Origin IGS: aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtagtataacagaaaacagttgcaaacgcaactgtttgtttttgctaatttggttttaaattaacaaattttcaaatcaatctatctaaaaaatggcttacctctaaagggcaaagccattttttatt Mask Tandem Repeat Region ================================================ aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac Find is-nt database================================================ Query_seq: SSA_0661:SSA_0662|SSA_0661:SSA_0662:Isoleucyl-tRNA synthetase, putative:Multiple antibiotic resistance operon transcription repressor (MarR), putative:-><-:647809..647936 128 aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0661:SSA_0662|SSA_0661:SSA_0662:Isoleucyl-tRNA synthetase, putative:Multiple antibiotic resistance operon transcription repressor (MarR), putative:-><-:647809..647936 128 aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0661:SSA_0662|SSA_0661:SSA_0662:Isoleucyl-tRNA synthetase, putative:Multiple antibiotic resistance operon transcription repressor (MarR), putative:-><-:647809..647936 128 aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac Predict ORF larger than 30AA ================================================ aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac 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: 82 Start: 97 End: 126 ................................................................................................GTTGCGTTTGCAACTGTTTTCTGTTATACT.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.9 Tail_Score: -4.75289 Start: 95 End: 112 Full_Region: ATTAGCAAAAACAAA CAGTTGC GTTT GCAACTG TTTTCTGTTATACTA ..............................................................................................CAGTTGCGTTTGCAACTG................ Find igs database================================================ Query_seq: SSA_0661:SSA_0662|SSA_0661:SSA_0662:Isoleucyl-tRNA synthetase, putative:Multiple antibiotic resistance operon transcription repressor (MarR), putative:-><-:647809..647936 128 aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_009009_SSA_0661_SSA_0662|Isoleucyl-tRNA synthetase, putative:Multiple antibiotic resistance operon transcription repressor (MarR), putative|POSITIVE:NEGATIVE|[647809,647936]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac aataaaaaatggctttgccctttagaggtaagccattttttagatagattgatttgaaaatttgttaatttaaaaccaaattagcaaaaacaaacagttgcgtttgcaactgttttctgttatactac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAAAAUGGCUUUGCCCUUUAGAGGUAAGCCAUUUUUUAGAUAGAUUGAUUUGAAAAUUUGUUAAUUUAAAACCAAAUUAGCAAAAACAAACAGUUGCGUUUGCAACUGUUUUCUGUUAUACUAC ..(((((((((((((.((((....).))))))))))))))))((((((............(((((((((((......)))))))))))...((((((((((....))))))))))))))))....... (-40.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAGUAUAACAGAAAACAGUUGCAAACGCAACUGUUUGUUUUUGCUAAUUUGGUUUUAAAUUAACAAAUUUUCAAAUCAAUCUAUCUAAAAAAUGGCUUACCUCUAAAGGGCAAAGCCAUUUUUUAUU .(((((.((((...(((((((((....)))))))))))))..)))))..(((((((.(((((....)))))..)))))))......(((((((((((((.(((....)))...))))))))))))).. (-37.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 57 11 217 160 NC_009009:SSA_0332|5end_hypothetical_protein_325909..326139_POSITIVE 254 36 11 28 2 NC_009009:SSA_2020|5end_hypothetical_protein_2019284..2019514_POSITIVE 253 43 2 175 136 NC_009009:SSA_0419|5end_Alpha-galactosidase,_putative_416213..416443_POSITIVE 245 120 90 31 1 NC_009009:SSA_2325|5end_3-methyladenine_DNA_glycosylase,_putative_2330721..2330951_NEGATIVE 243 119 84 87 46 NC_009009:SSA_0574|5end_YdjX_protein,_putative_569427..569657_NEGATIVE 241 52 14 49 4 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 241 35 11 173 148 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 241 32 5 156 126 NC_009009:SSA_1162|5end_Possible_fimbrial_assembly_protein_fimC,_putative_1189250..1189480_NEGATIVE 237 119 77 208 176 NC_009009:SSA_2085|5end_Glyoxylate_reductase,_NADH-dependent,_putative_2090404..2090634_NEGATIVE 237 57 13 59 13 NC_009009:SSA_0436|5end_Imidazolonepropionase,_putative_438869..439099_POSITIVE 235 45 11 151 119 NC_009009:SSA_0326|5end_Conserved_uncharacterized_BCR,_YbaB_family_319823..320053_NEGATIVE 232 115 75 202 161 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 229 119 81 168 120 NC_009009:SSA_0650|5end_GTP-binding_protein_TypA/BipA,_putative_632548..632778_POSITIVE 227 118 75 125 78 NC_009009:SSA_0924|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_933738..933968_POSITIVE 225 48 10 227 183 NC_009009:SSA_1600|5end_hypothetical_protein_1606595..1606825_NEGATIVE 225 78 33 60 1 NC_009009:SSA_0432|5end_Formate--tetrahydrofolate_ligase,_putative_434991..435221_NEGATIVE 223 57 11 186 143 NC_009009:SSA_2268|5end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_2267228..2267458_POSITIVE 223 34 10 29 4 NC_009009:SSA_1676|5end_Transcriptional_regulator,_LytTr_family,_putative_1671313..1671543_NEGATIVE 222 51 12 82 48 NC_009009:SSA_0390|5end_hypothetical_protein_385002..385232_POSITIVE 221 33 8 155 133 NC_009009:SSA_2131|5end_DNA-binding_protein,_putative_2133949..2134179_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 42 3 88 49 NC_009009:SSA_0661|3end_Isoleucyl-tRNA_synthetase,_putative_647748..647898_POSITIVE 253 43 2 66 27 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 241 32 5 70 40 NC_009009:SSA_1163|3end_GMP_synthase_[glutamine-hydrolyzing],_putative_1189336..1189486_NEGATIVE 234 35 10 148 119 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 228 34 9 150 122 NC_009009:SSA_0768|3end_Ribonucleoside-diphosphate_reductase_2,_beta_subunit,_putative_748136..748286_NEGATIVE 226 57 11 63 15 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 223 57 11 68 25 NC_009009:SSA_2267|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2267190..2267340_POSITIVE 222 51 12 82 48 NC_009009:SSA_0389|3end_hypothetical_protein_385082..385232_POSITIVE 221 33 8 146 124 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 220 59 15 59 12 NC_009009:SSA_1930|3end_Acetyl-CoA_carboxylase_alpha_subunit,_putative_1917777..1917927_NEGATIVE 217 44 11 120 88 NC_009009:SSA_2077|3end_hypothetical_protein_2081352..2081502_NEGATIVE 213 50 6 81 47 NC_009009:SSA_1734|3end_Cation_(Mg/Ni_uptake)_transport_ATPase,_putative_1717643..1717793_NEGATIVE 210 43 9 135 93 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 209 38 9 81 51 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 209 33 9 147 115 NC_009009:SSA_1341|3end_Carbamoyl-phosphate_synthase_large_chain,_putative_1356648..1356798_NEGATIVE 206 118 97 121 98 NC_009009:SSA_2315|3end_Conserved_uncharacterized_protein_2316487..2316637_NEGATIVE 205 113 75 132 97 NC_009009:SSA_1498|3end_50S_ribosomal_protein_L20,_putative_1503753..1503903_NEGATIVE 205 48 10 129 92 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 204 46 4 102 49 NC_009009:SSA_1590|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1593342..1593492_POSITIVE 202 55 16 65 12 NC_009009:SSA_2106|3end_Flavin_monoxygenase,_putative_2108015..2108165_NEGATIVE