Origin IGS: ttagtcttcaaaaaaagaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagcattgtttttaatcaaattgaaagttgacaatcaagagaaatttcaagtctaaaaggtgctcaattttatttagacaccttgacaaatatgtaaagaactgctagtatatccataagcagttctttttttgaagactaa Mask Tandem Repeat Region ================================================ ttagtcttcaaaaaaagaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc Find is-nt database================================================ Query_seq: SSA_1635:SSA_1636|SSA_1635:SSA_1636:hypothetical protein:ABC-type antibiotic exporter, ATPase component, putative:<-<-:1639312..1639453 142 ttagtcttcaaaaaaagaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1635:SSA_1636|SSA_1635:SSA_1636:hypothetical protein:ABC-type antibiotic exporter, ATPase component, putative:<-<-:1639312..1639453 142 ttagtcttcaaaaaaagaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1635:SSA_1636|SSA_1635:SSA_1636:hypothetical protein:ABC-type antibiotic exporter, ATPase component, putative:<-<-:1639312..1639453 142 ttagtcttcaaaaaaagaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttagtcttcaaaaaaagaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc Predict ORF larger than 30AA ================================================ ttagtcttcaaaaaaagaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc 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: 88 Start: 32 End: 61 ...............................CTTGACAAATATGTAAAGAACTGCTAGTAT................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttagtcttcaaaaaaagaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -4.9 Tail_Score: -5.41143 Start: 17 End: 44 Full_Region: tgacaaatatgtaaa gaactgctagt atatcc ataagcagttc tttttttgaagacta ................gaactgctagtatatccataagcagttc.................................................................................................. Find igs database================================================ Query_seq: SSA_1635:SSA_1636|SSA_1635:SSA_1636:hypothetical protein:ABC-type antibiotic exporter, ATPase component, putative:<-<-:1639312..1639453 142 ttagtcttcaaaaaaagaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc Intra-Species Hit: Count: 1 Min: 17 Max: 142 Len: 126 Subject: NC_009009_SSA_1635_SSA_1636|hypothetical protein:ABC-type antibiotic exporter, ATPase component, putative|NEGATIVE:NEGATIVE|[1639312,1639453]|142 HSP 1 e-value: 1.0E-65 bit: 250.0 Len: 126 Query Start:17 Query End:142 Subject Strand: POSITIVE Subject Start: 17 Subject End: 142 ................gaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc ................gaactgcttatggatatactagcagttctttacatatttgtcaaggtgtctaaataaaattgagcaccttttagacttgaaatttctcttgattgtcaactttcaatttgattaaaaacaatgctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACUGCUUAUGGAUAUACUAGCAGUUCUUUACAUAUUUGUCAAGGUGUCUAAAUAAAAUUGAGCACCUUUUAGACUUGAAAUUUCUCUUGAUUGUCAACUUUCAAUUUGAUUAAAAACAAUGCUC ((((((((...(......).))))))))...........(((((((((..(((......)))..))))))...)))...............(((((......((.....))......))))).... (-24.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCAUUGUUUUUAAUCAAAUUGAAAGUUGACAAUCAAGAGAAAUUUCAAGUCUAAAAGGUGCUCAAUUUUAUUUAGACACCUUGACAAAUAUGUAAAGAACUGCUAGUAUAUCCAUAAGCAGUUC ..(.((((((.....((.....)).....)))))))..............(((...((((((((.((......)))).)))))))))...........((((((((.((......)).)))))))) (-22.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 50 1 157 108 NC_009009:SSA_1635|5end_hypothetical_protein_1639221..1639451_NEGATIVE 262 55 11 121 67 NC_009009:SSA_2348|5end_Metal_dependent_hydrolase,_putative_2350720..2350950_NEGATIVE 255 50 4 148 109 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 249 50 4 121 76 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 244 50 1 213 177 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 243 50 3 103 62 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 242 110 68 226 183 NC_009009:SSA_1272|5end_50S_ribosomal_protein_L31_type_B,_putative_1295015..1295245_POSITIVE 241 50 4 181 128 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 237 45 4 140 102 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 234 52 19 41 7 NC_009009:SSA_2210|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2210475..2210705_POSITIVE 232 45 5 229 176 NC_009009:SSA_1693|5end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1686811..1687041_NEGATIVE 232 43 5 97 61 NC_009009:SSA_0371|5end_NADP-specific_glutamate_dehydrogenase,_putative_361759..361989_NEGATIVE 227 49 1 227 182 NC_009009:SSA_0944|5end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_951741..951971_POSITIVE 226 110 62 192 145 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 225 105 61 190 135 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 225 46 1 209 164 NC_009009:SSA_0141|5end_Copper_chaperone,_putative_136893..137123_POSITIVE 223 79 37 147 101 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 219 104 63 186 141 NC_009009:SSA_1937|5end_Malonyl-CoA:ACP_transacylase,_putative_1924771..1925001_NEGATIVE 219 100 60 209 171 NC_009009:SSA_0177|5end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_178405..178635_POSITIVE 216 48 3 110 51 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 50 4 121 76 NC_009009:SSA_1660|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1656819..1656969_NEGATIVE 244 49 3 149 93 NC_009009:SSA_1740|3end_hypothetical_protein_1727081..1727231_NEGATIVE 242 110 68 118 75 NC_009009:SSA_1271|3end_Conserved_uncharacterized_protein_1294987..1295137_POSITIVE 233 101 61 99 58 NC_009009:SSA_0999|3end_Biotin--[acetyl-CoA-carboxylase]_ligase,_putative_998781..998931_NEGATIVE 226 110 62 97 50 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 225 105 61 134 79 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 224 80 34 142 95 NC_009009:SSA_1563|3end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1566456..1566606_NEGATIVE 223 48 4 141 96 NC_009009:SSA_2024|3end_hypothetical_protein_2029105..2029255_NEGATIVE 223 79 37 144 98 NC_009009:SSA_0759|3end_Acetylglutamate_kinase,_putative_742658..742808_POSITIVE 216 48 3 126 67 NC_009009:SSA_1645|3end_hypothetical_protein_1645601..1645751_NEGATIVE 216 110 65 98 50 NC_009009:SSA_0753|3end_Foldase_protein_prsA_precursor,_putative_736055..736205_POSITIVE 215 65 21 49 2 NC_009009:SSA_0642|3end_Type_4_prepilin_peptidase,_putative_629391..629541_NEGATIVE 211 90 42 77 21 NC_009009:SSA_2015|3end_Phosphoglycerate_mutase,_putative_2014794..2014944_NEGATIVE 210 79 43 129 97 NC_009009:SSA_1695|3end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1687177..1687327_NEGATIVE 210 90 41 113 59 NC_009009:SSA_1690|3end_hypothetical_protein_1683348..1683498_POSITIVE 208 47 11 151 110 NC_009009:SSA_2349|3end_DTDP-4-dehydrorhamnose_3,5-epimerase,_putative_2350677..2350827_NEGATIVE 206 79 37 117 78 NC_009009:SSA_1196|3end_Acetyltransferase,_GNAT_family,_putative_1221528..1221678_NEGATIVE 206 96 51 105 61 NC_009009:SSA_0818|3end_SPX_domain-like_protein,_putative_800486..800636_POSITIVE 205 96 57 77 27 NC_009009:SSA_1868|3end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863096..1863246_NEGATIVE 205 42 7 147 100 NC_009009:SSA_0248|3end_hypothetical_protein_241844..241994_POSITIVE