Origin IGS: actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagtttccggtattcaaggataagagaaaggtcagttgacttttctctttatctgacttggagcacaagatgacaaaaatgtaagattggcaggcaaaatgaaagattaggttatggaaacttgtctgtctttccggtatgatagtagtatcaagttaaataaagaagaggttcgagt Mask Tandem Repeat Region ================================================ actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc Find is-nt database================================================ Query_seq: SSA_1660:SSA_1661|SSA_1660:SSA_1661:ABC-type antimicrobial peptide transport system, ATPase component, putative:hypothetical protein:<-<-:1657671..1657848 178 actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1660:SSA_1661|SSA_1660:SSA_1661:ABC-type antimicrobial peptide transport system, ATPase component, putative:hypothetical protein:<-<-:1657671..1657848 178 actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1660:SSA_1661|SSA_1660:SSA_1661:ABC-type antimicrobial peptide transport system, ATPase component, putative:hypothetical protein:<-<-:1657671..1657848 178 actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 36 End: 176 ................................... M I P E R Q T S F H N L I F H F A C Q S Y I F V I L C S K S D K E K S Q L T F L L S L N T G N .. actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc 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: 83 Start: 36 End: 65 ...................................ATGGAAACTTGTCTGTCTTTCCGGTATGAT................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -8.2 Tail_Score: -3.52652 Start: 132 End: 155 Full_Region: TCCAAGTCAGATAAA GAGAAAAGTC AACT GACCTTTCTC TTATCCTTGAATACC ...................................................................................................................................GAGAAAAGTCAACTGACCTTTCTC....................... Find igs database================================================ Query_seq: SSA_1660:SSA_1661|SSA_1660:SSA_1661:ABC-type antimicrobial peptide transport system, ATPase component, putative:hypothetical protein:<-<-:1657671..1657848 178 actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_009009_SSA_1660_SSA_1661|ABC-type antimicrobial peptide transport system, ATPase component, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1657671,1657848]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc actcgaacctcttctttatttaacttgatactactatcataccggaaagacagacaagtttccataacctaatctttcattttgcctgccaatcttacatttttgtcatcttgtgctccaagtcagataaagagaaaagtcaactgacctttctcttatccttgaataccggaaactc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCGAACCUCUUCUUUAUUUAACUUGAUACUACUAUCAUACCGGAAAGACAGACAAGUUUCCAUAACCUAAUCUUUCAUUUUGCCUGCCAAUCUUACAUUUUUGUCAUCUUGUGCUCCAAGUCAGAUAAAGAGAAAAGUCAACUGACCUUUCUCUUAUCCUUGAAUACCGGAAACUC .........((((((((........(((((....)))))......))))).)))..(((((((........................(((((....(((....)))....))).))..((((...(((((.((((((.(((....))).)))))))))))))))......))))))). (-34.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUUUCCGGUAUUCAAGGAUAAGAGAAAGGUCAGUUGACUUUUCUCUUUAUCUGACUUGGAGCACAAGAUGACAAAAAUGUAAGAUUGGCAGGCAAAAUGAAAGAUUAGGUUAUGGAAACUUGUCUGUCUUUCCGGUAUGAUAGUAGUAUCAAGUUAAAUAAAGAAGAGGUUCGAGU (((..((..((.(((((((((((((((((((((....)))))))))).)))))...))))))..))....((((..........((..(((((((((..................(....))))))))))..)).(((((.......)))))..)))).........))..))).... (-44.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 889 90 41 181 132 NC_009009:SSA_1660|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1657580..1657810_NEGATIVE 382 108 62 195 148 NC_009009:SSA_1682|5end_hypothetical_protein_1676885..1677115_NEGATIVE 346 90 41 89 30 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 288 150 108 47 3 NC_009009:SSA_0040|5end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_46308..46538_POSITIVE 287 90 43 172 113 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 282 126 86 39 7 NC_009009:SSA_0392|5end_hypothetical_protein_387876..388106_POSITIVE 281 109 61 179 143 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 281 126 81 114 54 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 281 121 82 104 63 NC_009009:SSA_0250|5end_GTP_pyrophosphokinase,_putative_242167..242397_POSITIVE 279 124 84 197 149 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 277 90 51 231 193 NC_009009:SSA_2212|5end_Possible_polysaccharide_transport_protein,_putative_2213928..2214158_NEGATIVE 276 127 83 211 165 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 274 124 83 104 65 NC_009009:SSA_1646|5end_hypothetical_protein_1646771..1647001_NEGATIVE 273 120 74 153 99 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 272 120 84 231 193 NC_009009:SSA_0777|5end_Glycogen_biosynthesis_protein_GlgD,_putative_759430..759660_POSITIVE 270 130 83 60 23 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 269 117 76 128 91 NC_009009:SSA_0169|5end_hypothetical_protein_167741..167971_POSITIVE 268 88 42 106 64 NC_009009:SSA_0283|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274559..274789_POSITIVE 265 116 79 124 82 NC_009009:SSA_1802|5end_Snf2_family_protein,_putative_1786470..1786700_NEGATIVE 264 99 54 149 97 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 106 62 75 31 NC_009009:SSA_1682|3end_hypothetical_protein_1676130..1676280_NEGATIVE 346 90 41 73 14 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 322 108 64 46 1 NC_009009:SSA_1683|3end_NrdI_protein,_putative_1677034..1677184_NEGATIVE 310 97 51 121 74 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 288 150 108 60 16 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 274 124 83 53 14 NC_009009:SSA_1647|3end_hypothetical_protein_1646822..1646972_NEGATIVE 268 88 42 85 43 NC_009009:SSA_0282|3end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIA_component,_putative_274618..274768_POSITIVE 263 127 84 53 4 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 252 117 73 77 30 NC_009009:SSA_2131|3end_DNA-binding_protein,_putative_2134247..2134397_POSITIVE 251 117 72 151 101 NC_009009:SSA_1402|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1414481..1414631_NEGATIVE 248 129 84 86 23 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 246 85 43 76 9 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 246 148 101 135 86 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 245 160 114 99 54 NC_009009:SSA_2355|3end_Conserved_uncharacterized_protein_2356325..2356475_NEGATIVE 245 127 86 83 47 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 242 126 82 138 102 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 241 90 42 124 62 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 240 120 75 147 98 NC_009009:SSA_1735|3end_UreX,_putative_1720461..1720611_NEGATIVE 238 126 91 113 70 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 238 126 86 119 83 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE