Origin IGS: cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttatactattataaatgaatttcggcttttttttaagtagtttttagagatttttattaaaaaaaagtataaaaagccgaaaattgatataggagttttttatatagatgacttttttaagtgcatcgaattaaggtttggtaag Mask Tandem Repeat Region ================================================ cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat Find is-nt database================================================ Query_seq: TDE2116:TDE2117|TDE2116:TDE2117:hypothetical protein:hypothetical protein:<-->:2147799..2147945 147 cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2116:TDE2117|TDE2116:TDE2117:hypothetical protein:hypothetical protein:<-->:2147799..2147945 147 cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2116:TDE2117|TDE2116:TDE2117:hypothetical protein:hypothetical protein:<-->:2147799..2147945 147 cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 56 End: 142 ....................................................... M S I F G F L Y F F L I K I S K N Y L K K S R N S F I I V * ..... Protein_Len: 32 Strand: - Start: 1 End: 96 K G F R L E I C K F F D D I Y F V G I D I K P K K Y K K K I F M ................................................... cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat 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: 109 End: 138 ............................................................................................................CTTAAAAAAAAGCCGAAATTCATTTATAAT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2116:TDE2117|TDE2116:TDE2117:hypothetical protein:hypothetical protein:<-->:2147799..2147945 147 cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: NC_002967_TDE2116_TDE2117|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2147799,2147945]|147 HSP 1 e-value: 1.0E-49 bit: 196.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacnnnnnnnnaataaaaatctctaaaaactacttnnnnnnnngccgaaattcatttataatagtataaat cttaccaaaccttaattcgatgcacttaaaaaagtcatctatataaaaaactcctatatcaattttcggctttttatacttttttttaataaaaatctctaaaaactacttaaaaaaaagccgaaattcatttataatagtataaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUACCAAACCUUAAUUCGAUGCACUUAAAAAAGUCAUCUAUAUAAAAAACUCCUAUAUCAAUUUUCGGCUUUUUAUACUUUUUUUUAAUAAAAAUCUCUAAAAACUACUUAAAAAAAAGCCGAAAUUCAUUUAUAAUAGUAUAAAU ..................((((.((((....))))))))..........(((..((((.....((((((((((((.......((((((...........)))))).........))))))))))))......))))..)))...... (-21.29) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAUACUAUUAUAAAUGAAUUUCGGCUUUUUUUUAAGUAGUUUUUAGAGAUUUUUAUUAAAAAAAAGUAUAAAAAGCCGAAAAUUGAUAUAGGAGUUUUUUAUAUAGAUGACUUUUUUAAGUGCAUCGAAUUAAGGUUUGGUAAG .....(((((...........((((((((((((.....(((.(((((...(((....)))...))))).)))))))))))))))....((((((((...)))))))).((((((((....)))).))))...........))))).. (-25.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 736 70 21 161 112 NC_002967:TDE2116|5end_hypothetical_protein_2147708..2147938_NEGATIVE 237 46 4 78 39 NC_002967:TDE2336|5end_sodium/dicarboxylate_symporter_family_protein_2373196..2373426_NEGATIVE 235 55 21 102 56 NC_002967:TDE1798|5end_hypothetical_protein_1836676..1836906_NEGATIVE 229 132 92 53 8 NC_002967:TDE2149|5end_transglycosylase,_SLT_family_2187293..2187523_NEGATIVE 227 88 53 228 187 NC_002967:TDE1863|5end_Holliday_junction_DNA_helicase_RuvA_1888579..1888809_NEGATIVE 