Origin IGS: aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgttttagacctcttttataacctaatattaaccgatttggcgcataaaaacaaggcaggagaatactataacccatgttgtcaataatattattcaagtattgatattttgatttttttgttatatcataattatgtaagtttaaatttaaaggagtaaatt Mask Tandem Repeat Region ================================================ aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca Find is-nt database================================================ Query_seq: TDE2485:TDE2486|TDE2485:TDE2486:hypothetical protein:hypothetical protein:<-->:2509214..2509376 163 aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2485:TDE2486|TDE2485:TDE2486:hypothetical protein:hypothetical protein:<-->:2509214..2509376 163 aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2485:TDE2486|TDE2485:TDE2486:hypothetical protein:hypothetical protein:<-->:2509214..2509376 163 aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 39 End: 161 ...................................... M T K K S K Y Q Y L N N I I D N M G Y S I L L P C F Y A P N R L I L G Y K R G L K .. aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca 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 .................................ATTGATATTTTGATTTTTTTGTTATATCAT.................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2485:TDE2486|TDE2485:TDE2486:hypothetical protein:hypothetical protein:<-->:2509214..2509376 163 aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_002967_TDE2485_TDE2486|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2509214,2509376]|163 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 aatttactcctttaaatttaaacttacataattatgatataacnnnnnnntcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca aatttactcctttaaatttaaacttacataattatgatataacaaaaaaatcaaaatatcaatacttgaataatattattgacaacatgggttatagtattctcctgccttgtttttatgcgccaaatcggttaatattaggttataaaagaggtctaaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUACUCCUUUAAAUUUAAACUUACAUAAUUAUGAUAUAACAAAAAAAUCAAAAUAUCAAUACUUGAAUAAUAUUAUUGACAACAUGGGUUAUAGUAUUCUCCUGCCUUGUUUUUAUGCGCCAAAUCGGUUAAUAUUAGGUUAUAAAAGAGGUCUAAAACA ..((((..(((((.............(((....))).((((((.......((((...........)))).((((((((.(((.((((.((((...((....))...)))))))).)))...(((.....))))))))))).))))))..)))))..))))... (-21.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUAGACCUCUUUUAUAACCUAAUAUUAACCGAUUUGGCGCAUAAAAACAAGGCAGGAGAAUACUAUAACCCAUGUUGUCAAUAAUAUUAUUCAAGUAUUGAUAUUUUGAUUUUUUUGUUAUAUCAUAAUUAUGUAAGUUUAAAUUUAAAGGAGUAAAUU ..........((((((((........((((..((..((((...........))))...))..)))).((((((.......(((((.(((((((.........))))))))))))......)))))).......................))))))))...... (-20.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 891 130 81 221 172 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 326 124 86 127 89 NC_002967:TDE2205|5end_enoate_reductase,_putative_2244755..2244985_NEGATIVE 296 124 88 79 43 NC_002967:TDE1881|5end_methyltransferase,_putative_1903000..1903230_POSITIVE 290 130 100 100 67 NC_002967:TDE0915|5end_hypothetical_protein_933320..933550_NEGATIVE 290 130 100 225 192 NC_002967:TDE0914|5end_hypothetical_protein_933195..933425_NEGATIVE 268 130 90 94 62 NC_002967:TDE0974|5end_hypothetical_protein_998694..998924_POSITIVE 265 131 91 128 87 NC_002967:TDE2423|5end_ribosomal_protein_L10_2454034..2454264_NEGATIVE 261 129 81 135 83 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 259 120 79 201 157 NC_002967:TDE2138|5end_ankyrin_repeat_protein_2171631..2171861_POSITIVE 259 126 86 122 77 NC_002967:TDE1452|5end_hypothetical_protein_1498891..1499121_POSITIVE 251 134 91 221 177 NC_002967:TDE0643|5end_peptidyl-tRNA_hydrolase_679827..680057_NEGATIVE 248 129 86 67 25 NC_002967:TDE0637|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_672491..672721_NEGATIVE 241 121 83 129 79 NC_002967:TDE0789|5end_30S_ribosomal_protein_S13_816562..816792_POSITIVE 240 142 102 57 22 NC_002967:TDE2243|5end_CutC_family_protein_2282954..2283184_NEGATIVE 238 124 85 61 27 NC_002967:TDE1387|5end_RNA_pseudouridylate_synthase_family_protein_1427732..1427962_NEGATIVE 236 148 108 100 54 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 234 147 102 65 9 NC_002967:TDE2613|5end_hypothetical_protein_2655372..2655602_POSITIVE 233 132 102 52 25 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 232 130 81 228 170 NC_002967:TDE2042|5end_hypothetical_protein_2072179..2072409_NEGATIVE 232 145 103 145 95 NC_002967:TDE1074|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1104555..1104785_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 124 88 57 21 NC_002967:TDE1880|3end_hypothetical_protein_1903058..1903208_POSITIVE 265 131 91 125 84 NC_002967:TDE2424|3end_50S_ribosomal_protein_L1_2454037..2454187_NEGATIVE 248 129 86 70 28 NC_002967:TDE0638|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_672488..672638_NEGATIVE 241 121 83 112 62 NC_002967:TDE0788|3end_ribosomal_protein_L36_816625..816775_POSITIVE 240 130 85 111 62 NC_002967:TDE0490|3end_hypothetical_protein_546272..546422_NEGATIVE 236 148 108 110 64 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 234 147 102 72 16 NC_002967:TDE2612|3end_hypothetical_protein_2655459..2655609_POSITIVE 233 130 94 110 77 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 233 142 104 65 30 NC_002967:TDE2336|3end_sodium/dicarboxylate_symporter_family_protein_2371925..2372075_NEGATIVE 232 145 103 145 95 NC_002967:TDE1073|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1104635..1104785_POSITIVE 231 129 82 145 106 NC_002967:TDE0059|3end_hypothetical_protein_67481..67631_POSITIVE 231 129 82 62 23 NC_002967:TDE0058|3end_hypothetical_protein_67398..67548_POSITIVE 229 129 84 75 18 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 226 136 103 54 25 NC_002967:TDE0200|3end_tetrapyrrole_methylase_family_protein_235372..235522_POSITIVE 225 144 104 146 113 NC_002967:TDE2739|3end_hypothetical_protein_2795169..2795319_POSITIVE 224 134 100 149 124 NC_002967:TDE1543|3end_conserved_hypothetical_protein_TIGR00247_1587170..1587320_POSITIVE 223 131 96 65 31 NC_002967:TDE1867|3end_hypothetical_protein_1892351..1892501_NEGATIVE 221 112 86 40 10 NC_002967:TDE0986|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014121..1014271_POSITIVE 220 124 87 114 75 NC_002967:TDE0609|3end_hypothetical_protein_645276..645426_NEGATIVE 219 129 85 114 64 NC_002967:TDE1387|3end_RNA_pseudouridylate_synthase_family_protein_1426815..1426965_NEGATIVE