Origin IGS: attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atccttccttttaaatgagattaattttcactttaatattatagcataaaaaaatgaggttatagtgaattaaattacaatataacctcaaatttttaaaat Mask Tandem Repeat Region ================================================ attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat Find is-nt database================================================ Query_seq: FN0821:FN0822|FN0821:FN0822:hypothetical protein:Shikimate kinase:->->:1481866..1481967 102 attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0821:FN0822|FN0821:FN0822:hypothetical protein:Shikimate kinase:->->:1481866..1481967 102 attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0821:FN0822|FN0821:FN0822:hypothetical protein:Shikimate kinase:->->:1481866..1481967 102 attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat Predict ORF larger than 30AA ================================================ attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat 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================================================ attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0821:FN0822|FN0821:FN0822:hypothetical protein:Shikimate kinase:->->:1481866..1481967 102 attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_003454_FN0821_FN0822|hypothetical protein:Shikimate kinase|POSITIVE:POSITIVE|[1481866,1481967]|102 HSP 1 e-value: 5.0E-39 bit: 161.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 attttaaaaatttgaggttatattgtaatttaattcactataacctcannnnnnnatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat attttaaaaatttgaggttatattgtaatttaattcactataacctcatttttttatgctataatattaaagtgaaaattaatctcatttaaaaggaaggat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUAAAAAUUUGAGGUUAUAUUGUAAUUUAAUUCACUAUAACCUCAUUUUUUUAUGCUAUAAUAUUAAAGUGAAAAUUAAUCUCAUUUAAAAGGAAGGAU ....((((((..((((((((((.((..........)).))))))))))..)))))).............((((((.........))))))............ (-18.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCUUCCUUUUAAAUGAGAUUAAUUUUCACUUUAAUAUUAUAGCAUAAAAAAAUGAGGUUAUAGUGAAUUAAAUUACAAUAUAACCUCAAAUUUUUAAAAU ..........((((((((((.....))))).)))))..........((((((..((((((((((((((......))))..))))))))))..)))))).... (-19.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 62 23 126 86 NC_003454:FN0677|5end_hypothetical_protein_1332641..1332871_POSITIVE 194 77 37 50 14 NC_003454:FN0196|5end_Transcriptional_regulator,_FUR_family_822317..822547_POSITIVE 189 74 40 129 95 NC_003454:FN0927|5end_hypothetical_protein_1582352..1582582_NEGATIVE 188 76 52 199 175 NC_003454:FN1785|5end_hypothetical_protein_266685..266915_NEGATIVE 185 54 15 85 47 NC_003454:FN1072|5end_GTP-binding_protein_1719301..1719531_POSITIVE 184 67 32 91 49 NC_003454:FN0138|5end_Transposase_771238..771468_POSITIVE 184 54 12 96 52 NC_003454:FN1592|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_D_103746..103976_NEGATIVE 177 47 11 182 152 NC_003454:FN2038|5end_LSU_ribosomal_protein_L10P_547696..547926_NEGATIVE 176 78 33 137 84 NC_003454:FN0015|5end_hypothetical_protein_653500..653730_NEGATIVE 175 66 22 80 28 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 171 57 14 220 163 NC_003454:FN0534|5end_hypothetical_protein_1188858..1189088_POSITIVE 168 43 15 218 190 NC_003454:FN0029|5end_Flavodoxin_667027..667257_NEGATIVE 166 62 34 155 120 NC_003454:FN0269|5end_Transposase_896041..896271_POSITIVE 165 60 11 206 163 NC_003454:FN2067|5end_Thiol:disulfide_interchange_protein_tlpA_577378..577608_NEGATIVE 165 79 43 126 96 NC_003454:FN1918|5end_SPO0B-associated_GTP-binding_protein_415026..415256_NEGATIVE 164 60 13 229 179 NC_003454:FN1145|5end_Oligoendopeptidase_F_1795931..1796161_NEGATIVE 164 58 36 226 204 NC_003454:FN0203|5end_Glutaconate_CoA-transferase_subunit_B_828748..828978_POSITIVE 163 76 45 57 24 NC_003454:FN1456|5end_UDP-N-acetylmuramate--alanine_ligase_2137922..2138152_NEGATIVE 163 90 43 164 112 NC_003454:FN1791|5end_Mutator_MutT_protein_272041..272271_POSITIVE 162 70 21 124 83 NC_003454:FN1741|5end_ATP_synthase_subunit_I_240477..240707_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 57 12 94 44 NC_003454:FN1109|3end_Dipeptide_transport_ATP-binding_protein_dppF_1752994..1753144_NEGATIVE 228 48 5 78 35 NC_003454:FN0821|3end_hypothetical_protein_1481805..1481955_POSITIVE 194 77 37 60 24 NC_003454:FN0195|3end_Dipeptide_transport_ATP-binding_protein_dppD_822407..822557_POSITIVE 189 74 40 99 65 NC_003454:FN0928|3end_O-sialoglycoprotein_endopeptidase_1582382..1582532_NEGATIVE 185 54 15 88 50 NC_003454:FN1071|3end_Integrase/recombinase_1719384..1719534_POSITIVE 184 67 32 53 11 NC_003454:FN0137|3end_Transposase_771280..771430_POSITIVE 184 54 12 99 55 NC_003454:FN1593|3end_NADH-ubiquinone_oxidoreductase_103743..103893_NEGATIVE 183 54 13 69 33 NC_003454:FN1985|3end_Inner_membrane_protein_487273..487423_NEGATIVE 166 62 34 120 85 NC_003454:FN0268|3end_DNA_repair_protein_recN_896086..896236_POSITIVE 165 76 58 73 55 NC_003454:FN1380|3end_Citrate_lyase_beta_chain_2028878..2029028_POSITIVE 165 60 11 139 96 NC_003454:FN2068|3end_dGTP_triphosphohydrolase_577445..577595_NEGATIVE 164 60 13 80 30 NC_003454:FN1146|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1796080..1796230_NEGATIVE 164 47 1 74 25 NC_003454:FN0224|3end_excinuclease_ABC_subunit_B_851673..851823_POSITIVE 163 76 45 76 43 NC_003454:FN1457|3end_UDP-N-acetylglucosamine-N-acetylmuramyl-_Pentapeptide_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_2137903..2138053_NEGATIVE 162 70 21 137 96 NC_003454:FN1742|3end_V-type_sodium_ATP_synthase_subunit_G_240464..240614_NEGATIVE 160 50 2 105 52 NC_003454:FN0834|3end_hypothetical_protein_1498088..1498238_POSITIVE 159 90 46 151 105 NC_003454:FN0544|3end_ADP-heptose:LPS_heptosyltransferase_II_1198128..1198278_POSITIVE 156 76 32 149 110 NC_003454:FN0803|3end_trifunctional_thioredoxin/methionine_sulfoxide_reductase_A/B_protein_1462450..1462600_NEGATIVE 155 88 44 59 7 NC_003454:FN1139|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_1789248..1789398_POSITIVE 154 60 15 88 39 NC_003454:FN1199|3end_DNA_polymerase_IV_1860193..1860343_POSITIVE