Origin IGS: aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgaaaggctttcaattctgccaatcgagactctgtaactgcggctaaattgaacttttttatcttcttatctaccatacatacacaaatccagatttttt Mask Tandem Repeat Region ================================================ aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg Find is-nt database================================================ Query_seq: TDE0911:TDE0912|TDE0911:TDE0912:type II restriction endonuclease TdeIII:hypothetical protein:->->:931390..931489 100 aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0911:TDE0912|TDE0911:TDE0912:type II restriction endonuclease TdeIII:hypothetical protein:->->:931390..931489 100 aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0911:TDE0912|TDE0911:TDE0912:type II restriction endonuclease TdeIII:hypothetical protein:->->:931390..931489 100 aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 6 End: 98 ..... M W I C V C M V D K K I K K F N L A A V T E S R L A E L K A F .. aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg 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: 81 Start: 24 End: 53 .......................ATTGAACTTTTTTATCTTCTTATCTACCAT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0911:TDE0912|TDE0911:TDE0912:type II restriction endonuclease TdeIII:hypothetical protein:->->:931390..931489 100 aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002967_TDE0911_TDE0912|type II restriction endonuclease TdeIII:hypothetical protein|POSITIVE:POSITIVE|[931390,931489]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg aaaaaatctggatttgtgtatgtatggtagataagaagataaaaaagttcaatttagccgcagttacagagtctcgattggcagaattgaaagcctttcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAUCUGGAUUUGUGUAUGUAUGGUAGAUAAGAAGAUAAAAAAGUUCAAUUUAGCCGCAGUUACAGAGUCUCGAUUGGCAGAAUUGAAAGCCUUUCG .....((((...(((((.(((.....))).))))).)))).......((((((((.((((..(..((...))..)...)))).))))))))......... (-15.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAAGGCUUUCAAUUCUGCCAAUCGAGACUCUGUAACUGCGGCUAAAUUGAACUUUUUUAUCUUCUUAUCUACCAUACAUACACAAAUCCAGAUUUUUU .((((((..(((((((..(((....................)))..)))))))))))))......................................... (-10.95) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 100 51 54 20 NC_002967:TDE0980|5end_asparaginyl-tRNA_synthetase_1005400..1005630_NEGATIVE 269 86 45 81 36 NC_002967:TDE2085|5end_uridylate_kinase_2114182..2114412_POSITIVE 263 100 58 209 171 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 261 89 44 152 104 NC_002967:TDE0259|5end_transcriptional_regulator,_MarR_family_293257..293487_POSITIVE 255 100 55 168 114 NC_002967:TDE0255|5end_ABC_transporter,_ATP-binding_protein_290742..290972_NEGATIVE 254 100 56 56 4 NC_002967:TDE1398|5end_hypothetical_protein_1437192..1437422_POSITIVE 249 90 47 221 169 NC_002967:TDE0404|5end_hypothetical_protein_455499..455729_NEGATIVE 248 91 55 136 98 NC_002967:TDE1512|5end_hypothetical_protein_1559203..1559433_POSITIVE 244 96 56 81 40 NC_002967:TDE0611|5end_hypothetical_protein_647389..647619_NEGATIVE 244 96 56 184 143 NC_002967:TDE0610|5end_3-hydroxyacyl-CoA_dehydrogenase,_putative_647286..647516_NEGATIVE 243 94 51 82 28 NC_002967:TDE0717|5end_hypothetical_protein_751779..752009_POSITIVE 243 100 60 191 153 NC_002967:TDE0406|5end_hypothetical_protein_457230..457460_POSITIVE 242 100 56 192 128 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 240 99 51 155 101 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 239 94 57 46 10 NC_002967:TDE1679|5end_ATP_synthase_subunit_K_1731049..1731279_NEGATIVE 238 90 56 219 186 NC_002967:TDE1850|5end_ABC_transporter,_permease_protein,_putative_1879561..1879791_NEGATIVE 237 96 57 65 33 NC_002967:TDE0849|5end_hypothetical_protein_871599..871829_POSITIVE 236 94 56 181 144 NC_002967:TDE0672|5end_hypothetical_protein_711110..711340_POSITIVE 234 98 55 139 99 NC_002967:TDE2693|5end_ankyrin_repeat_protein_2731133..2731363_POSITIVE 234 100 53 168 121 NC_002967:TDE1349|5end_rod_shape-determining_protein_MreB_1389286..1389516_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 96 57 124 83 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 292 96 56 92 51 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 274 100 57 40 1 NC_002967:TDE1314|3end_penicillin-binding_protein_1353116..1353266_POSITIVE 269 86 45 48 3 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE 249 96 57 59 6 NC_002967:TDE2571|3end_hypothetical_protein_2597922..2598072_NEGATIVE 248 91 55 47 9 NC_002967:TDE1511|3end_pathogen-specific_surface_antigen,_putative_1559194..1559344_POSITIVE 244 96 56 103 62 NC_002967:TDE0612|3end_hypothetical_protein_647367..647517_NEGATIVE 243 100 60 62 24 NC_002967:TDE0405|3end_major_outer_sheath_protein_457181..457331_POSITIVE 242 100 56 130 66 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 238 95 52 53 1 NC_002967:TDE0875|3end_ribosomal_large_subunit_pseudouridine_synthase_B_898273..898423_POSITIVE 236 94 56 69 32 NC_002967:TDE0671|3end_PIN_domain_protein_711078..711228_POSITIVE 235 99 52 50 12 NC_002967:TDE2209|3end_CarB_family_protein_2249300..2249450_POSITIVE 234 100 53 150 103 NC_002967:TDE1348|3end_TPR_domain_protein_1389348..1389498_POSITIVE 232 99 56 85 25 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 230 100 56 139 94 NC_002967:TDE0700|3end_hypothetical_protein_735331..735481_NEGATIVE 230 77 35 101 47 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 228 99 56 91 35 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 226 85 46 95 51 NC_002967:TDE1953|3end_transcriptional_regulator,_TetR_family_1969030..1969180_NEGATIVE 226 95 58 66 33 NC_002967:TDE1444|3end_metallo-beta-lactamase_family_protein_1489592..1489742_NEGATIVE 226 82 47 78 37 NC_002967:TDE0072|3end_methyl-accepting_chemotaxis_protein_83139..83289_POSITIVE