220 AGA 108.6812
221 AGC 97.937
222 AGG 113.4334
223 AGT 73.5561
224 ATA 169.427
225 ATC 136.5747
226 ATG 253.9338
227 ATT 167.5674
228 CAA 120.0452
229 CAC 66.7377
230 CAG 102.8959
231 CAT 78.1017
232 CCA 99.7966
233 CCC 45.6626
234 CCG 72.7296
235 CCT 59.5061
236 CGA 43.5964
237 CGC 22.728
238 CGG 37.8111
239 CGT 30.9927
240 CTA 166.1211
241 CTC 141.3269
242 CTG 215.7094
243 CTT 157.6497
244 GAA 86.573
245 GAC 38.431
246 GAG 54.5472
247 GAT 44.0097
248 GCA 61.5722
249 GCC 35.5383
250 GCG 47.5222
251 GCT 41.117
252 GGA 40.7038
253 GGC 24.5876
254 GGG 33.4722
255 GGT 31.406
256 GTA 107.6481
257 GTC 79.1348
258 GTG 150.4181
259 GTT 89.4657
260 TAA 114.0533
261 TAC 76.862
262 TAG 96.4907
263 TAT 76.6554
264 TCA 89.6723
265 TCC 59.5061
266 TCG 76.0355
267 TCT 60.3325
268 TGA 103.7224
269 TGC 66.5311
270 TGG 120.8717
271 TGT 64.0517
272 TTA 199.3866
273 TTC 168.6005
274 TTG 265.2978
275 TTT 181.2042
276 end consensus
277 type CDS
278 phase 2
279 begin consensus
280 AAA 231.6265
281 AAC 94.221
282 AAG 74.5916
283 AAT 155.1753
284 ACA 92.1547
285 ACC 74.385
286 ACG 56.6152
287 ACT 76.6578
288 AGA 200.2195
289 AGC 100.2131
290 AGG 77.2777
291 AGT 98.1468
292 ATA 54.549
293 ATC 103.5191
294 ATG 37.8124
295 ATT 135.7526
296 CAA 159.1012
297 CAC 66.5332
298 CAG 39.4654
299 CAT 102.6926
300 CCA 61.3676
301 CCC 45.4575
302 CCG 38.4322
303 CCT 45.8707
304 CGA 120.4623
305 CGC 46.0774
306 CGG 51.6562
307 CGT 59.7146
308 CTA 34.2997
309 CTC 69.426
310 CTG 25.4149
311 CTT 107.445
312 GAA 129.3472
313 GAC 50.2099
314 GAG 42.1515
315 GAT 75.0048
316 GCA 76.038
317 GCC 44.8376
318 GCG 33.06
319 GCT 57.855
320 GGA 138.2321
321 GGC 56.8219
322 GGG 46.0774
323 GGT 64.467
324 GTA 37.3991
325 GTC 52.4827
326 GTG 17.5631
327 GTT 92.568
328 TAA 224.8079
329 TAC 145.8772
330 TAG 80.7903
331 TAT 191.128
332 TCA 155.5886
333 TCC 139.6784
334 TCG 111.7841
335 TCT 118.6027
336 TGA 342.1709
337 TGC 191.5413
338 TGG 174.1848
339 TGT 177.4908
340 TTA 98.9733
341 TTC 177.0775
342 TTG 59.508
343 TTT 260.3474
344 end consensus
345 type Intron_Corr_Term
346 phase all
347 225.12
348 type Intron_Corr_Term
349 phase 0
350 524.049
351 type Intron_Corr_Term
352 phase 1
353 652.388
354 type Intron_Corr_Term
355 phase 2
356 998.969
357 type Intron_emission
358 begin consensus
359 A 123.3115
360 C 59.5593
361 G 67.0399
362 T 150.0893
363 end consensus
364 type Pyrimidine_emission
365 begin consensus
366 A 26.1549
367 C 86.9936
368 G 12.7932
369 T 274.0583
370 end consensus
371 type Spacer_emission
372 begin consensus
373 A 149.5231
374 C 60.7484
375 G 51.3573
376 T 138.3712
377 end consensus
378 type Intron_Stay_Prob
379 0.988929
380 type Central_Intron_Stay_Prob
381 0.983466
382 type Pyrimidine_Stay_Prob
383 0.904578
384 type No_Spacer_Prob
385 0.0743243
386 type Spacer_Stay_Prob
387 0.952081