Origin IGS: aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggcttcctcctcattcataataaagttggatagttttgtagtattcatgttttaacagaatctagtctaagtaccgtgtgaaaaagacaagcttcctcgcattcatcgaatgctgtgtcagctttctattttcactttgtgttttacacccttgatatcttaaactgaacacgagctaaaaccttggaaaatagataatccgttctaggagcatcgctccttcgtccgaatcgctaattttcagtcagttttgacgctctttgtatcttgtt Mask Tandem Repeat Region ================================================ aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct Find is-nt database================================================ Query_seq: SSA_0100:SSA_0101|SSA_0100:SSA_0101:DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative:Conserved uncharacterized protein:->->:103463..103735 273 aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0100:SSA_0101|SSA_0100:SSA_0101:DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative:Conserved uncharacterized protein:->->:103463..103735 273 aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0100:SSA_0101|SSA_0100:SSA_0101:DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative:Conserved uncharacterized protein:->->:103463..103735 273 aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 101 End: 208 .................................................................................................... M F S L R Y Q G C K T Q S E N R K L T Q H S M N A R K L V F F T R Y L D ................................................................. aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct 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================================================ aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -9.1 Tail_Score: -3.15663 Start: 53 End: 65 Full_Region: agataatccgttcta ggagc atc gctcc ttcgtccgaatcgct ....................................................ggagcatcgctcc................................................................................................................................................................................................................ TransTerm Strand: - Conf: 70 HP_score: -7.4 Tail_Score: -3.79633 Start: 147 End: 165 Full_Region: ttcctcgcattcatc gaatgctg tgt cagctttc tattttcactttgtg ..................................................................................................................................................gaatgctgtgtcagctttc............................................................................................................ TransTerm Strand: - Conf: 75 HP_score: -6.8 Tail_Score: -4.47679 Start: 151 End: 161 Full_Region: tcgcattcatcgaat gctg tgt cagc tttctattttcactt ......................................................................................................................................................gctgtgtcagc................................................................................................................ Find igs database================================================ Query_seq: SSA_0100:SSA_0101|SSA_0100:SSA_0101:DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative:Conserved uncharacterized protein:->->:103463..103735 273 aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct Intra-Species Hit: Count: 1 Min: 1 Max: 273 Len: 273 Subject: NC_009009_SSA_0100_SSA_0101|DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative:Conserved uncharacterized protein|POSITIVE:POSITIVE|[103463,103735]|273 HSP 1 e-value: 1.0E-153 bit: 541.0 Len: 273 Query Start:1 Query End:273 Subject Strand: POSITIVE Subject Start: 1 Subject End: 273 aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct aacaagatacaaagagcgtcaaaactgactgaaaattagcgattcggacgaaggagcgatgctcctagaacggattatctattttccaaggttttagctcgtgttcagtttaagatatcaagggtgtaaaacacaaagtgaaaatagaaagctgacacagcattcgatgaatgcgaggaagcttgtctttttcacacggtacttagactagattctgttaaaacatgaatactacaaaactatccaactttattatgaatgaggaggaagcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAGAUACAAAGAGCGUCAAAACUGACUGAAAAUUAGCGAUUCGGACGAAGGAGCGAUGCUCCUAGAACGGAUUAUCUAUUUUCCAAGGUUUUAGCUCGUGUUCAGUUUAAGAUAUCAAGGGUGUAAAACACAAAGUGAAAAUAGAAAGCUGACACAGCAUUCGAUGAAUGCGAGGAAGCUUGUCUUUUUCACACGGUACUUAGACUAGAUUCUGUUAAAACAUGAAUACUACAAAACUAUCCAACUUUAUUAUGAAUGAGGAGGAAGCCU .....(((((...((((...((((((....((((((..(..(((((..(..((((((...)))))).)..)))))..)..))))))...)))))).))))))))).((((((((.((((....(((.....)))...(((((((.((((((((..(...((((((...))))))..)..))))).))))))))))..))))))))))))..(((((((....))).))))............(((..((((((.....)))))).)))..... (-73.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUUCCUCCUCAUUCAUAAUAAAGUUGGAUAGUUUUGUAGUAUUCAUGUUUUAACAGAAUCUAGUCUAAGUACCGUGUGAAAAAGACAAGCUUCCUCGCAUUCAUCGAAUGCUGUGUCAGCUUUCUAUUUUCACUUUGUGUUUUACACCCUUGAUAUCUUAAACUGAACACGAGCUAAAACCUUGGAAAAUAGAUAAUCCGUUCUAGGAGCAUCGCUCCUUCGUCCGAAUCGCUAAUUUUCAGUCAGUUUUGACGCUCUUUGUAUCUUGUU ((((((((..((............))..))).)))))..((((((((.............(((((.((((((......((((((((((.(((((..(.(((((((...)))))).).)..)))))))).))))))).((((((((......................))))))))........))))))...)))))....((....((((((...)))))).))...)))).)))).......(((......)))................. (-55.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 503 90 44 180 134 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 336 88 41 105 59 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 327 58 16 40 1 NC_009009:SSA_0637|5end_Tryptophan_synthase_beta_chain,_putative_625719..625949_POSITIVE 324 200 157 182 139 NC_009009:SSA_1226|5end_ParC,_putative_1251233..1251463_NEGATIVE 323 107 61 77 24 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 321 147 101 128 81 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 313 99 58 118 76 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 306 220 175 81 23 NC_009009:SSA_2013|5end_hypothetical_protein_2013793..2014023_NEGATIVE 303 99 52 83 32 NC_009009:SSA_0203|5end_hypothetical_protein_201322..201552_POSITIVE 301 44 4 137 96 NC_009009:SSA_0914|5end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_924952..925182_POSITIVE 295 57 12 59 11 NC_009009:SSA_1304|5end_hypothetical_protein_1323449..1323679_NEGATIVE 292 93 52 45 2 NC_009009:SSA_0380|5end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_370916..371146_POSITIVE 288 200 152 167 117 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 286 60 16 117 65 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 286 110 61 219 169 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 278 60 11 58 4 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 277 189 150 205 162 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 276 120 80 113 61 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 276 99 52 186 143 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 275 68 39 183 149 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 58 15 50 10 NC_009009:SSA_0636|3end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625809..625959_POSITIVE 303 99 52 83 32 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 297 88 41 113 47 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 292 130 83 65 8 NC_009009:SSA_1303|3end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322474..1322624_NEGATIVE 291 199 151 53 5 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 276 120 80 103 51 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 271 74 31 70 28 NC_009009:SSA_0327|3end_Glycosyltransferase,_putative_320436..320586_POSITIVE 271 100 52 77 25 NC_009009:SSA_0100|3end_DNA_polymerase_I_-_3'-5'_exonuclease_and_polymerase_domains,_putative_103402..103552_POSITIVE 270 57 13 48 13 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 268 220 173 131 80 NC_009009:SSA_1494|3end_Conserved_uncharacterized_protein_1499514..1499664_NEGATIVE 267 86 51 145 97 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 265 76 46 134 96 NC_009009:SSA_0330|3end_hypothetical_protein_325162..325312_POSITIVE 263 99 51 108 55 NC_009009:SSA_1164|3end_hypothetical_protein_1191007..1191157_NEGATIVE 263 121 82 81 32 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 262 66 23 130 81 NC_009009:SSA_1693|3end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1685105..1685255_NEGATIVE 261 75 36 151 107 NC_009009:SSA_1496|3end_hypothetical_protein_1502473..1502623_NEGATIVE 260 187 141 74 42 NC_009009:SSA_2109|3end_Elongation_factor_G,_putative_2112787..2112937_NEGATIVE 260 75 43 34 7 NC_009009:SSA_0582|3end_Methylase,_putative_574583..574733_POSITIVE 258 88 45 69 35 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 254 219 171 79 32 NC_009009:SSA_0712|3end_P-type_ATPase-metal_cation_transport_(calcium_efflux),_putative_696761..696911_NEGATIVE