Origin IGS: acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat .........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 ataattttagaagtaataaatttttattaacaaagcgataggttgaagcttacaagattattcaaagcctaattctgacatagataagaaattttgttgagctctataaaaagaaaatggatgaattgagcattaaggatacaagtaaatacttataaatcctaatttaaggagatatgt Mask Tandem Repeat Region ================================================ acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat Find is-nt database================================================ Query_seq: TDE1774:TDE1775|TDE1774:TDE1775:hypothetical protein:hypothetical protein:<-<-:1817980..1818159 180 acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1774:TDE1775|TDE1774:TDE1775:hypothetical protein:hypothetical protein:<-<-:1817980..1818159 180 acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1774:TDE1775|TDE1774:TDE1775:hypothetical protein:hypothetical protein:<-<-:1817980..1818159 180 acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat Predict ORF larger than 30AA ================================================ acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat 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================================================ acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1774:TDE1775|TDE1774:TDE1775:hypothetical protein:hypothetical protein:<-<-:1817980..1818159 180 acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_002967_TDE1774_TDE1775|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1817980,1818159]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat acatatctccttaaattaggatttataagtatttacttgtatccttaatgctcaattcatccattttctttttatagagctcaacaaaatttcttatctatgtcagaattaggctttgaataatcttgtaagcttcaacctatcgctttgttaataaaaatttattacttctaaaattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUAUCUCCUUAAAUUAGGAUUUAUAAGUAUUUACUUGUAUCCUUAAUGCUCAAUUCAUCCAUUUUCUUUUUAUAGAGCUCAACAAAAUUUCUUAUCUAUGUCAGAAUUAGGCUUUGAAUAAUCUUGUAAGCUUCAACCUAUCGCUUUGUUAAUAAAAAUUUAUUACUUCUAAAAUUAU ................((((...(((((((....)))))))..((((.......(((((.((...((((...((((((..................))))))..))))...))...))))).......))))......)))).........((((((....))))))............. (-19.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUUUUAGAAGUAAUAAAUUUUUAUUAACAAAGCGAUAGGUUGAAGCUUACAAGAUUAUUCAAAGCCUAAUUCUGACAUAGAUAAGAAAUUUUGUUGAGCUCUAUAAAAAGAAAAUGGAUGAAUUGAGCAUUAAGGAUACAAGUAAAUACUUAUAAAUCCUAAUUUAAGGAGAUAUGU .......(((((((.....)))))))(((((((((...(((((((((.((....))....))))..))))).((((..........)))).))))))))).((((.((((.........((((.......)))).(((((..((((....))))....)))))..)))).))))...... (-23.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 787 140 91 231 182 NC_002967:TDE1774|5end_hypothetical_protein_1817889..1818119_NEGATIVE 266 83 42 198 163 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 239 118 76 117 66 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 237 146 111 53 21 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 231 146 102 222 173 NC_002967:TDE1917|5end_cytidylyltransferase_domain_protein_1937394..1937624_NEGATIVE 228 89 42 229 182 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 226 46 1 133 88 NC_002967:TDE0923|5end_ABC_transporter,_ATP-binding/permease_protein_945731..945961_NEGATIVE 224 151 112 162 128 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 223 150 108 197 154 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 221 108 67 42 2 NC_002967:TDE1442|5end_histidyl-tRNA_synthetase_1487416..1487646_POSITIVE 215 155 116 46 3 NC_002967:TDE1995|5end_magnesium_chelatase_family_protein_2012464..2012694_POSITIVE 212 103 64 165 124 NC_002967:TDE0035|5end_acetyltransferase,_GNAT_family_42020..42250_NEGATIVE 211 148 105 59 21 NC_002967:TDE0685|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_722620..722850_NEGATIVE 209 146 112 40 5 NC_002967:TDE2726|5end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2784169..2784399_NEGATIVE 209 148 104 100 55 NC_002967:TDE2578|5end_hypothetical_protein_2603154..2603384_NEGATIVE 209 90 41 109 62 NC_002967:TDE0504|5end_hypothetical_protein_558104..558334_NEGATIVE 206 151 113 55 14 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 205 141 111 133 108 NC_002967:TDE1242|5end_hypothetical_protein_1274565..1274795_POSITIVE 204 160 112 79 11 NC_002967:TDE2500|5end_DJ-1_family_protein_2524506..2524736_NEGATIVE 204 81 43 147 115 NC_002967:TDE1291|5end_HD_domain_protein_1329213..1329443_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 150 109 137 95 NC_002967:TDE0249|3end_flavoredoxin,_putative_283182..283332_POSITIVE 239 118 76 124 73 NC_002967:TDE0796|3end_histidinol_phosphate_phosphatase_HisJ_family_protein_820946..821096_POSITIVE 230 148 101 148 92 NC_002967:TDE1409|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1452381..1452531_POSITIVE 226 46 1 113 68 NC_002967:TDE0924|3end_ABC_transporter,_ATP-binding/permease_protein_945751..945901_NEGATIVE 225 145 104 62 26 NC_002967:TDE0763|3end_hypothetical_protein_804234..804384_NEGATIVE 219 88 42 151 105 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 218 82 42 123 88 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 215 146 104 119 79 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 214 150 104 57 8 NC_002967:TDE1463|3end_hypothetical_protein_1512206..1512356_NEGATIVE 212 103 64 50 9 NC_002967:TDE0036|3end_hypothetical_protein_42135..42285_NEGATIVE 209 54 18 133 100 NC_002967:TDE1084|3end_folylpolyglutamate_synthetase,_putative_1114934..1115084_NEGATIVE 205 141 111 140 115 NC_002967:TDE1241|3end_HD_domain_protein_1274652..1274802_POSITIVE 205 141 105 78 39 NC_002967:TDE0433|3end_hypothetical_protein_488553..488703_NEGATIVE 204 146 109 64 24 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 204 81 43 46 14 NC_002967:TDE1292|3end_TldD/PmbA_family_protein_1329314..1329464_NEGATIVE 203 150 113 100 65 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 203 149 101 80 37 NC_002967:TDE0663|3end_hypothetical_protein_697840..697990_NEGATIVE 200 48 1 99 40 NC_002967:TDE1477|3end_flagellar_filament_core_protein_1522473..1522623_NEGATIVE 198 118 78 149 104 NC_002967:TDE1460|3end_hypothetical_protein_1508707..1508857_NEGATIVE 197 154 111 75 15 NC_002967:TDE2639|3end_oligoendopeptidase_F_2680089..2680239_POSITIVE