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comparison orthologs/ucsb_hamster/lib/wisecfg/human.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
2 # Wed Jan 1 13:42:23 IST 1997
3 # Created by Mor Amitai (mor@compugen.co.il)
4 # dataset : hum1 and hum2 from embl48
5 # Consensi are read from top down. The value, for a sequence,
6 # is the number in the line of the first consensus that
7 # matches the sequence.
8 # Note: the set of sequences that are represented by a consensus
9 # are all the sequences that match this consensus and none of the
10 # previous consensi
11 #
12 # the numbers in types 5SS, 3SS, CDS, and the emissions are the number of
13 # occurrences of each sequence in the database.
14 # In case of a consensus this is the number of occurrences of sequences
15 # that are represented by the consensus in the database divided by the
16 # number of sequences that are represented by the consensus.
17 # *stay_prob is the probability of the transition from the state to itself.
18 # No_Spacer_Prob is the probability of transition from Pyrimidine directly
19 # to 3SS (no spacer).
20 type 5SS
21 center 3
22 phase all
23 begin consensus
24 C-GGTGAGTG 15.75
25 --GGTGAGTG 8.83333
26 CAGGTGAG-- 7.6
27 AAGGTGAG-- 6.86667
28 CAGGTAAG-- 4.3125
29 GAGGTGAG-- 4.26667
30 AAGGTAAG-- 4.1875
31 --GGTGAGT- 1.71795
32 ---GTGAGTG 1.66667
33 --GGTGAG-C 1.51282
34 -A-GTAAGT- 1.41071
35 -AGGTG-GT- 1.39583
36 -TGGTAAG-- 1.39062
37 CAGGTA-G-- 1.35417
38 AAGGTA-G-- 1.04167
39 -GGGTAAG-- 1
40 --GGTGAG-- 0.91453
41 -C-GTAAGT- 0.828125
42 ---GTGAGT- 0.729167
43 -AGGTAA--- 0.578704
44 -AGGTG-G-- 0.506944
45 CAGGTA---- 0.381944
46 --GGTA-GT- 0.339286
47 -AGGTGA--- 0.265625
48 --GGTCAG-- 0.207031
49 ---GTAAG-- 0.155556
50 -AGGTA---- 0.134921
51 -AGGT--G-- 0.111607
52 --GGT--G-- 0.0369898
53 -AGGT----- 0.0250947
54 --GGTA---- 0.0234375
55 --AGT--G-- 0.0132415
56 ---GT----- 0.00148067
57 end consensus
58 type 5SS
59 center 3
60 phase 0
61 begin consensus
62 A-GGTGAGTG 8.25
63 C-GGTGAGTG 7.75
64 AAGGTGAG-- 3.86667
65 CAGGTGAG-- 3.46667
66 AAGGTAAG-- 2.5
67 GAGGTGAG-- 2.4375
68 --GGTGAGT- 1.19565
69 -AGGTAAG-- 1.02083
70 -A-GTGAGT- 0.916667
71 -AGGT--GTG 0.785714
72 AAGGT-GG-- 0.716667
73 -C-GTGAGT- 0.666667
74 ---GTAAGTG 0.566667
75 --GGTGAG-- 0.423077
76 --GGTAAG-- 0.355556
77 CAGGT--G-- 0.3
78 ---GTAAGT- 0.284722
79 -AGGTAA--- 0.265625
80 --GGTA-GT- 0.196429
81 -AGGTAC--- 0.157895
82 AAGGTG---- 0.13964
83 -AGGTG---- 0.048048
84 -AGGT----- 0.0181818
85 --GGT--G-- 0.0129717
86 ---GTA---- 0.00291667
87 ---GT----- 0.000915751
88 end consensus
89 type 5SS
90 center 3
91 phase 1
92 begin consensus
93 --GGTGAGTG 4.375
94 CAGGTGAG-- 2.8
95 AAGGTGAG-- 2.26667
96 -AGGTAAG-- 1.01562
97 -TGGTAAG-- 0.8125
98 -TGGTGAG-- 0.7
99 G-GGTGAG-- 0.755556
100 CAGGT-GG-- 0.546875
101 --GGTGAG-- 0.428571
102 ---GTGAGTG 0.625
103 ---GTAAGT- 0.223214
104 AAGGT--G-- 0.200893
105 -AGGTAA--- 0.1875
106 --GGTA-G-G 0.175
107 CAGGT----- 0.0733945
108 ---GTGAG-- 0.0527778
109 --GGT--GT- 0.0512129
110 A-GGTA---- 0.046398
111 -AGGT----- 0.0137104
112 ---G-AAG-- 0.00972447
113 ---GT----- 0.00111909
114 end consensus
115 type 5SS
116 center 3
117 phase 2
118 begin consensus
119 -AGGTGAG-- 0.703125
120 C--GTGAGT- 0.516667
121 -AGGTAAG-- 0.5
122 ---GTAAGT- 0.241667
123 --GGTGAG-- 0.227778
124 CAGGTA---- 0.133333
125 ---GTGAG-- 0.0569444
126 -AGGT--G-- 0.0483491
127 ---GTAAG-- 0.0444444
128 --GGTA---- 0.00896991
129 ---GT----- 0.000797367
130 end consensus
131 type 3SS
132 center 3
133 phase all
134 begin consensus
135 CAGGTG 143
136 CAGGGT 120
137 CAGGGC 88
138 CAGGGA 82
139 CAGGCT 77
140 CAGGAG 73
141 CAGGGG 66
142 CAGGTA 60
143 CAGGCC 58
144 CAGGAA 54
145 CAGATC 50
146 CAGCTG 50
147 CAGG-C 43.5
148 CAGG-T 38.5
149 CAGA-C 35.6667
150 CAGAT- 29.3333
151 CAGA-A 27.3333
152 CAG-TC 25.5
153 TAGG-G 21.75
154 CAG-CA 21.6667
155 TAGGA- 21.3333
156 TAGGG- 20.6667
157 CAGA-G 19.3333
158 CAGTG- 18.75
159 CAGA-- 18
160 TAGG-- 13.8333
161 CAG-C- 11.8571
162 CAG-T- 10.4
163 CAG-A- 7.375
164 TAGA-- 6.0625
165 TAGC-- 3.3125
166 AAGG-- 3.125
167 -AGT-- 1.08333
168 -AG--- 0.714286
169 end consensus
170 type 3SS
171 center 3
172 phase 0
173 begin consensus
174 CAGGGT 88
175 CAGGTG 64
176 CAGGAG 43
177 CAGGG- 40.3333
178 CAGATC 32
179 CAGG-C 25
180 CAGG-A 19
181 CAGG-T 17.3333
182 CAGA-C 14.6667
183 CAG-TG 13
184 CAGAA- 13
185 CAGA-T 11.3333
186 CAGC-C 10.25
187 TAGG-- 9.8125
188 CAG--A 4.09091
189 CAGT-- 4.45455
190 TAG-T- 3.33333
191 TAG--- 1.36111
192 -AGG-- 1.06061
193 -AG--- 0.342857
194 end consensus
195 type 3SS
196 center 3
197 phase 1
198 begin consensus
199 CAGGTG 71
200 CAGGCT 36
201 CAGGG- 24.75
202 CAG-CC 17.5
203 CAG-TG 16.6667
204 CAGAG- 15.75
205 CAGG-- 14.5556
206 CAGA-A 13.3333
207 CAGTG- 10.75
208 CAG-TC 10.3333
209 TAGG-G 9.5
210 CAGA-- 6.16667
211 TAGG-- 5
212 CAGC-- 3.69231
213 TAG--- 1.66667
214 -AG--- 0.328467
215 end consensus
216 type 3SS
217 center 3
218 phase 2
219 begin consensus
220 CAGG-A 19.25
221 CAGG-T 14.75
222 CAG-G- 4.57143
223 CAG--T 4.66667
224 TAGG-- 3
225 CAG--- 2.87879
226 TAG--- 0.645833
227 AAG--- 0.25
228 end consensus
229 type CDS
230 phase all
231 begin consensus
232 AAA 5290.000000
233 AAC 4795.000000
234 AAG 8178.000000
235 AAT 3305.000000
236 ACA 6240.000000
237 ACC 7728.000000
238 ACG 3347.000000
239 ACT 4930.000000
240 AGA 8491.000000
241 AGC 8639.000000
242 AGG 8997.000000
243 AGT 4417.000000
244 ATA 1975.000000
245 ATC 4973.000000
246 ATG 6474.000000
247 ATT 3083.000000
248 CAA 7057.000000
249 CAC 6815.000000
250 CAG 11041.000000
251 CAT 5779.000000
252 CCA 10537.000000
253 CCC 10307.000000
254 CCG 5621.000000
