Origin IGS: tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtttaacactcccttatcatttacatttgtaatctaactcttcattagtttacatttgtaatcgtaatttgtcaagtatttttatcatcattttccgatatacaaaaaagaaggcgggaaaatcccgtcttcttactttatttata Mask Tandem Repeat Region ================================================ tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca Find is-nt database================================================ Query_seq: SSA_0138:SSA_0139|SSA_0138:SSA_0139:Metal-binding (Zn) permease, putative:Copper transport operon or penicillinase transcriptional repressor, putative:->->:134176..134322 147 tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0138:SSA_0139|SSA_0138:SSA_0139:Metal-binding (Zn) permease, putative:Copper transport operon or penicillinase transcriptional repressor, putative:->->:134176..134322 147 tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0138:SSA_0139|SSA_0138:SSA_0139:Metal-binding (Zn) permease, putative:Copper transport operon or penicillinase transcriptional repressor, putative:->->:134176..134322 147 tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 2 End: 94 . M N K V R R R D F P A F F F V Y R K M M I K I L D K L R L Q M ..................................................... Protein_Len: 31 Strand: - Start: 1 End: 93 I F L T L L R S K G A K K K T Y R F I I I F I S S L N R N C M ...................................................... tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca 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: 85 Start: 71 End: 100 ......................................................................CTTGACAAATTACGATTACAAATGTAAACT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 91 HP_score: -10.1 Tail_Score: -3.99091 Start: 18 End: 34 Full_Region: atatacaaaaaagaa ggcggga aaa tcccgtc ttcttactttattta .................ggcgggaaaatcccgtc................................................................................................................. Find igs database================================================ Query_seq: SSA_0138:SSA_0139|SSA_0138:SSA_0139:Metal-binding (Zn) permease, putative:Copper transport operon or penicillinase transcriptional repressor, putative:->->:134176..134322 147 tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: NC_009009_SSA_0138_SSA_0139|Metal-binding (Zn) permease, putative:Copper transport operon or penicillinase transcriptional repressor, putative|POSITIVE:POSITIVE|[134176,134322]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca tataaataaagtaagaagacgggattttcccgccttcttttttgtatatcggaaaatgatgataaaaatacttgacaaattacgattacaaatgtaaactaatgaagagttagattacaaatgtaaatgataagggagtgttaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAUAAAGUAAGAAGACGGGAUUUUCCCGCCUUCUUUUUUGUAUAUCGGAAAAUGAUGAUAAAAAUACUUGACAAAUUACGAUUACAAAUGUAAACUAAUGAAGAGUUAGAUUACAAAUGUAAAUGAUAAGGGAGUGUUAAACA .....((((((.((((((.((((.....)))).)))))))))))).(((((........))))).......((((((..(((((.(((((..(((((.(((((.....))))).)))))..))))).)).))).....))))))... (-33.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUAACACUCCCUUAUCAUUUACAUUUGUAAUCUAACUCUUCAUUAGUUUACAUUUGUAAUCGUAAUUUGUCAAGUAUUUUUAUCAUCAUUUUCCGAUAUACAAAAAAGAAGGCGGGAAAAUCCCGUCUUCUUACUUUAUUUAUA ......................((((..(((((.((((.......)))).)))))..))))((((.((..((....(((....)))...))..)).))))........(((((((((((.....)))))))))))............ (-30.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 34 7 42 19 NC_009009:SSA_2036|5end_Conserved_hypothetical_cytosolic_protein_2040799..2041029_NEGATIVE 271 47 3 219 171 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 255 44 6 56 18 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 245 52 14 188 142 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 242 43 7 214 173 NC_009009:SSA_1464|5end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1471516..1471746_NEGATIVE 239 60 14 45 2 NC_009009:SSA_0797|5end_Transcriptional_regulator,_putative_779521..779751_POSITIVE 238 52 19 49 2 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 237 41 4 226 177 NC_009009:SSA_1340|5end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1356372..1356602_NEGATIVE 232 60 14 229 177 NC_009009:SSA_1428|5end_hypothetical_protein_1436348..1436578_NEGATIVE 232 62 24 123 90 NC_009009:SSA_1143|5end_Na+-driven_multidrug_efflux_pump,_putative_1173497..1173727_NEGATIVE 231 58 16 224 174 NC_009009:SSA_0549|5end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_543556..543786_POSITIVE 228 45 10 193 148 NC_009009:SSA_1182|5end_Gid-like_protein,_putative_1210866..1211096_NEGATIVE 227 52 11 46 3 NC_009009:SSA_1276|5end_Conserved_uncharacterized_protein_1298446..1298676_NEGATIVE 226 46 20 231 201 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 225 59 13 198 147 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 222 63 29 67 31 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 220 51 18 126 80 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 216 53 21 167 125 NC_009009:SSA_0589|5end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_580745..580975_POSITIVE 214 58 12 177 117 NC_009009:SSA_1862|5end_hypothetical_protein_1858541..1858771_NEGATIVE 213 35 6 202 165 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 34 7 45 22 NC_009009:SSA_2037|3end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2040796..2040946_NEGATIVE 290 39 5 92 55 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 271 47 3 83 35 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 268 49 6 91 46 NC_009009:SSA_0138|3end_Metal-binding_(Zn)_permease,_putative_134115..134265_POSITIVE 255 44 6 63 25 NC_009009:SSA_0637|3end_Tryptophan_synthase_beta_chain,_putative_627022..627172_POSITIVE 242 43 7 82 41 NC_009009:SSA_1465|3end_Conserved_uncharacterized_protein_1471648..1471798_NEGATIVE 236 45 15 137 98 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 231 58 16 117 67 NC_009009:SSA_0548|3end_Alanine_racemase,_putative_543529..543679_POSITIVE 229 46 10 79 40 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 228 45 10 91 46 NC_009009:SSA_1183|3end_hypothetical_protein_1210968..1211118_NEGATIVE 227 35 8 82 50 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 227 53 17 146 106 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 221 60 11 111 56 NC_009009:SSA_0774|3end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_756075..756225_POSITIVE 220 51 18 48 2 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 218 47 14 81 42 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 217 34 5 78 40 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 216 53 21 49 7 NC_009009:SSA_0588|3end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_580707..580857_POSITIVE 214 58 12 129 69 NC_009009:SSA_1863|3end_NH(3)-dependent_NAD(+)_synthetase,_putative_1858589..1858739_NEGATIVE 214 37 18 26 5 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 212 62 21 142 97 NC_009009:SSA_0504|3end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503799..503949_POSITIVE