Origin IGS: tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatctcatctcctcgttacttttcaaaaataattgtaactccccgttacctaatattacctactactaagtatagttcgaactctaaaaaaagtcaagaattttactacataaaaatttctaaaatcaaagaataccaagggatgagacaaattgtcaatttaccaactatttaaatggtcatttatttatatttgaaacatcaagtaatttgagttttctttcaaagtgaatgttggacttttttaaaaaagatagtaggaataaaataagaagaggccaggaatcaagtatcccagccatatatctcaga Mask Tandem Repeat Region ================================================ tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata Find is-nt database================================================ Query_seq: SSA_0020:SSA_0021|SSA_0020:SSA_0021:Ribose-phosphate pyrophosphokinase 1, putative:hypothetical protein:->->:26670..26981 312 tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0020:SSA_0021|SSA_0020:SSA_0021:Ribose-phosphate pyrophosphokinase 1, putative:hypothetical protein:->->:26670..26981 312 tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0020:SSA_0021|SSA_0020:SSA_0021:Ribose-phosphate pyrophosphokinase 1, putative:hypothetical protein:->->:26670..26981 312 tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 2 End: 130 . M R Y M A G I L D S W P L L I L F L L S F L K K S N I H F E R K L K L L D V S N I N K ...................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 153 End: 254 ........................................................................................................................................................ M D N L S H P L V F F D F R N F Y V V K F L T F F R V R T I L S S R .......................................................... Protein_Len: 57 Strand: - Start: 141 End: 311 ............................................................................................................................................ I T P L N V I Q R M G Q Y E K I K S I K I Y Y F E Q S K K S N S S Y K T T P L I L Y R P T V I I K S F Y R P S S M . Protein_Len: 32 Strand: - Start: 85 End: 180 .................................................................................... K S L F S L N S S T E F I F L H G N L Y N T F Q C N T E D R P M .................................................................................................................................... tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata 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: 87 Start: 215 End: 244 ......................................................................................................................................................................................................................CTTGACTTTTTTTAGAGTTCGAACTATACT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -4.3 Tail_Score: -2.53831 Start: 264 End: 278 Full_Region: AGTAGGTAATATTAG GTAAC GGGGA GTTAC AATTATTTTTGAAAA .......................................................................................................................................................................................................................................................................GTAACGGGGAGTTAC.................................. Find igs database================================================ Query_seq: SSA_0020:SSA_0021|SSA_0020:SSA_0021:Ribose-phosphate pyrophosphokinase 1, putative:hypothetical protein:->->:26670..26981 312 tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata Intra-Species Hit: Count: 1 Min: 1 Max: 312 Len: 312 Subject: NC_009009_SSA_0020_SSA_0021|Ribose-phosphate pyrophosphokinase 1, putative:hypothetical protein|POSITIVE:POSITIVE|[26670,26981]|312 HSP 1 e-value: 1.0E-164 bit: 577.0 Len: 312 Query Start:1 Query End:312 Subject Strand: POSITIVE Subject Start: 1 Subject End: 312 tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgacnnnnnnnagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata tctgagatatatggctgggatacttgattcctggcctcttcttattttattcctactatcttttttaaaaaagtccaacattcactttgaaagaaaactcaaattacttgatgtttcaaatataaataaatgaccatttaaatagttggtaaattgacaatttgtctcatcccttggtattctttgattttagaaatttttatgtagtaaaattcttgactttttttagagttcgaactatacttagtagtaggtaatattaggtaacggggagttacaattatttttgaaaagtaacgaggagatgagata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUGAGAUAUAUGGCUGGGAUACUUGAUUCCUGGCCUCUUCUUAUUUUAUUCCUACUAUCUUUUUUAAAAAAGUCCAACAUUCACUUUGAAAGAAAACUCAAAUUACUUGAUGUUUCAAAUAUAAAUAAAUGACCAUUUAAAUAGUUGGUAAAUUGACAAUUUGUCUCAUCCCUUGGUAUUCUUUGAUUUUAGAAAUUUUUAUGUAGUAAAAUUCUUGACUUUUUUUAGAGUUCGAACUAUACUUAGUAGUAGGUAAUAUUAGGUAACGGGGAGUUACAAUUAUUUUUGAAAAGUAACGAGGAGAUGAGAUA ..(((((.....(((..(((........)))..)))...))))).........(((((.((..((((((...(((.....(((.....))).((((..((((.....))))..))))..............)))..)))))).)).)))))...........((((((((((((((...((((........)))).((((((.(((((..(((((((((((((....)))))).......(((((((((........)))))))))...)))))))...)))))...))))))....))))).))))))))) (-65.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUCAUCUCCUCGUUACUUUUCAAAAAUAAUUGUAACUCCCCGUUACCUAAUAUUACCUACUACUAAGUAUAGUUCGAACUCUAAAAAAAGUCAAGAAUUUUACUACAUAAAAAUUUCUAAAAUCAAAGAAUACCAAGGGAUGAGACAAAUUGUCAAUUUACCAACUAUUUAAAUGGUCAUUUAUUUAUAUUUGAAACAUCAAGUAAUUUGAGUUUUCUUUCAAAGUGAAUGUUGGACUUUUUUAAAAAAGAUAGUAGGAAUAAAAUAAGAAGAGGCCAGGAAUCAAGUAUCCCAGCCAUAUAUCUCAGA .........((((.((..((((((..........(((((.....)))))....((((.(((((((((.((((.(((((..(((........)))...))))).))))...((((((..(((((..((((((((.(((((.(((((.(((.....))).....((((..........))))))))).....(((((((....)))))))..))).)).)))))......)))...)))))..))))))....)).)))))))))))......)))))))).))))............................ (-53.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 39 13 212 188 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 322 60 12 218 149 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 304 42 1 225 175 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 304 42 11 201 166 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 302 40 12 182 151 NC_009009:SSA_1764|5end_hypothetical_protein_1750868..1751098_POSITIVE 286 37 2 159 123 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 280 60 12 220 177 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 276 56 12 73 16 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 274 47 1 187 136 NC_009009:SSA_1474|5end_Lipoprotein,_putative_1479741..1479971_NEGATIVE 274 48 3 161 117 NC_009009:SSA_1372|5end_hypothetical_protein_1389137..1389367_NEGATIVE 274 49 3 167 108 NC_009009:SSA_0577|5end_Ancient_RNA-binding_IF3-C_fold_(CRS1/YhbY_domain),_putative_571253..571483_POSITIVE 273 47 13 180 143 NC_009009:SSA_1967|5end_Threonine_desaminase,_putative_1963559..1963789_NEGATIVE 271 48 14 115 75 NC_009009:SSA_1992|5end_Fructose-bisphosphate_aldolase,_putative_1989972..1990202_NEGATIVE 268 60 12 79 26 NC_009009:SSA_2182|5end_hypothetical_protein_2181020..2181250_NEGATIVE 268 58 13 96 55 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 264 53 12 59 11 NC_009009:SSA_1528|5end_Phosphoglycerate_mutase,_putative_1535135..1535365_POSITIVE 260 42 1 39 5 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 259 52 13 157 119 NC_009009:SSA_1420|5end_Homoserine_O-succinyltransferase,_putative_1430625..1430855_NEGATIVE 258 57 11 226 182 NC_009009:SSA_0533|5end_Glycerol_dehydratase_large_subunit_pduC,_putative_528970..529200_POSITIVE 258 190 148 126 77 NC_009009:SSA_0388|5end_Mismatch_repair_ATPase_(MutS_family),_putative_382474..382704_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 39 3 42 9 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 338 57 13 95 48 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 322 60 12 96 27 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 288 37 1 70 30 NC_009009:SSA_1161|3end_hypothetical_protein_1188443..1188593_POSITIVE 286 42 3 86 51 NC_009009:SSA_0303|3end_surface_protein_C_301051..301201_POSITIVE 280 60 12 151 108 NC_009009:SSA_0250|3end_GTP_pyrophosphokinase,_putative_244466..244616_POSITIVE 273 47 13 80 43 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 271 49 13 104 61 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 257 49 4 59 1 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 254 191 160 52 15 NC_009009:SSA_2356|3end_Replicative_DNA_helicase,_putative_2356603..2356753_NEGATIVE 254 50 5 56 9 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 252 53 13 97 63 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 252 178 145 59 28 NC_009009:SSA_1418|3end_Conserved_uncharacterized_protein_1428139..1428289_NEGATIVE 252 37 3 61 29 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE 252 57 13 125 63 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 252 42 3 118 84 NC_009009:SSA_0381|3end_hypothetical_protein_373514..373664_POSITIVE 249 53 11 103 66 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 247 53 13 123 74 NC_009009:SSA_1862|3end_hypothetical_protein_1857981..1858131_NEGATIVE 245 57 11 95 46 NC_009009:SSA_1462|3end_Prephenate_dehydratase,_putative_1468934..1469084_NEGATIVE 244 55 14 108 54 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE