Origin IGS: tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct .........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 aggagctactccatgtggaattcctaattcatcgagaagatgattttcaaactgaggaatggtaagccaagctctgccttttaataattttatacgggagtcatctttattcggcataatattagtattctcttaaaggcatattttcttttttttgctttagcttgtcaatcgggttcgtttgtgctattattaaattacatgatatcgttttttacggaggagtttttaaa Mask Tandem Repeat Region ================================================ tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct Find is-nt database================================================ Query_seq: TDE2540:TDE2541|TDE2540:TDE2541:lipoprotein, putative:hypothetical protein:<-->:2568072..2568304 233 tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2540:TDE2541|TDE2540:TDE2541:lipoprotein, putative:hypothetical protein:<-->:2568072..2568304 233 tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2540:TDE2541|TDE2540:TDE2541:lipoprotein, putative:hypothetical protein:<-->:2568072..2568304 233 tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 114 End: 233 ................................................................................................................. M M P N K D D S R I K L L K G R A W L T I P Q F E N H L L D E L G I P H G V A P Protein_Len: 43 Strand: - Start: 3 End: 131 .. L F E E T F F S I M Y N L L L V F S G S Q C A L A F F L F Y A K L L I S I N H R I F M ...................................................................................................... Protein_Len: 31 Strand: - Start: 1 End: 93 K F V G G Y F V I D H L K I I A C V F G I S L S F C F F S F M ............................................................................................................................................ tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct 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: 41 End: 70 ........................................CTTGTCAATCGGGTTCGTTTGTGCTATTAT................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2540:TDE2541|TDE2540:TDE2541:lipoprotein, putative:hypothetical protein:<-->:2568072..2568304 233 tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: NC_002967_TDE2540_TDE2541|lipoprotein, putative:hypothetical protein|NEGATIVE:POSITIVE|[2568072,2568304]|233 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 233 Query Start:1 Query End:233 Subject Strand: POSITIVE Subject Start: 1 Subject End: 233 tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcnnnnnnnngaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct tttaaaaactcctccgtaaaaaacgatatcatgtaatttaataatagcacaaacgaacccgattgacaagctaaagcaaaaaaaagaaaatatgcctttaagagaatactaatattatgccgaataaagatgactcccgtataaaattattaaaaggcagagcttggcttaccattcctcagtttgaaaatcatcttctcgatgaattaggaattccacatggagtagctcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAAAACUCCUCCGUAAAAAACGAUAUCAUGUAAUUUAAUAAUAGCACAAACGAACCCGAUUGACAAGCUAAAGCAAAAAAAAGAAAAUAUGCCUUUAAGAGAAUACUAAUAUUAUGCCGAAUAAAGAUGACUCCCGUAUAAAAUUAUUAAAAGGCAGAGCUUGGCUUACCAUUCCUCAGUUUGAAAAUCAUCUUCUCGAUGAAUUAGGAAUUCCACAUGGAGUAGCUCCU ........((.((((((................................(((((......((.((..(((((((.((...............(((((((.......((.((((.((((((.(..............).)))))).)))).)))))))))..)))))))))..)).))....)))))....(((((.....)))))....((....))..)))))).))..... (-36.68) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAGCUACUCCAUGUGGAAUUCCUAAUUCAUCGAGAAGAUGAUUUUCAAACUGAGGAAUGGUAAGCCAAGCUCUGCCUUUUAAUAAUUUUAUACGGGAGUCAUCUUUAUUCGGCAUAAUAUUAGUAUUCUCUUAAAGGCAUAUUUUCUUUUUUUUGCUUUAGCUUGUCAAUCGGGUUCGUUUGUGCUAUUAUUAAAUUACAUGAUAUCGUUUUUUACGGAGGAGUUUUUAAA (((((((.((((..((((((..(.....(((((((((((((((((..(............(((((((...))).))))...(((.....)))...)..))))))))))..)))...(((((.((((((...(...((((((..............)))))).(((((.....)))))..)...)))))).)))))......))))....)..)))))))))).)))))))... (-49.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 824 140 91 231 182 NC_002967:TDE2540|5end_lipoprotein,_putative_2567981..2568211_NEGATIVE 298 180 136 199 139 NC_002967:TDE2380|5end_hypothetical_protein_2409819..2410049_POSITIVE 282 200 156 69 29 NC_002967:TDE0553|5end_hypothetical_protein_590307..590537_NEGATIVE 274 201 161 109 61 NC_002967:TDE2247|5end_PemK_family_protein_2286362..2286592_POSITIVE 269 202 161 158 125 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 263 186 146 203 156 NC_002967:TDE1646|5end_hypothetical_protein_1696180..1696410_NEGATIVE 263 168 127 146 104 NC_002967:TDE0259|5end_transcriptional_regulator,_MarR_family_293257..293487_POSITIVE 259 199 152 149 105 NC_002967:TDE2574|5end_conserved_hypothetical_protein_TIGR00650_2600376..2600606_POSITIVE 259 168 125 230 190 NC_002967:TDE2330|5end_hypothetical_protein_2366454..2366684_POSITIVE 259 179 134 137 77 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 257 198 154 144 96 NC_002967:TDE1104|5end_tRNA_pseudouridine_synthase_B_1137786..1138016_NEGATIVE 256 182 155 39 10 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 250 173 136 218 168 NC_002967:TDE2297|5end_TPR_domain_protein_2337019..2337249_NEGATIVE 250 188 144 53 3 NC_002967:TDE1427|5end_glycosyl_transferase,_group_1_family_protein_1469713..1469943_POSITIVE 248 178 156 225 195 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 248 198 156 64 23 NC_002967:TDE0512|5end_hypothetical_protein_561442..561672_NEGATIVE 246 180 134 156 99 NC_002967:TDE0556|5end_hypothetical_protein_592092..592322_NEGATIVE 240 196 155 225 190 NC_002967:TDE0776|5end_ribosomal_protein_S17_810818..811048_POSITIVE 239 192 155 223 185 NC_002967:TDE2155|5end_50S_ribosomal_protein_L35_2190165..2190395_NEGATIVE 237 199 155 157 99 NC_002967:TDE1474|5end_hypothetical_protein_1521353..1521583_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 179 132 74 8 NC_002967:TDE1499|3end_adenylosuccinate_lyase,_putative_1546788..1546938_POSITIVE 275 217 171 85 33 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 274 201 161 121 73 NC_002967:TDE2246|3end_hypothetical_protein_2286454..2286604_POSITIVE 259 168 125 60 20 NC_002967:TDE2328|3end_efflux_pump_component_MtrF_2366364..2366514_POSITIVE 259 179 134 61 1 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 257 198 154 129 81 NC_002967:TDE1105|3end_ribosome-binding_factor_A_1137801..1137951_NEGATIVE 256 182 155 42 13 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 251 180 137 57 7 NC_002967:TDE1426|3end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1469805..1469955_POSITIVE 250 173 136 124 74 NC_002967:TDE2298|3end_galactokinase,_putative_2337113..2337263_NEGATIVE 246 197 156 75 26 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 246 197 156 107 58 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 246 180 134 102 45 NC_002967:TDE0557|3end_hypothetical_protein_592146..592296_NEGATIVE 242 207 161 71 27 NC_002967:TDE0460|3end_transporter,_putative_515274..515424_NEGATIVE 240 198 152 151 108 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 234 199 154 136 77 NC_002967:TDE0041|3end_birA_bifunctional_protein_48635..48785_POSITIVE 231 199 155 151 105 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 228 219 171 140 87 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 224 165 134 107 70 NC_002967:TDE1281|3end_hypothetical_protein_1316852..1317002_POSITIVE 224 96 53 54 12 NC_002967:TDE0390|3end_hypothetical_protein_441583..441733_POSITIVE 223 179 134 91 61 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE