Origin IGS: gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta .........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 taagcaattaaaattaattaattttaagagaatgtatgctggaagatgactttgctaaagaacaaggaaatatgattatgagcattatttttacaacataggaattctagtaattactaggatttttatttttatgatattaataggtatcaatgtataactttatagtttaatttaaaaaaatatgagaccattgcaacttcttttttgcaatagtctcatttattttaattc Mask Tandem Repeat Region ================================================ gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta Find is-nt database================================================ Query_seq: FN0400:FN0401|FN0400:FN0401:Dipeptide transport ATP-binding protein dppF:hypothetical protein:-><-:1039761..1039994 234 gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0400:FN0401|FN0400:FN0401:Dipeptide transport ATP-binding protein dppF:hypothetical protein:-><-:1039761..1039994 234 gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0400:FN0401|FN0400:FN0401:Dipeptide transport ATP-binding protein dppF:hypothetical protein:-><-:1039761..1039994 234 gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta Predict ORF larger than 30AA ================================================ gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 53 HP_score: -5.1 Tail_Score: -3.28108 Start: 17 End: 46 Full_Region: tttaaaaaaatatga gaccattgcaa cttctttt ttgcaatagtc tcatttattttaatt ................gaccattgcaacttcttttttgcaatagtc............................................................................................................................................................................................ TransTerm Strand: - Conf: 78 HP_score: -5.9 Tail_Score: -4.98436 Start: 107 End: 136 Full_Region: attatttttacaaca taggaattctagt aatt actaggattttta tttttatgatattaa ..........................................................................................................taggaattctagtaattactaggattttta.................................................................................................. TransTerm Strand: - Conf: 84 HP_score: -4.9 Tail_Score: -5.69262 Start: 113 End: 130 Full_Region: tttacaacataggaa ttctagt aatt actagga tttttatttttatga ................................................................................................................ttctagtaattactagga........................................................................................................ Find igs database================================================ Query_seq: FN0400:FN0401|FN0400:FN0401:Dipeptide transport ATP-binding protein dppF:hypothetical protein:-><-:1039761..1039994 234 gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: NC_003454_FN0400_FN0401|Dipeptide transport ATP-binding protein dppF:hypothetical protein|POSITIVE:NEGATIVE|[1039761,1039994]|234 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 234 Query Start:1 Query End:234 Subject Strand: POSITIVE Subject Start: 1 Subject End: 234 gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatannnnnnnaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta gaattaaaataaatgagactattgcaaaaaagaagttgcaatggtctcatatttttttaaattaaactataaagttatacattgatacctattaatatcataaaaataaaaatcctagtaattactagaattcctatgttgtaaaaataatgctcataatcatatttccttgttctttagcaaagtcatcttccagcatacattctcttaaaattaattaattttaattgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUUAAAAUAAAUGAGACUAUUGCAAAAAAGAAGUUGCAAUGGUCUCAUAUUUUUUUAAAUUAAACUAUAAAGUUAUACAUUGAUACCUAUUAAUAUCAUAAAAAUAAAAAUCCUAGUAAUUACUAGAAUUCCUAUGUUGUAAAAAUAAUGCUCAUAAUCAUAUUUCCUUGUUCUUUAGCAAAGUCAUCUUCCAGCAUACAUUCUCUUAAAAUUAAUUAAUUUUAAUUGCUUA .(((((((((..(((((((((((((((........))))))))))))))).........((((((((((.....((((....(((((........))))).....))))......))))..(((..(((((...(((((((.........((((......((........))......))))...........))))))).)))))..)))..)))))).)))))))))..... (-39.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAAUUAAAAUUAAUUAAUUUUAAGAGAAUGUAUGCUGGAAGAUGACUUUGCUAAAGAACAAGGAAAUAUGAUUAUGAGCAUUAUUUUUACAACAUAGGAAUUCUAGUAAUUACUAGGAUUUUUAUUUUUAUGAUAUUAAUAGGUAUCAAUGUAUAACUUUAUAGUUUAAUUUAAAAAAAUAUGAGACCAUUGCAACUUCUUUUUUGCAAUAGUCUCAUUUAUUUUAAUUC (((((..