Origin IGS: ctctttttttatttttagagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgaaacttggtatgatggaagagttgagaaaagcagaagtgagagcttctcgccttgcgactaacgttgtctggctctacaggattcagtttcagtaatgaaatattatcgtgtagtgcgggtttgcgttagcaggtccgcacttgtttttctctaaaaataaaaaaagag Mask Tandem Repeat Region ================================================ ctctttttttatttttagagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt Find is-nt database================================================ Query_seq: SSA_1500:SSA_1501|SSA_1500:SSA_1501:Translation initiation factor IF-3, putative:Cytidylate kinase, putative:<-<-:1505012..1505184 173 ctctttttttatttttagagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1500:SSA_1501|SSA_1500:SSA_1501:Translation initiation factor IF-3, putative:Cytidylate kinase, putative:<-<-:1505012..1505184 173 ctctttttttatttttagagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1500:SSA_1501|SSA_1500:SSA_1501:Translation initiation factor IF-3, putative:Cytidylate kinase, putative:<-<-:1505012..1505184 173 ctctttttttatttttagagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctttttttatttttagagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 68 End: 172 ................................................................... M S L L K L N P V E P D N V S R K A R S S H F C F S Q L F H H T K F H . Protein_Len: 32 Strand: - Start: 77 End: 172 ............................................................................ Q F Q I R Y L W V V N T A L R S A R V E A K R L E E M M G L K M . ctctttttttatttttagagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt 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================================================ ctctttttttatttttagagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -5.9 Tail_Score: -4.9725 Start: 26 End: 59 Full_Region: atgaaatattatcgt gtagtgcgggtttgc gtta gcaggtccgcacttg tttttctctaaaaat .........................gtagtgcgggtttgcgttagcaggtccgcacttg.................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -12.0 Tail_Score: -4.58943 Start: 29 End: 56 Full_Region: aaatattatcgtgta gtgcgggtttgc gtta gcaggtccgcac ttgtttttctctaaa ............................gtgcgggtttgcgttagcaggtccgcac..................................................................................................................... Find igs database================================================ Query_seq: SSA_1500:SSA_1501|SSA_1500:SSA_1501:Translation initiation factor IF-3, putative:Cytidylate kinase, putative:<-<-:1505012..1505184 173 ctctttttttatttttagagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt Intra-Species Hit: Count: 1 Min: 17 Max: 173 Len: 157 Subject: NC_009009_SSA_1500_SSA_1501|Translation initiation factor IF-3, putative:Cytidylate kinase, putative|NEGATIVE:NEGATIVE|[1505012,1505184]|173 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 157 Query Start:17 Query End:173 Subject Strand: POSITIVE Subject Start: 17 Subject End: 173 ................agagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt ................agagaaaaacaagtgcggacctgctaacgcaaacccgcactacacgataatatttcattactgaaactgaatcctgtagagccagacaacgttagtcgcaaggcgagaagctctcacttctgcttttctcaactcttccatcataccaagtttcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGAAAAACAAGUGCGGACCUGCUAACGCAAACCCGCACUACACGAUAAUAUUUCAUUACUGAAACUGAAUCCUGUAGAGCCAGACAACGUUAGUCGCAAGGCGAGAAGCUCUCACUUCUGCUUUUCUCAACUCUUCCAUCAUACCAAGUUUCAUU ...........(((((((...(((....)))...)))))))....................(((((((.........((((.............(((....)))(((((((..........)))))))....))))............))))))).. (-37.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAAACUUGGUAUGAUGGAAGAGUUGAGAAAAGCAGAAGUGAGAGCUUCUCGCCUUGCGACUAACGUUGUCUGGCUCUACAGGAUUCAGUUUCAGUAAUGAAAUAUUAUCGUGUAGUGCGGGUUUGCGUUAGCAGGUCCGCACUUGUUUUUCUCU .....(((((..(......)..)))))(((((((((.(((((....)))))..(((..(((((....)))))..)))..((((.(((...((((((....))))))...))).))))((((((..((((....))))..))))))..))))))))). (-61.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1019 120 71 227 178 NC_009009:SSA_1500|5end_Translation_initiation_factor_IF-3,_putative_1504921..1505151_NEGATIVE 379 109 73 55 18 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 344 113 73 197 151 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 328 109 61 72 27 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 317 150 101 56 12 NC_009009:SSA_0652|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_635036..635266_POSITIVE 316 112 76 56 8 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 313 108 66 60 11 NC_009009:SSA_0004|5end_Lipoprotein,_putative_3704..3934_NEGATIVE 312 139 96 103 59 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 310 60 15 90 25 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 310 36 1 213 181 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 310 120 76 49 7 NC_009009:SSA_0324|5end_Conserved_uncharacterized_protein_317019..317249_POSITIVE 307 139 98 223 172 NC_009009:SSA_1084|5end_Conserved_uncharacterized_protein_1101675..1101905_POSITIVE 306 113 72 178 127 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 305 110 61 222 156 NC_009009:SSA_0141|5end_Copper_chaperone,_putative_136893..137123_POSITIVE 303 125 82 63 19 NC_009009:SSA_0257|5end_N-acetylmuramidase/lysin,_putative_248878..249108_POSITIVE 299 149 101 151 106 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 295 120 74 216 164 NC_009009:SSA_2310|5end_hypothetical_protein_2313418..2313648_NEGATIVE 294 127 82 210 153 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 293 112 72 218 184 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 292 130 94 218 174 NC_009009:SSA_2173|5end_Aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase,_putative_2171914..2172144_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 107 66 129 93 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 328 109 61 70 25 NC_009009:SSA_1403|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1416222..1416372_NEGATIVE 315 140 95 121 56 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 313 129 83 44 8 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 312 139 96 106 62 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 306 120 74 141 83 NC_009009:SSA_2175|3end_hypothetical_protein_2173146..2173296_NEGATIVE 306 113 72 53 2 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 299 104 67 91 60 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 294 129 81 83 30 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 294 127 82 92 35 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 292 130 94 141 97 NC_009009:SSA_2174|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2171991..2172141_NEGATIVE 291 139 102 118 80 NC_009009:SSA_2201|3end_hypothetical_protein_2202237..2202387_POSITIVE 290 118 72 63 22 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 286 124 95 142 115 NC_009009:SSA_0456|3end_Phosphotransferase_system_IIC_components,_glucose/maltose/N-acetylglucosamine-specific,_putative_460585..460735_POSITIVE 282 107 75 141 115 NC_009009:SSA_1897|3end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894154..1894304_NEGATIVE 282 130 81 91 35 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE 281 80 32 75 19 NC_009009:SSA_0153|3end_hypothetical_protein_149503..149653_POSITIVE 280 120 72 138 89 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 279 38 11 142 116 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 277 129 94 92 54 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE