Origin IGS: aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggttgtttcctttctttataatcactatctagttgtaattaaatttgttacattttaacaaagaaaaaacaagctgtcaagataagatcttgtttcgcttttggtatggataggtcaagtcttccgttagctaagctatagaagagatttgtgatt Mask Tandem Repeat Region ================================================ aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc Find is-nt database================================================ Query_seq: SSA_1686:SSA_1687|SSA_1686:SSA_1687:hypothetical protein:NADH-binding ferric-oxidoreductase, putative:->->:1680531..1680686 156 aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1686:SSA_1687|SSA_1686:SSA_1687:hypothetical protein:NADH-binding ferric-oxidoreductase, putative:->->:1680531..1680686 156 aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1686:SSA_1687|SSA_1686:SSA_1687:hypothetical protein:NADH-binding ferric-oxidoreductase, putative:->->:1680531..1680686 156 aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 2 End: 106 . M T N L F Y S L A N G R L D L S I P K A K Q D L I L T A C F F F V K M .................................................. Protein_Len: 32 Strand: - Start: 19 End: 114 .................. L K A L P L S S R D M G F A F C S R I K V A Q K K K T L I Y C M .......................................... aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc 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: 92 Start: 76 End: 105 ...........................................................................CTTGACAGCTTGTTTTTTCTTTGTTAAAAT................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -7.2 Tail_Score: -3.95448 Start: 65 End: 79 Full_Region: gaaaaaacaagctgt caagat aag atcttg tttcgcttttggtat ................................................................caagataagatcttg............................................................................. Find igs database================================================ Query_seq: SSA_1686:SSA_1687|SSA_1686:SSA_1687:hypothetical protein:NADH-binding ferric-oxidoreductase, putative:->->:1680531..1680686 156 aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_009009_SSA_1686_SSA_1687|hypothetical protein:NADH-binding ferric-oxidoreductase, putative|POSITIVE:POSITIVE|[1680531,1680686]|156 HSP 1 e-value: 1.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc aatcacaaatctcttctatagcttagctaacggaagacttgacctatccataccaaaagcgaaacaagatcttatcttgacagcttgttttttctttgttaaaatgtaacaaatttaattacaactagatagtgattataaagaaaggaaacaacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCACAAAUCUCUUCUAUAGCUUAGCUAACGGAAGACUUGACCUAUCCAUACCAAAAGCGAAACAAGAUCUUAUCUUGACAGCUUGUUUUUUCUUUGUUAAAAUGUAACAAAUUUAAUUACAACUAGAUAGUGAUUAUAAAGAAAGGAAACAACC ((((((.....((((((.((((...))))..)))))).......((((........((((....((((((...))))))...))))((..((..(((((((.....)))))))...))..)).....)))))))))).........(....).... (-26.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUGUUUCCUUUCUUUAUAAUCACUAUCUAGUUGUAAUUAAAUUUGUUACAUUUUAACAAAGAAAAAACAAGCUGUCAAGAUAAGAUCUUGUUUCGCUUUUGGUAUGGAUAGGUCAAGUCUUCCGUUAGCUAAGCUAUAGAAGAGAUUUGUGAUU ((((((...........)))))).(((((((..((((((.......))))))......(((((...(((((((..(((.......))))))))))...)))))...)))))))..((((((((....((((...)))).....))))))))..... (-29.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 443 56 11 183 140 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 280 69 21 220 158 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 268 68 23 152 94 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 268 80 38 74 38 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 263 68 26 62 28 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 252 42 10 215 183 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 237 53 14 220 186 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 237 64 21 74 31 NC_009009:SSA_0033|5end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_38957..39187_POSITIVE 236 94 51 202 159 NC_009009:SSA_1789|5end_Metal-dependent_phosphohydrolase,_HD_superfamily,_putative_1772856..1773086_NEGATIVE 235 84 43 130 95 NC_009009:SSA_0066|5end_hypothetical_protein_67602..67832_POSITIVE 233 60 15 58 3 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 233 49 21 39 14 NC_009009:SSA_1985|5end_hypothetical_protein_1981773..1982003_NEGATIVE 233 54 21 94 55 NC_009009:SSA_0425|5end_Glycosyltransferase,_putative_423279..423509_NEGATIVE 232 60 11 118 68 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 232 88 41 72 17 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 230 49 17 169 129 NC_009009:SSA_2109|5end_Elongation_factor_G,_putative_2114868..2115098_NEGATIVE 230 79 31 207 153 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 229 69 21 190 128 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 229 98 51 193 126 NC_009009:SSA_0349|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_341110..341340_POSITIVE 228 60 12 120 69 NC_009009:SSA_0594|5end_Transcriptional_regulator,_AraC_family,_putative_585630..585860_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 443 56 11 137 94 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE 249 55 12 144 98 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 245 46 12 67 33 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 239 66 23 57 8 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 239 90 44 96 40 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 237 64 21 77 34 NC_009009:SSA_0032|3end_Phosphoribosylformylglycinamidine_cyclo-ligase,_putative_39040..39190_POSITIVE 235 84 43 125 90 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE 234 85 55 61 32 NC_009009:SSA_1691|3end_Transcriptional_regulator,_XRE_family,_putative_1683570..1683720_POSITIVE 232 60 11 125 75 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 232 88 41 72 17 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 231 49 12 150 105 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 229 69 21 125 63 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 229 98 51 117 50 NC_009009:SSA_0348|3end_CAAX_amino_terminal_protease_family,_putative_341114..341264_POSITIVE 227 60 11 141 94 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 227 60 20 86 45 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 226 60 11 128 77 NC_009009:SSA_1550|3end_hypothetical_protein_1552228..1552378_NEGATIVE 225 54 12 132 96 NC_009009:SSA_0227|3end_Collagen-binding_surface_protein,_putative_222970..223120_POSITIVE 224 89 53 43 11 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 219 49 4 139 97 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 216 54 11 135 94 NC_009009:SSA_0245|3end_hypothetical_protein_239608..239758_POSITIVE