Origin IGS: tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaattaaaaagaaatttgaaaaaaaactaaaaaaaacttgacttttactcaaaagaggcttagaatgtattc .........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 gaatacattctaagcctcttttgagtaaaagtcaagttttttttagttttttttcaaatttctttttaattgcaaaataaaagcctttatccggcggttgaagaatataacagttacaagaatgaatatctaaattgacttgaatttacccttattttctgctataatttaagggaaaatatcggaggcaaaaca Mask Tandem Repeat Region ================================================ tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaattaaaaagaaatttgaaaaaaaactaaaaaaaacttgacttttactcaaaagaggcttagaatgtattc Find is-nt database================================================ Query_seq: TDE0061:TDE0062|TDE0061:TDE0062:fic family protein:PTS system, IIA component:<-->:69035..69229 195 tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaattaaaaagaaatttgaaaaaaaactaaaaaaaacttgacttttactcaaaagaggcttagaatgtattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0061:TDE0062|TDE0061:TDE0062:fic family protein:PTS system, IIA component:<-->:69035..69229 195 tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaattaaaaagaaatttgaaaaaaaactaaaaaaaacttgacttttactcaaaagaggcttagaatgtattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0061:TDE0062|TDE0061:TDE0062:fic family protein:PTS system, IIA component:<-->:69035..69229 195 tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaattaaaaagaaatttgaaaaaaaactaaaaaaaacttgacttttactcaaaagaggcttagaatgtattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaattaaaaagaaatttgaaaaaaaactaaaaaaaacttgacttttactcaaaagaggcttagaatgtattc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 51 End: 161 .................................................. M Q V N L D I H S C N C Y I L Q P P D K G F Y F A I K K K F E K K L K K T .................................. tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaattaaaaagaaatttgaaaaaaaactaaaaaaaacttgacttttactcaaaagaggcttagaatgtattc 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: 90 Start: 28 End: 57 ...........................CTTGAATTTACCCTTATTTTCTGCTATAAT.......................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 88 Start: 160 End: 189 ...............................................................................................................................................................CTTGACTTTTACTCAAAAGAGGCTTAGAAT...... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 63 End: 92 ..............................................................TTAGATATTCATTCTTGTAACTGTTATATT....................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaattaaaaagaaatttgaaaaaaaactaaaaaaaacttgacttttactcaaaagaggcttagaatgtattc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0061:TDE0062|TDE0061:TDE0062:fic family protein:PTS system, IIA component:<-->:69035..69229 195 tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaattaaaaagaaatttgaaaaaaaactaaaaaaaacttgacttttactcaaaagaggcttagaatgtattc Intra-Species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: NC_002967_TDE0061_TDE0062|fic family protein:PTS system, IIA component|NEGATIVE:POSITIVE|[69035,69229]|195 HSP 1 e-value: 1.0E-66 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaatt................................................................... tgttttgcctccgatattttcccttaaattatagcagaaaataagggtaaattcaagtcaatttagatattcattcttgtaactgttatattcttcaaccgccggataaaggcttttattttgcaatt................................................................... HSP 2 e-value: 8.0E-12 bit: 71.9 Len: 36 Query Start:160 Query End:195 Subject Strand: POSITIVE Subject Start: 160 Subject End: 195 ...............................................................................................................................................................cttgacttttactcaaaagaggcttagaatgtattc ...............................................................................................................................................................cttgacttttactcaaaagaggcttagaatgtattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUGCCUCCGAUAUUUUCCCUUAAAUUAUAGCAGAAAAUAAGGGUAAAUUCAAGUCAAUUUAGAUAUUCAUUCUUGUAACUGUUAUAUUCUUCAACCGCCGGAUAAAGGCUUUUAUUUUGCAAUUAAAAAGAAAUUUGAAAAAAAACUAAAAAAAACUUGACUUUUACUCAAAAGAGGCUUAGAAUGUAUUC .