255 CCT 10134.000000
256 CGA 3377.000000
257 CGC 5146.000000
258 CGG 5375.000000
259 CGT 2765.000000
260 CTA 3502.000000
261 CTC 7465.000000
262 CTG 13780.000000
263 CTT 5453.000000
264 GAA 7461.000000
265 GAC 6937.000000
266 GAG 9975.000000
267 GAT 4949.000000
268 GCA 7747.000000
269 GCC 10890.000000
270 GCG 4828.000000
271 GCT 9371.000000
272 GGA 10143.000000
273 GGC 10400.000000
274 GGG 8869.000000
275 GGT 5567.000000
276 GTA 2143.000000
277 GTC 4593.000000
278 GTG 8189.000000
279 GTT 3021.000000
280 TAA 1775.000000
281 TAC 3687.000000
282 TAG 1333.000000
283 TAT 2477.000000
284 TCA 6180.000000
285 TCC 7668.000000
286 TCG 2875.000000
287 TCT 5767.000000
288 TGA 7315.000000
289 TGC 8625.000000
290 TGG 11718.000000
291 TGT 5197.000000
292 TTA 1664.000000
293 TTC 5462.000000
294 TTG 4420.000000
295 TTT 3453.000000
296 end consensus
297 type CDS
298 phase 0
299 begin consensus
300 AAA 2167.000000
301 AAC 2839.000000
302 AAG 4830.000000
303 AAT 1616.000000
304 ACA 1543.000000
305 ACC 3187.000000
306 ACG 983.000000
307 ACT 1484.000000
308 AGA 995.000000
309 AGC 2722.000000
310 AGG 1326.000000
311 AGT 1093.000000
312 ATA 585.000000
313 ATC 3281.000000
314 ATG 2538.000000
315 ATT 1584.000000
316 CAA 1141.000000
317 CAC 1981.000000
318 CAG 4796.000000
319 CAT 1016.000000
320 CCA 2021.000000
321 CCC 3183.000000
322 CCG 1104.000000
323 CCT 2289.000000
324 CGA 770.000000
325 CGC 2011.000000
326 CGG 1762.000000
327 CGT 687.000000
328 CTA 745.000000
329 CTC 2964.000000
330 CTG 6980.000000
331 CTT 1200.000000
332 GAA 2729.000000
333 GAC 3946.000000
334 GAG 6121.000000
335 GAT 2318.000000
336 GCA 1767.000000
337 GCC 4902.000000
338 GCG 1288.000000
339 GCT 2556.000000
340 GGA 2322.000000
341 GGC 4338.000000
342 GGG 2688.000000
343 GGT 1903.000000
344 GTA 690.000000
345 GTC 2172.000000
346 GTG 4546.000000
347 GTT 1020.000000
348 TAA 0.000000
349 TAC 2405.000000
350 TAG 0.000000
351 TAT 1323.000000
352 TCA 990.000000
353 TCC 2579.000000
354 TCG 684.000000
355 TCT 1522.000000
356 TGA 0.000000
357 TGC 1747.000000
358 TGG 1766.000000
359 TGT 931.000000
360 TTA 397.000000
361 TTC 3156.000000
362 TTG 1313.000000
363 TTT 1697.000000
364 end consensus
365 type CDS
366 phase 1
367 begin consensus
368 AAA 1534.000000
369 AAC 1140.000000
370 AAG 2597.000000
371 AAT 767.000000
372 ACA 3632.000000
373 ACC 3429.000000
374 ACG 1849.000000
375 ACT 2262.000000
376 AGA 4427.000000
377 AGC 4014.000000
378 AGG 5377.000000
379 AGT 1927.000000
380 ATA 953.000000
381 ATC 1055.000000
382 ATG 3488.000000
383 ATT 777.000000
384 CAA 998.000000
385 CAC 1332.000000
386 CAG 3260.000000
387 CAT 731.000000
388 CCA 4701.000000
389 CCC 3908.000000
390 CCG 2252.000000
391 CCT 2992.000000
392 CGA 471.000000
393 CGC 1361.000000
394 CGG 1785.000000
395 CGT 443.000000
396 CTA 825.000000
397 CTC 1766.000000
398 CTG 4378.000000
399 CTT 882.000000
400 GAA 924.000000
401 GAC 843.000000
402 GAG 1897.000000
403 GAT 424.000000
404 GCA 3140.000000
405 GCC 3275.000000
406 GCG 1806.000000
407 GCT 2595.000000
408 GGA 1911.000000
409 GGC 2034.000000
410 GGG 2835.000000
411 GGT 762.000000
412 GTA 577.000000
413 GTC 968.000000
414 GTG 2506.000000
415 GTT 563.000000
416 TAA 622.000000
417 TAC 561.000000
418 TAG 912.000000
419 TAT 322.000000
420 TCA 3963.000000
421 TCC 3535.000000
422 TCG 1466.000000
423 TCT 2607.000000
424 TGA 3311.000000
425 TGC 4099.000000
426 TGG 6194.000000
427 TGT 1772.000000
428 TTA 773.000000
429 TTC 1353.000000
430 TTG 2662.000000
431 TTT 713.000000
432 end consensus
433 type CDS
434 phase 2
435 begin consensus
436 AAA 1589.000000
437 AAC 816.000000
438 AAG 751.000000
439 AAT 922.000000
440 ACA 1065.000000
441 ACC 1112.000000
442 ACG 515.000000
443 ACT 1184.000000
444 AGA 3069.000000
445 AGC 1903.000000
446 AGG 2294.000000
447 AGT 1397.000000
448 ATA 437.000000
449 ATC 637.000000
450 ATG 448.000000
451 ATT 722.000000
452 CAA 4918.000000
453 CAC 3502.000000
454 CAG 2985.000000
455 CAT 4032.000000
456 CCA 3815.000000
457 CCC 3216.000000
458 CCG 2265.000000
459 CCT 4853.000000
460 CGA 2136.000000
461 CGC 1774.000000
462 CGG 1828.000000
463 CGT 1635.000000
464 CTA 1932.000000
465 CTC 2735.000000
466 CTG 2422.000000
467 CTT 3371.000000
468 GAA 3808.000000
469 GAC 2148.000000
470 GAG 1957.000000
471 GAT 2207.000000
472 GCA 2840.000000
473 GCC 2713.000000
474 GCG 1734.000000
475 GCT 4220.000000
476 GGA 5910.000000
477 GGC 4028.000000
478 GGG 3346.000000
479 GGT 2902.000000
480 GTA 876.000000
481 GTC 1453.000000
482 GTG 1137.000000
483 GTT 1438.000000
484 TAA 1153.000000
485 TAC 721.000000
486 TAG 421.000000
487 TAT 832.000000
488 TCA 1227.000000
489 TCC 1554.000000
490 TCG 725.000000
491 TCT 1638.000000
492 TGA 4004.000000
493 TGC 2779.000000
494 TGG 3758.000000
495 TGT 2494.000000
496 TTA 494.000000
497 TTC 953.000000
498 TTG 445.000000
499 TTT 1043.000000
500 end consensus
501 type Intron_Corr_Term
502 phase all
503 65.6094
504 type Intron_Corr_Term
505 phase 0
506 141.429
507 type Intron_Corr_Term
508 phase 1
509 172.738
510 type Intron_Corr_Term
511 phase 2
512 371.127
513 type Intron_emission
514 begin consensus
515 A 399845.000000
516 C 371259.000000
517 G 393779.000000
518 T 425926.000000
519 end consensus
520 type Pyrimidine_emission
521 begin consensus
522 A 2299.000000
523 C 18610.000000
524 G 2345.000000
525 T 17132.000000
526 end consensus
527 type Spacer_emission
528 begin consensus
529 A 3020.000000
530 C 3834.000000
531 G 3644.000000
532 T 4224.000000
533 end consensus
534 type Central_Intron_Stay_Prob
535 0.99853
536 type Pyrimidine_Stay_Prob
537 0.944485
538 type No_Spacer_Prob
539 0.331508
540 type Spacer_Stay_Prob
541 0.902704