((((((((....)))))))).((((((.(((((.(((.((..(((((........)))))..))....)).).)))))))))))((((..((((((((((((((....)))))))))))))).....(((((((....))))))).))))..........)))))..((((((....(((((((.(((((((........))))))).)))))))...))))))... (-48.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 199 154 193 148 NC_003454:FN0266|5end_membrane_protein_related_to_metalloendopeptidase_892320..892550_POSITIVE 257 198 153 93 47 NC_003454:FN1318|5end_RNA_polymerase_sigma_factor_rpoD_1972096..1972326_NEGATIVE 251 48 9 69 20 NC_003454:FN2068|5end_dGTP_triphosphohydrolase_578986..579216_NEGATIVE 246 56 15 218 174 NC_003454:FN1949|5end_Xaa-Pro_dipeptidase_454922..455152_NEGATIVE 242 210 165 203 167 NC_003454:FN0644|5end_UROPORPHYRINOGEN-III_SYNTHASE_1301344..1301574_NEGATIVE 239 179 131 112 67 NC_003454:FN0206|5end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_832758..832988_POSITIVE 237 200 151 76 20 NC_003454:FN0156|5end_Phosphopantetheine_adenylyltransferase_784403..784633_POSITIVE 236 208 164 49 4 NC_003454:FN0329|5end_50S_ribosomal_protein_L13_964133..964363_POSITIVE 235 210 163 218 183 NC_003454:FN0133|5end_hypothetical_protein_769121..769351_POSITIVE 224 195 164 32 3 NC_003454:FN0909|5end_DNA_repair_protein_radC_1567654..1567884_NEGATIVE 223 47 6 64 24 NC_003454:FN1275|5end_Acriflavin_resistance_protein_B_1931725..1931955_POSITIVE 223 210 162 69 25 NC_003454:FN0091|5end_Phosphoserine_phosphatase_726788..727018_POSITIVE 219 197 156 218 183 NC_003454:FN1214|5end_Fe-S_oxidoreductase_1875473..1875703_NEGATIVE 219 217 172 64 10 NC_003454:FN1971|5end_Hemin_receptor_471106..471336_NEGATIVE 216 208 169 176 147 NC_003454:FN1475|5end_N-acetylneuraminate_lyase_2157785..2158015_POSITIVE 213 208 166 101 64 NC_003454:FN0366|5end_Phosphoacetylglucosamine_mutase_996366..996596_NEGATIVE 212 209 169 45 10 NC_003454:FN0080|5end_ethanolamine_ammonia-lyase_small_subunit_719041..719271_POSITIVE 208 210 172 107 64 NC_003454:FN0268|5end_DNA_repair_protein_recN_894330..894560_POSITIVE 207 189 145 220 173 NC_003454:FN0460|5end_delta-aminolevulinic_acid_dehydratase_1105482..1105712_POSITIVE 206 197 156 210 176 NC_003454:FN0089|5end_Ethanolamine_permease_725222..725452_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 50 6 78 36 NC_003454:FN0400|3end_Dipeptide_transport_ATP-binding_protein_dppF_1039700..1039850_POSITIVE 268 46 17 101 75 NC_003454:FN1044|3end_hypothetical_protein_1694453..1694603_NEGATIVE 262 208 163 128 85 NC_003454:FN0502|3end_Phosphoheptose_isomerase_1152063..1152213_NEGATIVE 249 50 5 88 44 NC_003454:FN1132|3end_Nicotinamide-nucleotide_adenylyltransferase_1780254..1780404_POSITIVE 246 56 15 77 33 NC_003454:FN1950|3end_Serine_protease_455063..455213_NEGATIVE 245 59 16 90 48 NC_003454:FN0515|3end_Acriflavin_resistance_protein_D_1163938..1164088_NEGATIVE 242 47 1 78 29 NC_003454:FN0514|3end_hypothetical_protein_1163912..1164062_POSITIVE 239 179 131 82 37 NC_003454:FN0205|3end_Sodium/glutamate_symport_carrier_protein_832808..832958_POSITIVE 223 47 6 64 24 NC_003454:FN1274|3end_Acriflavin_resistance_protein_E_1931805..1931955_POSITIVE 223 210 162 45 1 NC_003454:FN0090|3end_Ethanolamine_utilization_protein_eutQ_726844..726994_POSITIVE 219 199 167 140 106 NC_003454:FN1419|3end_methionine_gamma-lyase_2081832..2081982_POSITIVE 213 208 166 84 47 NC_003454:FN0367|3end_Integral_membrane_protein_996383..996533_NEGATIVE 211 183 152 143 113 NC_003454:FN0212|3end_hypothetical_protein_837583..837733_NEGATIVE 210 210 162 75 12 NC_003454:FN0155|3end_hypothetical_protein_784462..784612_POSITIVE 209 197 164 115 82 NC_003454:FN0011|3end_Transcriptional_regulator_651620..651770_POSITIVE 208 210 172 128 85 NC_003454:FN0267|3end_ATP-NAD_kinase_894431..894581_POSITIVE 206 193 153 47 17 NC_003454:FN1829|3end_hypothetical_protein_317717..317867_NEGATIVE 198 210 162 107 63 NC_003454:FN1349|3end_ABC_transporter_permease_protein_2001150..2001300_NEGATIVE 198 189 158 65 29 NC_003454:FN1990|3end_Tetratricopeptide_repeat_protein_494692..494842_POSITIVE 197 219 171 77 24 NC_003454:FN1622|3end_Uridylate_kinase_130439..130589_POSITIVE