((((((((((...(((((((.((........))..))))))).(((((((.((((((...(((((.......(((((.(((.(((..............(((.......))).........))).)))..))))).(((....)))..)))))....))))))..)))))))....)))))..)))))...... (-33.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUACAUUCUAAGCCUCUUUUGAGUAAAAGUCAAGUUUUUUUUAGUUUUUUUUCAAAUUUCUUUUUAAUUGCAAAAUAAAAGCCUUUAUCCGGCGGUUGAAGAAUAUAACAGUUACAAGAAUGAAUAUCUAAAUUGACUUGAAUUUACCCUUAUUUUCUGCUAUAAUUUAAGGGAAAAUAUCGGAGGCAAAACA .............((((((.....(((((..(((((((...(((((..(((.(((.......(((((((((((...(((((....)))))...))))))))))).((.......))...))).)))...)))))..))))))).)))))...((((((((..((.....))..))))))))..))))))...... (-38.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 810 120 71 211 162 NC_002967:TDE0061|5end_fic_family_protein_68944..69174_NEGATIVE 320 126 84 124 78 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 296 49 2 145 101 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 273 113 84 105 78 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 265 113 75 199 161 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 261 127 83 170 129 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 256 126 86 117 72 NC_002967:TDE1885|5end_hypothetical_protein_1906857..1907087_POSITIVE 253 120 76 171 129 NC_002967:TDE0407|5end_glutamate_synthase_(NADPH),_homotetrameric_460522..460752_NEGATIVE 252 116 74 214 176 NC_002967:TDE1160|5end_hypothetical_protein_1195841..1196071_NEGATIVE 250 119 100 203 181 NC_002967:TDE0795|5end_hypothetical_protein_819974..820204_NEGATIVE 249 115 74 60 17 NC_002967:TDE0389|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_440008..440238_POSITIVE 247 115 76 65 31 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 246 107 62 203 163 NC_002967:TDE0508|5end_hypothetical_protein_559759..559989_NEGATIVE 239 128 81 211 156 NC_002967:TDE1597|5end_transporter,_putative_1647402..1647632_NEGATIVE 237 115 75 46 3 NC_002967:TDE0165|5end_hypothetical_protein_194122..194352_POSITIVE 235 135 95 213 165 NC_002967:TDE2764|5end_flagellar_protein_2819331..2819561_NEGATIVE 235 109 74 110 79 NC_002967:TDE1329|5end_ATPase,_AAA_family_1363503..1363733_POSITIVE 231 112 84 107 78 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 229 125 92 80 33 NC_002967:TDE1225|5end_zinc_ABC_transporter,_ATP-binding_protein_1259518..1259748_NEGATIVE 229 124 99 201 165 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 49 2 139 95 NC_002967:TDE2233|3end_iron_compound_ABC_transporter,_permease_protein,_putative_2271291..2271441_NEGATIVE 236 118 76 137 97 NC_002967:TDE2627|3end_transcriptional_regulator,_TetR_family_2668532..2668682_NEGATIVE 234 113 84 68 42 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 229 125 92 53 6 NC_002967:TDE1226|3end_zinc_ABC_transporter,_periplasmic_zinc-binding_protein_1259545..1259695_NEGATIVE 224 113 71 55 8 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 224 50 1 64 9 NC_002967:TDE1666|3end_hypothetical_protein_1720021..1720171_POSITIVE 222 124 84 102 66 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 221 98 51 140 93 NC_002967:TDE2786|3end_DNA_polymerase_III_subunit_alpha_2839223..2839373_NEGATIVE 220 124 99 141 108 NC_002967:TDE0872|3end_recA_protein_896165..896315_POSITIVE 219 117 74 148 96 NC_002967:TDE0960|3end_neuB_family_protein_983595..983745_POSITIVE 218 119 75 102 50 NC_002967:TDE2729|3end_hypothetical_protein_2785756..2785906_NEGATIVE 218 113 72 36 3 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 217 47 5 114 72 NC_002967:TDE2550|3end_hypothetical_protein_2575520..2575670_NEGATIVE 215 117 77 142 94 NC_002967:TDE2342|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2379238..2379388_NEGATIVE 213 50 4 64 10 NC_002967:TDE2346|3end_elongation_factor_Ts_2382587..2382737_NEGATIVE 213 124 84 63 19 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 213 115 71 59 16 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 211 117 74 72 28 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 211 47 8 33 9 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 210 117 75 133 99 NC_002967:TDE1616|3end_glycerate_dehydrogenase_1663755..1663905_NEGATIVE