Origin IGS: aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattcacctcctttcgggcatctcttgcccggtgtctgtgtaagttattcgaaccgttgttctaattaacttacagctataatatacaacaaatcgcttgtaacgtcaatagaacttctgatttttt Mask Tandem Repeat Region ================================================ aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt Find is-nt database================================================ Query_seq: TDE0673:TDE0674|TDE0673:TDE0674:hypothetical protein:hypothetical protein:->->:713174..713300 127 aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0673:TDE0674|TDE0673:TDE0674:hypothetical protein:hypothetical protein:->->:713174..713300 127 aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0673:TDE0674|TDE0673:TDE0674:hypothetical protein:hypothetical protein:->->:713174..713300 127 aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt Predict ORF larger than 30AA ================================================ aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt 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: 86 Start: 18 End: 47 .................ATTGACGTTACAAGCGATTTGTTGTATATT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0673:TDE0674|TDE0673:TDE0674:hypothetical protein:hypothetical protein:->->:713174..713300 127 aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_002967_TDE0673_TDE0674|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[713174,713300]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt aaaaaatcagaagttctattgacgttacaagcgatttgttgtatattatagctgtaagttaattagaacaacggttcgaataacttacacagacaccgggcaagagatgcccgaaaggaggtgaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAUCAGAAGUUCUAUUGACGUUACAAGCGAUUUGUUGUAUAUUAUAGCUGUAAGUUAAUUAGAACAACGGUUCGAAUAACUUACACAGACACCGGGCAAGAGAUGCCCGAAAGGAGGUGAAUU ............(((((((((((.(((((.((..................)))))))))))).))))))..................(((...(..((((((.....))))))...)...))).... (-28.07) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCACCUCCUUUCGGGCAUCUCUUGCCCGGUGUCUGUGUAAGUUAUUCGAACCGUUGUUCUAAUUAACUUACAGCUAUAAUAUACAACAAAUCGCUUGUAACGUCAAUAGAACUUCUGAUUUUUU ...(((.......(((((((.....)))))))..(((((((((((((...((((....))))....))))))))..........(((((........)))))......))))).....)))...... (-27.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 120 89 61 27 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 270 119 72 188 134 NC_002967:TDE2061|5end_hypothetical_protein_2087792..2088022_NEGATIVE 265 117 88 33 4 NC_002967:TDE0210|5end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_245551..245781_POSITIVE 259 120 90 135 85 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 259 110 65 76 36 NC_002967:TDE0472|5end_hypothetical_protein_528376..528606_POSITIVE 249 59 11 195 146 NC_002967:TDE1911|5end_hypothetical_protein_1929098..1929328_NEGATIVE 241 120 77 37 1 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 241 113 71 63 18 NC_002967:TDE0008|5end_copper-translocating_P-type_ATPase_10891..11121_POSITIVE 240 113 72 62 29 NC_002967:TDE0847|5end_hypothetical_protein_870894..871124_POSITIVE 237 44 10 205 166 NC_002967:TDE0787|5end_preprotein_translocase_SecY_815068..815298_POSITIVE 236 116 73 222 163 NC_002967:TDE0101|5end_alpha-amylase_family_protein_121161..121391_NEGATIVE 234 119 76 71 28 NC_002967:TDE2729|5end_hypothetical_protein_2786457..2786687_NEGATIVE 233 107 62 70 20 NC_002967:TDE2567|5end_hypothetical_protein_2595076..2595306_NEGATIVE 233 100 66 79 43 NC_002967:TDE2321|5end_hypothetical_protein_2357301..2357531_NEGATIVE 232 60 11 199 151 NC_002967:TDE2386|5end_hypothetical_protein_2415411..2415641_POSITIVE 232 114 72 91 44 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 230 99 51 209 149 NC_002967:TDE2466|5end_hypothetical_protein_2489860..2490090_NEGATIVE 230 110 72 137 98 NC_002967:TDE2094|5end_hypothetical_protein_2121319..2121549_NEGATIVE 229 115 85 68 34 NC_002967:TDE0953|5end_branched-chain_amino_acid_ABC_transporter,_permease_protein_976863..977093_POSITIVE 227 118 89 202 169 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 120 89 48 14 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 255 119 84 67 35 NC_002967:TDE2144|3end_hypothetical_protein_2180451..2180601_NEGATIVE 253 120 73 86 34 NC_002967:TDE2117|3end_hypothetical_protein_2149175..2149325_POSITIVE 248 119 71 65 15 NC_002967:TDE1062|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1090387..1090537_POSITIVE 247 120 71 65 26 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 243 109 61 90 27 NC_002967:TDE1003|3end_hypothetical_protein_1029325..1029475_POSITIVE 233 100 66 46 10 NC_002967:TDE2322|3end_flagellar_protein_FliL-related_protein_2357334..2357484_NEGATIVE 231 116 72 77 44 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 229 115 85 71 37 NC_002967:TDE0952|3end_ABC_transporter,_ATP-binding_protein_976946..977096_POSITIVE 229 118 82 118 68 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 228 120 77 146 98 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 227 118 90 47 15 NC_002967:TDE1855|3end_hypothetical_protein_1883213..1883363_POSITIVE 222 120 72 143 86 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 222 118 71 77 27 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 220 118 71 82 44 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 219 113 72 124 86 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 219 118 87 66 18 NC_002967:TDE1692|3end_hypothetical_protein_1748471..1748621_POSITIVE 218 120 85 59 28 NC_002967:TDE1712|3end_flagellar_filament_outer_layer_protein_1766866..1767016_NEGATIVE 214 78 31 115 76 NC_002967:TDE1907|3end_holo-(acyl-carrier-protein)_synthase_1924726..1924876_NEGATIVE 214 112 72 91 49 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE