Origin IGS: ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagcacctcctttggaatcgtttacgattattattatacctctttaattttcaatgtcaagcactttctatcaaaaacttccattttctatctttttgccgaacaaaaaaagagctgggctatatccaactccttacatatgttgcataactgccaaataaaaggcaa Mask Tandem Repeat Region ================================================ ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt Find is-nt database================================================ Query_seq: SSA_1079:SSA_1080|SSA_1079:SSA_1080:hypothetical protein:Transcriptional repressor of the fructose operon, DeoR family, putative:->->:1097509..1097677 169 ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1079:SSA_1080|SSA_1079:SSA_1080:hypothetical protein:Transcriptional repressor of the fructose operon, DeoR family, putative:->->:1097509..1097677 169 ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1079:SSA_1080|SSA_1079:SSA_1080:hypothetical protein:Transcriptional repressor of the fructose operon, DeoR family, putative:->->:1097509..1097677 169 ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 11 End: 115 .......... K A T I C C I Y P T P Y L G A R K K N P L F I S F P L K Q Y F T S S M ...................................................... Protein_Len: 50 Strand: - Start: 3 End: 152 .. G K I Q C N H L M H L S N S I A W S K K Q E A F L Y F I S T K S L F H K V N F I L S T Y Y Y D Y V M ................. ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt 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================================================ ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1079:SSA_1080|SSA_1079:SSA_1080:hypothetical protein:Transcriptional repressor of the fructose operon, DeoR family, putative:->->:1097509..1097677 169 ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: NC_009009_SSA_1079_SSA_1080|hypothetical protein:Transcriptional repressor of the fructose operon, DeoR family, putative|POSITIVE:POSITIVE|[1097509,1097677]|169 HSP 1 e-value: 9.0E-79 bit: 293.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctcnnnnnnngttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt ttgccttttatttggcagttatgcaacatatgtaaggagttggatatagcccagctctttttttgttcggcaaaaagatagaaaatggaagtttttgatagaaagtgcttgacattgaaaattaaagaggtataataataatcgtaaacgattccaaaggaggtgcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCCUUUUAUUUGGCAGUUAUGCAACAUAUGUAAGGAGUUGGAUAUAGCCCAGCUCUUUUUUUGUUCGGCAAAAAGAUAGAAAAUGGAAGUUUUUGAUAGAAAGUGCUUGACAUUGAAAAUUAAAGAGGUAUAAUAAUAAUCGUAAACGAUUCCAAAGGAGGUGCUUU ..(((((...(((((..(((((((..(......((((((((((.......))))))))))...((((.((((........((((((....)))))).........)))).))))............)..)))))))...(((((....)))))))))).)))))..... (-40.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCACCUCCUUUGGAAUCGUUUACGAUUAUUAUUAUACCUCUUUAAUUUUCAAUGUCAAGCACUUUCUAUCAAAAACUUCCAUUUUCUAUCUUUUUGCCGAACAAAAAAAGAGCUGGGCUAUAUCCAACUCCUUACAUAUGUUGCAUAACUGCCAAAUAAAAGGCAA ..(((.((.....(((((..((((..((..((((...........))))..))..((.....))...........))))))))).......(((((((.........)))))))...))))).(((.((((...........)))).)))..((((........)))). (-22.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 69 21 204 153 NC_009009:SSA_2067|5end_hypothetical_protein_2070254..2070484_POSITIVE 308 57 11 88 36 NC_009009:SSA_1672|5end_hypothetical_protein_1670389..1670619_NEGATIVE 294 57 17 169 132 NC_009009:SSA_1067|5end_hypothetical_protein_1086399..1086629_POSITIVE 294 96 51 48 4 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 293 97 53 207 155 NC_009009:SSA_1200|5end_Formate--tetrahydrofolate_ligase,_putative_1225591..1225821_NEGATIVE 292 61 34 148 121 NC_009009:SSA_2202|5end_Elongation_factor_Ts,_putative_2203350..2203580_NEGATIVE 284 68 21 192 132 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 276 57 11 73 33 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 271 59 11 172 114 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 268 73 31 163 117 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 266 55 15 49 12 NC_009009:SSA_1623|5end_50S_ribosomal_protein_L11,_putative_1625968..1626198_NEGATIVE 261 59 12 54 10 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 259 69 21 157 105 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 259 73 35 52 8 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 258 89 41 187 134 NC_009009:SSA_0665|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes_(MutT/NUDIX_family)_649603..649833_NEGATIVE 258 81 42 48 9 NC_009009:SSA_0387|5end_Transcriptional_regulator,_GntR_family,_putative_382343..382573_NEGATIVE 252 55 14 64 26 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 251 71 37 222 171 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 250 85 46 158 113 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 249 59 14 160 110 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 70 34 100 59 NC_009009:SSA_0718|3end_Conserved_uncharacterized_protein_704935..705085_POSITIVE 294 57 17 66 29 NC_009009:SSA_1066|3end_ABC-type_oligopeptide_transport_system,_putative_1086376..1086526_POSITIVE 292 61 34 75 48 NC_009009:SSA_2203|3end_30S_ribosomal_protein_S2,_putative_2203423..2203573_NEGATIVE 284 72 34 59 20 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 269 67 21 91 46 NC_009009:SSA_1373|3end_ATPase_components_of_ABC_transporters_with_duplicated_ATPase_domains,_multidrug_transport_system,_putative_1391313..1391463_POSITIVE 268 73 31 107 61 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE 265 88 43 124 76 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 261 59 12 70 26 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 259 71 32 40 3 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 259 73 35 48 4 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 258 89 41 109 56 NC_009009:SSA_0666|3end_hypothetical_protein_649681..649831_NEGATIVE 249 59 14 79 29 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE 243 45 1 120 75 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 242 70 22 139 86 NC_009009:SSA_1695|3end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1687177..1687327_NEGATIVE 242 88 49 150 111 NC_009009:SSA_1111|3end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1137940..1138090_POSITIVE 241 66 36 43 11 NC_009009:SSA_1671|3end_hypothetical_protein_1670337..1670487_POSITIVE 241 73 32 113 67 NC_009009:SSA_0667|3end_Transcriptional_regulator,_putative_650757..650907_POSITIVE 240 80 35 43 2 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 236 62 23 92 54 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 235 71 34 128 95 NC_009009:SSA_1869|3end_ATP-dependent_RNA_helicase,_putative_1864152..1864302_NEGATIVE