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