Origin IGS: cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag .........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 ctctgattcctttcataagatatgtgagctttagcgactaaaaataacaatttctagataacatcttatttccaagcttcagctcacctttactttgacaagctagggacgctgaattatttaccatccgctagctcttttcttcagcttcttcctaccattcttcaggaattcgcatcatttcattttaccatatttcagg Mask Tandem Repeat Region ================================================ cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag Find is-nt database================================================ Query_seq: SSA_0568:SSA_0569|SSA_0568:SSA_0569:Aspartyl-tRNA synthetase 1, putative:Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C, putative:->->:563551..563752 202 cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0568:SSA_0569|SSA_0568:SSA_0569:Aspartyl-tRNA synthetase 1, putative:Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C, putative:->->:563551..563752 202 cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0568:SSA_0569|SSA_0568:SSA_0569:Aspartyl-tRNA synthetase 1, putative:Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C, putative:->->:563551..563752 202 cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 2 End: 145 . Q F I T F H F S A F E Q L I T P L L Q L F S S A S P L Y N L T G L K D F Y L H A S A Q F Y S T M ......................................................... cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag 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================================================ cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0568:SSA_0569|SSA_0568:SSA_0569:Aspartyl-tRNA synthetase 1, putative:Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C, putative:->->:563551..563752 202 cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: NC_009009_SSA_0568_SSA_0569|Aspartyl-tRNA synthetase 1, putative:Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C, putative|POSITIVE:POSITIVE|[563551,563752]|202 HSP 1 e-value: 1.0E-111 bit: 400.0 Len: 202 Query Start:1 Query End:202 Subject Strand: POSITIVE Subject Start: 1 Subject End: 202 cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag cctgaaatatggtaaaatgaaatgatgcgaattcctgaagaatggtaggaagaagctgaagaaaagagctagcggatggtaaataattcagcgtccctagcttgtcaaagtaaaggtgagctgaagcttggaaataagatgttatctagaaattgttatttttagtcgctaaagctcacatatcttatgaaaggaatcagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUGAAAUAUGGUAAAAUGAAAUGAUGCGAAUUCCUGAAGAAUGGUAGGAAGAAGCUGAAGAAAAGAGCUAGCGGAUGGUAAAUAAUUCAGCGUCCCUAGCUUGUCAAAGUAAAGGUGAGCUGAAGCUUGGAAAUAAGAUGUUAUCUAGAAAUUGUUAUUUUUAGUCGCUAAAGCUCACAUAUCUUAUGAAAGGAAUCAGAG (((...(((.((((............((...((((((........))))))...))....((...(((((((.(((((.(.........).)))))))))))).)).........(((((((..(((((((((((((.(..((.....))...).))))))))))..)))..))))))).)))).)))...)))........ (-51.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUGAUUCCUUUCAUAAGAUAUGUGAGCUUUAGCGACUAAAAAUAACAAUUUCUAGAUAACAUCUUAUUUCCAAGCUUCAGCUCACCUUUACUUUGACAAGCUAGGGACGCUGAAUUAUUUACCAUCCGCUAGCUCUUUUCUUCAGCUUCUUCCUACCAUUCUUCAGGAAUUCGCAUCAUUUCAUUUUACCAUAUUUCAGG ..((((............((((((.(((((..((((.(((.((((....)))).)))....................((((((((.(((...(((....)))..))))).))))))............))))))))).........((...(((((..........)))))...))...............)))))))))). (-34.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 129 89 41 1 NC_009009:SSA_0462|5end_ABC-type_multidrug_transport_system_(phospholipid,_LPS,_lipid_A_and_drug_exporter),_ATPase_and_permease_components,_putative_464815..465045_POSITIVE 337 98 55 101 49 NC_009009:SSA_1904|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1899279..1899509_NEGATIVE 333 69 27 222 176 NC_009009:SSA_2092|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095975..2096205_NEGATIVE 331 130 88 216 165 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 331 128 87 212 169 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 331 138 91 184 140 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 326 129 87 48 3 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 326 107 67 182 134 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 317 76 35 47 4 NC_009009:SSA_1750|5end_Extracellular_nuclease,_putative_1737922..1738152_NEGATIVE 316 104 72 61 31 NC_009009:SSA_0921|5end_Zn-dependeant_threonine_dehydrogenase,_putative_931047..931277_POSITIVE 309 107 65 107 59 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 303 76 43 53 22 NC_009009:SSA_2204|5end_hypothetical_protein_2204663..2204893_POSITIVE 302 117 71 55 11 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 299 130 85 192 136 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 295 90 43 192 148 NC_009009:SSA_0113|5end_30S_ribosomal_protein_S3,_putative_111322..111552_POSITIVE 292 130 94 68 35 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 291 107 64 41 2 NC_009009:SSA_2023|5end_Fructan_beta-fructosidase_precursor,_putative_2028826..2029056_NEGATIVE 288 74 43 181 150 NC_009009:SSA_0917|5end_Cobalamin-independent_methionine_synthase_II,_putative_930250..930480_NEGATIVE 287 131 92 58 19 NC_009009:SSA_0720|5end_hypothetical_protein_705106..705336_POSITIVE 285 121 92 52 23 NC_009009:SSA_0249|5end_hypothetical_protein_241751..241981_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 129 83 51 5 NC_009009:SSA_0461|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_464905..465055_POSITIVE 337 98 55 104 52 NC_009009:SSA_1905|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1899276..1899426_NEGATIVE 331 130 84 42 3 NC_009009:SSA_1231|3end_hypothetical_protein_1253649..1253799_NEGATIVE 302 117 71 51 7 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 285 79 31 140 93 NC_009009:SSA_1943|3end_Aspartate_kinase,_putative_1930159..1930309_POSITIVE 285 121 92 65 36 NC_009009:SSA_0248|3end_hypothetical_protein_241844..241994_POSITIVE 280 80 31 105 43 NC_009009:SSA_1541|3end_Peptidase,_U32_family,_putative_1545311..1545461_NEGATIVE 279 99 51 88 47 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 278 133 91 136 97 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 278 95 54 61 26 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 274 104 63 48 2 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 273 99 55 116 61 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 271 96 53 141 98 NC_009009:SSA_1828|3end_Glycerol_uptake_facilitator_protein,_putative_1818791..1818941_POSITIVE 268 127 92 49 13 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 264 150 102 79 29 NC_009009:SSA_0964|3end_DEAD_RNA_helicase,_putative_972954..973104_NEGATIVE 258 127 86 46 2 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 257 128 97 30 3 NC_009009:SSA_1748|3end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1733543..1733693_NEGATIVE 256 100 54 116 59 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 255 127 90 145 109 NC_009009:SSA_0780|3end_Acid_phosphatase_(PAP2_family),_putative_765328..765478_POSITIVE 255 124 90 146 108 NC_009009:SSA_0607|3end_ABC_transporter,_permease_component,_putative_594590..594740_NEGATIVE