Origin IGS: gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct .........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 agaagaaatgcagtctggtaacagattgcttttttcttgaattatttgctggtctattttgttttccgtatgattgcttgattatttttctattttctcaaaactctagacacatacatttcttcctatcctcttgaaatatcagcctaattttgttacactagatagaaagactgtgaaggagac Mask Tandem Repeat Region ================================================ gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct Find is-nt database================================================ Query_seq: SSA_1851:SSA_1852|SSA_1851:SSA_1852:Guanylate kinase, putative:Metal dependent phosphohydrolase (HD motif), putative:<-<-:1846773..1846958 186 gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1851:SSA_1852|SSA_1851:SSA_1852:Guanylate kinase, putative:Metal dependent phosphohydrolase (HD motif), putative:<-<-:1846773..1846958 186 gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1851:SSA_1852|SSA_1851:SSA_1852:Guanylate kinase, putative:Metal dependent phosphohydrolase (HD motif), putative:<-<-:1846773..1846958 186 gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 53 End: 172 .................................................... S S L F F H I H R S N Q S F L F I I L C D Y P F C F L G A F L E L F F C D T V M .............. gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct 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: 86 Start: 25 End: 54 ........................CTTGAAATATCAGCCTAATTTTGTTACACT.................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 113 End: 142 ................................................................................................................TTTGCTGGTCTATTTTGTTTTCCGTATGAT............................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1851:SSA_1852|SSA_1851:SSA_1852:Guanylate kinase, putative:Metal dependent phosphohydrolase (HD motif), putative:<-<-:1846773..1846958 186 gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct Intra-Species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: NC_009009_SSA_1851_SSA_1852|Guanylate kinase, putative:Metal dependent phosphohydrolase (HD motif), putative|NEGATIVE:NEGATIVE|[1846773,1846958]|186 HSP 1 e-value: 1.0E-101 bit: 369.0 Len: 186 Query Start:1 Query End:186 Subject Strand: POSITIVE Subject Start: 1 Subject End: 186 gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct gtctccttcacagtctttctatctagtgtaacaaaattaggctgatatttcaagaggataggaagaaatgtatgtgtctagagttttgagaaaatagaaaaataatcaagcaatcatacggaaaacaaaatagaccagcaaataattcaagaaaaaagcaatctgttaccagactgcatttcttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUCCUUCACAGUCUUUCUAUCUAGUGUAACAAAAUUAGGCUGAUAUUUCAAGAGGAUAGGAAGAAAUGUAUGUGUCUAGAGUUUUGAGAAAAUAGAAAAAUAAUCAAGCAAUCAUACGGAAAACAAAAUAGACCAGCAAAUAAUUCAAGAAAAAAGCAAUCUGUUACCAGACUGCAUUUCUUCU ((((.........(((((((((((.((.(((.....))).)).((....))....)))))))))))..((((((((.((.(((((((...........)))))..)).))))..))))))...........)))).............((((((...(((.((((....)))).))).)))))).. (-31.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAGAAAUGCAGUCUGGUAACAGAUUGCUUUUUUCUUGAAUUAUUUGCUGGUCUAUUUUGUUUUCCGUAUGAUUGCUUGAUUAUUUUUCUAUUUUCUCAAAACUCUAGACACAUACAUUUCUUCCUAUCCUCUUGAAAUAUCAGCCUAAUUUUGUUACACUAGAUAGAAAGACUGUGAAGGAGAC .((((((((((((((((....))))))))....................(((((((....(((((..(((....)))..((..((......))..))..)))))..))))).))...)))))))).....(((((.......(((.((..(((((((......))))))))).)))...))))).. (-34.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 90 41 181 132 NC_009009:SSA_1851|5end_Guanylate_kinase,_putative_1846682..1846912_NEGATIVE 266 55 15 144 109 NC_009009:SSA_0256|5end_Metalloregulator_ScaR_(Fe/Mn-dependent_transcriptional_repressor),_putative_248699..248929_NEGATIVE 265 46 2 122 81 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 260 44 1 229 183 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 259 177 136 189 151 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 257 177 132 53 4 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 254 167 126 97 47 NC_009009:SSA_1665|5end_hypothetical_protein_1665353..1665583_NEGATIVE 246 35 2 134 101 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 246 177 136 140 86 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 244 45 3 146 97 NC_009009:SSA_0401|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_398462..398692_POSITIVE 243 66 21 139 94 NC_009009:SSA_1739|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1725540..1725770_POSITIVE 240 36 1 63 24 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 234 44 1 159 98 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 234 45 5 137 82 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 234 78 41 230 200 NC_009009:SSA_1029|5end_hypothetical_protein_1047009..1047239_NEGATIVE 233 78 37 206 165 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 230 179 149 61 27 NC_009009:SSA_0418|5end_AraC-type_DNA-binding_domain-containing_protein,_putative_415256..415486_POSITIVE 227 96 52 133 93 NC_009009:SSA_0662|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_648302..648532_NEGATIVE 223 53 12 48 4 NC_009009:SSA_1824|5end_hypothetical_protein_1812746..1812976_NEGATIVE 222 46 2 139 98 NC_009009:SSA_0166|5end_hypothetical_protein_164641..164871_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 46 2 78 37 NC_009009:SSA_0487|3end_Delta-aminolevulinic_acid_dehydratase,_putative_488400..488550_POSITIVE 259 177 136 89 51 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 254 167 126 75 25 NC_009009:SSA_1666|3end_Collagen-binding_surface_protein,_putative_1665375..1665525_NEGATIVE 246 35 2 95 62 NC_009009:SSA_2233|3end_hypothetical_protein_2232967..2233117_NEGATIVE 234 44 1 134 73 NC_009009:SSA_2240|3end_Holliday_junction_resolvase,_putative_2237258..2237408_NEGATIVE 223 31 1 55 16 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 221 43 4 64 28 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 219 44 4 70 15 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 218 51 11 55 7 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 218 66 39 68 39 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 216 88 41 106 65 NC_009009:SSA_1134|3end_Xanthine_phosphoribosyltransferase,_putative_1160316..1160466_POSITIVE 215 89 41 73 13 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE 213 43 4 149 110 NC_009009:SSA_1636|3end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1639364..1639514_NEGATIVE 212 42 5 48 17 NC_009009:SSA_1889|3end_Conserved_uncharacterized_protein_1886283..1886433_NEGATIVE 207 47 6 48 3 NC_009009:SSA_0383|3end_Beta-glucosidase,_putative_376053..376203_POSITIVE 206 46 3 41 1 NC_009009:SSA_0165|3end_hypothetical_protein_164623..164773_POSITIVE 204 48 1 116 84 NC_009009:SSA_1254|3end_hypothetical_protein_1281242..1281392_NEGATIVE 203 97 51 106 61 NC_009009:SSA_1164|3end_hypothetical_protein_1191007..1191157_NEGATIVE 201 58 12 61 17 NC_009009:SSA_0998|3end_hypothetical_protein_998758..998908_POSITIVE 201 176 137 60 24 NC_009009:SSA_0099|3end_hypothetical_protein_100134..100284_NEGATIVE