Origin IGS: ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttcaaaaaacttgtaaaacattaaaaagacttgtaaaaacttatttgctatgttatactctatttagaaaagcaaggagggacaagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcttgtccctccttgcttttctaaatagagtataacatagcaaataagtttttacaagtctttttaatgttttacaagttttttgaaatgcgcaggagaaaatcaaaaaaccgagcaaatctcggttttcatgaattataataatcgaaacatgtttttcaa Mask Tandem Repeat Region ================================================ ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttcaaaaaacttgtaaaacattaaaaagacttgtaaaaacttatttgctatgttatactctatttagaaaagcaaggagggacaagc Find is-nt database================================================ Query_seq: SSA_2327:SSA_2328|SSA_2327:SSA_2328:hypothetical protein:Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative:->->:2331461..2331622 162 ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttcaaaaaacttgtaaaacattaaaaagacttgtaaaaacttatttgctatgttatactctatttagaaaagcaaggagggacaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2327:SSA_2328|SSA_2327:SSA_2328:hypothetical protein:Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative:->->:2331461..2331622 162 ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttcaaaaaacttgtaaaacattaaaaagacttgtaaaaacttatttgctatgttatactctatttagaaaagcaaggagggacaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2327:SSA_2328|SSA_2327:SSA_2328:hypothetical protein:Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative:->->:2331461..2331622 162 ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttcaaaaaacttgtaaaacattaaaaagacttgtaaaaacttatttgctatgttatactctatttagaaaagcaaggagggacaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttcaaaaaacttgtaaaacattaaaaagacttgtaaaaacttatttgctatgttatactctatttagaaaagcaaggagggacaagc Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 18 End: 161 ................. M I I I H E N R D L L G F L I F S C A F Q K T C K T L K R L V K T Y L L C Y T L F R K A R R D K . Protein_Len: 38 Strand: - Start: 25 End: 138 ........................ L E H F G L N A R N K S K R R R M E F F K Y F M L F V Q L F K N A I N Y E M ........................ ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttcaaaaaacttgtaaaacattaaaaagacttgtaaaaacttatttgctatgttatactctatttagaaaagcaaggagggacaagc 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: 105 End: 134 ........................................................................................................CTTGTAAAAACTTATTTGCTATGTTATACT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttcaaaaaacttgtaaaacattaaaaagacttgtaaaaacttatttgctatgttatactctatttagaaaagcaaggagggacaagc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -7.5 Tail_Score: -4.4648 Start: 29 End: 60 Full_Region: TTCGATTATTATAAT TCATGAAAACCGAG ATTTG CTCGGTTTTTTGA TTTTCTCCTGCGCAT ............................TCATGAAAACCGAGATTTGCTCGGTTTTTTGA...................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -7.1 Tail_Score: -4.32049 Start: 38 End: 52 Full_Region: gagaaaatcaaaaaa ccgag caaat ctcgg ttttcatgaattata .....................................ccgagcaaatctcgg.............................................................................................................. Find igs database================================================ Query_seq: SSA_2327:SSA_2328|SSA_2327:SSA_2328:hypothetical protein:Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative:->->:2331461..2331622 162 ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttcaaaaaacttgtaaaacattaaaaagacttgtaaaaacttatttgctatgttatactctatttagaaaagcaaggagggacaagc Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: NC_009009_SSA_2327_SSA_2328|hypothetical protein:Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative|POSITIVE:POSITIVE|[2331461,2331622]|162 HSP 1 e-value: 5.0E-37 bit: 155.0 Len: 78 Query Start:1 Query End:78 Subject Strand: POSITIVE Subject Start: 1 Subject End: 78 ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttc.................................................................................... ttgaaaaacatgtttcgattattataattcatgaaaaccgagatttgctcggttttttgattttctcctgcgcatttc.................................................................................... HSP 2 e-value: 4.0E-19 bit: 95.6 Len: 48 Query Start:115 Query End:162 Subject Strand: POSITIVE Subject Start: 115 Subject End: 162 ..................................................................................................................cttatttgctatgttatactctatttagaaaagcaaggagggacaagc ..................................................................................................................cttatttgctatgttatactctatttagaaaagcaaggagggacaagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAAAAACAUGUUUCGAUUAUUAUAAUUCAUGAAAACCGAGAUUUGCUCGGUUUUUUGAUUUUCUCCUGCGCAUUUCAAAAAACUUGUAAAACAUUAAAAAGACUUGUAAAAACUUAUUUGCUAUGUUAUACUCUAUUUAGAAAAGCAAGGAGGGACAAGC ((((((......))))))..........(((.((((((((((.....))))))))))))).(..(((((..((.((((.(((.....(((.(((((...........(((((......))))).))))).)))....))).)))).)).)))))..)..... (-35.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUGUCCCUCCUUGCUUUUCUAAAUAGAGUAUAACAUAGCAAAUAAGUUUUUACAAGUCUUUUUAAUGUUUUACAAGUUUUUUGAAAUGCGCAGGAGAAAAUCAAAAAACCGAGCAAAUCUCGGUUUUCAUGAAUUAUAAUAAUCGAAACAUGUUUUUCAA ........((((((((.((((.((((...(((.(((((.......(((...........)))....))))).)))..))))...)))).))).)))))....(((.(((((((((.....)))))))))..)))............((((......)))).. (-28.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 80 37 81 26 NC_009009:SSA_2004|5end_Zinc_metalloprotease_zmpB_precursor,_putative_2004930..2005160_NEGATIVE 300 79 33 66 18 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 274 78 34 66 20 NC_009009:SSA_0006|5end_Peptidyl-tRNA_hydrolase,_putative_5009..5239_POSITIVE 265 68 27 185 148 NC_009009:SSA_1801|5end_hypothetical_protein_1783314..1783544_NEGATIVE 263 62 28 138 101 NC_009009:SSA_2161|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160600..2160830_NEGATIVE 262 78 39 79 34 NC_009009:SSA_1646|5end_hypothetical_protein_1646771..1647001_NEGATIVE 262 74 38 205 168 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 261 58 14 132 87 NC_009009:SSA_0392|5end_hypothetical_protein_387876..388106_POSITIVE 258 78 37 59 14 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 254 80 38 116 61 NC_009009:SSA_0739|5end_Carbamate_kinase,_putative_721087..721317_POSITIVE 248 128 85 176 128 NC_009009:SSA_1253|5end_hypothetical_protein_1281245..1281475_NEGATIVE 246 75 38 176 141 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 245 72 48 179 155 NC_009009:SSA_1134|5end_Xanthine_phosphoribosyltransferase,_putative_1159628..1159858_POSITIVE 243 70 28 49 17 NC_009009:SSA_0968|5end_hypothetical_protein_976699..976929_POSITIVE 243 78 40 101 56 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 240 78 37 203 152 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 235 72 32 222 168 NC_009009:SSA_0012|5end_Beta-lactamase_class_A,_putative_9916..10146_POSITIVE 235 72 32 101 47 NC_009009:SSA_0011|5end_hypothetical_protein_9795..10025_POSITIVE 234 89 41 206 158 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 230 80 39 200 152 NC_009009:SSA_1515|5end_hypothetical_protein_1522129..1522359_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 71 31 48 4 NC_009009:SSA_1570|3end_hypothetical_protein_1573137..1573287_POSITIVE 265 68 27 130 93 NC_009009:SSA_1802|3end_Snf2_family_protein,_putative_1783369..1783519_NEGATIVE 259 73 39 137 100 NC_009009:SSA_1630|3end_hypothetical_protein_1631508..1631658_POSITIVE 258 76 37 108 49 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 256 70 28 145 106 NC_009009:SSA_1719|3end_Conserved_uncharacterized_protein_1705924..1706074_NEGATIVE 248 75 46 86 51 NC_009009:SSA_2348|3end_Metal_dependent_hydrolase,_putative_2349875..2350025_NEGATIVE 245 72 48 136 112 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 243 78 40 55 10 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 240 66 31 82 44 NC_009009:SSA_1571|3end_Threonyl-tRNA_synthetase,_putative_1573211..1573361_NEGATIVE 235 72 32 98 44 NC_009009:SSA_0010|3end_Cell_division_protein_DivIC,_putative_9872..10022_POSITIVE 234 89 41 150 102 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 231 66 37 103 69 NC_009009:SSA_0267|3end_ROK_family_protein,_putative_260873..261023_NEGATIVE 230 79 37 134 87 NC_009009:SSA_1128|3end_Voltage_gated_chloride_channel_EriC,_putative_1154886..1155036_POSITIVE 228 73 31 55 8 NC_009009:SSA_2371|3end_Zn-dependent_peptidase,_putative_2372422..2372572_NEGATIVE 228 79 36 133 93 NC_009009:SSA_1173|3end_Lipoate_protein_ligase_A,_putative_1200092..1200242_NEGATIVE 227 58 12 111 53 NC_009009:SSA_1882|3end_Subtilisin-like_serine_proteases,_putative_1876277..1876427_NEGATIVE 223 74 39 40 1 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 221 106 66 52 6 NC_009009:SSA_0445|3end_hypothetical_protein_444776..444926_POSITIVE 220 158 117 131 82 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 219 73 31 110 55 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE