Origin IGS: tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttttctcctttgtctttttattcgtaaaagattgcaaaaaaataaaacaagccgagaatattttcagcttgtcatattttaaaatctttattttgcaagaagtcgtatagtcgtatagatagaaaggccattgacaaaaatagaagctgcaata Mask Tandem Repeat Region ================================================ tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat Find is-nt database================================================ Query_seq: SSA_0714:SSA_0715|SSA_0714:SSA_0715:hypothetical protein:DNA uptake protein, putative:->->:700710..700865 156 tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0714:SSA_0715|SSA_0714:SSA_0715:hypothetical protein:DNA uptake protein, putative:->->:700710..700865 156 tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0714:SSA_0715|SSA_0714:SSA_0715:hypothetical protein:DNA uptake protein, putative:->->:700710..700865 156 tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 64 End: 156 ............................................................... M K I L K Y D K L K I F S A C F I F L Q S F T N K K T K E K N Protein_Len: 32 Strand: - Start: 2 End: 97 . N C S R N K D I A K R D I R S Y S K K C F L S K L I H C A S F M ........................................................... tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat 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================================================ tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -6.0 Tail_Score: -5.55855 Start: 84 End: 107 Full_Region: GATTTTAAAATATGA CAAGCTGAAA ATAT TCTCGGCTTG TTTTATTTTTTTGCA ...................................................................................CAAGCTGAAAATATTCTCGGCTTG................................................. Find igs database================================================ Query_seq: SSA_0714:SSA_0715|SSA_0714:SSA_0715:hypothetical protein:DNA uptake protein, putative:->->:700710..700865 156 tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_009009_SSA_0714_SSA_0715|hypothetical protein:DNA uptake protein, putative|POSITIVE:POSITIVE|[700710,700865]|156 HSP 1 e-value: 5.0E-71 bit: 268.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttannnnnnngcaatcttttacgaataaaaagacaaaggagaaaaat tattgcagcttctatttttgtcaatggcctttctatctatacgactatacgacttcttgcaaaataaagattttaaaatatgacaagctgaaaatattctcggcttgttttatttttttgcaatcttttacgaataaaaagacaaaggagaaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUGCAGCUUCUAUUUUUGUCAAUGGCCUUUCUAUCUAUACGACUAUACGACUUCUUGCAAAAUAAAGAUUUUAAAAUAUGACAAGCUGAAAAUAUUCUCGGCUUGUUUUAUUUUUUUGCAAUCUUUUACGAAUAAAAAGACAAAGGAGAAAAAU .........((((.((((((((...................((......)).....((((((((...........(((((.((((((((((........)))))))))).))))))))))))).................)))))))))))).... (-30.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUCUCCUUUGUCUUUUUAUUCGUAAAAGAUUGCAAAAAAAUAAAACAAGCCGAGAAUAUUUUCAGCUUGUCAUAUUUUAAAAUCUUUAUUUUGCAAGAAGUCGUAUAGUCGUAUAGAUAGAAAGGCCAUUGACAAAAAUAGAAGCUGCAAUA ((((((.((..(.(((((((((((..((...(((((....((((((..((((((.((((....)))).))))))..))))))....((((........)))).......))))).))..))))))))))).)..)).))))))............. (-31.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 60 19 178 124 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 264 117 81 216 178 NC_009009:SSA_0679|5end_DNA_repair_and_genetic_recombination,_putative_660714..660944_POSITIVE 256 132 94 170 132 NC_009009:SSA_1564|5end_Histidine_kinase,_putative_1568615..1568845_NEGATIVE 248 60 11 128 78 NC_009009:SSA_1854|5end_Conserved_uncharacterized_protein_1850884..1851114_NEGATIVE 248 129 90 160 125 NC_009009:SSA_1512|5end_hypothetical_protein_1517936..1518166_NEGATIVE 237 46 5 221 174 NC_009009:SSA_2310|5end_hypothetical_protein_2313418..2313648_NEGATIVE 237 30 5 149 122 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 236 56 11 183 141 NC_009009:SSA_1817|5end_Conserved_uncharacterized_protein_1805595..1805825_NEGATIVE 236 44 5 64 22 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 233 46 6 119 67 NC_009009:SSA_2337|5end_hypothetical_protein_2338680..2338910_POSITIVE 232 44 4 75 23 NC_009009:SSA_1072|5end_Glutamate_5-kinase,_putative_1089755..1089985_POSITIVE 231 129 86 218 164 NC_009009:SSA_1031|5end_DNA_topology_modulation_protein_FlaR,_putative_1048255..1048485_NEGATIVE 231 61 28 128 95 NC_009009:SSA_0066|5end_hypothetical_protein_67602..67832_POSITIVE 230 113 76 63 21 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 229 90 42 219 160 NC_009009:SSA_0568|5end_Aspartyl-tRNA_synthetase_1,_putative_561674..561904_POSITIVE 228 47 8 227 185 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 227 60 17 56 12 NC_009009:SSA_2316|5end_General_secretory_pathway_protein_F,_putative_2318342..2318572_NEGATIVE 227 129 81 176 124 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 224 119 97 24 2 NC_009009:SSA_1246|5end_hypothetical_protein_1271225..1271455_NEGATIVE 223 60 18 132 91 NC_009009:SSA_1302|5end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1322484..1322714_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 60 11 115 65 NC_009009:SSA_1855|3end_hypothetical_protein_1850897..1851047_NEGATIVE 248 129 90 101 66 NC_009009:SSA_1513|3end_Glycosyltransferase,_putative_1517995..1518145_NEGATIVE 243 37 1 79 41 NC_009009:SSA_1769|3end_hypothetical_protein_1756939..1757089_NEGATIVE 236 56 11 123 81 NC_009009:SSA_1818|3end_Very_short_patch_repair_endonuclease,_putative_1805655..1805805_NEGATIVE 236 121 88 88 55 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE 234 119 72 92 47 NC_009009:SSA_2374|3end_Inosine-5'-monophosphate_dehydrogenase,_putative_2375534..2375684_NEGATIVE 233 46 6 144 92 NC_009009:SSA_2336|3end_Transcriptional_regulator,_PadR_family,_putative_2338785..2338935_POSITIVE 231 61 28 123 90 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE 227 60 17 52 8 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE 225 60 20 130 94 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 224 119 97 27 5 NC_009009:SSA_1247|3end_hypothetical_protein_1271222..1271372_NEGATIVE 223 60 18 142 101 NC_009009:SSA_1303|3end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322474..1322624_NEGATIVE 223 57 25 62 22 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 222 45 5 138 102 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE 222 60 11 145 101 NC_009009:SSA_0219|3end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215884..216034_POSITIVE 220 62 26 107 63 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 219 37 3 144 111 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 218 129 82 75 40 NC_009009:SSA_0419|3end_Alpha-galactosidase,_putative_418530..418680_POSITIVE 216 116 87 87 55 NC_009009:SSA_1591|3end_Dipeptidase,_putative_1593403..1593553_NEGATIVE 216 103 80 31 7 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE