Origin IGS: ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatttcctcaaaaactttttctagtttgtagatacctaaatcttatcatatcaagccttaactgtcaaatttcacaatattttttgagcctgactcctatcttttcaacccctttttgtgatacaatgagacagattaagtgacttaaaaacgaataaaataccacagccaaaataaacaggtaagcaatggctaactcctagataatagtagctgataaaaaactcaacctagtcttagccaaacttatctctgaaaggaaatcacaa Mask Tandem Repeat Region ================================================ ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt Find is-nt database================================================ Query_seq: SSA_0323:SSA_0324|SSA_0323:SSA_0324:Flavoprotein, putative:Conserved uncharacterized protein:<-->:316890..317158 269 ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0323:SSA_0324|SSA_0323:SSA_0324:Flavoprotein, putative:Conserved uncharacterized protein:<-->:316890..317158 269 ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0323:SSA_0324|SSA_0323:SSA_0324:Flavoprotein, putative:Conserved uncharacterized protein:<-->:316890..317158 269 ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 52 End: 162 ................................................... M S Y Y Y L G V S H C L P V Y F G C G I L F V F K S L N L S H C I T K R G ........................................................................................................... Protein_Len: 41 Strand: + Start: 80 End: 202 ............................................................................... M A Y L F I L A V V F Y S F L S H L I C L I V S Q K G V E K I G V R L K K Y C E I ................................................................... Protein_Len: 32 Strand: - Start: 130 End: 225 ................................................................................................................................. K I Q R M T D C F P T S F I P T L S L F Y Q S I Q C N L S S I M ............................................ ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt 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: 87 Start: 201 End: 230 ........................................................................................................................................................................................................TTTGACAGTTAAGGCTTGATATGATAAGAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0323:SSA_0324|SSA_0323:SSA_0324:Flavoprotein, putative:Conserved uncharacterized protein:<-->:316890..317158 269 ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 269 Len: 269 Subject: NC_009009_SSA_0323_SSA_0324|Flavoprotein, putative:Conserved uncharacterized protein|NEGATIVE:POSITIVE|[316890,317158]|269 HSP 1 e-value: 1.0E-150 bit: 533.0 Len: 269 Query Start:1 Query End:269 Subject Strand: POSITIVE Subject Start: 1 Subject End: 269 ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt ttgtgatttcctttcagagataagtttggctaagactaggttgagttttttatcagctactattatctaggagttagccattgcttacctgtttattttggctgtggtattttattcgtttttaagtcacttaatctgtctcattgtatcacaaaaaggggttgaaaagataggagtcaggctcaaaaaatattgtgaaatttgacagttaaggcttgatatgataagatttaggtatctacaaactagaaaaagtttttgaggaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUGAUUUCCUUUCAGAGAUAAGUUUGGCUAAGACUAGGUUGAGUUUUUUAUCAGCUACUAUUAUCUAGGAGUUAGCCAUUGCUUACCUGUUUAUUUUGGCUGUGGUAUUUUAUUCGUUUUUAAGUCACUUAAUCUGUCUCAUUGUAUCACAAAAAGGGGUUGAAAAGAUAGGAGUCAGGCUCAAAAAAUAUUGUGAAAUUUGACAGUUAAGGCUUGAUAUGAUAAGAUUUAGGUAUCUACAAACUAGAAAAAGUUUUUGAGGAAAUU ....(((((((((.(((.(.(((((.(((((((..((((((..(((............)))...))))))...)))))))..)))))))))....((((((.(((((.(((((((.(((..((((((..(((((.(((((.....((.((((((...(((.((((...........)))).)))........)))))).))..)))))))))))))))).))))))))))........)))))..)))))).........))))))))) (-63.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCCUCAAAAACUUUUUCUAGUUUGUAGAUACCUAAAUCUUAUCAUAUCAAGCCUUAACUGUCAAAUUUCACAAUAUUUUUUGAGCCUGACUCCUAUCUUUUCAACCCCUUUUUGUGAUACAAUGAGACAGAUUAAGUGACUUAAAAACGAAUAAAAUACCACAGCCAAAAUAAACAGGUAAGCAAUGGCUAACUCCUAGAUAAUAGUAGCUGAUAAAAAACUCAACCUAGUCUUAGCCAAACUUAUCUCUGAAAGGAAAUCACAA .(((((((...............((((((.((((.........)))).....((((((((((((((..(((((((((......(((((...((......))..))))).......))))))...)))..))))).))))).).)))....)))))).........(((...........(((((((...(((((((...((((.....(((............)))....))))..)))))))..))))))))))..)))))))..... (-44.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 110 61 201 152 NC_009009:SSA_0323|5end_Flavoprotein,_putative_316799..317029_NEGATIVE 337 217 173 131 97 NC_009009:SSA_1774|5end_RRNA_methylase,_putative_1761043..1761273_NEGATIVE 331 130 83 99 49 NC_009009:SSA_1279|5end_Oxidoreductase,_putative_1300832..1301062_NEGATIVE 296 92 55 73 33 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 295 59 16 49 4 NC_009009:SSA_0396|5end_hypothetical_protein_393595..393825_NEGATIVE 288 58 24 47 11 NC_009009:SSA_0450|5end_Elongation_factor_P,_putative_450587..450817_POSITIVE 287 180 131 166 117 NC_009009:SSA_1522|5end_Cell_division_protein_FtsW,_putative_1531962..1532192_NEGATIVE 284 49 7 142 95 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 282 184 143 187 128 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 280 107 70 121 76 NC_009009:SSA_1579|5end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1582851..1583081_POSITIVE 279 58 11 147 105 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 274 185 141 169 123 NC_009009:SSA_0564|5end_Potential_aminotransferase,_putative_555694..555924_POSITIVE 271 107 63 202 148 NC_009009:SSA_0220|5end_PTS_system,_mannose-specific_IIB_component,_putative_215848..216078_POSITIVE 270 100 53 182 126 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 270 107 67 159 107 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 270 180 136 147 100 NC_009009:SSA_0289|5end_Leucyl-tRNA_synthetase,_putative_281406..281636_POSITIVE 267 60 11 227 168 NC_009009:SSA_1087|5end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1104524..1104754_POSITIVE 267 99 51 67 4 NC_009009:SSA_0442|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_442237..442467_POSITIVE 266 114 83 220 189 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 266 198 156 148 108 NC_009009:SSA_0735|5end_Integral_membrane_protein,_putative_717103..717333_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 92 55 76 36 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 284 49 7 67 20 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 282 184 143 74 15 NC_009009:SSA_0814|3end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_795519..795669_NEGATIVE 280 107 70 119 74 NC_009009:SSA_1578|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1582929..1583079_POSITIVE 279 58 11 146 104 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 270 100 53 123 67 NC_009009:SSA_0792|3end_hypothetical_protein_774880..775030_POSITIVE 263 181 143 56 13 NC_009009:SSA_1638|3end_hypothetical_protein_1641017..1641167_NEGATIVE 258 43 6 135 93 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 258 78 35 151 105 NC_009009:SSA_0100|3end_DNA_polymerase_I_-_3'-5'_exonuclease_and_polymerase_domains,_putative_103402..103552_POSITIVE 257 90 48 139 89 NC_009009:SSA_1594|3end_Metalloendopeptidase,_putative_1598457..1598607_NEGATIVE 255 45 5 39 2 NC_009009:SSA_0493|3end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_494483..494633_POSITIVE 252 153 114 103 66 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 251 164 121 140 98 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 249 105 65 108 62 NC_009009:SSA_2000|3end_hypothetical_protein_1996987..1997137_NEGATIVE 249 107 69 107 53 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 247 110 62 121 78 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 246 182 148 50 4 NC_009009:SSA_2369|3end_hypothetical_protein_2370239..2370389_NEGATIVE 246 44 8 63 21 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 246 100 54 61 20 NC_009009:SSA_0634|3end_Anthranilate_phosphoribosyltransferase,_putative_624471..624621_POSITIVE 245 147 101 137 81 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE