Origin IGS: accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttttatagtactacaaattttgctttttgaaaagggagtaagtataattgtaagtttactttaattgtatcttaataatttttatattttatgatataatcataaccggt Mask Tandem Repeat Region ================================================ accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat Find is-nt database================================================ Query_seq: TDE0086:TDE0087|TDE0086:TDE0087:hypothetical protein:Trk system potassium uptake protein TrkA:<-->:103967..104078 112 accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0086:TDE0087|TDE0086:TDE0087:hypothetical protein:Trk system potassium uptake protein TrkA:<-->:103967..104078 112 accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0086:TDE0087|TDE0086:TDE0087:hypothetical protein:Trk system potassium uptake protein TrkA:<-->:103967..104078 112 accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat Predict ORF larger than 30AA ================================================ accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat 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: 86 Start: 11 End: 40 ..........CTTAATAATTTTTATATTTTATGATATAAT........................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 63 End: 92 ..............................................................TTTGCTTTTTGAAAAGGGAGTAAGTATAAT.................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 77 End: 106 ............................................................................CTTTTCAAAAAGCAAAATTTGTAGTACTAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0086:TDE0087|TDE0086:TDE0087:hypothetical protein:Trk system potassium uptake protein TrkA:<-->:103967..104078 112 accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002967_TDE0086_TDE0087|hypothetical protein:Trk system potassium uptake protein TrkA|NEGATIVE:POSITIVE|[103967,104078]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat accggttatgattatatcataaaatataaaaattattaagatacaattaaagtaaacttacaattatacttactcccttttcaaaaagcaaaatttgtagtactataaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGGUUAUGAUUAUAUCAUAAAAUAUAAAAAUUAUUAAGAUACAAUUAAAGUAAACUUACAAUUAUACUUACUCCCUUUUCAAAAAGCAAAAUUUGUAGUACUAUAAAAAU .....(((((((...)))))))..........((((.....(((((...(((((............))))).....((((....))))......))))).....)))).... ( -7.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUAUAGUACUACAAAUUUUGCUUUUUGAAAAGGGAGUAAGUAUAAUUGUAAGUUUACUUUAAUUGUAUCUUAAUAAUUUUUAUAUUUUAUGAUAUAAUCAUAACCGGU .....(((((...........(((((((((....)))))))))(((((((((.(((....))))))))))))...........)))))..(((((((...)))))))..... (-15.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 704 100 51 191 142 NC_002967:TDE0086|5end_hypothetical_protein_103876..104106_NEGATIVE 218 76 39 102 64 NC_002967:TDE0155|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_180154..180384_NEGATIVE 202 105 67 87 55 NC_002967:TDE1145|5end_hypothetical_protein_1184811..1185041_NEGATIVE 195 50 1 188 137 NC_002967:TDE1699|5end_hypothetical_protein_1757920..1758150_NEGATIVE 191 99 56 119 81 NC_002967:TDE2739|5end_hypothetical_protein_2794673..2794903_POSITIVE 183 56 19 71 35 NC_002967:TDE1940|5end_hypothetical_protein_1956508..1956738_NEGATIVE 161 99 58 124 82 NC_002967:TDE0365|5end_hypothetical_protein_412421..412651_NEGATIVE 160 90 67 193 169 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 157 101 70 35 3 NC_002967:TDE1282|5end_hypothetical_protein_1316801..1317031_POSITIVE 156 98 68 28 1 NC_002967:TDE1516|5end_ABC_transporter,_ATP-binding_protein,_putative_1563127..1563357_POSITIVE 156 107 63 50 9 NC_002967:TDE1172|5end_hypothetical_protein_1201006..1201236_POSITIVE 155 108 74 45 13 NC_002967:TDE1277|5end_Fe-hydrogenase_large_subunit_family_protein_1310681..1310911_POSITIVE 155 99 57 118 73 NC_002967:TDE0119|5end_flagellar_protein_FliS_137498..137728_NEGATIVE 154 102 63 192 151 NC_002967:TDE1241|5end_HD_domain_protein_1272269..1272499_POSITIVE 154 107 69 137 87 NC_002967:TDE0128|5end_HAMP_domain/GGDEF_domain/EAL_domain_protein_146240..146470_POSITIVE 152 78 36 199 157 NC_002967:TDE2681|5end_hypothetical_protein_2721407..2721637_NEGATIVE 152 89 64 231 203 NC_002967:TDE1136|5end_M23/M37_peptidase_domain_protein_1166049..1166279_NEGATIVE 150 99 51 190 128 NC_002967:TDE0163|5end_flavodoxin_193383..193613_NEGATIVE 149 109 67 134 83 NC_002967:TDE2769|5end_flagellar_hook_assembly_protein_2823032..2823262_NEGATIVE 148 84 60 106 81 NC_002967:TDE2085|5end_uridylate_kinase_2114182..2114412_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 202 105 67 74 42 NC_002967:TDE1146|3end_hypothetical_protein_1184824..1184974_NEGATIVE 200 90 44 119 71 NC_002967:TDE2555|3end_precorrin-8X_methylmutase_2582316..2582466_POSITIVE 183 56 19 74 38 NC_002967:TDE1941|3end_hypothetical_protein_1956505..1956655_NEGATIVE 172 100 73 73 41 NC_002967:TDE2610|3end_hypothetical_protein_2651854..2652004_NEGATIVE 171 90 70 151 132 NC_002967:TDE0194|3end_hypothetical_protein_230739..230889_NEGATIVE 164 43 3 117 84 NC_002967:TDE2141|3end_hypothetical_protein_2175583..2175733_NEGATIVE 161 99 58 123 81 NC_002967:TDE0366|3end_type_I_restriction-modification_system,_R_subunit_412422..412572_NEGATIVE 160 90 67 116 92 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 159 100 69 134 95 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 152 100 51 131 80 NC_002967:TDE1173|3end_site-specific_recombinase,_phage_integrase_family_1201257..1201407_NEGATIVE 152 91 57 98 55 NC_002967:TDE0912|3end_hypothetical_protein_931528..931678_POSITIVE 149 109 67 122 71 NC_002967:TDE2770|3end_flagellar_hook-length_control_protein_FliK_2823044..2823194_NEGATIVE 148 82 69 27 14 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 148 84 60 73 48 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE 148 33 2 70 31 NC_002967:TDE0629|3end_chaperone_protein_DnaJ_663848..663998_POSITIVE 148 100 61 118 82 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 147 106 64 75 28 NC_002967:TDE2748|3end_acetyltransferase,_GNAT_family_2805646..2805796_POSITIVE 147 83 41 104 47 NC_002967:TDE0230|3end_DNA_replication_and_repair_protein_RecF_262799..262949_NEGATIVE 146 104 76 41 7 NC_002967:TDE1983|3end_hypothetical_protein_1993376..1993526_NEGATIVE 146 98 59 104 56 NC_002967:TDE0390|3end_hypothetical_protein_441583..441733_POSITIVE