Origin IGS: aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa .........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 ttcgttctgcttttttcataggattagcctctattctatagcttctttttgaaattttcaagatattttcaacaatgttatcaaaacgaaaagagtcacaaaattgtgagaactgctgacagccctaaaaaagccgccttttggcagctctgttaagattcaaaaagtagattttcctagcct Mask Tandem Repeat Region ================================================ aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa Find is-nt database================================================ Query_seq: SSA_0597:SSA_0599|SSA_0597:SSA_0599:hypothetical protein:hypothetical protein:->->:588624..588806 183 aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0597:SSA_0599|SSA_0597:SSA_0599:hypothetical protein:hypothetical protein:->->:588624..588806 183 aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0597:SSA_0599|SSA_0597:SSA_0599:hypothetical protein:hypothetical protein:->->:588624..588806 183 aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 25 End: 123 ........................ M L T E L P K G G F F R A V S S S H N F V T L F V L I T L L K I S ............................................................ Protein_Len: 35 Strand: - Start: 31 End: 135 .............................. C L Q W F A A K K P S D A T R V I K H S K E N Q Y C Q Q F Y R S F K M ................................................ aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa 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: 86 Start: 122 End: 151 .........................................................................................................................CTTGAAAATTTCAAAAAGAAGCTATAGAAT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0597:SSA_0599|SSA_0597:SSA_0599:hypothetical protein:hypothetical protein:->->:588624..588806 183 aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: NC_009009_SSA_0597_SSA_0599|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[588624,588806]|183 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa aggctaggaaaatctactttttgaatcttaacagagctgccaaaaggcggcttttttagggctgtcagcagttctcacaattttgtgactcttttcgttttgataacattgttgaaaatatcttgaaaatttcaaaaagaagctatagaatagaggctaatcctatgaaaaaagcagaacgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUAGGAAAAUCUACUUUUUGAAUCUUAACAGAGCUGCCAAAAGGCGGCUUUUUUAGGGCUGUCAGCAGUUCUCACAAUUUUGUGACUCUUUUCGUUUUGAUAACAUUGUUGAAAAUAUCUUGAAAAUUUCAAAAAGAAGCUAUAGAAUAGAGGCUAAUCCUAUGAAAAAAGCAGAACGAA ....(((((.......(((((((((.(((((.(((((((((....))))))))).)))))....(((((((...(((((....)))))........(((.....))).)))))))...............))))))))).((((..........))))..))))).................. (-43.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGUUCUGCUUUUUUCAUAGGAUUAGCCUCUAUUCUAUAGCUUCUUUUUGAAAUUUUCAAGAUAUUUUCAACAAUGUUAUCAAAACGAAAAGAGUCACAAAAUUGUGAGAACUGCUGACAGCCCUAAAAAAGCCGCCUUUUGGCAGCUCUGUUAAGAUUCAAAAAGUAGAUUUUCCUAGCCU .....((((((((((..(((((((........))))))).((.((((((((...((((.(.((((((......)))))).).)))))))))))).(((((....))))).....)).(((((.........(((.(((....))).)))))))).......))))))))))............ (-35.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 78 33 149 104 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 369 78 32 81 38 NC_009009:SSA_0900|5end_Tetratricopeptide_repeat_(TPR)_family_protein_891068..891298_POSITIVE 356 74 36 62 23 NC_009009:SSA_1848|5end_Methionyl-tRNA_formyltransferase,_putative_1843178..1843408_NEGATIVE 346 89 46 49 15 NC_009009:SSA_0567|5end_Isochorismitase_family_protein,_putative_560805..561035_POSITIVE 337 78 36 217 164 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 337 69 23 55 15 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 333 80 33 57 16 NC_009009:SSA_1245|5end_Transcriptional_regulator,_LysR_family,_putative_1268722..1268952_POSITIVE 327 77 37 186 141 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 322 79 33 140 92 NC_009009:SSA_0563|5end_Universal_stress_protein_family,_putative_555399..555629_NEGATIVE 322 65 31 186 146 NC_009009:SSA_0215|5end_Periplasmic_sugar-binding_protein_(ribose_porter),_putative_210891..211121_POSITIVE 313 73 36 74 33 NC_009009:SSA_0814|5end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_796835..797065_NEGATIVE 310 76 32 62 24 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 310 77 33 215 160 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 310 73 32 213 162 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 308 70 31 162 125 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 306 73 32 73 11 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 305 74 37 40 4 NC_009009:SSA_2210|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2210475..2210705_POSITIVE 304 77 36 72 17 NC_009009:SSA_1003|5end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1003875..1004105_POSITIVE 302 79 34 219 173 NC_009009:SSA_0177|5end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_178405..178635_POSITIVE 301 80 38 223 160 NC_009009:SSA_2173|5end_Aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase,_putative_2171914..2172144_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 78 32 94 51 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 351 75 33 58 16 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 346 89 46 49 15 NC_009009:SSA_0566|3end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560885..561035_POSITIVE 312 80 35 120 61 NC_009009:SSA_0242|3end_hypothetical_protein_235810..235960_POSITIVE 304 77 36 59 4 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 301 80 38 146 83 NC_009009:SSA_2174|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2171991..2172141_NEGATIVE 299 80 33 151 95 NC_009009:SSA_1954|3end_Aminotransferase,_class-V,_putative_1950066..1950216_NEGATIVE 299 74 37 144 98 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 299 89 46 48 10 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 298 70 33 130 95 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 297 77 37 148 99 NC_009009:SSA_0582|3end_Methylase,_putative_574583..574733_POSITIVE 291 69 31 151 115 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 291 76 32 83 36 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 290 70 37 78 50 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 288 98 54 143 108 NC_009009:SSA_0119|3end_50S_ribosomal_protein_L5,_putative_114314..114464_POSITIVE 286 52 13 41 1 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 285 78 31 90 39 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 285 80 31 66 10 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE 281 68 27 79 28 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 277 79 32 95 41 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE