Origin IGS: tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtatttttactctatttctttgtttataacagcttctcttgtttttctatggtattaaataagataatatgctataattaacaagttaaattactaggaaggaaataaaaa Mask Tandem Repeat Region ================================================ tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt Find is-nt database================================================ Query_seq: FN1601:FN1602|FN1601:FN1602:Hypothetical cytosolic protein:Hypothetical cytosolic protein:<-<-:110999..111111 113 tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1601:FN1602|FN1601:FN1602:Hypothetical cytosolic protein:Hypothetical cytosolic protein:<-<-:110999..111111 113 tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1601:FN1602|FN1601:FN1602:Hypothetical cytosolic protein:Hypothetical cytosolic protein:<-<-:110999..111111 113 tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt Predict ORF larger than 30AA ================================================ tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt 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================================================ tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1601:FN1602|FN1601:FN1602:Hypothetical cytosolic protein:Hypothetical cytosolic protein:<-<-:110999..111111 113 tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_003454_FN1601_FN1602|Hypothetical cytosolic protein:Hypothetical cytosolic protein|NEGATIVE:NEGATIVE|[110999,111111]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt tttttatttccttcctagtaatttaacttgttaattatagcatattatcttatttaataccatagaaaaacaagagaagctgttataaacaaagaaatagagtaaaaatactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAUUUCCUUCCUAGUAAUUUAACUUGUUAAUUAUAGCAUAUUAUCUUAUUUAAUACCAUAGAAAAACAAGAGAAGCUGUUAUAAACAAAGAAAUAGAGUAAAAAUACUU .(((((((((......(((......)))......((((((((.....((((.(((............))).)))).....)))))))).....)))))))))........... (-11.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAUUUUUACUCUAUUUCUUUGUUUAUAACAGCUUCUCUUGUUUUUCUAUGGUAUUAAAUAAGAUAAUAUGCUAUAAUUAACAAGUUAAAUUACUAGGAAGGAAAUAAAAA .((((....)))).(((((((((.((..(((........((((((....((((((((.............))))))))...)))))).....)))..)).))))))))).... (-17.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 690 90 41 181 132 NC_003454:FN1601|5end_Hypothetical_cytosolic_protein_110908..111138_NEGATIVE 236 50 12 98 66 NC_003454:FN0087|5end_Ethanolamine_utilization_protein_eutN_724626..724856_POSITIVE 224 41 4 132 94 NC_003454:FN1197|5end_hypothetical_protein_1857676..1857906_NEGATIVE 220 48 1 162 112 NC_003454:FN1200|5end_hypothetical_protein_1861006..1861236_NEGATIVE 215 48 1 132 85 NC_003454:FN0019|5end_Transcription-repair_coupling_factor_656549..656779_POSITIVE 209 50 6 178 133 NC_003454:FN1051|5end_hypothetical_protein_1699781..1700011_POSITIVE 205 43 6 135 95 NC_003454:FN1732|5end_hypothetical_protein_232078..232308_NEGATIVE 201 43 2 170 130 NC_003454:FN0846|5end_hypothetical_protein_1504242..1504472_POSITIVE 200 50 8 51 4 NC_003454:FN1759|5end_Hydroxymethylpyrimidine_kinase_254765..254995_NEGATIVE 199 48 2 137 91 NC_003454:FN1432|5end_Leucine-,_isoleucine-,_valine-,_threonine-,_and_alanine-binding_protein_2101580..2101810_NEGATIVE 199 43 1 144 94 NC_003454:FN1844|5end_Ketoacyl_reductase_hetN_333593..333823_POSITIVE 196 43 4 91 43 NC_003454:FN0492|5end_hypothetical_protein_1137651..1137881_NEGATIVE 195 50 6 197 152 NC_003454:FN1587|5end_Acetyltransferase_98841..99071_POSITIVE 192 50 1 83 42 NC_003454:FN1918|5end_SPO0B-associated_GTP-binding_protein_415026..415256_NEGATIVE 189 90 41 112 64 NC_003454:FN0764|5end_Transporter,_LysE_family_1420327..1420557_POSITIVE 188 44 1 158 109 NC_003454:FN0100|5end_Flavodoxins/hemoproteins_735766..735996_NEGATIVE 188 89 41 143 89 NC_003454:FN1877|5end_Guanine-hypoxanthine_permease_366537..366767_NEGATIVE 187 53 14 135 96 NC_003454:FN2121|5end_Hypothetical_exported_24-amino_acid_repeat_protein_629728..629958_NEGATIVE 186 50 2 137 96 NC_003454:FN0058|5end_Cysteine_desulfhydrase_693907..694137_POSITIVE 186 43 3 136 94 NC_003454:FN1801|5end_Sodium/glutamate_symport_carrier_protein_283877..284107_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 50 1 133 81 NC_003454:FN0224|3end_excinuclease_ABC_subunit_B_851673..851823_POSITIVE 236 50 12 96 64 NC_003454:FN0086|3end_hypothetical_protein_724704..724854_POSITIVE 224 41 4 129 91 NC_003454:FN1198|3end_Transporter_1857679..1857829_NEGATIVE 201 43 2 72 32 NC_003454:FN0845|3end_hypothetical_protein_1504224..1504374_POSITIVE 196 43 4 119 71 NC_003454:FN0493|3end_hypothetical_protein_1137623..1137773_NEGATIVE 189 90 41 145 97 NC_003454:FN0763|3end_Transporter,_LysE_family_1420440..1420590_POSITIVE 189 105 62 78 37 NC_003454:FN0691|3end_hypothetical_protein_1345827..1345977_NEGATIVE 187 53 14 65 26 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 186 50 2 50 9 NC_003454:FN0057|3end_Endonuclease_III_693900..694050_POSITIVE 185 49 1 76 24 NC_003454:FN0709|3end_Virulence_factor_mviN_1368888..1369038_POSITIVE 183 104 72 90 62 NC_003454:FN1806|3end_Integral_membrane_protein_288667..288817_POSITIVE 181 86 48 46 13 NC_003454:FN1125|3end_LemA_protein_1769260..1769410_NEGATIVE 179 45 3 59 13 NC_003454:FN0688|3end_hypothetical_protein_1344609..1344759_POSITIVE 170 35 1 95 63 NC_003454:FN1272|3end_Transcriptional_regulator,_TetR_family_1929353..1929503_POSITIVE 169 89 45 54 22 NC_003454:FN0627|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1286155..1286305_NEGATIVE 168 89 64 34 8 NC_003454:FN1363|3end_Dipeptide_transport_ATP-binding_protein_dppF_2015333..2015483_POSITIVE 165 49 15 92 58 NC_003454:FN1045|3end_hypothetical_protein_1695178..1695328_NEGATIVE 162 50 9 118 85 NC_003454:FN1734|3end_V-type_ATP_synthase_subunit_B_232882..233032_NEGATIVE 161 28 7 119 97 NC_003454:FN0722|3end_WD-repeat_family_protein_1381604..1381754_POSITIVE 161 49 7 123 75 NC_003454:FN0106|3end_hypothetical_protein_741462..741612_POSITIVE