Origin IGS: ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcattctctggaaagccgacaaaactcagctgggcagccagctgagttcgtcttcacccgacagttagtcctctttacaggtcaagactgtccctttcaattttcc Mask Tandem Repeat Region ================================================ ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat Find is-nt database================================================ Query_seq: SSA_0546:SSA_0547|SSA_0546:SSA_0547:Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthatase), possibly tyr-sensitive, putative:Acyl carrier protein synthase, putative:->->:542024..542130 107 ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0546:SSA_0547|SSA_0546:SSA_0547:Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthatase), possibly tyr-sensitive, putative:Acyl carrier protein synthase, putative:->->:542024..542130 107 ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0546:SSA_0547|SSA_0546:SSA_0547:Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthatase), possibly tyr-sensitive, putative:Acyl carrier protein synthase, putative:->->:542024..542130 107 ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 1 End: 99 S F Q F P C D Q G T F L V L Q R T F V F E A P Q G A S N Q R S E M ........ ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat 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================================================ ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.5 Tail_Score: -4.44974 Start: 61 End: 82 Full_Region: TCGGGTGAAGACGAA CTCAGCTGG CTGC CCAGCTGAG TTTTGTCGGCTTTCC ............................................................CTCAGCTGGCTGCCCAGCTGAG......................... Find igs database================================================ Query_seq: SSA_0546:SSA_0547|SSA_0546:SSA_0547:Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthatase), possibly tyr-sensitive, putative:Acyl carrier protein synthase, putative:->->:542024..542130 107 ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_009009_SSA_0546_SSA_0547|Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthatase), possibly tyr-sensitive, putative:Acyl carrier protein synthase, putative|POSITIVE:POSITIVE|[542024,542130]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat ggaaaattgaaagggacagtcttgacctgtaaagaggactaactgtcgggtgaagacgaactcagctggctgcccagctgagttttgtcggctttccagagaatgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAAUUGAAAGGGACAGUCUUGACCUGUAAAGAGGACUAACUGUCGGGUGAAGACGAACUCAGCUGGCUGCCCAGCUGAGUUUUGUCGGCUUUCCAGAGAAUGAU (((((.((((........(((((.(((((...((........))..))))).))))).(((((((((((....)))))))))))...)))).))))).......... (-40.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUUCUCUGGAAAGCCGACAAAACUCAGCUGGGCAGCCAGCUGAGUUCGUCUUCACCCGACAGUUAGUCCUCUUUACAGGUCAAGACUGUCCCUUUCAAUUUUCC ...........(((((..(((..(((((((((((....))))))))))).))).......(((((((.(.(((......))).)..))))))).)))))........ (-36.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 433 80 36 159 106 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 419 94 53 152 112 NC_009009:SSA_0350|5end_Helicase,_putative_344218..344448_NEGATIVE 415 89 46 143 102 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 410 99 54 67 27 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 378 80 33 177 124 NC_009009:SSA_1469|5end_Shikimate_dehydrogenase,_putative_1476317..1476547_NEGATIVE 361 89 41 165 115 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 344 97 55 57 21 NC_009009:SSA_0814|5end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_796835..797065_NEGATIVE 342 100 63 156 126 NC_009009:SSA_0944|5end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_951741..951971_POSITIVE 339 88 45 54 3 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 333 69 21 227 173 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 331 98 57 90 42 NC_009009:SSA_2350|5end_30S_ribosomal_protein_S4,_putative_2352648..2352878_NEGATIVE 330 80 45 225 185 NC_009009:SSA_2008|5end_Molecular_chaperone_GrpE_(HSP-70_cofactor),_putative_2010062..2010292_NEGATIVE 330 80 35 203 148 NC_009009:SSA_0165|5end_hypothetical_protein_163938..164168_POSITIVE 328 74 31 228 186 NC_009009:SSA_0980|5end_3-isopropylmalate_dehydratase_large_subunit,_putative_984004..984234_POSITIVE 325 79 43 227 191 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 325 80 35 164 123 NC_009009:SSA_0050|5end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_54612..54842_POSITIVE 325 88 47 163 118 NC_009009:SSA_0018|5end_Cell-shape_determining_protein_MreD,_putative_23628..23858_POSITIVE 321 97 66 41 2 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 320 84 43 65 25 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 320 49 6 70 21 NC_009009:SSA_0157|5end_hypothetical_protein_153513..153743_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 503 89 47 81 29 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 456 99 55 48 2 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 433 80 36 149 96 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 419 94 53 92 52 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 415 89 46 88 47 NC_009009:SSA_0354|3end_Uncharacterized_membrane_protein_346872..347022_POSITIVE 364 93 64 74 44 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 345 95 51 58 14 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 342 100 63 145 115 NC_009009:SSA_0943|3end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_951810..951960_POSITIVE 339 88 45 54 3 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 336 80 43 142 102 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 324 99 51 61 3 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 320 84 43 57 17 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 312 87 43 132 91 NC_009009:SSA_1946|3end_Oligopeptide_transport_system_permease_protein,_putative_1937698..1937848_NEGATIVE 306 87 49 75 34 NC_009009:SSA_1619|3end_Ribosome_recycling_factor,_putative_1621679..1621829_NEGATIVE 302 92 56 59 18 NC_009009:SSA_1775|3end_Potassium_uptake_protein,_Trk_family,_putative_1762713..1762863_POSITIVE 302 76 33 60 14 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 300 98 62 60 25 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 298 78 31 75 32 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 298 100 52 95 53 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 297 100 57 72 31 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE