Origin IGS: gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tattctttaaatcaaaaaagccgagacagcagtgtttcggctttgacttttgaataaaatatgtggataggaaattagctattgtgcgggcttctaaaaaggtgaaagcctcttggccttgtcagctttttcttttcggtgtataataagtgaaaatatttctttacaggaggtgttc Mask Tandem Repeat Region ================================================ gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata Find is-nt database================================================ Query_seq: SSA_2264:SSA_2265|SSA_2264:SSA_2265:hypothetical protein:Maltodextrin phosphorylase, putative:<-<-:2261848..2262025 178 gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2264:SSA_2265|SSA_2264:SSA_2265:hypothetical protein:Maltodextrin phosphorylase, putative:<-<-:2261848..2262025 178 gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2264:SSA_2265|SSA_2264:SSA_2265:hypothetical protein:Maltodextrin phosphorylase, putative:<-<-:2261848..2262025 178 gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 36 End: 125 ................................... V G F L F L Q C P W S A K V K K S A R V I A L K R D V Y K M ..................................................... gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata 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: 91 Start: 32 End: 61 ...............................CTTGTCAGCTTTTTCTTTTCGGTGTATAAT..................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.7 Tail_Score: -5.37593 Start: 138 End: 159 Full_Region: TATTCAAAAGTCAAA GCCGAAACA CTGC TGTCTCGGC TTTTTTGATTTAAAG .........................................................................................................................................GCCGAAACACTGCTGTCTCGGC................... Find igs database================================================ Query_seq: SSA_2264:SSA_2265|SSA_2264:SSA_2265:hypothetical protein:Maltodextrin phosphorylase, putative:<-<-:2261848..2262025 178 gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_009009_SSA_2264_SSA_2265|hypothetical protein:Maltodextrin phosphorylase, putative|NEGATIVE:NEGATIVE|[2261848,2262025]|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 gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata gaacacctcctgtaaagaaatattttcacttattatacaccgaaaagaaaaagctgacaaggccaagaggctttcacctttttagaagcccgcacaatagctaatttcctatccacatattttattcaaaagtcaaagccgaaacactgctgtctcggcttttttgatttaaagaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACACCUCCUGUAAAGAAAUAUUUUCACUUAUUAUACACCGAAAAGAAAAAGCUGACAAGGCCAAGAGGCUUUCACCUUUUUAGAAGCCCGCACAAUAGCUAAUUUCCUAUCCACAUAUUUUAUUCAAAAGUCAAAGCCGAAACACUGCUGUCUCGGCUUUUUUGAUUUAAAGAAUA ................(((((..........................((((((.(((..(((((....)))))))).))))))........((......))..)))))..............(((((..(((((((((((((.(((....))).))))))...)))))))...))))) (-31.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUCUUUAAAUCAAAAAAGCCGAGACAGCAGUGUUUCGGCUUUGACUUUUGAAUAAAAUAUGUGGAUAGGAAAUUAGCUAUUGUGCGGGCUUCUAAAAAGGUGAAAGCCUCUUGGCCUUGUCAGCUUUUUCUUUUCGGUGUAUAAUAAGUGAAAAUAUUUCUUUACAGGAGGUGUUC (((((...((.((((...((((((((((....)))))))))))))).))..)))))..(((..(.((.((((((..((((.....(((((((.......((((....))))...)))).))).)))).)))))).)).)..)))..........(((((((((.....))))))))). (-48.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 968 100 51 191 142 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 326 128 81 224 169 NC_009009:SSA_0666|5end_hypothetical_protein_649788..650018_NEGATIVE 309 99 52 54 5 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 308 110 62 43 1 NC_009009:SSA_2225|5end_Transcriptional_attenuator_LytR,_putative_2226947..2227177_NEGATIVE 302 95 53 155 104 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 294 100 53 230 177 NC_009009:SSA_0811|5end_hypothetical_protein_792469..792699_POSITIVE 293 161 135 136 106 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 289 72 40 177 141 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 285 98 57 143 97 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 285 111 86 50 29 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 284 107 61 186 144 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 283 93 54 216 173 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 280 96 53 175 99 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 279 98 53 94 43 NC_009009:SSA_1422|5end_hypothetical_protein_1431555..1431785_NEGATIVE 278 93 54 198 167 NC_009009:SSA_0892|5end_ATP-binding_cassette_lipoprotein,_putative_884226..884456_POSITIVE 277 92 52 44 5 NC_009009:SSA_0332|5end_hypothetical_protein_325909..326139_POSITIVE 276 168 121 131 87 NC_009009:SSA_1278|5end_Rhodanese-like_domain_protein,_putative_1299877..1300107_NEGATIVE 274 109 63 131 88 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 272 102 61 51 10 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 271 165 137 230 203 NC_009009:SSA_2194|5end_Nicotinamide_mononucleotide_transporter,_putative_2195663..2195893_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 99 58 151 105 NC_009009:SSA_0859|3end_Triosephosphate_isomerase,_putative_847485..847635_POSITIVE 293 161 135 83 53 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 289 72 40 52 16 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 289 110 68 55 13 NC_009009:SSA_1047|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_1062845..1062995_POSITIVE 289 96 53 151 101 NC_009009:SSA_0759|3end_Acetylglutamate_kinase,_putative_742658..742808_POSITIVE 287 170 121 97 50 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 287 92 51 142 107 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 284 107 61 91 49 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 279 98 53 88 37 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 277 92 52 47 8 NC_009009:SSA_0331|3end_C3-degrading_proteinase,_putative_325992..326142_POSITIVE 276 168 121 138 94 NC_009009:SSA_1279|3end_Oxidoreductase,_putative_1299870..1300020_NEGATIVE 275 162 130 85 53 NC_009009:SSA_0452|3end_Nitrogen_utilization_substance_protein_B,_putative_452060..452210_POSITIVE 274 109 63 97 54 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 272 71 41 63 31 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 269 165 132 75 33 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 268 89 52 151 110 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 264 97 53 138 83 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 262 150 101 135 91 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 260 119 71 126 69 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 256 170 121 138 90 NC_009009:SSA_1254|3end_hypothetical_protein_1281242..1281392_NEGATIVE