Origin IGS: taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatccttttaatttttgcttaattttttaaacaaactacacaattttttatacaatatttagctatagattatattattttaatacaatacatattattgacatacttaatttatagatatataataaaaatacaggattaaaccattttatttaaattttaaggaggctat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atagcctccttaaaatttaaataaaatggtttaatcctgtatttttattatatatctataaattaagtatgtcaataatatgtattgtattaaaataatataatctatagctaaatattgtataaaaaattgtgtagtttgtttaaaaaattaagcaaaaattaaaaggattaacttttgcttcttacaaaagtcaatccttattagtaagttaaattatccaactttttagagtcagtacatattcataaaaaatttcagatattatatttgtaatagcaatcatttttaatggtattagtta Mask Tandem Repeat Region ================================================ taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatccttttaatttttgcttaattttttaaacaaactacacaattttttatacaatatttagctatagattatattattttaatacaatacatattattgacatacttaatttatagatatataataaaaatacaggattaaaccattttatttaaattttaaggaggctat Find is-nt database================================================ Query_seq: FN1410:FN1411|FN1410:FN1411:Transporter:Threonine dehydratase:->->:2070566..2070869 304 taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatccttttaatttttgcttaattttttaaacaaactacacaattttttatacaatatttagctatagattatattattttaatacaatacatattattgacatacttaatttatagatatataataaaaatacaggattaaaccattttatttaaattttaaggaggctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1410:FN1411|FN1410:FN1411:Transporter:Threonine dehydratase:->->:2070566..2070869 304 taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatccttttaatttttgcttaattttttaaacaaactacacaattttttatacaatatttagctatagattatattattttaatacaatacatattattgacatacttaatttatagatatataataaaaatacaggattaaaccattttatttaaattttaaggaggctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1410:FN1411|FN1410:FN1411:Transporter:Threonine dehydratase:->->:2070566..2070869 304 taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatccttttaatttttgcttaattttttaaacaaactacacaattttttatacaatatttagctatagattatattattttaatacaatacatattattgacatacttaatttatagatatataataaaaatacaggattaaaccattttatttaaattttaaggaggctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatccttttaatttttgcttaattttttaaacaaactacacaattttttatacaatatttagctatagattatattattttaatacaatacatattattgacatacttaatttatagatatataataaaaatacaggattaaaccattttatttaaattttaaggaggctat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 182 End: 271 ..................................................................................................................................................................................... M Q Y L A I D Y I I L I Q Y I L L T Y L I Y R Y I I K I Q D ................................. taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatccttttaatttttgcttaattttttaaacaaactacacaattttttatacaatatttagctatagattatattattttaatacaatacatattattgacatacttaatttatagatatataataaaaatacaggattaaaccattttatttaaattttaaggaggctat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 89 Start: 229 End: 258 ....................................................................................................................................................................................................................................ATTGACATACTTAATTTATAGATATATAAT.............................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 12 End: 41 ...........ATTAAAAATGATTGCTATTACAAATATAAT....................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatccttttaatttttgcttaattttttaaacaaactacacaattttttatacaatatttagctatagattatattattttaatacaatacatattattgacatacttaatttatagatatataataaaaatacaggattaaaccattttatttaaattttaaggaggctat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -7.4 Tail_Score: -4.97312 Start: 99 End: 143 Full_Region: GATAATTTAACTTAC TAATAAGGATTGACTTTTGT AAGAA GCAAAAGTTAATCCTTTTAA TTTTTGCTTAATTTT ..................................................................................................TAATAAGGATTGACTTTTGTAAGAAGCAAAAGTTAATCCTTTTAA................................................................................................................................................................. TransTerm Strand: + Conf: 95 HP_score: -10.8 Tail_Score: -4.81523 Start: 105 End: 137 Full_Region: TTAACTTACTAATAA GGATTGACTTTTGT AAGAA GCAAAAGTTAATCC TTTTAATTTTTGCTT ........................................................................................................GGATTGACTTTTGTAAGAAGCAAAAGTTAATCC....................................................................................................................................................................... TransTerm Strand: - Conf: 74 HP_score: -7.9 Tail_Score: -3.75105 Start: 105 End: 137 Full_Region: aagcaaaaattaaaa ggattaacttttg cttctta caaaagtcaatcc ttattagtaagttaa ........................................................................................................ggattaacttttgcttcttacaaaagtcaatcc....................................................................................................................................................................... TransTerm Strand: + Conf: 57 HP_score: -2.3 Tail_Score: -5.00884 Start: 120 End: 154 Full_Region: GGATTGACTTTTGTA AGAAGCAAAAGTTAA TCCTT TTAATTTTTGCTTAA TTTTTTAAACAAACT .......................................................................................................................AGAAGCAAAAGTTAATCCTTTTAATTTTTGCTTAA...................................................................................................................................................... TransTerm Strand: + Conf: 71 HP_score: -7.5 Tail_Score: -3.93166 Start: 124 End: 150 Full_Region: TGACTTTTGTAAGAA GCAAAAGTTAA TCCTT TTAATTTTTGC TTAATTTTTTAAACA ...........................................................................................................................GCAAAAGTTAATCCTTTTAATTTTTGC.......................................................................................................................................................... TransTerm Strand: - Conf: 59 HP_score: -5.3 Tail_Score: -3.62046 Start: 124 End: 150 Full_Region: tgtttaaaaaattaa gcaaaaattaa aagga ttaacttttgc ttcttacaaaagtca ...........................................................................................................................gcaaaaattaaaaggattaacttttgc.......................................................................................................................................................... Find igs database================================================ Query_seq: FN1410:FN1411|FN1410:FN1411:Transporter:Threonine dehydratase:->->:2070566..2070869 304 taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatccttttaatttttgcttaattttttaaacaaactacacaattttttatacaatatttagctatagattatattattttaatacaatacatattattgacatacttaatttatagatatataataaaaatacaggattaaaccattttatttaaattttaaggaggctat Intra-Species Hit: Count: 1 Min: 1 Max: 304 Len: 304 Subject: NC_003454_FN1410_FN1411|Transporter:Threonine dehydratase|POSITIVE:POSITIVE|[2070566,2070869]|304 HSP 1 e-value: 7.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatcc....................................................................................................................................................................... taactaataccattaaaaatgattgctattacaaatataatatctgaaattttttatgaatatgtactgactctaaaaagttggataatttaacttactaataaggattgacttttgtaagaagcaaaagttaatcc....................................................................................................................................................................... HSP 2 e-value: 3.0E-12 bit: 73.8 Len: 37 Query Start:268 Query End:304 Subject Strand: POSITIVE Subject Start: 268 Subject End: 304 ...........................................................................................................................................................................................................................................................................ggattaaaccattttatttaaattttaaggaggctat ...........................................................................................................................................................................................................................................................................ggattaaaccattttatttaaattttaaggaggctat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUAAUACCAUUAAAAAUGAUUGCUAUUACAAAUAUAAUAUCUGAAAUUUUUUAUGAAUAUGUACUGACUCUAAAAAGUUGGAUAAUUUAACUUACUAAUAAGGAUUGACUUUUGUAAGAAGCAAAAGUUAAUCCUUUUAAUUUUUGCUUAAUUUUUUAAACAAACUACACAAUUUUUUAUACAAUAUUUAGCUAUAGAUUAUAUUAUUUUAAUACAAUACAUAUUAUUGACAUACUUAAUUUAUAGAUAUAUAAUAAAAAUACAGGAUUAAACCAUUUUAUUUAAAUUUUAAGGAGGCUAU .........((.((((((....(((......)))...((((.((((....(((((((..((((((........((((((((((...................((((((((((((((((.....))))))))))))))))......((((.((((....)))).)))).....))))))))))............((((((((((...(((.((((((..........)))))).)))..)))))))))))))))).)))))))..))))))))................))))))))....... (-48.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGCCUCCUUAAAAUUUAAAUAAAAUGGUUUAAUCCUGUAUUUUUAUUAUAUAUCUAUAAAUUAAGUAUGUCAAUAAUAUGUAUUGUAUUAAAAUAAUAUAAUCUAUAGCUAAAUAUUGUAUAAAAAAUUGUGUAGUUUGUUUAAAAAAUUAAGCAAAAAUUAAAAGGAUUAACUUUUGCUUCUUACAAAAGUCAAUCCUUAUUAGUAAGUUAAAUUAUCCAACUUUUUAGAGUCAGUACAUAUUCAUAAAAAAUUUCAGAUAUUAUAUUUGUAAUAGCAAUCAUUUUUAAUGGUAUUAGUUA ...(((...((((((.((((((......))))))...((.(((.(((((((((((((..(((((...((((.....(((((((((((.(((...(((((((.............))))))).((((((.(((..((((((((((((....))))))....((((((((((((.(((((((.......))))))).))))))).))))).....))))))..))).)))))).))))))))))))))))))...))))).)))))).......))))))).))))).)))))).)))........ (-48.93) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 110 63 134 78 NC_003454:FN1530|5end_Transposase_43625..43855_POSITIVE 369 139 103 204 168 NC_003454:FN0864|5end_hypothetical_protein_1522900..1523130_NEGATIVE 251 148 103 209 166 NC_003454:FN0496|5end_hypothetical_protein_1140910..1141140_POSITIVE 230 147 111 225 188 NC_003454:FN0846|5end_hypothetical_protein_1504242..1504472_POSITIVE 224 145 105 166 127 NC_003454:FN1343|5end_seC-independent_protein_TATD_1997232..1997462_NEGATIVE 212 167 126 61 16 NC_003454:FN2071|5end_hypothetical_protein_582375..582605_NEGATIVE 206 149 103 214 170 NC_003454:FN0733|5end_peptidase_T_1389564..1389794_POSITIVE 206 141 103 159 121 NC_003454:FN1997|5end_Transcriptional_regulator_499758..499988_POSITIVE 201 158 116 166 124 NC_003454:FN1753|5end_thiamine_biosynthesis_protein_ThiH_250344..250574_NEGATIVE 196 135 103 231 199 NC_003454:FN1844|5end_Ketoacyl_reductase_hetN_333593..333823_POSITIVE 195 152 120 226 195 NC_003454:FN1387|5end_Metal_dependent_hydrolase_2043603..2043833_NEGATIVE 194 44 3 161 113 NC_003454:FN1502|5end_Nickel_transport_system_permease_protein_nikC_7522..7752_NEGATIVE 192 160 111 81 24 NC_003454:FN1748|5end_Pyruvate-flavodoxin_oxidoreductase_247252..247482_POSITIVE 189 88 45 55 4 NC_003454:FN1465|5end_Permease_2147986..2148216_POSITIVE 188 147 104 113 65 NC_003454:FN0436|5end_Urea_carboxylase_1078861..1079091_NEGATIVE 188 135 98 38 3 NC_003454:FN1725|5end_Potassium_uptake_protein_KtrB_224671..224901_NEGATIVE 183 44 2 166 127 NC_003454:FN1349|5end_ABC_transporter_permease_protein_2002355..2002585_NEGATIVE 181 119 72 97 39 NC_003454:FN0900|5end_Metal_dependent_hydrolase_1559180..1559410_POSITIVE 181 258 217 224 189 NC_003454:FN0615|5end_Export_ABC_transporter_1273187..1273417_POSITIVE 179 84 43 116 71 NC_003454:FN2041|5end_Transcription_antitermination_protein_nusG_549659..549889_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 653 140 91 141 92 NC_003454:FN1447|3end_Transposase_2117342..2117492_POSITIVE 653 140 91 141 92 NC_003454:FN0841|3end_Transposase_1502804..1502954_POSITIVE 653 140 91 141 92 NC_003454:FN0486|3end_Transposase_1131710..1131860_POSITIVE 653 140 91 141 92 NC_003454:FN0139|3end_Transposase_771640..771790_POSITIVE 653 140 91 141 92 NC_003454:FN1889|3end_Transposase_373027..373177_POSITIVE 613 110 63 111 58 NC_003454:FN1442|3end_Transposase_2110155..2110305_NEGATIVE 613 110 63 111 58 NC_003454:FN0787|3end_Transposase_1443908..1444058_POSITIVE 549 140 91 141 92 NC_003454:FN1680|3end_Transposase_175971..176121_NEGATIVE 369 139 103 64 28 NC_003454:FN0865|3end_hypothetical_protein_1523040..1523190_NEGATIVE 362 145 112 34 1 NC_003454:FN1800|3end_Peptidyl-prolyl_cis-trans_isomerase_282534..282684_POSITIVE 336 142 103 80 41 NC_003454:FN1235|3end_Ankyrin_repeat_proteins_1892428..1892578_POSITIVE 320 160 119 42 1 NC_003454:FN1530|3end_Transposase_44061..44211_POSITIVE 259 140 103 76 43 NC_003454:FN0723|3end_hypothetical_protein_1383464..1383614_POSITIVE 252 141 103 60 22 NC_003454:FN1801|3end_Sodium/glutamate_symport_carrier_protein_282636..282786_NEGATIVE 251 148 103 74 31 NC_003454:FN0495|3end_Acetyl-CoA_acetyltransferase_1140855..1141005_POSITIVE 235 160 111 140 90 NC_003454:FN0845|3end_hypothetical_protein_1504224..1504374_POSITIVE 209 159 113 47 1 NC_003454:FN1236|3end_Choline_transport_protein_1892512..1892662_NEGATIVE 206 149 103 110 66 NC_003454:FN0732|3end_hypothetical_protein_1389540..1389690_POSITIVE 206 139 105 35 1 NC_003454:FN0209|3end_Hypothetical_cytosolic_protein_836800..836950_POSITIVE 206 141 103 63 25 NC_003454:FN1996|3end_Transporter_499742..499892_POSITIVE