Origin IGS: actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggccgtaaattcgagcgatataaatgtaaaaaaggagggatatgacaatttacgtcgcgttaaataagtttaaacacggtattatgtattgcataggttatttgcaatgcatacttttgtaccaaaacatagaacagt Mask Tandem Repeat Region ================================================ actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc Find is-nt database================================================ Query_seq: TF1662:TF1663|TF1662:TF1663:possible transcriptional regulator, PadR family:ABC transporter, permease component:->->:1777681..1777819 139 actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1662:TF1663|TF1662:TF1663:possible transcriptional regulator, PadR family:ABC transporter, permease component:->->:1777681..1777819 139 actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1662:TF1663|TF1662:TF1663:possible transcriptional regulator, PadR family:ABC transporter, permease component:->->:1777681..1777819 139 actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 2 End: 97 . Q E I N Q Y L L I C Q L Y G I C Y M I G H K F K N L A V Y I T M .......................................... actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc 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================================================ actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 58 HP_score: -2.8 Tail_Score: -4.36914 Start: 25 End: 57 Full_Region: agtttaaacacggta ttatgtattgcata ggtta tttgcaatgcatac ttttgtaccaaaaca ........................ttatgtattgcataggttatttgcaatgcatac.................................................................................. TransTerm Strand: - Conf: 61 HP_score: -6.3 Tail_Score: -3.21934 Start: 26 End: 56 Full_Region: gtttaaacacggtat tatgtattgcata ggtta tttgcaatgcata cttttgtaccaaaac .........................tatgtattgcataggttatttgcaatgcata................................................................................... Find igs database================================================ Query_seq: TF1662:TF1663|TF1662:TF1663:possible transcriptional regulator, PadR family:ABC transporter, permease component:->->:1777681..1777819 139 actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: tfor_TF1662_TF1663|possible transcriptional regulator, PadR family:ABC transporter, permease component|POSITIVE:POSITIVE|[1777681,1777819]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc actgttctatgttttggtacaaaagtatgcattgcaaataacctatgcaatacataataccgtgtttaaacttatttaacgcgacgtaaattgtcatatccctccttttttacatttatatcgctcgaatttacggccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGUUCUAUGUUUUGGUACAAAAGUAUGCAUUGCAAAUAACCUAUGCAAUACAUAAUACCGUGUUUAAACUUAUUUAACGCGACGUAAAUUGUCAUAUCCCUCCUUUUUUACAUUUAUAUCGCUCGAAUUUACGGCCC ..(((.(((.....))).)))....((((.((((((.........)))))).))))...(((((.(((((....))))).((((..(((((.((.................)))))))..)))).......)))))... (-20.53) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGCCGUAAAUUCGAGCGAUAUAAAUGUAAAAAAGGAGGGAUAUGACAAUUUACGUCGCGUUAAAUAAGUUUAAACACGGUAUUAUGUAUUGCAUAGGUUAUUUGCAAUGCAUACUUUUGUACCAAAACAUAGAACAGU (((((((........((((..(((((......................)))))..)))).(((((....)))))..)))))..(((((((((((.........)))))))))))........))............... (-27.45) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 129 81 79 24 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 256 108 62 117 78 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 247 65 25 141 108 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 246 126 81 74 45 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 244 107 62 211 171 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 244 107 62 199 159 tfor:TF1171|5end_ABC_transporter,_ATP-binding_protein_1251850..1252080_POSITIVE 242 100 60 210 154 tfor:TF1718|5end_conserved_hypothetical_protein_1840462..1840692_POSITIVE 242 54 16 166 125 tfor:TF1260|5end_chaperone_protein_DnaJ_1345325..1345555_POSITIVE 238 114 80 211 173 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 235 128 81 218 175 tfor:TF2090|5end_phosphoribosylglycinamide_formyltransferase_2258692..2258922_POSITIVE 227 129 81 61 11 tfor:TF1322|5end_conserved_hypothetical_protein;_possible_surface_protein_1401864..1402094_POSITIVE 227 129 86 88 46 tfor:TF1222|5end_conserved_hypothetical_protein_1308250..1308480_POSITIVE 222 117 80 93 49 tfor:TF2889|5end_50S_ribosomal_protein_L27_3078333..3078563_POSITIVE 219 127 81 220 165 tfor:TF1768|5end_conserved_hypothetical_protein;_possible_transposase_1906526..1906756_POSITIVE 217 87 46 158 117 tfor:TF2769|5end_cell-division_protein;_ftsX_family_permease_2955348..2955578_POSITIVE 217 101 76 212 183 tfor:TF2082|5end_DNA_topoisomerase_IV,_subunit_B_2248965..2249195_POSITIVE 216 128 83 186 151 tfor:TF0200|5end_2-nitropropane_dioxygenase_225061..225291_POSITIVE 215 110 61 85 35 tfor:TF2556|5end_conserved_hypothetical_protein_2736131..2736361_POSITIVE 214 127 85 127 76 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 214 102 61 63 28 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 129 81 62 7 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 258 119 77 57 22 tfor:TF2999|3end_conserved_hypothetical_protein_3215891..3216041_POSITIVE 243 103 77 137 105 tfor:TF3094|3end_translation_elongation_factor_Ts_3327023..3327173_POSITIVE 238 114 80 142 104 tfor:TF2831|3end_ABC_transporter,_permease_component_3022671..3022821_POSITIVE 228 108 61 89 31 tfor:TF2613|3end_conserved_hypothetical_protein_2789798..2789948_POSITIVE 227 116 76 139 88 tfor:TF1761|3end_hypothetical_protein_1899579..1899729_POSITIVE 227 129 86 121 79 tfor:TF1221|3end_conserved_hypothetical_protein_1308363..1308513_POSITIVE 226 35 2 131 98 tfor:TF0081|3end_pantothenate_kinase_88494..88644_POSITIVE 223 49 8 72 17 tfor:TF0362|3end_hypothetical_protein_380199..380349_POSITIVE 222 117 80 69 25 tfor:TF2888|3end_50S_ribosomal_protein_L21_3078389..3078539_POSITIVE 217 129 81 99 58 tfor:TF0258|3end_hypothetical_protein_289534..289684_POSITIVE 215 122 92 41 5 tfor:TF1259|3end_hypothetical_protein_1345204..1345354_POSITIVE 214 127 85 100 49 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 214 102 61 56 21 tfor:TF1766|3end_alanyl-tRNA_synthetase_1905565..1905715_POSITIVE 213 128 82 110 63 tfor:TF1249|3end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1332356..1332506_POSITIVE 211 100 62 148 111 tfor:TF1085|3end_Fe-S_oxidoreductase_1156611..1156761_POSITIVE 210 33 1 45 9 tfor:TF1955|3end_amino_acid_exporter,_possible_threonine_efflux_protein_2107649..2107799_POSITIVE 209 126 100 120 99 tfor:TF1250|3end_possible_cation_efflux_pump_1333801..1333951_POSITIVE 207 49 8 144 89 tfor:TF2172|3end_hypothetical_protein_2346135..2346285_POSITIVE 207 49 8 72 17 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE