Origin IGS: ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt .........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 aactgcactcctttcattgatattatagttaaggttgtttattatttacaccattaactattaagtatattataaaatatctttttaaaaaacgcaagtcttcttttaagttttttttattttatactgacaaagttataaaaaatgcttatattattaagtaaattagtgtagaatttataaataaaacaggaaaaatcggtaaaatacttaaaa Mask Tandem Repeat Region ================================================ ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt Find is-nt database================================================ Query_seq: TDE1667:TDE1668|TDE1667:TDE1668:translation initiation factor IF-2B subunit alpha:amino acid permease family protein:<-->:1721142..1721357 216 ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1667:TDE1668|TDE1667:TDE1668:translation initiation factor IF-2B subunit alpha:amino acid permease family protein:<-->:1721142..1721357 216 ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1667:TDE1668|TDE1667:TDE1668:translation initiation factor IF-2B subunit alpha:amino acid permease family protein:<-->:1721142..1721357 216 ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 56 End: 157 ....................................................... K I I Y A N K I V K D T Y F L F F K F S S K R K K F L Y K I I Y K M ........................................................... ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt 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: 87 Start: 172 End: 201 ...........................................................................................................................................................................ATTGATATTATAGTTAAGGTTGTTTATTAT............... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 119 End: 148 ......................................................................................................................CTTGCGTTTTTTAAAAAGATATTTTATAAT.................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 144 End: 173 ...............................................................................................................................................ATTTACACCATTAACTATTAAGTATATTAT........................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 62 End: 91 .............................................................ACTGACAAAGTTATAAAAAATGCTTATATT............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1667:TDE1668|TDE1667:TDE1668:translation initiation factor IF-2B subunit alpha:amino acid permease family protein:<-->:1721142..1721357 216 ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt Intra-Species Hit: Count: 1 Min: 1 Max: 216 Len: 216 Subject: NC_002967_TDE1667_TDE1668|translation initiation factor IF-2B subunit alpha:amino acid permease family protein|NEGATIVE:POSITIVE|[1721142,1721357]|216 HSP 1 e-value: 1.0E-105 bit: 381.0 Len: 216 Query Start:1 Query End:216 Subject Strand: POSITIVE Subject Start: 1 Subject End: 216 ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaatnnnnnnnncttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt ttttaagtattttaccgatttttcctgttttatttataaattctacactaatttacttaataatataagcattttttataactttgtcagtataaaataaaaaaaacttaaaagaagacttgcgttttttaaaaagatattttataatatacttaatagttaatggtgtaaataataaacaaccttaactataatatcaatgaaaggagtgcagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAGUAUUUUACCGAUUUUUCCUGUUUUAUUUAUAAAUUCUACACUAAUUUACUUAAUAAUAUAAGCAUUUUUUAUAACUUUGUCAGUAUAAAAUAAAAAAAACUUAAAAGAAGACUUGCGUUUUUUAAAAAGAUAUUUUAUAAUAUACUUAAUAGUUAAUGGUGUAAAUAAUAAACAACCUUAACUAUAAUAUCAAUGAAAGGAGUGCAGUU ..(((((((..(((..((....)).(((...(((....)))...))).)))..)))))))........(((((((((...........((((((..((((((....(((...(((((((....)))))))...)))...))))))..))))))..((((((((.(((((.........)).)))))))))))...........))))))))).... (-30.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUGCACUCCUUUCAUUGAUAUUAUAGUUAAGGUUGUUUAUUAUUUACACCAUUAACUAUUAAGUAUAUUAUAAAAUAUCUUUUUAAAAAACGCAAGUCUUCUUUUAAGUUUUUUUUAUUUUAUACUGACAAAGUUAUAAAAAAUGCUUAUAUUAUUAAGUAAAUUAGUGUAGAAUUUAUAAAUAAAACAGGAAAAAUCGGUAAAAUACUUAAAA .((((...((((....(((((......)))))..((((((((..(((((((...(((((....((((((..((((((......(((((((.((....))....)))))))....))))))..)))))).....))))).......((((((......)))))).....)))))))....))))))))...)))).....))))............. (-35.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 652 130 81 221 172 NC_002967:TDE1667|5end_translation_initiation_factor_IF-2B_subunit_alpha_1721051..1721281_NEGATIVE 251 57 11 139 93 NC_002967:TDE1572|5end_hypothetical_protein_1620863..1621093_POSITIVE 239 93 68 144 117 NC_002967:TDE1481|5end_hypothetical_protein_1525657..1525887_POSITIVE 208 49 1 138 91 NC_002967:TDE1916|5end_glycerol_kinase_1934767..1934997_NEGATIVE 201 34 4 121 91 NC_002967:TDE2699|5end_antigen,_putative_2742716..2742946_POSITIVE 200 36 8 41 14 NC_002967:TDE0826|5end_hypothetical_protein_847604..847834_POSITIVE 189 45 13 103 61 NC_002967:TDE1683|5end_V-type_ATP_synthase_subunit_A_1736614..1736844_NEGATIVE 186 154 111 100 52 NC_002967:TDE1293|5end_TldD/PmbA_family_protein_1332003..1332233_NEGATIVE 185 207 163 142 90 NC_002967:TDE1600|5end_ABC_transporter,_ATP-binding/permease_protein_1652396..1652626_NEGATIVE 182 45 11 182 156 NC_002967:TDE0565|5end_hypothetical_protein_597031..597261_POSITIVE 182 60 12 145 106 NC_002967:TDE0480|5end_alpha-L-fucosidase_family_protein_536689..536919_POSITIVE 181 137 113 144 119 NC_002967:TDE2694|5end_hypothetical_protein_2736301..2736531_NEGATIVE 181 45 1 159 122 NC_002967:TDE2487|5end_acetyltransferase,_GNAT_family_2509807..2510037_POSITIVE 181 170 122 115 73 NC_002967:TDE1116|5end_hypothetical_protein_1149664..1149894_NEGATIVE 177 57 11 128 87 NC_002967:TDE2090|5end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2118636..2118866_NEGATIVE 176 42 5 162 127 NC_002967:TDE1784|5end_transcriptional_activator,_AraC_family_1824423..1824653_NEGATIVE 176 172 134 157 119 NC_002967:TDE1530|5end_hypothetical_protein_1575872..1576102_NEGATIVE 174 45 4 132 85 NC_002967:TDE0555|5end_hypothetical_protein_591522..591752_NEGATIVE 173 100 66 138 96 NC_002967:TDE1338|5end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_1374889..1375119_POSITIVE 173 48 7 165 133 NC_002967:TDE1148|5end_hypothetical_protein_1186357..1186587_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 57 16 42 2 NC_002967:TDE1571|3end_hypothetical_protein_1620846..1620996_POSITIVE 208 49 1 141 94 NC_002967:TDE1917|3end_cytidylyltransferase_domain_protein_1934764..1934914_NEGATIVE 201 34 4 100 70 NC_002967:TDE2698|3end_hypothetical_protein_2742775..2742925_POSITIVE 185 207 163 149 97 NC_002967:TDE1601|3end_transcriptional_regulator,_TetR_family_1652389..1652539_NEGATIVE 183 132 106 84 55 NC_002967:TDE0803|3end_hypothetical_protein_826875..827025_POSITIVE 182 45 11 86 60 NC_002967:TDE0564|3end_hypothetical_protein_597015..597165_POSITIVE 181 137 113 71 46 NC_002967:TDE2695|3end_transcript_cleavage_factor/unknown_domain_fusion_protein_2736374..2736524_NEGATIVE 181 45 1 143 106 NC_002967:TDE2486|3end_hypothetical_protein_2509871..2510021_POSITIVE 177 154 112 48 1 NC_002967:TDE1294|3end_phosphocarrier_protein_HPr_1332055..1332205_NEGATIVE 175 169 135 80 47 NC_002967:TDE1833|3end_hypothetical_protein_1866277..1866427_NEGATIVE 175 169 135 80 47 NC_002967:TDE1777|3end_hypothetical_protein_1819956..1820106_NEGATIVE 174 61 21 135 95 NC_002967:TDE0673|3end_hypothetical_protein_713113..713263_POSITIVE 174 45 4 116 69 NC_002967:TDE0556|3end_hypothetical_protein_591538..591688_NEGATIVE 173 48 7 96 64 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 168 45 10 131 100 NC_002967:TDE1485|3end_hypothetical_protein_1530382..1530532_POSITIVE 164 58 11 108 54 NC_002967:TDE1455|3end_prevent-host-death_family_protein_1503211..1503361_POSITIVE 160 58 14 80 42 NC_002967:TDE0784|3end_ribosomal_protein_S5_814492..814642_POSITIVE 158 34 1 109 71 NC_002967:TDE0767|3end_ribosomal_protein_L3_807061..807211_POSITIVE 156 38 15 80 60 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 156 140 106 137 89 NC_002967:TDE1541|3end_metallo-beta-lactamase_family_protein_1585940..1586090_POSITIVE