Origin IGS: tttagaacaagataaaaataaaataaatgaaagaaaaatcaaattattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaagattatatttttttataattttcctatttttagtaattattttttac .........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 gtaaaaaataattactaaaaataggaaaattataaaaaaatataatcttcctatttttttatttctcattatgtattataatataagagtaaaatgaatgaccacttggtcaatatttttggaggaataaaatgaaactacagaataatttgatttttctttcatttattttatttttatcttgttctaaa Mask Tandem Repeat Region ================================================ tttagaacaagataaaaataaaataaatgaaagaaaaatcaaattattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaagattatatttttttataattttcctatttttagtaattattttttac Find is-nt database================================================ Query_seq: FN0517:FN0518|FN0517:FN0518:Outer membrane protein tolC:Hypothetical exported 24-amino acid repeat protein:<-<-:1169526..1169716 191 tttagaacaagataaaaataaaataaatgaaagaaaaatcaaattattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaagattatatttttttataattttcctatttttagtaattattttttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0517:FN0518|FN0517:FN0518:Outer membrane protein tolC:Hypothetical exported 24-amino acid repeat protein:<-<-:1169526..1169716 191 tttagaacaagataaaaataaaataaatgaaagaaaaatcaaattattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaagattatatttttttataattttcctatttttagtaattattttttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0517:FN0518|FN0517:FN0518:Outer membrane protein tolC:Hypothetical exported 24-amino acid repeat protein:<-<-:1169526..1169716 191 tttagaacaagataaaaataaaataaatgaaagaaaaatcaaattattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaagattatatttttttataattttcctatttttagtaattattttttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttagaacaagataaaaataaaataaatgaaagaaaaatcaaattattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaagattatatttttttataattttcctatttttagtaattattttttac Predict ORF larger than 30AA ================================================ tttagaacaagataaaaataaaataaatgaaagaaaaatcaaattattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaagattatatttttttataattttcctatttttagtaattattttttac 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: 81 Start: 110 End: 139 .............................................................................................................ATTTTTTTATTTCTCATTATGTATTATAAT.................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttagaacaagataaaaataaaataaatgaaagaaaaatcaaattattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaagattatatttttttataattttcctatttttagtaattattttttac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -8.3 Tail_Score: -4.83593 Start: 139 End: 170 Full_Region: TGAGAAATAAAAAAA TAGGAAGATTATA TTTTTT TATAATTTTCCTA TTTTTAGTAATTATT ..........................................................................................................................................TAGGAAGATTATATTTTTTTATAATTTTCCTA..................... Find igs database================================================ Query_seq: FN0517:FN0518|FN0517:FN0518:Outer membrane protein tolC:Hypothetical exported 24-amino acid repeat protein:<-<-:1169526..1169716 191 tttagaacaagataaaaataaaataaatgaaagaaaaatcaaattattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaagattatatttttttataattttcctatttttagtaattattttttac Intra-Species Hit: Count: 1 Min: 45 Max: 145 Len: 101 Subject: NC_003454_FN0517_FN0518|Outer membrane protein tolC:Hypothetical exported 24-amino acid repeat protein|NEGATIVE:NEGATIVE|[1169526,1169716]|191 HSP 1 e-value: 1.0E-50 bit: 200.0 Len: 101 Query Start:45 Query End:145 Subject Strand: POSITIVE Subject Start: 45 Subject End: 145 ............................................tattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaag.............................................. ............................................tattctgtagtttcattttattcctccaaaaatattgaccaagtggtcattcattttactcttatattataatacataatgagaaataaaaaaataggaag.............................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUCUGUAGUUUCAUUUUAUUCCUCCAAAAAUAUUGACCAAGUGGUCAUUCAUUUUACUCUUAUAUUAUAAUACAUAAUGAGAAAUAAAAAAAUAGGAAG ..((((((..(((.(((((.........(((((..(((((....)))))...))))).......((((((.....)))))).))))).)))..)))))).. (-14.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCCUAUUUUUUUAUUUCUCAUUAUGUAUUAUAAUAUAAGAGUAAAAUGAAUGACCACUUGGUCAAUAUUUUUGGAGGAAUAAAAUGAAACUACAGAAUA (((((......((((((((((.((((((......)))))))))..)))))))(((((....)))))........)))))...................... (-18.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 760 50 1 185 136 NC_003454:FN0517|5end_Outer_membrane_protein_tolC_1169435..1169665_NEGATIVE 269 50 11 137 86 NC_003454:FN1116|5end_Peptidase_E_1759521..1759751_POSITIVE 267 59 11 177 125 NC_003454:FN2121|5end_Hypothetical_exported_24-amino_acid_repeat_protein_629728..629958_NEGATIVE 251 57 14 98 53 NC_003454:FN1713|5end_tRNA_(Uracil-5-)_-methyltransferase_207494..207724_POSITIVE 242 58 11 125 71 NC_003454:FN0108|5end_Microcin_C7_self-immunity_protein_mccF_743219..743449_POSITIVE 241 27 2 102 76 NC_003454:FN0739|5end_Formiminotetrahydrofolate_cyclodeaminase_1397655..1397885_NEGATIVE 234 36 1 109 77 NC_003454:FN0008|5end_quinolinate_synthetase_648010..648240_POSITIVE 230 60 11 152 96 NC_003454:FN1196|5end_hypothetical_protein_1857045..1857275_NEGATIVE 227 58 12 115 72 NC_003454:FN0343|5end_hypothetical_protein_976653..976883_NEGATIVE 219 71 31 125 83 NC_003454:FN1702|5end_undecaprenyl_pyrophosphate_phosphatase_197964..198194_NEGATIVE 216 50 3 133 74 NC_003454:FN1979|5end_SSU_ribosomal_protein_S15P_481736..481966_POSITIVE 211 31 1 107 75 NC_003454:FN0515|5end_Acriflavin_resistance_protein_D_1167006..1167236_NEGATIVE 209 68 24 109 52 NC_003454:FN1965|5end_Tetratricopeptide_repeat_family_protein_465097..465327_NEGATIVE 207 54 11 122 86 NC_003454:FN1303|5end_Adenosylcobalamin-dependent_DIOL_dehydratase_gamma_subunit_1960284..1960514_NEGATIVE 207 48 6 124 80 NC_003454:FN1064|5end_hypothetical_protein_1710528..1710758_POSITIVE 207 47 3 124 80 NC_003454:FN1753|5end_thiamine_biosynthesis_protein_ThiH_250344..250574_NEGATIVE 206 28 4 103 81 NC_003454:FN0648|5end_Exoenzyme_regulatory_protein_aepA_precursor_1306061..1306291_NEGATIVE 206 62 24 113 76 NC_003454:FN0130|5end_ABC_transporter_ATP-binding_protein_758586..758816_POSITIVE 204 47 5 96 51 NC_003454:FN1578|5end_hypothetical_protein_88796..89026_NEGATIVE 203 29 1 91 58 NC_003454:FN2126|5end_DNA_gyrase_subunit_B_638225..638455_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 50 11 135 84 NC_003454:FN1115|3end_Hypothetical_membrane-spanning_protein_1759599..1759749_POSITIVE 267 59 11 107 55 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 251 57 14 132 87 NC_003454:FN1712|3end_hypothetical_protein_207608..207758_POSITIVE 242 58 11 66 12 NC_003454:FN0107|3end_Sodium/proline_symporter_743240..743390_POSITIVE 241 27 2 84 58 NC_003454:FN0740|3end_imidazolonepropionase_1397673..1397823_NEGATIVE 227 58 12 146 103 NC_003454:FN0344|3end_Methyltransferase_976622..976772_NEGATIVE 220 51 21 145 114 NC_003454:FN0636|3end_hypothetical_protein_1295609..1295759_POSITIVE 219 71 31 95 53 NC_003454:FN1703|3end_ADP-L-glycero-D-manno-heptose-6-epimerase_197994..198144_NEGATIVE 211 31 1 110 78 NC_003454:FN0516|3end_Acriflavin_resistance_protein_E_1167003..1167153_NEGATIVE 207 54 11 107 71 NC_003454:FN1304|3end_Single-strand_DNA_binding_protein_1960299..1960449_NEGATIVE 207 48 6 105 61 NC_003454:FN1063|3end_N-acyl-L-amino_acid_amidohydrolase_1710589..1710739_POSITIVE 207 59 11 119 76 NC_003454:FN0385|3end_hypothetical_protein_1018920..1019070_POSITIVE 207 47 3 124 80 NC_003454:FN1754|3end_thiazole_synthase_250344..250494_NEGATIVE 206 28 4 75 53 NC_003454:FN0649|3end_Exoenzyme_regulatory_protein_aepA_precursor_1306089..1306239_NEGATIVE 204 47 5 108 63 NC_003454:FN1579|3end_Cysteinyl-tRNA_synthetase_88784..88934_NEGATIVE 203 29 1 90 57 NC_003454:FN2127|3end_hypothetical_protein_638226..638376_NEGATIVE 199 38 14 94 71 NC_003454:FN0537|3end_Hypothetical_membrane-spanning_protein_1191169..1191319_NEGATIVE 192 70 25 111 58 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 191 70 23 99 59 NC_003454:FN1606|3end_3-deoxy-D-manno-octulosonic-acid_transferase_115286..115436_NEGATIVE 190 81 42 134 95 NC_003454:FN0152|3end_Ribonuclease_III_780812..780962_POSITIVE