Origin IGS: tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa .........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 ttaaatttacctaaattgagtacattataaataaagaaattatattgtcaagcacgaaaatacaccaagaatcgtcgttaaagtaaattataaattctcataatttactttaagcctttaaagtaaattataacttgctattttgctaaatttatgttaaaataaatccattgggagaaaaa Mask Tandem Repeat Region ================================================ tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa Find is-nt database================================================ Query_seq: TDE0233:TDE0234|TDE0233:TDE0234:fic family protein:ABC transporter, ATP-binding protein, HlyB family:<-->:267011..267192 182 tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0233:TDE0234|TDE0233:TDE0234:fic family protein:ABC transporter, ATP-binding protein, HlyB family:<-->:267011..267192 182 tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0233:TDE0234|TDE0233:TDE0234:fic family protein:ABC transporter, ATP-binding protein, HlyB family:<-->:267011..267192 182 tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa Predict ORF larger than 30AA ================================================ tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa 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: 89 Start: 20 End: 49 ...................CTTGCTATTTTGCTAAATTTATGTTAAAAT..................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -9.4 Tail_Score: -2.72856 Start: 50 End: 85 Full_Region: gtaaattataaattc tcataatttactttaa gcct ttaaagtaaattataa cttgctattttgcta .................................................tcataatttactttaagcctttaaagtaaattataa................................................................................................. TransTerm Strand: - Conf: 84 HP_score: -11.1 Tail_Score: -2.63041 Start: 53 End: 82 Full_Region: aattataaattctca taatttactttaa gcct ttaaagtaaatta taacttgctattttg ....................................................taatttactttaagcctttaaagtaaatta.................................................................................................... TransTerm Strand: - Conf: 75 HP_score: -8.4 Tail_Score: -3.44792 Start: 56 End: 79 Full_Region: tataaattctcataa tttactttaa gcct ttaaagtaaa ttataacttgctatt .......................................................tttactttaagcctttaaagtaaa....................................................................................................... Find igs database================================================ Query_seq: TDE0233:TDE0234|TDE0233:TDE0234:fic family protein:ABC transporter, ATP-binding protein, HlyB family:<-->:267011..267192 182 tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_002967_TDE0233_TDE0234|fic family protein:ABC transporter, ATP-binding protein, HlyB family|NEGATIVE:POSITIVE|[267011,267192]|182 HSP 1 e-value: 5.0E-99 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa tttttctcccaatggatttattttaacataaatttagcaaaatagcaagttataatttactttaaaggcttaaagtaaattatgagaatttataatttactttaacgacgattcttggtgtattttcgtgcttgacaatataatttctttatttataatgtactcaatttaggtaaatttaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCUCCCAAUGGAUUUAUUUUAACAUAAAUUUAGCAAAAUAGCAAGUUAUAAUUUACUUUAAAGGCUUAAAGUAAAUUAUGAGAAUUUAUAAUUUACUUUAACGACGAUUCUUGGUGUAUUUUCGUGCUUGACAAUAUAAUUUCUUUAUUUAUAAUGUACUCAAUUUAGGUAAAUUUAA ...(((((....(((((((((......)))))))))((......)).....((((((((((((((....))))))))))))))))))).....(((((((((..((((.(((.(.....).))).)))).....(((.(((((.........))))).))).........)))))))))... (-29.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAUUUACCUAAAUUGAGUACAUUAUAAAUAAAGAAAUUAUAUUGUCAAGCACGAAAAUACACCAAGAAUCGUCGUUAAAGUAAAUUAUAAAUUCUCAUAAUUUACUUUAAGCCUUUAAAGUAAAUUAUAACUUGCUAUUUUGCUAAAUUUAUGUUAAAAUAAAUCCAUUGGGAGAAAAA ...(((((((.........(.(((.(((((.........))))).)))).(((((((..............)))).)))...))))))).....(((((.(((((((((((((....)))))))))))))......((......))...((((((......)))))).......)))))... (-24.84) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 759 140 91 231 182 NC_002967:TDE0233|5end_fic_family_protein_266920..267150_NEGATIVE 232 146 115 213 172 NC_002967:TDE0585|5end_hypothetical_protein_625024..625254_NEGATIVE 221 148 110 101 65 NC_002967:TDE1472|5end_flagellar_hook-associated_protein_1520715..1520945_NEGATIVE 209 157 112 139 105 NC_002967:TDE1360|5end_xanthine/uracil_permease_family_protein_1399297..1399527_POSITIVE 207 148 106 159 107 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 205 134 97 202 152 NC_002967:TDE2472|5end_ISTde1,_transposase_2494962..2495192_POSITIVE 202 150 114 104 64 NC_002967:TDE0110|5end_M23/M37_peptidase_domain_protein_130581..130811_POSITIVE 201 157 112 223 172 NC_002967:TDE0269|5end_hypothetical_protein_300687..300917_NEGATIVE 200 131 96 124 78 NC_002967:TDE2156|5end_translation_initiation_factor_IF-3_2190719..2190949_NEGATIVE 199 139 105 154 121 NC_002967:TDE2506|5end_radical_SAM_domain_protein_2530581..2530811_POSITIVE 196 129 81 91 39 NC_002967:TDE0921|5end_ABC_transporter,_ATP-binding/permease_protein_941857..942087_NEGATIVE 196 133 101 151 114 NC_002967:TDE0652|5end_hypothetical_protein_688177..688407_POSITIVE 194 139 105 219 182 NC_002967:TDE1590|5end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1637516..1637746_POSITIVE 190 135 96 99 60 NC_002967:TDE2271|5end_HAM1_protein_2309065..2309295_NEGATIVE 190 138 100 124 86 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 190 149 106 65 22 NC_002967:TDE0254|5end_hypothetical_protein_288654..288884_POSITIVE 188 140 106 207 180 NC_002967:TDE0286|5end_ABC_transporter,_ATP-binding_protein_317378..317608_NEGATIVE 187 163 127 121 89 NC_002967:TDE2482|5end_hypothetical_protein_2505536..2505766_POSITIVE 187 150 101 75 23 NC_002967:TDE1917|5end_cytidylyltransferase_domain_protein_1937394..1937624_NEGATIVE 186 119 82 195 164 NC_002967:TDE2656|5end_cobalt_chelatase_2693065..2693295_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 148 110 56 20 NC_002967:TDE1473|3end_flagellin_FlaG,_putative_1520760..1520910_NEGATIVE 218 136 106 55 12 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 213 127 81 71 24 NC_002967:TDE2014|3end_ankyrin_repeat_protein_2035435..2035585_NEGATIVE 209 131 99 130 95 NC_002967:TDE0826|3end_hypothetical_protein_847860..848010_POSITIVE 201 157 112 65 14 NC_002967:TDE0270|3end_hypothetical_protein_300845..300995_NEGATIVE 199 139 105 114 81 NC_002967:TDE2505|3end_hypothetical_protein_2530621..2530771_POSITIVE 196 135 97 51 7 NC_002967:TDE2074|3end_radical_SAM_enzyme,_Cfr_family_2101537..2101687_POSITIVE 196 129 81 101 49 NC_002967:TDE0922|3end_ABC_transporter,_ATP-binding/permease_protein_941847..941997_NEGATIVE 190 149 106 56 13 NC_002967:TDE0253|3end_hypothetical_protein_288725..288875_POSITIVE 187 150 101 78 26 NC_002967:TDE1918|3end_hypothetical_protein_1937391..1937541_NEGATIVE 186 119 82 49 18 NC_002967:TDE2654|3end_macrolide_efflux_protein,_putative_2692999..2693149_POSITIVE 184 64 33 70 35 NC_002967:TDE1595|3end_cobalamin_biosynthesis_protein_CbiD_1644948..1645098_NEGATIVE 184 141 109 102 76 NC_002967:TDE1537|3end_polyprenyl_synthetase_family_protein_1580472..1580622_NEGATIVE 183 157 111 95 37 NC_002967:TDE0507|3end_hypothetical_protein_558783..558933_NEGATIVE 182 151 112 50 11 NC_002967:TDE1108|3end_hypothetical_protein_1142413..1142563_NEGATIVE 181 136 106 47 20 NC_002967:TDE0263|3end_spermidine_N1-acetyltransferase,_putative_296400..296550_NEGATIVE 181 136 105 150 113 NC_002967:TDE0002|3end_DNA_gyrase,_B_subunit_3540..3690_POSITIVE 180 129 82 135 82 NC_002967:TDE0799|3end_glycerophosphoryl_diester_phosphodiesterase,_putative_823468..823618_POSITIVE 178 148 101 81 39 NC_002967:TDE1864|3end_crossover_junction_endodeoxyribonuclease_RuvC_1888572..1888722_NEGATIVE 178 72 36 54 24 NC_002967:TDE1313|3end_signal_peptidase_I_1351266..1351416_POSITIVE