Origin IGS: ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcttgtaaaaggctgagtttcctttgggaagcagcctttttgtgtaaatttacaaggggttgacaagattgtaaacttttaaagactatttttcgcttcctttacccttcttaa Mask Tandem Repeat Region ================================================ ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag Find is-nt database================================================ Query_seq: SSA_2358:SSA_2359|SSA_2358:SSA_2359:hypothetical protein:Glucose inhibited division protein A, putative:<-<-:2360588..2360702 115 ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2358:SSA_2359|SSA_2358:SSA_2359:hypothetical protein:Glucose inhibited division protein A, putative:<-<-:2360588..2360702 115 ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2358:SSA_2359|SSA_2358:SSA_2359:hypothetical protein:Glucose inhibited division protein A, putative:<-<-:2360588..2360702 115 ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 26 End: 115 ......................... M V F K S L Q S C Q P L V N L H K K A A S Q R K L S L L Q E ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag 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: 39 End: 68 ......................................GTTTACAATCTTGTCAACCCCTTGTAAATT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2358:SSA_2359|SSA_2358:SSA_2359:hypothetical protein:Glucose inhibited division protein A, putative:<-<-:2360588..2360702 115 ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_009009_SSA_2358_SSA_2359|hypothetical protein:Glucose inhibited division protein A, putative|NEGATIVE:NEGATIVE|[2360588,2360702]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag ttaagaagggtaaaggaagcgaaaaatagtctttaaaagtttacaatcttgtcaaccccttgtaaatttacacaaaaaggctgcttcccaaaggaaactcagccttttacaagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAGAAGGGUAAAGGAAGCGAAAAAUAGUCUUUAAAAGUUUACAAUCUUGUCAACCCCUUGUAAAUUUACACAAAAAGGCUGCUUCCCAAAGGAAACUCAGCCUUUUACAAGAG ....(((((((...((((((.......(((((((..((((((((((.............))))))))))......)))))))))))))...((....))..)))))))....... (-25.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUGUAAAAGGCUGAGUUUCCUUUGGGAAGCAGCCUUUUUGUGUAAAUUUACAAGGGGUUGACAAGAUUGUAAACUUUUAAAGACUAUUUUUCGCUUCCUUUACCCUUCUUAA ((((((((((((((((...((((....)))).))))))...........))))))))))......((((..(((((........((.......))......)))))...)))).. (-24.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 873 100 51 191 142 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 306 100 57 221 177 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 287 109 72 204 160 NC_009009:SSA_2279|5end_hypothetical_protein_2281910..2282140_NEGATIVE 287 108 76 223 189 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 278 90 47 156 109 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 269 89 46 202 143 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 261 103 61 52 2 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 259 87 43 49 3 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 256 42 4 168 131 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 254 98 56 205 160 NC_009009:SSA_0516|5end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_514485..514715_POSITIVE 249 107 72 175 149 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 248 103 74 53 20 NC_009009:SSA_0384|5end_hypothetical_protein_376240..376470_POSITIVE 246 108 79 190 162 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 245 90 44 159 116 NC_009009:SSA_1423|5end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1433783..1434013_NEGATIVE 244 110 76 159 121 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 244 104 79 47 20 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 240 105 67 62 20 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 239 60 15 180 135 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 234 104 78 41 14 NC_009009:SSA_1188|5end_Ribonuclease_HII,_putative_1216819..1217049_NEGATIVE 233 103 61 169 121 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 100 57 64 20 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 269 89 46 66 7 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 263 95 54 68 13 NC_009009:SSA_2367|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368845..2368995_NEGATIVE 251 103 75 60 31 NC_009009:SSA_0680|3end_Serine/threonine_protein_phosphatase,_putative_663233..663383_POSITIVE 249 107 72 79 53 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 245 90 44 53 10 NC_009009:SSA_1424|3end_Hydrolase,_putative_1433889..1434039_NEGATIVE 244 110 76 94 56 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 234 104 78 54 27 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 233 103 61 75 27 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 226 105 79 122 100 NC_009009:SSA_1386|3end_NADPH-dependent_FMN_reductase,_putative_1403428..1403578_POSITIVE 226 60 18 71 33 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 223 108 74 100 69 NC_009009:SSA_1862|3end_hypothetical_protein_1857981..1858131_NEGATIVE 223 60 14 99 64 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 220 86 45 84 44 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 217 105 64 45 7 NC_009009:SSA_1659|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1654831..1654981_NEGATIVE 215 106 70 149 107 NC_009009:SSA_1024|3end_Alpha-amylase,_putative_1041182..1041332_NEGATIVE 214 87 47 150 111 NC_009009:SSA_0102|3end_Kinase,_putative_104627..104777_POSITIVE 212 33 5 49 16 NC_009009:SSA_1086|3end_TRNA_nucleotidyltransferase,_putative_1104607..1104757_POSITIVE 211 88 41 85 33 NC_009009:SSA_1707|3end_Conserved_uncharacterized_protein_1698248..1698398_POSITIVE 210 104 78 121 95 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE