Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff orthologs/ucsb_hamster/lib/wisecfg/pombe.gf @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
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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--- /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