Origin IGS: accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actcaatcctccactacaaaatatctaaaattaaaaaagcgtatctgccgcaccattatgcggccttaccatacatttaagggttcatattacactaaaatgcataaaaagtcaatacaaaattgaaaagatgataaaatatcggt Mask Tandem Repeat Region ================================================ accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt Find is-nt database================================================ Query_seq: TDE1024:TDE1025|TDE1024:TDE1025:conserved hypothetical protein TIGR01319:ribosomal protein L32:->->:1057095..1057240 146 accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1024:TDE1025|TDE1024:TDE1025:conserved hypothetical protein TIGR01319:ribosomal protein L32:->->:1057095..1057240 146 accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1024:TDE1025|TDE1024:TDE1025:conserved hypothetical protein TIGR01319:ribosomal protein L32:->->:1057095..1057240 146 accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt Predict ORF larger than 30AA ================================================ accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt 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: 31 End: 60 ..............................ATTGACTTTTTATGCATTTTAGTGTAATAT...................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1024:TDE1025|TDE1024:TDE1025:conserved hypothetical protein TIGR01319:ribosomal protein L32:->->:1057095..1057240 146 accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_002967_TDE1024_TDE1025|conserved hypothetical protein TIGR01319:ribosomal protein L32|POSITIVE:POSITIVE|[1057095,1057240]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt accgatattttatcatcttttcaattttgtattgactttttatgcattttagtgtaatatgaacccttaaatgtatggtaaggccgcataatggtgcggcagatacgcttttttaattttagatattttgtagtggaggattgagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGAUAUUUUAUCAUCUUUUCAAUUUUGUAUUGACUUUUUAUGCAUUUUAGUGUAAUAUGAACCCUUAAAUGUAUGGUAAGGCCGCAUAAUGGUGCGGCAGAUACGCUUUUUUAAUUUUAGAUAUUUUGUAGUGGAGGAUUGAGU ...((((...)))).....(((((((((.(((((.(((.((((((((((.((.((.......)).)).)))))))))).)))(((((((....)))))))..............................))))).))))))))). (-32.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCAAUCCUCCACUACAAAAUAUCUAAAAUUAAAAAAGCGUAUCUGCCGCACCAUUAUGCGGCCUUACCAUACAUUUAAGGGUUCAUAUUACACUAAAAUGCAUAAAAAGUCAAUACAAAAUUGAAAAGAUGAUAAAAUAUCGGU .....................(((((............(.(((...((((((......))))))..))))...(((((.((.((.......)).)).))))).........(((((.....)))))..)))))............. (-19.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 107 73 184 150 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 316 128 81 222 164 NC_002967:TDE2089|5end_signal_recognition_particle_protein_2117563..2117793_NEGATIVE 304 110 63 215 173 NC_002967:TDE0294|5end_TrkA_domain_protein_324210..324440_NEGATIVE 297 99 64 231 194 NC_002967:TDE0093|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_111257..111487_POSITIVE 292 111 75 155 112 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 289 139 93 204 152 NC_002967:TDE0995|5end_hypothetical_protein_1022576..1022806_NEGATIVE 284 110 62 117 71 NC_002967:TDE2199|5end_racemase,_Asp/Glu/Hydantoin_family_2237150..2237380_NEGATIVE 281 103 61 145 93 NC_002967:TDE1014|5end_hypothetical_protein_1045544..1045774_NEGATIVE 276 103 64 164 119 NC_002967:TDE2008|5end_ABC_transporter,_ATP-binding/permease_protein_2028578..2028808_POSITIVE 272 50 15 94 51 NC_002967:TDE1855|5end_hypothetical_protein_1882846..1883076_POSITIVE 270 129 82 104 59 NC_002967:TDE2460|5end_aminotransferase,_class_V_2485983..2486213_POSITIVE 268 110 66 54 6 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 266 109 81 37 6 NC_002967:TDE1042|5end_deoxyuridine_5'triphosphate_nucleotidohydrolase_1070492..1070722_POSITIVE 261 126 81 219 180 NC_002967:TDE0904|5end_hypothetical_protein_922406..922636_NEGATIVE 260 136 94 218 176 NC_002967:TDE1909|5end_conserved_hypothetical_protein_TIGR00159_1926872..1927102_NEGATIVE 259 108 63 187 130 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 259 104 64 93 60 NC_002967:TDE0292|5end_hypothetical_protein_322014..322244_NEGATIVE 257 107 65 191 144 NC_002967:TDE0079|5end_DNA-binding_protein_90670..90900_NEGATIVE 255 103 69 47 2 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 254 99 65 204 166 NC_002967:TDE2747|5end_type_I_restriction-modification_system,_R_subunit_2804942..2805172_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 108 62 80 31 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 280 109 76 48 17 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 276 103 64 147 102 NC_002967:TDE2007|3end_ABC_transporter,_ATP-binding/permease_protein_2028641..2028791_POSITIVE 272 109 64 135 87 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 260 109 76 144 114 NC_002967:TDE0007|3end_hypothetical_protein_10808..10958_POSITIVE 259 108 63 143 86 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 259 104 64 89 56 NC_002967:TDE0293|3end_MATE_efflux_family_protein_322018..322168_NEGATIVE 257 107 65 133 86 NC_002967:TDE0080|3end_betaine_aldehyde_dehydrogenase_90728..90878_NEGATIVE 255 103 69 50 5 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 255 110 64 151 96 NC_002967:TDE2555|3end_precorrin-8X_methylmutase_2582316..2582466_POSITIVE 253 100 77 146 117 NC_002967:TDE2050|3end_hypothetical_protein_2079707..2079857_NEGATIVE 251 100 51 150 95 NC_002967:TDE1335|3end_alginate_O-acetylation_protein,_putative_1372368..1372518_POSITIVE 250 101 64 103 49 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 249 100 63 78 32 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 246 109 69 126 79 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 246 111 71 101 60 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 244 110 63 85 37 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 244 109 82 144 111 NC_002967:TDE0609|3end_hypothetical_protein_645276..645426_NEGATIVE 243 110 67 128 91 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 242 100 82 61 38 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE