Origin IGS: tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac .........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 gtagcttctcctatttcttacagtattcttactttcaggtctaattcagtagctttgtcctatagttgaaagcaattcctgctaaaattatagcatattctcaactctatgcccatctatgatcaatacgaatcaagcagtaaaaaacgcagataagcctgtctgcgttctttgtttatcaactga Mask Tandem Repeat Region ================================================ tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac Find is-nt database================================================ Query_seq: SSA_0148:SSA_0149|SSA_0148:SSA_0149:Sugar ABC transporter, ATP-binding protein, putative:hypothetical protein:->->:143528..143713 186 tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0148:SSA_0149|SSA_0148:SSA_0149:Sugar ABC transporter, ATP-binding protein, putative:hypothetical protein:->->:143528..143713 186 tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0148:SSA_0149|SSA_0148:SSA_0149:Sugar ABC transporter, ATP-binding protein, putative:hypothetical protein:->->:143528..143713 186 tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. T S L C L V C V P K D A N K V A Q N T N I M S P C L T S F M .............................................................................................. tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac 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: 83 Start: 71 End: 100 ......................................................................ATGGGCATAGAGTTGAGAATATGCTATAAT...................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -6.9 Tail_Score: -4.56367 Start: 17 End: 42 Full_Region: gaatcaagcagtaaa aaacgcagata agcc tgtctgcgttc tttgtttatcaactg ................aaacgcagataagcctgtctgcgttc................................................................................................................................................ TransTerm Strand: - Conf: 90 HP_score: -8.6 Tail_Score: -4.38748 Start: 20 End: 39 Full_Region: tcaagcagtaaaaaa cgcagata agcc tgtctgcg ttctttgtttatcaa ...................cgcagataagcctgtctgcg................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0148:SSA_0149|SSA_0148:SSA_0149:Sugar ABC transporter, ATP-binding protein, putative:hypothetical protein:->->:143528..143713 186 tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac Intra-Species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: NC_009009_SSA_0148_SSA_0149|Sugar ABC transporter, ATP-binding protein, putative:hypothetical protein|POSITIVE:POSITIVE|[143528,143713]|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 tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac tcagttgataaacaaagaacgcagacaggcttatctgcgttttttactgcttgattcgtattgatcatagatgggcatagagttgagaatatgctataattttagcaggaattgctttcaactataggacaaagctactgaattagacctgaaagtaagaatactgtaagaaataggagaagctac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAGUUGAUAAACAAAGAACGCAGACAGGCUUAUCUGCGUUUUUUACUGCUUGAUUCGUAUUGAUCAUAGAUGGGCAUAGAGUUGAGAAUAUGCUAUAAUUUUAGCAGGAAUUGCUUUCAACUAUAGGACAAAGCUACUGAAUUAGACCUGAAAGUAAGAAUACUGUAAGAAAUAGGAGAAGCUAC ..((((((.....((((((((((((........))))))))))))....((..((((....((..((....))..))..))))..))....(((((......)))))..........)))))).........((((.((...(((...((...((((....))))...))...))).)).)))).. (-41.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAGCUUCUCCUAUUUCUUACAGUAUUCUUACUUUCAGGUCUAAUUCAGUAGCUUUGUCCUAUAGUUGAAAGCAAUUCCUGCUAAAAUUAUAGCAUAUUCUCAACUCUAUGCCCAUCUAUGAUCAAUACGAAUCAAGCAGUAAAAAACGCAGAUAAGCCUGUCUGCGUUCUUUGUUUAUCAACUGA ..((((.((...(((.(((..((((....))))...)))...)))..)).))))........(((((((((((((...(((((.........(((((..........))))).......((((........))))))))).....((((((((((....))))))))))..)))))).))))))). (-38.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 57 14 164 111 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 321 65 21 58 5 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 308 70 23 93 44 NC_009009:SSA_0933|5end_Acetyltransferase,_GNAT_family,_putative_942734..942964_POSITIVE 305 78 34 193 157 NC_009009:SSA_1521|5end_Phosphoenolpyruvate_carboxylase,_putative_1530683..1530913_NEGATIVE 304 150 107 176 136 NC_009009:SSA_2354|5end_hypothetical_protein_2356237..2356467_NEGATIVE 302 48 14 155 118 NC_009009:SSA_1024|5end_Alpha-amylase,_putative_1042648..1042878_NEGATIVE 301 77 31 135 88 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 299 50 8 46 8 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 297 117 72 228 171 NC_009009:SSA_1696|5end_Tagatose_1,6-diphosphate_aldolase_2,_putative_1689187..1689417_NEGATIVE 284 87 41 222 177 NC_009009:SSA_0901|5end_Alpha-acetolactate_decarboxylase,_putative_892447..892677_POSITIVE 282 78 31 145 88 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 278 80 37 93 53 NC_009009:SSA_1152|5end_Protein_chain_release_factor_A,_putative_1180759..1180989_POSITIVE 272 109 61 206 164 NC_009009:SSA_1657|5end_hypothetical_protein_1653231..1653461_NEGATIVE 265 68 21 187 127 NC_009009:SSA_0518|5end_Ethanolamine_utilization_protein_EutA,_putative_516610..516840_POSITIVE 261 83 46 77 38 NC_009009:SSA_1506|5end_Lipopolysaccharide_biosynthesis_protein,_putative_1511222..1511452_NEGATIVE 259 59 13 91 37 NC_009009:SSA_2152|5end_ABC-type_transporter_(uncharacterized),_ATPase_component,_putative_2153801..2154031_NEGATIVE 259 69 21 88 37 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 259 58 20 171 121 NC_009009:SSA_0675|5end_Exodeoxyribonuclease_VII_small_subunit,_putative_658389..658619_POSITIVE 258 49 1 214 176 NC_009009:SSA_0020|5end_Ribose-phosphate_pyrophosphokinase_1,_putative_25564..25794_POSITIVE 255 58 11 226 173 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 45 14 77 46 NC_009009:SSA_0148|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_143467..143617_POSITIVE 332 57 14 109 56 NC_009009:SSA_0354|3end_Uncharacterized_membrane_protein_346872..347022_POSITIVE 308 70 23 83 34 NC_009009:SSA_0932|3end_hypothetical_protein_942804..942954_POSITIVE 305 78 34 146 110 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 304 150 107 88 48 NC_009009:SSA_2355|3end_Conserved_uncharacterized_protein_2356325..2356475_NEGATIVE 299 50 8 46 8 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 295 53 12 89 48 NC_009009:SSA_1052|3end_hypothetical_protein_1066846..1066996_NEGATIVE 284 87 41 72 27 NC_009009:SSA_0900|3end_Tetratricopeptide_repeat_(TPR)_family_protein_892377..892527_POSITIVE 282 78 31 145 88 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 280 119 76 144 106 NC_009009:SSA_0127|3end_Multispanning_membrane_protein,_translocator_of_proteins,_putative_119107..119257_POSITIVE 279 58 12 79 31 NC_009009:SSA_0062|3end_Aldose_1-epimerase,_putative_64858..65008_POSITIVE 278 80 37 56 16 NC_009009:SSA_1151|3end_Thymidine_kinase,_putative_1180802..1180952_POSITIVE 273 74 31 151 110 NC_009009:SSA_0620|3end_hypothetical_protein_611951..612101_NEGATIVE 265 60 14 78 27 NC_009009:SSA_2343|3end_hypothetical_protein_2343703..2343853_NEGATIVE 265 68 21 73 13 NC_009009:SSA_0517|3end_Sensor_histidine_kinase,_putative_516576..516726_POSITIVE 264 80 32 128 79 NC_009009:SSA_1893|3end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1889421..1889571_NEGATIVE 261 83 46 60 21 NC_009009:SSA_1507|3end_ABC-type_lipopolysaccharide_transport_system,_ATPase_component,_putative_1511239..1511389_NEGATIVE 259 59 13 94 40 NC_009009:SSA_2153|3end_ABC-type_transporter_(uncharacterized),_permease_component,_putative_2153798..2153948_NEGATIVE 258 137 93 133 85 NC_009009:SSA_1317|3end_hypothetical_protein_1333398..1333548_NEGATIVE 258 49 1 89 51 NC_009009:SSA_0019|3end_Secreted_antigen_GbpB/SagA;_peptidoglycan_hydrolase;_PcsB_protein_precursor,_putative_25519..25669_POSITIVE