Origin IGS: ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtaaatctcctataaaaactttttgtagcaaatatcagacccttgcggttctgttctgcaaggaaattttttatcgtatccgctaaagcggatagcgaa Mask Tandem Repeat Region ================================================ ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt Find is-nt database================================================ Query_seq: TDE0692:TDE0693|TDE0692:TDE0693:hypothetical protein:phosphomethylpyrimidine kinase:->->:729981..730081 101 ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0692:TDE0693|TDE0692:TDE0693:hypothetical protein:phosphomethylpyrimidine kinase:->->:729981..730081 101 ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0692:TDE0693|TDE0692:TDE0693:hypothetical protein:phosphomethylpyrimidine kinase:->->:729981..730081 101 ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt Predict ORF larger than 30AA ================================================ ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0692:TDE0693|TDE0692:TDE0693:hypothetical protein:phosphomethylpyrimidine kinase:->->:729981..730081 101 ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_002967_TDE0692_TDE0693|hypothetical protein:phosphomethylpyrimidine kinase|POSITIVE:POSITIVE|[729981,730081]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt ttcgctatccgctttagcggatacgataaaaaatttccttgcagaacagaaccgcaagggtctgatatttgctacaaaaagtttttataggagatttactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGCUAUCCGCUUUAGCGGAUACGAUAAAAAAUUUCCUUGCAGAACAGAACCGCAAGGGUCUGAUAUUUGCUACAAAAAGUUUUUAUAGGAGAUUUACUU .(((.(((((((....))))))))))....(((((((((.(((((.((((.((....)).))))...)))))................))))))))).... (-33.63) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAAAUCUCCUAUAAAAACUUUUUGUAGCAAAUAUCAGACCCUUGCGGUUCUGUUCUGCAAGGAAAUUUUUUAUCGUAUCCGCUAAAGCGGAUAGCGAA ...........(((((((.....)))))))............((((((((.......))))))))..........((((((((((....)))))).)))). (-29.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 46 2 202 165 NC_002967:TDE2225|5end_thioesterase_family_protein_2264868..2265098_POSITIVE 316 46 2 77 40 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 295 46 2 204 165 NC_002967:TDE1195|5end_prolyl_endopeptidase_1229691..1229921_NEGATIVE 285 94 63 186 155 NC_002967:TDE1326|5end_hypothetical_protein_1361661..1361891_POSITIVE 282 26 2 189 165 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 282 97 52 193 148 NC_002967:TDE0122|5end_dihydrouridine_synthase,_putative_141539..141769_NEGATIVE 274 94 53 184 147 NC_002967:TDE1583|5end_hypothetical_protein_1631808..1632038_POSITIVE 268 94 53 76 38 NC_002967:TDE1902|5end_hypothetical_protein_1922475..1922705_NEGATIVE 266 71 32 149 97 NC_002967:TDE0112|5end_hypothetical_protein_132044..132274_POSITIVE 265 50 4 177 136 NC_002967:TDE2040|5end_lipoprotein_releasing_system,_ATP-binding_protein_2070221..2070451_NEGATIVE 264 55 11 100 39 NC_002967:TDE1096|5end_hydroxymethylbutenyl_pyrophosphate_reductase_1130989..1131219_POSITIVE 263 55 11 173 117 NC_002967:TDE0768|5end_50S_ribosomal_protein_L4_806996..807226_POSITIVE 260 75 31 66 24 NC_002967:TDE2752|5end_hypothetical_protein_2809118..2809348_POSITIVE 259 58 11 228 177 NC_002967:TDE0609|5end_hypothetical_protein_646166..646396_NEGATIVE 258 64 34 161 131 NC_002967:TDE1136|5end_M23/M37_peptidase_domain_protein_1166049..1166279_NEGATIVE 257 72 41 32 2 NC_002967:TDE0142|5end_hypothetical_protein_164074..164304_NEGATIVE 253 45 1 207 152 NC_002967:TDE2096|5end_hypothetical_protein_2123200..2123430_POSITIVE 253 55 11 81 33 NC_002967:TDE1408|5end_flagellar_filament_outer_layer_protein_FlaA,_putative_1450829..1451059_POSITIVE 251 73 34 151 114 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 251 73 37 43 1 NC_002967:TDE0046|5end_formiminotransferase-cyclodeaminase_family_protein_55849..56079_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 93 53 112 75 NC_002967:TDE2393|3end_hypothetical_protein_2422588..2422738_POSITIVE 316 46 2 80 43 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 316 46 2 103 65 NC_002967:TDE0692|3end_hypothetical_protein_729920..730070_POSITIVE 295 46 2 104 65 NC_002967:TDE1196|3end_hypothetical_protein_1229791..1229941_NEGATIVE 266 71 32 139 87 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 264 55 11 76 15 NC_002967:TDE1095|3end_alanine_racemase_1131045..1131195_POSITIVE 262 42 1 94 51 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 260 75 31 62 20 NC_002967:TDE2751|3end_hypothetical_protein_2809194..2809344_POSITIVE 258 64 34 144 114 NC_002967:TDE1137|3end_hypothetical_protein_1166066..1166216_NEGATIVE 257 72 41 127 97 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 248 76 39 95 59 NC_002967:TDE0903|3end_ATP-dependent_DNA_helicase_PcrA_922296..922446_POSITIVE 246 63 34 79 51 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 245 45 3 81 47 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 245 58 18 146 104 NC_002967:TDE1446|3end_hypothetical_protein_1492679..1492829_POSITIVE 243 66 26 52 11 NC_002967:TDE2708|3end_hypothetical_protein_2755136..2755286_NEGATIVE 242 73 34 65 26 NC_002967:TDE0300|3end_leucyl_aminopeptidase_332353..332503_POSITIVE 234 55 11 66 22 NC_002967:TDE0273|3end_ABC_transporter,_ATP-binding/permease_protein_302867..303017_NEGATIVE 231 73 52 35 9 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 230 90 43 85 34 NC_002967:TDE0296|3end_formiminotransferase,_putative_326842..326992_NEGATIVE 228 97 51 64 18 NC_002967:TDE0271|3end_hypothetical_protein_302199..302349_POSITIVE