Origin IGS: ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attataactcctttaatattcttttacatatatattatatcataagaattacttttttttaaaataaaaatcccacagaaaattctgtgggaaatattgtatatacttttgtaa Mask Tandem Repeat Region ================================================ ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat Find is-nt database================================================ Query_seq: FN0330:FN0331|FN0330:FN0331:SSU ribosomal protein S9P:hypothetical protein:->->:965125..965238 114 ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0330:FN0331|FN0330:FN0331:SSU ribosomal protein S9P:hypothetical protein:->->:965125..965238 114 ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0330:FN0331|FN0330:FN0331:SSU ribosomal protein S9P:hypothetical protein:->->:965125..965238 114 ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat Predict ORF larger than 30AA ================================================ ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat 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: 84 Start: 52 End: 81 ...................................................TTTAAAAAAAAGTAATTCTTATGATATAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -9.6 Tail_Score: -2.63113 Start: 22 End: 45 Full_Region: ttttttaaaataaaa atcccacaga aaat tctgtgggaa atattgtatatactt .....................atcccacagaaaattctgtgggaa..................................................................... Find igs database================================================ Query_seq: FN0330:FN0331|FN0330:FN0331:SSU ribosomal protein S9P:hypothetical protein:->->:965125..965238 114 ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_003454_FN0330_FN0331|SSU ribosomal protein S9P:hypothetical protein|POSITIVE:POSITIVE|[965125,965238]|114 HSP 1 e-value: 2.0E-44 bit: 178.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttnnnnnnnngtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat ttacaaaagtatatacaatatttcccacagaattttctgtgggatttttattttaaaaaaaagtaattcttatgatataatatatatgtaaaagaatattaaaggagttataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACAAAAGUAUAUACAAUAUUUCCCACAGAAUUUUCUGUGGGAUUUUUAUUUUAAAAAAAAGUAAUUCUUAUGAUAUAAUAUAUAUGUAAAAGAAUAUUAAAGGAGUUAUAAU .............((.((((..(((((((((....)))))))))....)))).)).......(((((((((.((((((.................)))))).)))))))))... (-23.83) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUAACUCCUUUAAUAUUCUUUUACAUAUAUAUUAUAUCAUAAGAAUUACUUUUUUUUAAAAUAAAAAUCCCACAGAAAAUUCUGUGGGAAAUAUUGUAUAUACUUUUGUAA .......................((((((((((((.((((..((((((.......)))))).........(((((((((....))))))))).)))).)))))))....))))) (-21.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 215 50 8 45 9 NC_003454:FN0704|5end_hypothetical_protein_1361855..1362085_NEGATIVE 215 50 8 176 140 NC_003454:FN0703|5end_N-acyl-L-amino_acid_amidohydrolase_1361724..1361954_NEGATIVE 200 107 64 229 179 NC_003454:FN0814|5end_Propionate_CoA-transferase_1472717..1472947_POSITIVE 193 48 23 156 126 NC_003454:FN0523|5end_Exonuclease_SBCD_1176887..1177117_NEGATIVE 188 49 3 85 34 NC_003454:FN1954|5end_Glycerophosphoryl_diester_phosphodiesterase_459992..460222_NEGATIVE 187 77 37 159 118 NC_003454:FN1357|5end_Transposase_2008189..2008419_POSITIVE 187 77 37 159 118 NC_003454:FN0509|5end_Transposase_1160059..1160289_NEGATIVE 187 58 21 81 45 NC_003454:FN1968|5end_Hemin_transport_system_ATP-binding_protein_hmuV_467189..467419_NEGATIVE 187 77 37 159 118 NC_003454:FN1883|5end_Transposase_368863..369093_POSITIVE 187 57 15 49 3 NC_003454:FN1876|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme_365064..365294_NEGATIVE 177 38 6 148 112 NC_003454:FN0447|5end_NIFS_protein_1089343..1089573_POSITIVE 174 48 13 126 93 NC_003454:FN0832|5end_hypothetical_protein_1494305..1494535_POSITIVE 173 55 12 124 73 NC_003454:FN0077|5end_Ethanolamine_two-component_sensor_kinase_714704..714934_POSITIVE 173 54 23 85 51 NC_003454:FN2078|5end_Transcriptional_regulator,_DeoR_family_590266..590496_NEGATIVE 172 66 21 225 174 NC_003454:FN1505|5end_6,7-dimethyl-8-ribityllumazine_synthase_10396..10626_POSITIVE 171 48 5 118 80 NC_003454:FN1586|5end_O-succinylbenzoate-CoA_synthase_98542..98772_NEGATIVE 167 45 1 113 72 NC_003454:FN0195|5end_Dipeptide_transport_ATP-binding_protein_dppD_820558..820788_POSITIVE 164 54 16 87 49 NC_003454:FN0751|5end_L-asparaginase_I_1410731..1410961_NEGATIVE 164 107 62 197 140 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 163 55 11 129 86 NC_003454:FN0189|5end_Two-component_response_regulator_yesN_813203..813433_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 44 23 68 47 NC_003454:FN0330|3end_SSU_ribosomal_protein_S9P_965064..965214_POSITIVE 187 77 37 50 9 NC_003454:FN1356|3end_hypothetical_protein_2008160..2008310_POSITIVE 187 77 37 50 9 NC_003454:FN0510|3end_hypothetical_protein_1160168..1160318_NEGATIVE 187 58 21 84 48 NC_003454:FN1969|3end_Hemin_transport_system_permease_protein_hmuU_467186..467336_NEGATIVE 187 77 37 50 9 NC_003454:FN1882|3end_hypothetical_protein_368834..368984_POSITIVE 177 38 6 129 93 NC_003454:FN0446|3end_hypothetical_protein_1089404..1089554_POSITIVE 177 101 61 61 11 NC_003454:FN1823|3end_Transcriptional_regulator,_TetR_family_312270..312420_POSITIVE 173 55 12 124 73 NC_003454:FN0076|3end_Ethanolamine_two-component_response_regulator_714784..714934_POSITIVE 165 70 25 142 102 NC_003454:FN0575|3end_hypothetical_protein_1225584..1225734_POSITIVE 164 54 16 97 59 NC_003454:FN0752|3end_Proline_iminopeptidase_1410721..1410871_NEGATIVE 163 55 11 98 55 NC_003454:FN0188|3end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_813252..813402_POSITIVE 162 54 20 87 46 NC_003454:FN0899|3end_3-oxoacyl-[acyl-carrier_protein]_reductase_1559253..1559403_POSITIVE 161 40 17 29 3 NC_003454:FN1029|3end_Zinc_protease_1682385..1682535_NEGATIVE 159 55 20 93 52 NC_003454:FN1224|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1882540..1882690_NEGATIVE 159 54 19 149 100 NC_003454:FN0458|3end_hypothetical_protein_1104645..1104795_POSITIVE 158 76 45 52 22 NC_003454:FN0467|3end_murein_hydrolase_exporter_1113300..1113450_POSITIVE 155 49 8 77 32 NC_003454:FN1512|3end_Phophatidylinositol-4-phosphate_5-kinase_17115..17265_POSITIVE 153 52 21 75 42 NC_003454:FN0982|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1634137..1634287_NEGATIVE 153 70 25 77 27 NC_003454:FN0674|3end_Transporter_1330401..1330551_POSITIVE 153 106 66 42 1 NC_003454:FN0518|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1169627..1169777_NEGATIVE