Origin IGS: cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagttaataatgggaaaagagtatgcaagttacatcatgatgataccggccttgaataaaaaatggctgctttaacggagaataaacgtaagaccgagacagaattgattcagcagcagtatattttatagtatctaacgattaag Mask Tandem Repeat Region ================================================ cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc Find is-nt database================================================ Query_seq: SSA_1473:SSA_1474|SSA_1473:SSA_1474:hypothetical protein:Lipoprotein, putative:<-<-:1479011..1479156 146 cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1473:SSA_1474|SSA_1473:SSA_1474:hypothetical protein:Lipoprotein, putative:<-<-:1479011..1479156 146 cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1473:SSA_1474|SSA_1473:SSA_1474:hypothetical protein:Lipoprotein, putative:<-<-:1479011..1479156 146 cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 18 End: 140 ................. M K Y T A A E S I L S R S Y V Y S P L K Q P F F I Q G R Y H H D V T C I L F S H Y ...... cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc 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================================================ cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1473:SSA_1474|SSA_1473:SSA_1474:hypothetical protein:Lipoprotein, putative:<-<-:1479011..1479156 146 cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_009009_SSA_1473_SSA_1474|hypothetical protein:Lipoprotein, putative|NEGATIVE:NEGATIVE|[1479011,1479156]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc cttaatcgttagatactataaaatatactgctgctgaatcaattctgtctcggtcttacgtttattctccgttaaagcagccattttttattcaaggccggtatcatcatgatgtaacttgcatactcttttcccattattaactc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAAUCGUUAGAUACUAUAAAAUAUACUGCUGCUGAAUCAAUUCUGUCUCGGUCUUACGUUUAUUCUCCGUUAAAGCAGCCAUUUUUUAUUCAAGGCCGGUAUCAUCAUGAUGUAACUUGCAUACUCUUUUCCCAUUAUUAACUC .......(((((.....((((((......((((((...............((......))...............))))))....)))))).....((.(((..(((....)))..))).)).................))))).. (-18.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUUAAUAAUGGGAAAAGAGUAUGCAAGUUACAUCAUGAUGAUACCGGCCUUGAAUAAAAAAUGGCUGCUUUAACGGAGAAUAAACGUAAGACCGAGACAGAAUUGAUUCAGCAGCAGUAUAUUUUAUAGUAUCUAACGAUUAAG ...(((((....(((..(((((((((......(((....))).......................(((((....(((.........)))......(((.(......).))).))))).)))))))))......)))....))))). (-20.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 891 80 31 171 122 NC_009009:SSA_1473|5end_hypothetical_protein_1478920..1479150_NEGATIVE 311 83 42 45 4 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 307 88 45 95 46 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 303 139 95 148 100 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 300 69 28 54 7 NC_009009:SSA_2325|5end_3-methyladenine_DNA_glycosylase,_putative_2330721..2330951_NEGATIVE 299 63 27 176 138 NC_009009:SSA_1192|5end_hypothetical_protein_1219034..1219264_NEGATIVE 299 105 64 197 151 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 295 105 64 210 158 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 292 79 31 128 75 NC_009009:SSA_2068|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_2071311..2071541_NEGATIVE 287 100 51 217 171 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 285 64 27 178 145 NC_009009:SSA_1190|5end_Conserved_uncharacterized_protein_1218137..1218367_NEGATIVE 283 83 42 157 108 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 281 80 48 40 7 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 280 80 33 87 33 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 279 89 45 96 51 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 278 71 45 228 203 NC_009009:SSA_0628|5end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_617892..618122_POSITIVE 277 112 71 219 174 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 277 90 46 128 78 NC_009009:SSA_1304|5end_hypothetical_protein_1323449..1323679_NEGATIVE 277 79 31 95 37 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 275 104 65 217 180 NC_009009:SSA_2253|5end_3-Methyladenine_DNA_glycosylase_I,_constitutive,_putative_2249424..2249654_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 63 27 115 77 NC_009009:SSA_1193|3end_Dihydrodipicolinate_synthase,_putative_1219095..1219245_NEGATIVE 297 106 64 69 20 NC_009009:SSA_0156|3end_ATPase_with_chaperone_activity,_ATP-binding_subunit,_putative_153322..153472_POSITIVE 285 64 27 93 60 NC_009009:SSA_1191|3end_hypothetical_protein_1218222..1218372_NEGATIVE 283 83 42 149 100 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 281 80 48 43 10 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 279 89 45 86 41 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 277 90 46 52 2 NC_009009:SSA_1305|3end_hypothetical_protein_1323525..1323675_NEGATIVE 267 75 35 88 35 NC_009009:SSA_0753|3end_Foldase_protein_prsA_precursor,_putative_736055..736205_POSITIVE 266 82 46 130 73 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 266 57 16 86 36 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 259 125 81 88 40 NC_009009:SSA_0578|3end_Nicotinate-nucleotide_adenylyltransferase,_putative_572303..572453_POSITIVE 256 98 55 40 3 NC_009009:SSA_0835|3end_Accessory_secretory_protein_Asp3,_putative_821595..821745_POSITIVE 255 80 31 76 17 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 255 83 41 55 6 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 250 81 46 127 80 NC_009009:SSA_0606|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_593789..593939_NEGATIVE 244 111 76 45 3 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 241 63 29 148 103 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 241 109 76 49 14 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 241 89 52 151 101 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 240 134 92 130 91 NC_009009:SSA_2303|3end_hypothetical_protein_2304113..2304263_NEGATIVE