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diff orthologs/ucsb_hamster/lib/wisecfg/pombe.gf @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/ucsb_hamster/lib/wisecfg/pombe.gf	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,1664 @@
+# Splice sites and intron regions information for GeneWise-21
+# Fri May 15 13:20:38 IDT 1998
+# 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- 0.0869141
+---GT----- 0.000821553
+end consensus
+type 5SS
+center 3
+phase 0
+begin consensus
+---GTA-GT- 0.0371094
+---GT----- 0.000356523
+end consensus
+type 5SS
+center 3
+phase 1
+begin consensus
+---GTA-GT- 0.0292969
+---GT----- 0.000294519
+end consensus
+type 5SS
+center 3
+phase 2
+begin consensus
+---GT----- 0.000488281
+end consensus
+type 5SS_codon
+phase all
+begin consensus
+AAA 1.864078
+AAC 0.621359
+AAG 6.524272
+AAT 1.864078
+AAN 2.71845
+ACA 0.932039
+ACC 0.310680
+ACG 1.553398
+ACT 0.932039
+ACN 0.932039
+AGA 1.553398
+AGC 0.310680
+AGG 1.553398
+AGT 1.864078
+AGN 1.32039
+ATA 0.932039
+ATC 0.621359
+ATG 2.796117
+ATT 1.553398
+ATN 1.47573
+ANA 1.32039
+ANC 0.46602
+ANG 3.1068
+ANT 1.5534
+ANN 1.61165
+CAA 1.242718
+CAC 0.310680
+CAG 3.417476
+CAT 0.621359
+CAN 1.39806
+CCA 0.310680
+CCC 0.310680
+CCG 0.621359
+CCT 0.310680
+CCN 0.38835
+CGA 0.621359
+CGC 0.310680
+CGG 1.242718
+CGT 0.310680
+CGN 0.621359
+CTA 0.310680
+CTC 0.310680
+CTG 1.864078
+CTT 0.621359
+CTN 0.776699
+CNA 0.621359
+CNC 0.31068
+CNG 1.78641
+CNT 0.46602
+CNN 0.796117
+GAA 0.310680
+GAC 0.621359
+GAG 3.106796
+GAT 1.242718
+GAN 1.32039
+GCA 0.621359
+GCC 0.621359
+GCG 0.310680
+GCT 0.621359
+GCN 0.543689
+GGA 0.310680
+GGC 0.310680
+GGG 0.310680
+GGT 0.310680
+GGN 0.31068
+GTA 0.310680
+GTC 0.310680
+GTG 0.932039
+GTT 0.310680
+GTN 0.46602
+GNA 0.38835
+GNC 0.46602
+GNG 1.16505
+GNT 0.621359
+GNN 0.660194
+TAA 0.621359
+TAC 0.932039
+TAG 0.932039
+TAT 0.621359
+TAN 0.776699
+TCA 0.621359
+TCC 0.310680
+TCG 0.621359
+TCT 0.932039
+TCN 0.621359
+TGA 0.621359
+TGC 0.621359
+TGG 1.242718
+TGT 0.621359
+TGN 0.776699
+TTA 0.621359
+TTC 0.621359
+TTG 3.106796
+TTT 1.864078
+TTN 1.5534
+TNA 0.621359
+TNC 0.621359
+TNG 1.47573
+TNT 1.00971
+TNN 0.932039
+NAA 1.00971
+NAC 0.621359
+NAG 3.49515
+NAT 1.08738
+NAN 1.5534
+NCA 0.621359
+NCC 0.38835
+NCG 0.776699
+NCT 0.699029
+NCN 0.621359
+NGA 0.776699
+NGC 0.38835
+NGG 1.08738
+NGT 0.776699
+NGN 0.757282
+NTA 0.543689
+NTC 0.46602
+NTG 2.17476
+NTT 1.08738
+NTN 1.06796
+NNA 0.737864
+NNC 0.46602
+NNG 1.8835
+NNT 0.912621
+NNN 1
+end consensus
+type 5SS_codon
+phase 0
+begin consensus
+AAA 0.512000
+AAC 0.512000
+AAG 6.144000
+AAT 1.536000
+AAN 2.176
+ACA 1.024000
+ACC 0.512000
+ACG 0.512000
+ACT 0.512000
+ACN 0.64
+AGA 0.512000
+AGC 0.512000
+AGG 1.536000
+AGT 1.024000
+AGN 0.896
+ATA 0.512000
+ATC 0.512000
+ATG 2.048000
+ATT 1.536000
+ATN 1.152
+ANA 0.64
+ANC 0.512
+ANG 2.56
+ANT 1.152
+ANN 1.216
+CAA 1.024000
+CAC 0.512000
+CAG 4.608000
+CAT 1.024000
+CAN 1.792
+CCA 0.512000
+CCC 0.512000
+CCG 1.024000
+CCT 0.512000
+CCN 0.64
+CGA 0.512000
+CGC 0.512000
+CGG 1.024000
+CGT 0.512000
+CGN 0.64
+CTA 0.512000
+CTC 0.512000
+CTG 1.536000
+CTT 1.024000
+CTN 0.896
+CNA 0.64
+CNC 0.512
+CNG 2.048
+CNT 0.768
+CNN 0.992
+GAA 0.512000
+GAC 0.512000
+GAG 4.096000
+GAT 1.536000
+GAN 1.664
+GCA 1.024000
+GCC 1.024000
+GCG 0.512000
+GCT 1.024000
+GCN 0.896
+GGA 0.512000
+GGC 0.512000
+GGG 0.512000
+GGT 0.512000
+GGN 0.512
+GTA 0.512000
+GTC 0.512000
+GTG 1.536000
+GTT 0.512000
+GTN 0.768
+GNA 0.64
+GNC 0.64
+GNG 1.664
+GNT 0.896
+GNN 0.96
+TAA 0.512000
+TAC 1.536000
+TAG 0.512000
+TAT 0.512000
+TAN 0.768
+TCA 0.512000
+TCC 0.512000
+TCG 0.512000
+TCT 1.536000
+TCN 0.768
+TGA 0.512000
+TGC 0.512000
+TGG 0.512000
+TGT 0.512000
+TGN 0.512
+TTA 1.024000
+TTC 0.512000
+TTG 2.048000
+TTT 1.536000
+TTN 1.28
+TNA 0.64
+TNC 0.768
+TNG 0.896
+TNT 1.024
+TNN 0.832
+NAA 0.64
+NAC 0.768
+NAG 3.84
+NAT 1.152
+NAN 1.6
+NCA 0.768
+NCC 0.64
+NCG 0.64
+NCT 0.896
+NCN 0.736
+NGA 0.512
+NGC 0.512
+NGG 0.896
+NGT 0.64
+NGN 0.64
+NTA 0.64
+NTC 0.512
+NTG 1.792
+NTT 1.152
+NTN 1.024
+NNA 0.64
+NNC 0.608
+NNG 1.792
+NNT 0.96
+NNN 1
+end consensus
+type 5SS_codon
+phase 1
+begin consensus
+AAA 1.699115
+AAC 0.566372
+AAG 3.964602
+AAT 1.132743
+AAN 1.84071
+ACA 1.132743
+ACC 0.566372
+ACG 2.265487
+ACT 1.699115
+ACN 1.41593
+AGA 1.132743
+AGC 0.566372
+AGG 1.699115
+AGT 1.132743
+AGN 1.13274
+ATA 1.699115
+ATC 1.132743
+ATG 2.831858
+ATT 1.699115
+ATN 1.84071
+ANA 1.41593
+ANC 0.707965
+ANG 2.69027
+ANT 1.41593
+ANN 1.55752
+CAA 1.132743
+CAC 0.566372
+CAG 1.132743
+CAT 0.566372
+CAN 0.849557
+CCA 0.566372
+CCC 0.566372
+CCG 0.566372
+CCT 0.566372
+CCN 0.566372
+CGA 0.566372
+CGC 0.566372
+CGG 1.699115
+CGT 0.566372
+CGN 0.849558
+CTA 0.566372
+CTC 0.566372
+CTG 2.265487
+CTT 0.566372
+CTN 0.991151
+CNA 0.707965
+CNC 0.566372
+CNG 1.41593
+CNT 0.566372
+CNN 0.814159
+GAA 0.566372
+GAC 1.132743
+GAG 1.699115
+GAT 0.566372
+GAN 0.99115
+GCA 0.566372
+GCC 0.566372
+GCG 0.566372
+GCT 0.566372
+GCN 0.566372
+GGA 0.566372
+GGC 0.566372
+GGG 0.566372
+GGT 0.566372
+GGN 0.566372
+GTA 0.566372
+GTC 0.566372
+GTG 0.566372
+GTT 0.566372
+GTN 0.566372
+GNA 0.566372
+GNC 0.707965
+GNG 0.849558
+GNT 0.566372
+GNN 0.672567
+TAA 0.566372
+TAC 0.566372
+TAG 0.566372
+TAT 1.132743
+TAN 0.707965
+TCA 0.566372
+TCC 0.566372
+TCG 0.566372
+TCT 0.566372
+TCN 0.566372
+TGA 0.566372
+TGC 0.566372
+TGG 1.699115
+TGT 0.566372
+TGN 0.849558
+TTA 0.566372
+TTC 0.566372
+TTG 3.964602
+TTT 1.699115
+TTN 1.69912
+TNA 0.566372
+TNC 0.566372
+TNG 1.69912
+TNT 0.99115
+TNN 0.955752
+NAA 0.99115
+NAC 0.707965
+NAG 1.84071
+NAT 0.849557
+NAN 1.09735
+NCA 0.707965
+NCC 0.566372
+NCG 0.991151
+NCT 0.849558
+NCN 0.778761
+NGA 0.707965
+NGC 0.566372
+NGG 1.41593
+NGT 0.707965
+NGN 0.849558
+NTA 0.849558
+NTC 0.707965
+NTG 2.40708
+NTT 1.13274
+NTN 1.27434
+NNA 0.814159
+NNC 0.637168
+NNG 1.66372
+NNT 0.884956
+NNN 1
+end consensus
+type 5SS_codon
+phase 2
+begin consensus
+AAA 2.666667
+AAC 1.333333
+AAG 2.666667
+AAT 2.000000
+AAN 2.16667
+ACA 0.666667
+ACC 0.666667
+ACG 1.333333
+ACT 0.666667
+ACN 0.833334
+AGA 2.666667
+AGC 0.666667
+AGG 0.666667
+AGT 2.666667
+AGN 1.66667
+ATA 0.666667
+ATC 0.666667
+ATG 1.333333
+ATT 0.666667
+ATN 0.833334
+ANA 1.66667
+ANC 0.833333
+ANG 1.5
+ANT 1.5
+ANN 1.375
+CAA 1.333333
+CAC 0.666667
+CAG 1.333333
+CAT 0.666667
+CAN 1
+CCA 0.666667
+CCC 0.666667
+CCG 0.666667
+CCT 0.666667
+CCN 0.666667
+CGA 1.333333
+CGC 0.666667
+CGG 0.666667
+CGT 0.666667
+CGN 0.833333
+CTA 0.666667
+CTC 0.666667
+CTG 0.666667
+CTT 0.666667
+CTN 0.666667
+CNA 1
+CNC 0.666667
+CNG 0.833333
+CNT 0.666667
+CNN 0.791667
+GAA 0.666667
+GAC 0.666667
+GAG 0.666667
+GAT 1.333333
+GAN 0.833334
+GCA 0.666667
+GCC 0.666667
+GCG 0.666667
+GCT 0.666667
+GCN 0.666667
+GGA 0.666667
+GGC 0.666667
+GGG 0.666667
+GGT 0.666667
+GGN 0.666667
+GTA 0.666667
+GTC 0.666667
+GTG 0.666667
+GTT 0.666667
+GTN 0.666667
+GNA 0.666667
+GNC 0.666667
+GNG 0.666667
+GNT 0.833333
+GNN 0.708334
+TAA 1.333333
+TAC 0.666667
+TAG 2.000000
+TAT 0.666667
+TAN 1.16667
+TCA 1.333333
+TCC 0.666667
+TCG 1.333333
+TCT 0.666667
+TCN 1
+TGA 1.333333
+TGC 1.333333
+TGG 1.333333
+TGT 1.333333
+TGN 1.33333
+TTA 0.666667
+TTC 1.333333
+TTG 0.666667
+TTT 1.333333
+TTN 1
+TNA 1.16667
+TNC 1
+TNG 1.33333
+TNT 1
+TNN 1.125
+NAA 1.5
+NAC 0.833333
+NAG 1.66667
+NAT 1.16667
+NAN 1.29167
+NCA 0.833334
+NCC 0.666667
+NCG 1
+NCT 0.666667
+NCN 0.791667
+NGA 1.5
+NGC 0.833334
+NGG 0.833334
+NGT 1.33333
+NGN 1.125
+NTA 0.666667
+NTC 0.833334
+NTG 0.833333
+NTT 0.833334
+NTN 0.791667
+NNA 1.125
+NNC 0.791667
+NNG 1.08333
+NNT 1
+NNN 1
+end consensus
+type 3SS
+center 3
+phase all
+begin consensus
+TAG--- 1.64062
+-AG--- 0.229167
+end consensus
+type 3SS
+center 3
+phase 0
+begin consensus
+TAG--- 0.765625
+-AG--- 0.09375
+end consensus
+type 3SS
+center 3
+phase 1
+begin consensus
+TAG--- 0.515625
+-AG--- 0.0885417
+end consensus
+type 3SS
+center 3
+phase 2
+begin consensus
+-AG--- 0.125
+end consensus
+type 3SS_codon
+phase all
+begin consensus
+AAA 1.802817
+AAC 1.502347
+AAG 0.300469
+AAT 1.802817
+AAN 1.35211
+ACA 0.300469
+ACC 1.802817
+ACG 0.300469
+ACT 0.901408
+ACN 0.826291
+AGA 0.600939
+AGC 0.300469
+AGG 0.600939
+AGT 1.502347
+AGN 0.751173
+ATA 1.502347
+ATC 2.103286
+ATG 1.502347
+ATT 2.103286
+ATN 1.80282
+ANA 1.05164
+ANC 1.42723
+ANG 0.676056
+ANT 1.57746
+ANN 1.1831
+CAA 2.103286
+CAC 0.300469
+CAG 0.300469
+CAT 1.201878
+CAN 0.976526
+CCA 0.600939
+CCC 0.600939
+CCG 0.901408
+CCT 0.600939
+CCN 0.676056
+CGA 0.300469
+CGC 0.300469
+CGG 0.300469
+CGT 0.901408
+CGN 0.450704
+CTA 0.901408
+CTC 0.600939
+CTG 1.201878
+CTT 1.201878
+CTN 0.976526
+CNA 0.976526
+CNC 0.450704
+CNG 0.676056
+CNT 0.976526
+CNN 0.769953
+GAA 1.802817
+GAC 0.300469
+GAG 1.201878
+GAT 2.403756
+GAN 1.42723
+GCA 0.901408
+GCC 0.300469
+GCG 1.201878
+GCT 1.502347
+GCN 0.976526
+GGA 0.901408
+GGC 0.600939
+GGG 0.600939
+GGT 1.201878
+GGN 0.826291
+GTA 1.201878
+GTC 1.502347
+GTG 0.600939
+GTT 1.502347
+GTN 1.20188
+GNA 1.20188
+GNC 0.676056
+GNG 0.901408
+GNT 1.65258
+GNN 1.10798
+TAA 0.600939
+TAC 0.300469
+TAG 0.300469
+TAT 1.502347
+TAN 0.676056
+TCA 1.201878
+TCC 0.901408
+TCG 0.901408
+TCT 1.201878
+TCN 1.05164
+TGA 0.300469
+TGC 0.300469
+TGG 0.901408
+TGT 1.502347
+TGN 0.751173
+TTA 0.600939
+TTC 0.600939
+TTG 1.201878
+TTT 2.704225
+TTN 1.277
+TNA 0.676056
+TNC 0.525821
+TNG 0.826291
+TNT 1.7277
+TNN 0.938967
+NAA 1.57746
+NAC 0.600939
+NAG 0.525821
+NAT 1.7277
+NAN 1.10798
+NCA 0.751173
+NCC 0.901408
+NCG 0.826291
+NCT 1.05164
+NCN 0.882629
+NGA 0.525821
+NGC 0.375587
+NGG 0.600939
+NGT 1.277
+NGN 0.694835
+NTA 1.05164
+NTC 1.20188
+NTG 1.12676
+NTT 1.87793
+NTN 1.31455
+NNA 0.976526
+NNC 0.769953
+NNG 0.769953
+NNT 1.48357
+NNN 1
+end consensus
+type 3SS_codon
+phase 0
+begin consensus
+AAA 1.465649
+AAC 1.465649
+AAG 0.488550
+AAT 1.954198
+AAN 1.34351
+ACA 0.488550
+ACC 1.954198
+ACG 0.488550
+ACT 0.977099
+ACN 0.977099
+AGA 0.488550
+AGC 0.488550
+AGG 0.488550
+AGT 1.954198
+AGN 0.854962
+ATA 1.465649
+ATC 0.488550
+ATG 0.977099
+ATT 1.465649
+ATN 1.09924
+ANA 0.9771
+ANC 1.09924
+ANG 0.610687
+ANT 1.58779
+ANN 1.0687
+CAA 2.931298
+CAC 0.488550
+CAG 0.488550
+CAT 0.977099
+CAN 1.22137
+CCA 0.977099
+CCC 0.488550
+CCG 0.488550
+CCT 0.977099
+CCN 0.732824
+CGA 0.488550
+CGC 0.488550
+CGG 0.488550
+CGT 0.488550
+CGN 0.48855
+CTA 1.465649
+CTC 0.977099
+CTG 0.488550
+CTT 0.977099
+CTN 0.977099
+CNA 1.46565
+CNC 0.610687
+CNG 0.48855
+CNT 0.854962
+CNN 0.854962
+GAA 1.954198
+GAC 0.488550
+GAG 0.977099
+GAT 2.931298
+GAN 1.58779
+GCA 0.977099
+GCC 0.488550
+GCG 0.977099
+GCT 0.488550
+GCN 0.732824
+GGA 0.488550
+GGC 0.977099
+GGG 0.977099
+GGT 1.465649
+GGN 0.977099
+GTA 1.465649
+GTC 0.977099
+GTG 0.488550
+GTT 1.465649
+GTN 1.09924
+GNA 1.22137
+GNC 0.732824
+GNG 0.854962
+GNT 1.58779
+GNN 1.09924
+TAA 0.488550
+TAC 0.488550
+TAG 0.488550
+TAT 0.977099
+TAN 0.610687
+TCA 1.465649
+TCC 1.465649
+TCG 0.977099
+TCT 1.954198
+TCN 1.46565
+TGA 0.488550
+TGC 0.488550
+TGG 0.977099
+TGT 0.488550
+TGN 0.610687
+TTA 0.977099
+TTC 0.488550
+TTG 0.488550
+TTT 2.931298
+TTN 1.22137
+TNA 0.854962
+TNC 0.732825
+TNG 0.732824
+TNT 1.58779
+TNN 0.977099
+NAA 1.70992
+NAC 0.732825
+NAG 0.610687
+NAT 1.70992
+NAN 1.19084
+NCA 0.977099
+NCC 1.09924
+NCG 0.732824
+NCT 1.09924
+NCN 0.977099
+NGA 0.48855
+NGC 0.610687
+NGG 0.732824
+NGT 1.09924
+NGN 0.732825
+NTA 1.34351
+NTC 0.732824
+NTG 0.610687
+NTT 1.70992
+NTN 1.09924
+NNA 1.12977
+NNC 0.793893
+NNG 0.671756
+NNT 1.40458
+NNN 1
+end consensus
+type 3SS_codon
+phase 1
+begin consensus
+AAA 1.684211
+AAC 1.122807
+AAG 0.561404
+AAT 1.684211
+AAN 1.26316
+ACA 0.561404
+ACC 1.684211
+ACG 0.561404
+ACT 0.561404
+ACN 0.842106
+AGA 1.122807
+AGC 0.561404
+AGG 1.122807
+AGT 0.561404
+AGN 0.842106
+ATA 1.122807
+ATC 2.245614
+ATG 2.245614
+ATT 1.684211
+ATN 1.82456
+ANA 1.12281
+ANC 1.40351
+ANG 1.12281
+ANT 1.12281
+ANN 1.19298
+CAA 0.561404
+CAC 0.561404
+CAG 0.561404
+CAT 1.122807
+CAN 0.701755
+CCA 0.561404
+CCC 0.561404
+CCG 1.122807
+CCT 0.561404
+CCN 0.701755
+CGA 0.561404
+CGC 0.561404
+CGG 0.561404
+CGT 1.684211
+CGN 0.842106
+CTA 0.561404
+CTC 0.561404
+CTG 2.245614
+CTT 1.684211
+CTN 1.26316
+CNA 0.561404
+CNC 0.561404
+CNG 1.12281
+CNT 1.26316
+CNN 0.877193
+GAA 1.684211
+GAC 0.561404
+GAG 1.684211
+GAT 1.122807
+GAN 1.26316
+GCA 1.122807
+GCC 0.561404
+GCG 0.561404
+GCT 1.122807
+GCN 0.842105
+GGA 1.122807
+GGC 0.561404
+GGG 0.561404
+GGT 1.122807
+GGN 0.842105
+GTA 1.122807
+GTC 1.684211
+GTG 1.122807
+GTT 1.122807
+GTN 1.26316
+GNA 1.26316
+GNC 0.842106
+GNG 0.982457
+GNT 1.12281
+GNN 1.05263
+TAA 0.561404
+TAC 0.561404
+TAG 0.561404
+TAT 0.561404
+TAN 0.561404
+TCA 0.561404
+TCC 0.561404
+TCG 0.561404
+TCT 0.561404
+TCN 0.561404
+TGA 0.561404
+TGC 0.561404
+TGG 1.122807
+TGT 1.122807
+TGN 0.842105
+TTA 0.561404
+TTC 1.122807
+TTG 2.245614
+TTT 2.245614
+TTN 1.54386
+TNA 0.561404
+TNC 0.701755
+TNG 1.12281
+TNT 1.12281
+TNN 0.877193
+NAA 1.12281
+NAC 0.701755
+NAG 0.842106
+NAT 1.12281
+NAN 0.947369
+NCA 0.701755
+NCC 0.842106
+NCG 0.701755
+NCT 0.701755
+NCN 0.736842
+NGA 0.842106
+NGC 0.561404
+NGG 0.842105
+NGT 1.12281
+NGN 0.842106
+NTA 0.842106
+NTC 1.40351
+NTG 1.96491
+NTT 1.68421
+NTN 1.47368
+NNA 0.877193
+NNC 0.877193
+NNG 1.08772
+NNT 1.15789
+NNN 1
+end consensus
+type 3SS_codon
+phase 2
+begin consensus
+AAA 1.333333
+AAC 1.333333
+AAG 0.666667
+AAT 0.666667
+AAN 1
+ACA 0.666667
+ACC 0.666667
+ACG 0.666667
+ACT 1.333333
+ACN 0.833334
+AGA 0.666667
+AGC 0.666667
+AGG 0.666667
+AGT 1.333333
+AGN 0.833334
+ATA 1.333333
+ATC 2.666667
+ATG 0.666667
+ATT 2.000000
+ATN 1.66667
+ANA 1
+ANC 1.33333
+ANG 0.666667
+ANT 1.33333
+ANN 1.08333
+CAA 1.333333
+CAC 0.666667
+CAG 0.666667
+CAT 1.333333
+CAN 1
+CCA 0.666667
+CCC 1.333333
+CCG 1.333333
+CCT 0.666667
+CCN 1
+CGA 0.666667
+CGC 0.666667
+CGG 0.666667
+CGT 0.666667
+CGN 0.666667
+CTA 0.666667
+CTC 0.666667
+CTG 0.666667
+CTT 0.666667
+CTN 0.666667
+CNA 0.833333
+CNC 0.833333
+CNG 0.833333
+CNT 0.833333
+CNN 0.833334
+GAA 0.666667
+GAC 0.666667
+GAG 0.666667
+GAT 1.333333
+GAN 0.833334
+GCA 0.666667
+GCC 0.666667
+GCG 2.000000
+GCT 2.666667
+GCN 1.5
+GGA 1.333333
+GGC 0.666667
+GGG 0.666667
+GGT 0.666667
+GGN 0.833333
+GTA 0.666667
+GTC 1.333333
+GTG 0.666667
+GTT 1.333333
+GTN 1
+GNA 0.833334
+GNC 0.833334
+GNG 1
+GNT 1.5
+GNN 1.04167
+TAA 1.333333
+TAC 0.666667
+TAG 0.666667
+TAT 2.666667
+TAN 1.33333
+TCA 1.333333
+TCC 0.666667
+TCG 1.333333
+TCT 0.666667
+TCN 1
+TGA 0.666667
+TGC 0.666667
+TGG 0.666667
+TGT 2.666667
+TGN 1.16667
+TTA 0.666667
+TTC 0.666667
+TTG 0.666667
+TTT 0.666667
+TTN 0.666667
+TNA 1
+TNC 0.666667
+TNG 0.833333
+TNT 1.66667
+TNN 1.04167
+NAA 1.16667
+NAC 0.833333
+NAG 0.666667
+NAT 1.5
+NAN 1.04167
+NCA 0.833334
+NCC 0.833333
+NCG 1.33333
+NCT 1.33333
+NCN 1.08333
+NGA 0.833334
+NGC 0.666667
+NGG 0.666667
+NGT 1.33333
+NGN 0.875
+NTA 0.833333
+NTC 1.33333
+NTG 0.666667
+NTT 1.16667
+NTN 1
+NNA 0.916667
+NNC 0.916667
+NNG 0.833334
+NNT 1.33333
+NNN 1
+end consensus
+type CDS
+phase all
+begin consensus
+AAA 2.386335
+AAC 1.053160
+AAG 1.564912
+AAT 1.686987
+AAN 1.67285
+ACA 0.987639
+ACC 0.645552
+ACG 0.588997
+ACT 1.051091
+ACN 0.81832
+AGA 1.264206
+AGC 0.831769
+AGG 0.727625
+AGT 0.865564
+AGN 0.922291
+ATA 0.993847
+ATC 1.040746
+ATG 1.394558
+ATT 1.851134
+ATN 1.32007
+ANA 1.40801
+ANC 0.892807
+ANG 1.06902
+ANT 1.36369
+ANN 1.18338
+CAA 1.498701
+CAC 0.575203
+CAG 0.708314
+CAT 0.951086
+CAN 0.933326
+CCA 0.795215
+CCC 0.491751
+CCG 0.455887
+CCT 0.832459
+CCN 0.643828
+CGA 0.706935
+CGC 0.368985
+CGG 0.354502
+CGT 0.741419
+CGN 0.54296
+CTA 0.836597
+CTC 0.861426
+CTG 0.917980
+CTT 1.436629
+CTN 1.01316
+CNA 0.959362
+CNC 0.574341
+CNG 0.609171
+CNT 0.990398
+CNN 0.783318
+GAA 1.682160
+GAC 0.641414
+GAG 0.823493
+GAT 1.255930
+GAN 1.10075
+GCA 0.793146
+GCC 0.515890
+GCG 0.364847
+GCT 0.964880
+GCN 0.659691
+GGA 0.946258
+GGC 0.470370
+GGG 0.352433
+GGT 0.846942
+GGN 0.654001
+GTA 0.737281
+GTC 0.688313
+GTG 0.724867
+GTT 1.275931
+GTN 0.856598
+GNA 1.03971
+GNC 0.578997
+GNG 0.56641
+GNT 1.08592
+GNN 0.81776
+TAA 1.130406
+TAC 0.999364
+TAG 0.591066
+TAT 1.385592
+TAN 1.02661
+TCA 1.159373
+TCC 0.921429
+TCG 0.764179
+TCT 1.205582
+TCN 1.01264
+TGA 1.487666
+TGC 0.967638
+TGG 1.180064
+TGT 0.966949
+TGN 1.15058
+TTA 1.538704
+TTC 1.455251
+TTG 1.566981
+TTT 2.128391
+TTN 1.67233
+TNA 1.32904
+TNC 1.08592
+TNG 1.02557
+TNT 1.42163
+TNN 1.21554
+NAA 1.6744
+NAC 0.817285
+NAG 0.921946
+NAT 1.3199
+NAN 1.18338
+NCA 0.933843
+NCC 0.643655
+NCG 0.543477
+NCT 1.0135
+NCN 0.78362
+NGA 1.10127
+NGC 0.65969
+NGG 0.653656
+NGT 0.855218
+NGN 0.817458
+NTA 1.02661
+NTC 1.01143
+NTG 1.1511
+NTT 1.67302
+NTN 1.21554
+NNA 1.18403
+NNC 0.783016
+NNG 0.817544
+NNT 1.21541
+NNN 1
+end consensus
+type CDS
+phase 0
+begin consensus
+AAA 2.488005
+AAC 1.039424
+AAG 1.727552
+AAT 2.175971
+AAN 1.85774
+ACA 0.874108
+ACC 0.690194
+ACG 0.386426
+ACT 1.630428
+ACN 0.895289
+AGA 0.702593
+AGC 0.514546
+AGG 0.276904
+AGT 0.880307
+AGN 0.593587
+ATA 0.741855
+ATC 0.721191
+ATG 1.264667
+ATT 2.516935
+ATN 1.31116
+ANA 1.20164
+ANC 0.741339
+ANG 0.913887
+ANT 1.80091
+ANN 1.16444
+CAA 1.702754
+CAC 0.394692
+CAG 0.702593
+CAT 1.045623
+CAN 0.961415
+CCA 0.774918
+CCC 0.566207
+CCG 0.258306
+CCT 1.444448
+CCN 0.76097
+CGA 0.481483
+CGC 0.421556
+CGG 0.171515
+CGT 1.318395
+CGN 0.598237
+CTA 0.506280
+CTC 0.477350
+CTG 0.343031
+CTT 1.657292
+CTN 0.745988
+CNA 0.866359
+CNC 0.464951
+CNG 0.368861
+CNT 1.36644
+CNN 0.766653
+GAA 2.884763
+GAC 1.039424
+GAG 1.504375
+GAT 2.576862
+GAN 2.00136
+GCA 1.004294
+GCC 0.745988
+GCG 0.291369
+GCT 1.905266
+GCN 0.986729
+GGA 1.049756
+GGC 0.599270
+GGG 0.264506
+GGT 1.582900
+GGN 0.874108
+GTA 0.762520
+GTC 0.750121
+GTG 0.495948
+GTT 2.006522
+GTN 1.00378
+GNA 1.42533
+GNC 0.783701
+GNG 0.639049
+GNT 2.01789
+GNN 1.21649
+TAA 0.000000
+TAC 0.770786
+TAG 0.000000
+TAT 1.477511
+TAN 0.562074
+TCA 1.024959
+TCC 0.772852
+TCG 0.415356
+TCT 1.826741
+TCN 1.00998
+TGA 0.000000
+TGC 0.322366
+TGG 0.588938
+TGT 0.485616
+TGN 0.34923
+TTA 1.630428
+TTC 0.907171
+TTG 1.450647
+TTT 1.965193
+TTN 1.48836
+TNA 0.663847
+TNC 0.693294
+TNG 0.613735
+TNT 1.43877
+TNN 0.85241
+NAA 1.76888
+NAC 0.811082
+NAG 0.98363
+NAT 1.81899
+NAN 1.34565
+NCA 0.91957
+NCC 0.69381
+NCG 0.337864
+NCT 1.70172
+NCN 0.913241
+NGA 0.558458
+NGC 0.464434
+NGG 0.325466
+NGT 1.0668
+NGN 0.603791
+NTA 0.910271
+NTC 0.713958
+NTG 0.888573
+NTT 2.03649
+NTN 1.13732
+NNA 1.03929
+NNC 0.670821
+NNG 0.633883
+NNT 1.656
+NNN 1
+end consensus
+type CDS
+phase 1
+begin consensus
+AAA 2.349249
+AAC 1.177724
+AAG 2.219080
+AAT 1.330621
+AAN 1.76917
+ACA 1.167393
+ACC 0.504148
+ACG 0.816142
+ACT 0.756223
+ACN 0.810976
+AGA 1.086812
+AGC 0.979370
+AGG 1.134334
+AGT 0.735561
+AGN 0.984019
+ATA 1.694270
+ATC 1.365747
+ATG 2.539338
+ATT 1.675674
+ATN 1.81876
+ANA 1.57443
+ANC 1.00675
+ANG 1.67722
+ANT 1.12452
+ANN 1.34573
+CAA 1.200452
+CAC 0.667377
+CAG 1.028959
+CAT 0.781017
+CAN 0.919451
+CCA 0.997966
+CCC 0.456626
+CCG 0.727296
+CCT 0.595061
+CCN 0.694237
+CGA 0.435964
+CGC 0.227280
+CGG 0.378111
+CGT 0.309927
+CGN 0.337821
+CTA 1.661211
+CTC 1.413269
+CTG 2.157094
+CTT 1.576497
+CTN 1.70202
+CNA 1.0739
+CNC 0.691138
+CNG 1.07286
+CNT 0.815626
+CNN 0.913382
+GAA 0.865730
+GAC 0.384310
+GAG 0.545472
+GAT 0.440097
+GAN 0.558902
+GCA 0.615722
+GCC 0.355383
+GCG 0.475222
+GCT 0.411170
+GCN 0.464374
+GGA 0.407038
+GGC 0.245876
+GGG 0.334722
+GGT 0.314060
+GGN 0.325424
+GTA 1.076481
+GTC 0.791348
+GTG 1.504181
+GTT 0.894657
+GTN 1.06667
+GNA 0.741243
+GNC 0.444229
+GNG 0.714899
+GNT 0.514996
+GNN 0.603842
+TAA 1.140533
+TAC 0.768620
+TAG 0.964907
+TAT 0.766554
+TAN 0.910154
+TCA 0.896723
+TCC 0.595061
+TCG 0.760355
+TCT 0.603325
+TCN 0.713866
+TGA 1.037224
+TGC 0.665311
+TGG 1.208717
+TGT 0.640517
+TGN 0.887942
+TTA 1.993866
+TTC 1.686005
+TTG 2.652978
+TTT 1.812042
+TTN 2.03622
+TNA 1.26709
+TNC 0.928749
+TNG 1.39674
+TNT 0.95561
+TNN 1.13705
+NAA 1.38899
+NAC 0.749508
+NAG 1.1896
+NAT 0.829572
+NAN 1.03942
+NCA 0.919451
+NCC 0.477804
+NCG 0.694754
+NCT 0.591445
+NCN 0.670863
+NGA 0.741759
+NGC 0.529459
+NGG 0.763971
+NGT 0.500016
+NGN 0.633801
+NTA 1.60646
+NTC 1.31409
+NTG 2.2134
+NTT 1.48972
+NTN 1.65592
+NNA 1.16416
+NNC 0.767716
+NNG 1.21543
+NNT 0.852688
+NNN 1
+end consensus
+type CDS
+phase 2
+begin consensus
+AAA 2.316265
+AAC 0.942210
+AAG 0.745916
+AAT 1.551753
+AAN 1.38904
+ACA 0.921547
+ACC 0.743850
+ACG 0.566152
+ACT 0.766578
+ACN 0.749532
+AGA 2.002195
+AGC 1.002131
+AGG 0.772777
+AGT 0.981468
+AGN 1.18964
+ATA 0.545490
+ATC 1.035191
+ATG 0.378124
+ATT 1.357526
+ATN 0.829083
+ANA 1.44637
+ANC 0.930845
+ANG 0.615742
+ANT 1.16433
+ANN 1.03932
+CAA 1.591012
+CAC 0.665332
+CAG 0.394654
+CAT 1.026926
+CAN 0.919481
+CCA 0.613676
+CCC 0.454575
+CCG 0.384322
+CCT 0.458707
+CCN 0.47782
+CGA 1.204623
+CGC 0.460774
+CGG 0.516562
+CGT 0.597146
+CGN 0.694776
+CTA 0.342997
+CTC 0.694260
+CTG 0.254149
+CTT 1.074450
+CTN 0.591464
+CNA 0.938077
+CNC 0.568735
+CNG 0.387422
+CNT 0.789307
+CNN 0.670885
+GAA 1.293472
+GAC 0.502099
+GAG 0.421515
+GAT 0.750048
+GAN 0.741783
+GCA 0.760380
+GCC 0.448376
+GCG 0.330600
+GCT 0.578550
+GCN 0.529477
+GGA 1.382321
+GGC 0.568219
+GGG 0.460774
+GGT 0.644670
+GGN 0.763996
+GTA 0.373991
+GTC 0.524827
+GTG 0.175631
+GTT 0.925680
+GTN 0.500032
+GNA 0.952541
+GNC 0.51088
+GNG 0.34713
+GNT 0.724737
+GNN 0.633822
+TAA 2.248079
+TAC 1.458772
+TAG 0.807903
+TAT 1.911280
+TAN 1.60651
+TCA 1.555886
+TCC 1.396784
+TCG 1.117841
+TCT 1.186027
+TCN 1.31413
+TGA 3.421709
+TGC 1.915413
+TGG 1.741848
+TGT 1.774908
+TGN 2.21347
+TTA 0.989733
+TTC 1.770775
+TTG 0.595080
+TTT 2.603474
+TTN 1.48977
+TNA 2.05385
+TNC 1.63544
+TNG 1.06567
+TNT 1.86892
+TNN 1.65597
+NAA 1.86221
+NAC 0.892103
+NAG 0.592497
+NAT 1.31
+NAN 1.1642
+NCA 0.962872
+NCC 0.760896
+NCG 0.599729
+NCT 0.747465
+NCN 0.767741
+NGA 2.00271
+NGC 0.986634
+NGG 0.87299
+NGT 0.999548
+NGN 1.21547
+NTA 0.563053
+NTC 1.00626
+NTG 0.350746
+NTT 1.49028
+NTN 0.852586
+NNA 1.34771
+NNC 0.911474
+NNG 0.603991
+NNT 1.13682
+NNN 1
+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 1.233115
+C 0.595593
+G 0.670399
+T 1.500893
+end consensus
+type Pyrimidine_emission
+begin consensus
+A 0.261549
+C 0.869936
+G 0.127932
+T 2.740583
+end consensus
+type Spacer_emission
+begin consensus
+A 1.495231
+C 0.607484
+G 0.513573
+T 1.383712
+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