Origin IGS: agagtctccctcttagattaaaaatctaagacctaaataatacaaaaaaacttaaaattagtaaataaatgaggataaattcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt .........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 aaataggtctccagtataatttagagtattttgattacaatttataaattaggatacttacaaaatatccggttaagatatgattgtgcaaaaatatcatattttcgaatttttttcaagcggttaagataaaaaaataaaattttatcactaatacatgattgcccacataggtaagaatttatcctcatttatttactaattttaagtttttttgtattatttaggtcttagatttttaatctaagagggagactct Mask Tandem Repeat Region ================================================ agagtctccctcttagattaaaaatctaagacctaaataatacaaaaaaacttaaaattagtaaataaatgaggataaattcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt Find is-nt database================================================ Query_seq: TDE0337:TDE0338|TDE0337:TDE0338:glucosamine-6-phosphate deaminase:methyl-accepting chemotaxis protein-like protein:<-->:377198..377456 259 agagtctccctcttagattaaaaatctaagacctaaataatacaaaaaaacttaaaattagtaaataaatgaggataaattcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0337:TDE0338|TDE0337:TDE0338:glucosamine-6-phosphate deaminase:methyl-accepting chemotaxis protein-like protein:<-->:377198..377456 259 agagtctccctcttagattaaaaatctaagacctaaataatacaaaaaaacttaaaattagtaaataaatgaggataaattcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0337:TDE0338|TDE0337:TDE0338:glucosamine-6-phosphate deaminase:methyl-accepting chemotaxis protein-like protein:<-->:377198..377456 259 agagtctccctcttagattaaaaatctaagacctaaataatacaaaaaaacttaaaattagtaaataaatgaggataaattcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agagtctccctcttagattaaaaatctaagacctaaataatacaaaaaaacttaaaattagtaaataaatgaggataaattcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 69 End: 215 .................................................................... M R I N S Y L C G Q S C I S D K I L F F Y L N R L K K I R K Y D I F A Q S Y L N R I F C K Y P N L ............................................ Protein_Len: 34 Strand: - Start: 131 End: 232 .................................................................................................................................. R L R K F F I R F Y S I K A C D Y R L R I N Q L Y G L K Y I T I L M ........................... agagtctccctcttagattaaaaatctaagacctaaataatacaaaaaaacttaaaattagtaaataaatgaggataaattcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt 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: 84 Start: 37 End: 66 ....................................ATTTACTAATTTTAAGTTTTTTTGTATTAT................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 140 End: 169 ...........................................................................................................................................CTTGAAAAAAATTCGAAAATATGATATTTT.......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agagtctccctcttagattaaaaatctaagacctaaataatacaaaaaaacttaaaattagtaaataaatgaggataaattcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0337:TDE0338|TDE0337:TDE0338:glucosamine-6-phosphate deaminase:methyl-accepting chemotaxis protein-like protein:<-->:377198..377456 259 agagtctccctcttagattaaaaatctaagacctaaataatacaaaaaaacttaaaattagtaaataaatgaggataaattcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt Intra-Species Hit: Count: 1 Min: 81 Max: 259 Len: 179 Subject: NC_002967_TDE0337_TDE0338|glucosamine-6-phosphate deaminase:methyl-accepting chemotaxis protein-like protein|NEGATIVE:POSITIVE|[377198,377456]|259 HSP 1 e-value: 6.0E-72 bit: 272.0 Len: 179 Query Start:81 Query End:259 Subject Strand: POSITIVE Subject Start: 81 Subject End: 259 ................................................................................tcttacctatgtgggcaatcatgtattagtgataaaattttannnnnnnatcttaaccgcttgnnnnnnnttcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt ................................................................................tcttacctatgtgggcaatcatgtattagtgataaaattttatttttttatcttaaccgcttgaaaaaaattcgaaaatatgatatttttgcacaatcatatcttaaccggatattttgtaagtatcctaatttataaattgtaatcaaaatactctaaattatactggagacctattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUACCUAUGUGGGCAAUCAUGUAUUAGUGAUAAAAUUUUAUUUUUUUAUCUUAACCGCUUGAAAAAAAUUCGAAAAUAUGAUAUUUUUGCACAAUCAUAUCUUAACCGGAUAUUUUGUAAGUAUCCUAAUUUAUAAAUUGUAAUCAAAAUACUCUAAAUUAUACUGGAGACCUAUUU ..........(((((..(((((((......(((((((........)))))))........(((((.....)))))..)))))))..(((((.(((((.(((..(((...(((((((.....))))))))))..)))..)))))...)))))..(((((........))))).))))).. (-26.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAGGUCUCCAGUAUAAUUUAGAGUAUUUUGAUUACAAUUUAUAAAUUAGGAUACUUACAAAAUAUCCGGUUAAGAUAUGAUUGUGCAAAAAUAUCAUAUUUUCGAAUUUUUUUCAAGCGGUUAAGAUAAAAAAAUAAAAUUUUAUCACUAAUACAUGAUUGCCCACAUAGGUAAGA .............((((......(((((((((((((..........))))))))))))).........(((...((((((((((.((......)))))))))))).(((.....)))...)))....(((((((........)))))))....))))....(((((......))))).. (-29.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 725 60 11 231 182 NC_002967:TDE0337|5end_glucosamine-6-phosphate_deaminase_377107..377337_NEGATIVE 289 93 55 168 126 NC_002967:TDE1326|5end_hypothetical_protein_1361661..1361891_POSITIVE 244 120 86 54 21 NC_002967:TDE2346|5end_elongation_factor_Ts_2383429..2383659_NEGATIVE 210 128 90 228 195 NC_002967:TDE1744|5end_chromate_transport_protein_1799090..1799320_NEGATIVE 208 98 59 201 162 NC_002967:TDE1754|5end_desulfoferrodoxin/neelaredoxin_1807023..1807253_NEGATIVE 197 129 81 197 143 NC_002967:TDE0737|5end_hypothetical_protein_775674..775904_NEGATIVE 196 123 81 43 2 NC_002967:TDE1843|5end_hypothetical_protein_1873005..1873235_NEGATIVE 193 94 57 42 4 NC_002967:TDE1953|5end_transcriptional_regulator,_TetR_family_1969671..1969901_NEGATIVE 193 111 71 185 139 NC_002967:TDE0753|5end_hypothetical_protein_793200..793430_POSITIVE 192 70 28 224 175 NC_002967:TDE0709|5end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_745434..745664_NEGATIVE 191 126 92 188 155 NC_002967:TDE2674|5end_hypothetical_protein_2713277..2713507_NEGATIVE 190 126 103 146 118 NC_002967:TDE0085|5end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_101015..101245_NEGATIVE 187 113 71 229 184 NC_002967:TDE0673|5end_hypothetical_protein_711990..712220_POSITIVE 187 66 38 120 86 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 184 123 84 207 168 NC_002967:TDE2275|5end_tRNA_pseudouridine_synthase_A_2311076..2311306_POSITIVE 182 130 83 173 120 NC_002967:TDE2454|5end_hypothetical_protein_2483376..2483606_NEGATIVE 182 128 81 89 37 NC_002967:TDE2334|5end_hypothetical_protein_2368629..2368859_POSITIVE 182 63 41 104 80 NC_002967:TDE1682|5end_V-type_ATP_synthase_subunit_B_1734843..1735073_NEGATIVE 182 36 1 229 183 NC_002967:TDE0397|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_446777..447007_POSITIVE 181 130 90 123 91 NC_002967:TDE2430|5end_bacteriocin_ABC_transporter,_bacteriocin-binding_protein,_putative_2459173..2459403_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 222 132 108 147 122 NC_002967:TDE0007|3end_hypothetical_protein_10808..10958_POSITIVE 211 129 100 107 70 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 204 119 81 76 32 NC_002967:TDE0525|3end_hypothetical_protein_571163..571313_POSITIVE 190 126 103 122 94 NC_002967:TDE0086|3end_hypothetical_protein_101039..101189_NEGATIVE 182 63 41 102 78 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 181 130 90 126 94 NC_002967:TDE2431|3end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_2459170..2459320_NEGATIVE 181 73 38 120 86 NC_002967:TDE2263|3end_acetyl_hydrolase,_putative_2299277..2299427_NEGATIVE 181 100 52 146 90 NC_002967:TDE1667|3end_translation_initiation_factor_IF-2B_subunit_alpha_1719993..1720143_NEGATIVE 181 74 42 68 37 NC_002967:TDE1146|3end_hypothetical_protein_1184824..1184974_NEGATIVE 180 127 91 90 41 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 179 128 81 85 27 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 177 129 108 123 101 NC_002967:TDE2342|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2379238..2379388_NEGATIVE 175 129 82 125 73 NC_002967:TDE2612|3end_hypothetical_protein_2655459..2655609_POSITIVE 175 126 85 145 101 NC_002967:TDE1291|3end_HD_domain_protein_1328638..1328788_NEGATIVE 174 33 1 130 89 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 173 98 51 144 105 NC_002967:TDE1435|3end_hypothetical_protein_1479543..1479693_POSITIVE 169 109 66 80 32 NC_002967:TDE0597|3end_hypothetical_protein_636019..636169_NEGATIVE 169 79 37 136 88 NC_002967:TDE0343|3end_hydrolase,_alpha/beta_fold_family_384247..384397_NEGATIVE 168 126 109 64 47 NC_002967:TDE1261|3end_choline/carnitine/betaine_transporter_family_protein_1297241..1297391_POSITIVE 167 118 75 45 7 NC_002967:TDE1692|3end_hypothetical_protein_1748471..1748621_POSITIVE