214 43 1 119 65 NC_002967:TDE1875|5end_hypothetical_protein_1896906..1897136_NEGATIVE 214 74 33 103 56 NC_002967:TDE1094|5end_hypothetical_protein_1128065..1128295_POSITIVE 211 75 35 120 85 NC_002967:TDE0296|5end_formiminotransferase,_putative_327741..327971_NEGATIVE 210 68 21 187 136 NC_002967:TDE1659|5end_alanyl-tRNA_synthetase_1710633..1710863_NEGATIVE 209 42 4 113 72 NC_002967:TDE2166|5end_hydrogenase_nickel_insertion_protein_HypA_2198084..2198314_NEGATIVE 209 99 52 118 66 NC_002967:TDE1355|5end_hypothetical_protein_1395109..1395339_POSITIVE 204 105 65 107 56 NC_002967:TDE1753|5end_UDP-glucose_4-epimerase_1806540..1806770_NEGATIVE 204 84 50 135 97 NC_002967:TDE1212|5end_flagellar_basal-body_rod_protein_FlgB_1245374..1245604_POSITIVE 202 75 41 112 70 NC_002967:TDE1245|5end_hypothetical_protein_1278894..1279124_NEGATIVE 200 104 67 105 64 NC_002967:TDE2155|5end_50S_ribosomal_protein_L35_2190165..2190395_NEGATIVE 198 102 61 42 3 NC_002967:TDE2585|5end_methyl-accepting_chemotaxis_domain/unknown_domain_protein_2620303..2620533_NEGATIVE 198 86 51 166 127 NC_002967:TDE0990|5end_hypothetical_protein_1017398..1017628_POSITIVE 197 74 51 127 99 NC_002967:TDE0182|5end_ABC_transporter,_ATP-binding_protein_216783..217013_NEGATIVE 194 42 10 105 73 NC_002967:TDE2263|5end_acetyl_hydrolase,_putative_2300191..2300421_NEGATIVE 190 46 5 192 147 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 55 21 89 43 NC_002967:TDE1799|3end_hypothetical_protein_1836689..1836839_NEGATIVE 229 132 92 92 47 NC_002967:TDE2150|3end_hypothetical_protein_2187254..2187404_NEGATIVE 222 69 31 128 83 NC_002967:TDE1305|3end_DNA-binding_protein_1340398..1340548_POSITIVE 214 43 1 86 32 NC_002967:TDE1876|3end_glycosyl_transferase,_WecB/TagA/CpsF_family_1896939..1897089_NEGATIVE 214 74 33 116 69 NC_002967:TDE1093|3end_hypothetical_protein_1128158..1128308_POSITIVE 211 75 35 65 30 NC_002967:TDE0297|3end_hypothetical_protein_327796..327946_NEGATIVE 210 68 21 110 59 NC_002967:TDE1660|3end_leucine_Rich_Repeat_domain_protein_1710710..1710860_NEGATIVE 209 42 4 94 53 NC_002967:TDE2167|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2198103..2198253_NEGATIVE 209 99 52 134 82 NC_002967:TDE1354|3end_hypothetical_protein_1395205..1395355_POSITIVE 204 84 50 83 45 NC_002967:TDE1211|3end_ATP-dependent_protease_ATP-binding_subunit_1245402..1245552_POSITIVE 201 91 51 128 88 NC_002967:TDE0241|3end_hypothetical_protein_274701..274851_NEGATIVE 200 104 67 78 37 NC_002967:TDE2156|3end_translation_initiation_factor_IF-3_2190192..2190342_NEGATIVE 198 102 61 94 55 NC_002967:TDE2586|3end_DNA_polymerase_III_subunits_gamma_and_tau_2620251..2620401_NEGATIVE 198 86 51 136 97 NC_002967:TDE0989|3end_hypothetical_protein_1017448..1017598_POSITIVE 197 74 51 127 99 NC_002967:TDE0183|3end_ABC_transporter,_permease_protein_216783..216933_NEGATIVE 194 42 10 53 21 NC_002967:TDE2264|3end_ABC_transporter,_ATP-binding/permease_protein_2300243..2300393_NEGATIVE 190 46 5 147 102 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 190 75 33 134 93 NC_002967:TDE2370|3end_hypothetical_protein_2403607..2403757_POSITIVE 188 100 51 147 87 NC_002967:TDE1144|3end_hypothetical_protein_1181848..1181998_NEGATIVE 187 108 67 65 10 NC_002967:TDE2029|3end_hydrolase,_TatD_family_2057148..2057298_NEGATIVE