Origin IGS: atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattaaaattccttaatgtaatctaaattttctttactataacaaaactctgccccgccatatcaatatgatccttatactcttctacagtcagcttgaaaaggttttgcacataaaaaagctcttttttttcaaaagagcataagaaacctttgcttttttatattttttataaaaaagctcatcttaaaaaaatgaccagctgcctgcaaaagatcgccgaaacagattccaatgccggaaaacttcaatattccgtgataatacaacaaaaaacaaagattttcaataggttacagctatttaaaacaaaatgtctacat Mask Tandem Repeat Region ================================================ atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt Find is-nt database================================================ Query_seq: TDE1412:TDE1413|TDE1412:TDE1413:sodium/hydrogen exchanger family protein:cytidylyltransferase/phosphoenolpyruvate phosphomutase, putative:->->:1455327..1455649 323 atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1412:TDE1413|TDE1412:TDE1413:sodium/hydrogen exchanger family protein:cytidylyltransferase/phosphoenolpyruvate phosphomutase, putative:->->:1455327..1455649 323 atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1412:TDE1413|TDE1412:TDE1413:sodium/hydrogen exchanger family protein:cytidylyltransferase/phosphoenolpyruvate phosphomutase, putative:->->:1455327..1455649 323 atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 45 End: 134 ............................................ M F F V V L S R N I E V F R H W N L F R R S F A G S W S F F ............................................................................................................................................................................................. Protein_Len: 52 Strand: + Start: 34 End: 189 ................................. M E N L C F L L Y Y H G I L K F S G I G I C F G D L L Q A A G H F F K M S F F I K N I K K Q R F L M L F ...................................................................................................................................... Protein_Len: 31 Strand: - Start: 182 End: 274 ..................................................................................................................................................................................... A R K F F F L K K I H L V K E L Q S Y F L I L I M N I H R P M ................................................. Protein_Len: 57 Strand: - Start: 1 End: 171 H L C K T K F L Q L R N F I K T K Q Q I I V S Y Q L K G A N S D T E A I K Q L C S T M K K L H A K K Y F I Y F L M ........................................................................................................................................................ atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt 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: 88 Start: 34 End: 63 .................................ATTGAAAATCTTTGTTTTTTGTTGTATTAT.................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -3.3 Tail_Score: -5.24531 Start: 124 End: 144 Full_Region: CTTTTGCAGGCAGCT GGTCATTTT TTT AAGATGAGC TTTTTTATAAAAAAT ...........................................................................................................................GGTCATTTTTTTAAGATGAGC................................................................................................................................................................................... TransTerm Strand: + Conf: 44 HP_score: -3.6 Tail_Score: -2.52404 Start: 140 End: 172 Full_Region: GTCATTTTTTTAAGA TGAGCTTTTTTATA AAAAA TATAAAAAAGCAAA GGTTTCTTATGCTCT ...........................................................................................................................................TGAGCTTTTTTATAAAAAATATAAAAAAGCAAA....................................................................................................................................................... TransTerm Strand: - Conf: 46 HP_score: -3.6 Tail_Score: -3.02511 Start: 140 End: 172 Full_Region: agagcataagaaacc tttgcttttttata ttttt tataaaaaagctca tcttaaaaaaatgac ...........................................................................................................................................tttgcttttttatattttttataaaaaagctca....................................................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -9.7 Tail_Score: -2.73994 Start: 143 End: 169 Full_Region: gcataagaaaccttt gcttttttata ttttt tataaaaaagc tcatcttaaaaaaat ..............................................................................................................................................gcttttttatattttttataaaaaagc.......................................................................................................................................................... TransTerm Strand: + Conf: 95 HP_score: -8.4 Tail_Score: -5.36441 Start: 183 End: 203 Full_Region: GCAAAGGTTTCTTAT GCTCTTTT GAAAA AAAAGAGC TTTTTTATGTGCAAA ......................................................................................................................................................................................GCTCTTTTGAAAAAAAAGAGC........................................................................................................................ Find igs database================================================ Query_seq: TDE1412:TDE1413|TDE1412:TDE1413:sodium/hydrogen exchanger family protein:cytidylyltransferase/phosphoenolpyruvate phosphomutase, putative:->->:1455327..1455649 323 atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt Intra-Species Hit: Count: 1 Min: 1 Max: 323 Len: 323 Subject: NC_002967_TDE1412_TDE1413|sodium/hydrogen exchanger family protein:cytidylyltransferase/phosphoenolpyruvate phosphomutase, putative|POSITIVE:POSITIVE|[1455327,1455649]|323 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 323 Query Start:1 Query End:323 Subject Strand: POSITIVE Subject Start: 1 Subject End: 323 atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcannnnnnnaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgnnnnnnnngagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt atgtagacattttgttttaaatagctgtaacctattgaaaatctttgttttttgttgtattatcacggaatattgaagttttccggcattggaatctgtttcggcgatcttttgcaggcagctggtcatttttttaagatgagcttttttataaaaaatataaaaaagcaaaggtttcttatgctcttttgaaaaaaaagagcttttttatgtgcaaaaccttttcaagctgactgtagaagagtataaggatcatattgatatggcggggcagagttttgttatagtaaagaaaatttagattacattaaggaattttaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUAGACAUUUUGUUUUAAAUAGCUGUAACCUAUUGAAAAUCUUUGUUUUUUGUUGUAUUAUCACGGAAUAUUGAAGUUUUCCGGCAUUGGAAUCUGUUUCGGCGAUCUUUUGCAGGCAGCUGGUCAUUUUUUUAAGAUGAGCUUUUUUAUAAAAAAUAUAAAAAAGCAAAGGUUUCUUAUGCUCUUUUGAAAAAAAAGAGCUUUUUUAUGUGCAAAACCUUUUCAAGCUGACUGUAGAAGAGUAUAAGGAUCAUAUUGAUAUGGCGGGGCAGAGUUUUGUUAUAGUAAAGAAAAUUUAGAUUACAUUAAGGAAUUUUAAUU ...(((..((((......))))..)))...(((..((..(((((..(((((((....((((((.(((((((.........(((((....)))))(((((..((.(..((((((((((.(((((..((((((.....))))))(((((((((((.....))))))))))).(((((((..(((((((((((.....))))))))........)))..)))))))....))))).))))))))))........(((.....)))..).))..)))))))))))).)))))).)))))))..))))).))...))).......... (-82.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAAAUUCCUUAAUGUAAUCUAAAUUUUCUUUACUAUAACAAAACUCUGCCCCGCCAUAUCAAUAUGAUCCUUAUACUCUUCUACAGUCAGCUUGAAAAGGUUUUGCACAUAAAAAAGCUCUUUUUUUUCAAAAGAGCAUAAGAAACCUUUGCUUUUUUAUAUUUUUUAUAAAAAAGCUCAUCUUAAAAAAAUGACCAGCUGCCUGCAAAAGAUCGCCGAAACAGAUUCCAAUGCCGGAAAACUUCAAUAUUCCGUGAUAAUACAACAAAAAACAAAGAUUUUCAAUAGGUUACAGCUAUUUAAAACAAAAUGUCUACAU ................(((((((((.....(((((.............((((...((.(..(((.....)))........((((...(((.(((((.(.(((((((((............((((((((.....))))))))....)))))))))(((((((((((.....))))))))))).................).))))).)))...))))..).))...)))).........(((((..........)))))...................))))).......)))))))))......................... (-54.89) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 123 83 60 16 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 343 127 84 209 159 NC_002967:TDE2008|5end_ABC_transporter,_ATP-binding/permease_protein_2028578..2028808_POSITIVE 343 122 81 172 122 NC_002967:TDE1165|5end_hypothetical_protein_1198390..1198620_NEGATIVE 337 127 84 217 172 NC_002967:TDE1096|5end_hydroxymethylbutenyl_pyrophosphate_reductase_1130989..1131219_POSITIVE 337 137 96 197 159 NC_002967:TDE0931|5end_MATE_efflux_family_protein_955107..955337_NEGATIVE 326 120 80 90 57 NC_002967:TDE2373|5end_precorrin-6Y_C5,15-methyltransferase,_putative_2405123..2405353_POSITIVE 324 76 31 147 100 NC_002967:TDE2416|5end_hypothetical_protein_2442799..2443029_NEGATIVE 320 118 73 82 30 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 319 128 83 97 46 NC_002967:TDE0587|5end_hypothetical_protein_625749..625979_POSITIVE 318 230 184 150 104 NC_002967:TDE1644|5end_methionyl-tRNA_formyltransferase_1695546..1695776_NEGATIVE 318 135 95 197 158 NC_002967:TDE0837|5end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_857109..857339_NEGATIVE 317 124 83 62 9 NC_002967:TDE2644|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2683651..2683881_POSITIVE 316 150 101 209 150 NC_002967:TDE0859|5end_hypothetical_protein_880100..880330_POSITIVE 312 105 63 58 18 NC_002967:TDE2574|5end_conserved_hypothetical_protein_TIGR00650_2600376..2600606_POSITIVE 304 130 84 92 44 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 301 128 83 66 13 NC_002967:TDE1356|5end_lipoprotein,_putative_1396669..1396899_NEGATIVE 300 136 94 65 20 NC_002967:TDE0574|5end_surface_protein,_putative_604925..605155_POSITIVE 295 125 82 84 33 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 295 127 83 223 171 NC_002967:TDE1300|5end_hypothetical_protein_1337419..1337649_NEGATIVE 293 127 84 200 134 NC_002967:TDE2057|5end_hypothetical_protein_2085343..2085573_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 125 83 150 98 NC_002967:TDE0994|3end_hypothetical_protein_1022447..1022597_POSITIVE 382 126 83 61 12 NC_002967:TDE1347|3end_hypothetical_protein_1388032..1388182_POSITIVE 326 120 80 86 53 NC_002967:TDE2372|3end_hypothetical_protein_2405199..2405349_POSITIVE 324 76 31 134 87 NC_002967:TDE2417|3end_nitroimidazole_resistance_protein,_putative_2442812..2442962_NEGATIVE 317 124 83 65 12 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 312 105 63 61 21 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 309 125 81 149 100 NC_002967:TDE2066|3end_exodeoxyribonuclease_VII,_small_subunit_2092222..2092372_POSITIVE 306 128 83 148 96 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 301 226 184 147 107 NC_002967:TDE1645|3end_polypeptide_deformylase_1695543..1695693_NEGATIVE 298 118 76 55 1 NC_002967:TDE2179|3end_voltage-gated_chloride_channel_2210614..2210764_POSITIVE 296 128 83 62 5 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 295 135 98 134 96 NC_002967:TDE0871|3end_hypothetical_protein_894657..894807_NEGATIVE 293 113 73 146 91 NC_002967:TDE0996|3end_hypothetical_protein_1023998..1024148_POSITIVE 292 115 71 141 79 NC_002967:TDE2609|3end_MiaB-like_tRNA_modifying_enzyme_YliG,_TIGR01125_2651904..2652054_POSITIVE 292 290 250 85 27 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 292 124 84 124 73 NC_002967:TDE0790|3end_30S_ribosomal_protein_S11_817411..817561_POSITIVE 291 124 81 46 5 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 290 127 84 151 105 NC_002967:TDE0937|3end_RNA_polymerase_sigma-70_factor_family_protein_960891..961041_POSITIVE 287 123 84 130 96 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 286 149 102 70 1 NC_002967:TDE1194|3end_hypothetical_protein_1227623..1227773_POSITIVE