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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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# Splice sites and intron regions information for GeneWise-21 May 1500 # Created by Mor Amitai (mor@compugen.co.il) # dataset : ~/ftp/pub/PomBase/temp/cds_cdna ~/ftp/pub/PomBase/temp/cds_ex # Consensi are read from top down. The value, for a sequence, # is the number in the line of the first consensus that # matches the sequence. # Note: the set of sequences that are represented by a consensus # are all the sequences that match this consensus and none of the # previous consensi # # the numbers in types 5SS, 3SS, CDS, and the emissions are the number of # occurrences of each sequence in the database. # In case of a consensus this is the number of occurrences of sequences # that are represented by the consensus in the database divided by the # number of sequences that are represented by the consensus. # *stay_prob is the probability of the transition from the state to itself. # No_Spacer_Prob is the probability of transition from Pyrimidine directly # to 3SS (no spacer). type 5SS center 3 phase all begin consensus ---GTA-GT- 8.69141 ---GT----- 0.0821553 end consensus type 5SS center 3 phase 0 begin consensus ---GTA-GT- 3.71094 ---GT----- 0.0356523 end consensus type 5SS center 3 phase 1 begin consensus ---GTA-GT- 2.92969 ---GT----- 0.0294519 end consensus type 5SS center 3 phase 2 begin consensus ---GT----- 0.0488281 end consensus type 3SS center 3 phase all begin consensus TAG--- 1.64062 -AG--- 22.9167 end consensus type 3SS center 3 phase 0 begin consensus TAG--- 0.765625 -AG--- 9.375 end consensus type 3SS center 3 phase 1 begin consensus TAG--- 0.515625 -AG--- 8.85417 end consensus type 3SS center 3 phase 2 begin consensus -AG--- 12.5 end consensus type CDS phase all begin consensus AAA 238.6335 AAC 105.316 AAG 156.4912 AAT 168.6987 ACA 98.7639 ACC 64.5552 ACG 58.8997 ACT 105.1091 AGA 126.4206 AGC 83.1769 AGG 72.7625 AGT 86.5564 ATA 99.3847 ATC 104.0746 ATG 139.4558 ATT 185.1134 CAA 149.8701 CAC 57.5203 CAG 70.8314 CAT 95.1086 CCA 79.5215 CCC 49.1751 CCG 45.5887 CCT 83.2459 CGA 70.6935 CGC 36.8985 CGG 35.4502 CGT 74.1419 CTA 83.6597 CTC 86.1426 CTG 91.798 CTT 143.6629 GAA 168.216 GAC 64.1414 GAG 82.3493 GAT 125.593 GCA 79.3146 GCC 51.589 GCG 36.4847 GCT 96.488 GGA 94.6258 GGC 47.037 GGG 35.2433 GGT 84.6942 GTA 73.7281 GTC 68.8313 GTG 72.4867 GTT 127.5931 TAA 113.0406 TAC 99.9364 TAG 59.1066 TAT 138.5592 TCA 115.9373 TCC 92.1429 TCG 76.4179 TCT 120.5582 TGA 148.7666 TGC 96.7638 TGG 118.0064 TGT 96.6949 TTA 153.8704 TTC 145.5251 TTG 156.6981 TTT 212.8391 end consensus type CDS phase 0 begin consensus AAA 248.8005 AAC 103.9424 AAG 172.7552 AAT 217.5971 ACA 87.4108 ACC 69.0194 ACG 38.6426 ACT 163.0428 AGA 70.2593 AGC 51.4546 AGG 27.6904 AGT 88.0307 ATA 74.1855 ATC 72.1191 ATG 126.4667 ATT 251.6935 CAA 170.2754 CAC 39.4692 CAG 70.2593 CAT 104.5623 CCA 77.4918 CCC 56.6207 CCG 25.8306 CCT 144.4448 CGA 48.1483 CGC 42.1556 CGG 17.1515 CGT 131.8395 CTA 50.628 CTC 47.735 CTG 34.3031 CTT 165.7292 GAA 288.4763 GAC 103.9424 GAG 150.4375 GAT 257.6862 GCA 100.4294 GCC 74.5988 GCG 29.1369 GCT 190.5266 GGA 104.9756 GGC 59.927 GGG 26.4506 GGT 158.29 GTA 76.252 GTC 75.0121 GTG 49.5948 GTT 200.6522 TAA 0 TAC 77.0786 TAG 0 TAT 147.7511 TCA 102.4959 TCC 77.2852 TCG 41.5356 TCT 182.6741 TGA 0 TGC 32.2366 TGG 58.8938 TGT 48.5616 TTA 163.0428 TTC 90.7171 TTG 145.0647 TTT 196.5193 end consensus type CDS phase 1 begin consensus AAA 234.9249 AAC 117.7724 AAG 221.908 AAT 133.0621 ACA 116.7393 ACC 50.4148 ACG 81.6142 ACT 75.6223 AGA 108.6812 AGC 97.937 AGG 113.4334 AGT 73.5561 ATA 169.427 ATC 136.5747 ATG 253.9338 ATT 167.5674 CAA 120.0452 CAC 66.7377 CAG 102.8959 CAT 78.1017 CCA 99.7966 CCC 45.6626 CCG 72.7296 CCT 59.5061 CGA 43.5964 CGC 22.728 CGG 37.8111 CGT 30.9927 CTA 166.1211 CTC 141.3269 CTG 215.7094 CTT 157.6497 GAA 86.573 GAC 38.431 GAG 54.5472 GAT 44.0097 GCA 61.5722 GCC 35.5383 GCG 47.5222 GCT 41.117 GGA 40.7038 GGC 24.5876 GGG 33.4722 GGT 31.406 GTA 107.6481 GTC 79.1348 GTG 150.4181 GTT 89.4657 TAA 114.0533 TAC 76.862 TAG 96.4907 TAT 76.6554 TCA 89.6723 TCC 59.5061 TCG 76.0355 TCT 60.3325 TGA 103.7224 TGC 66.5311 TGG 120.8717 TGT 64.0517 TTA 199.3866 TTC 168.6005 TTG 265.2978 TTT 181.2042 end consensus type CDS phase 2 begin consensus AAA 231.6265 AAC 94.221 AAG 74.5916 AAT 155.1753 ACA 92.1547 ACC 74.385 ACG 56.6152 ACT 76.6578 AGA 200.2195 AGC 100.2131 AGG 77.2777 AGT 98.1468 ATA 54.549 ATC 103.5191 ATG 37.8124 ATT 135.7526 CAA 159.1012 CAC 66.5332 CAG 39.4654 CAT 102.6926 CCA 61.3676 CCC 45.4575 CCG 38.4322 CCT 45.8707 CGA 120.4623 CGC 46.0774 CGG 51.6562 CGT 59.7146 CTA 34.2997 CTC 69.426 CTG 25.4149 CTT 107.445 GAA 129.3472 GAC 50.2099 GAG 42.1515 GAT 75.0048 GCA 76.038 GCC 44.8376 GCG 33.06 GCT 57.855 GGA 138.2321 GGC 56.8219 GGG 46.0774 GGT 64.467 GTA 37.3991 GTC 52.4827 GTG 17.5631 GTT 92.568 TAA 224.8079 TAC 145.8772 TAG 80.7903 TAT 191.128 TCA 155.5886 TCC 139.6784 TCG 111.7841 TCT 118.6027 TGA 342.1709 TGC 191.5413 TGG 174.1848 TGT 177.4908 TTA 98.9733 TTC 177.0775 TTG 59.508 TTT 260.3474 end consensus type Intron_Corr_Term phase all 225.12 type Intron_Corr_Term phase 0 524.049 type Intron_Corr_Term phase 1 652.388 type Intron_Corr_Term phase 2 998.969 type Intron_emission begin consensus A 123.3115 C 59.5593 G 67.0399 T 150.0893 end consensus type Pyrimidine_emission begin consensus A 26.1549 C 86.9936 G 12.7932 T 274.0583 end consensus type Spacer_emission begin consensus A 149.5231 C 60.7484 G 51.3573 T 138.3712 end consensus type Intron_Stay_Prob 0.988929 type Central_Intron_Stay_Prob 0.983466 type Pyrimidine_Stay_Prob 0.904578 type No_Spacer_Prob 0.0743243 type Spacer_Stay_Prob 0.952081