Origin IGS: aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca .........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 tgattttctcattctttccttttatgatacaataaattataacacaaaaatgacatacaatcacatgaattgcagaaaagaaaagctggagtaatatctatgcaataggattgaaaactatatgaaaatataatgtattttttcaactctgcatcataactacaaggagaaaaaggattt Mask Tandem Repeat Region ================================================ aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca Find is-nt database================================================ Query_seq: SSA_0551:SSA_0552|SSA_0551:SSA_0552:L-asparaginase, putative:Cof family protein, putative:<-->:547384..547563 180 aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0551:SSA_0552|SSA_0551:SSA_0552:L-asparaginase, putative:Cof family protein, putative:<-->:547384..547563 180 aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0551:SSA_0552|SSA_0551:SSA_0552:L-asparaginase, putative:Cof family protein, putative:<-->:547384..547563 180 aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 35 End: 169 .................................. M K K Y I I F S Y S F Q S Y C I D I T P A F L F C N S C D C M S F L C Y N L L Y H K R K E ........... Protein_Len: 32 Strand: + Start: 84 End: 179 ................................................................................... M L L Q L F F S A I H V I V C H F C V I I Y C I I K G K N E K I . aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca 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: 83 Start: 116 End: 145 ...................................................................................................................TGTGATTGTATGTCATTTTTGTGTTATAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0551:SSA_0552|SSA_0551:SSA_0552:L-asparaginase, putative:Cof family protein, putative:<-->:547384..547563 180 aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_009009_SSA_0551_SSA_0552|L-asparaginase, putative:Cof family protein, putative|NEGATIVE:POSITIVE|[547384,547563]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca aaatcctttttctccttgtagttatgatgcagagttgaaaaaatacattatattttcatatagttttcaatcctattgcatagatattactccagcttttcttttctgcaattcatgtgattgtatgtcatttttgtgttataatttattgtatcataaaaggaaagaatgagaaaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCCUUUUUCUCCUUGUAGUUAUGAUGCAGAGUUGAAAAAAUACAUUAUAUUUUCAUAUAGUUUUCAAUCCUAUUGCAUAGAUAUUACUCCAGCUUUUCUUUUCUGCAAUUCAUGUGAUUGUAUGUCAUUUUUGUGUUAUAAUUUAUUGUAUCAUAAAAGGAAAGAAUGAGAAAAUCA .......(((((((...(((((....((((((.(((((((......(((((((....))))))))))))))....))))))....))))).....((((((((((.((((((......(((((((...(((....))).))))))).))))))....))))))))))...)))))))... (-34.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUCUCAUUCUUUCCUUUUAUGAUACAAUAAAUUAUAACACAAAAAUGACAUACAAUCACAUGAAUUGCAGAAAAGAAAAGCUGGAGUAAUAUCUAUGCAAUAGGAUUGAAAACUAUAUGAAAAUAUAAUGUAUUUUUUCAACUCUGCAUCAUAACUACAAGGAGAAAAAGGAUUU ...(((((((...........(((((((.......)))))))......................((((..((((((........((((((......)))).)).....((..(((.(((((((....)))))..)).)))..))...)))))))))).........)))))))....... (-28.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 821 120 71 211 162 NC_009009:SSA_0551|5end_L-asparaginase,_putative_547293..547523_NEGATIVE 293 136 92 59 22 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 282 100 53 62 10 NC_009009:SSA_1197|5end_DNA_alkylation_repair_enzyme,_putative_1222699..1222929_NEGATIVE 278 96 51 140 82 NC_009009:SSA_0895|5end_ATP-binding_cassette_transporter-like_protein,_putative_886466..886696_POSITIVE 265 116 71 91 35 NC_009009:SSA_1005|5end_Sugar_ABC_transporter,_permease_protein,_putative_1006028..1006258_POSITIVE 255 140 91 88 27 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 255 109 66 108 60 NC_009009:SSA_0166|5end_hypothetical_protein_164641..164871_POSITIVE 251 147 104 96 51 NC_009009:SSA_0962|5end_Lactoylglutathione_lyase,_putative_970965..971195_POSITIVE 250 118 73 127 69 NC_009009:SSA_0966|5end_Uridine_kinase,_putative_975063..975293_POSITIVE 249 118 73 149 105 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 247 118 71 227 179 NC_009009:SSA_1330|5end_hypothetical_protein_1346368..1346598_NEGATIVE 246 132 92 187 138 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 244 38 10 122 96 NC_009009:SSA_0273|5end_hypothetical_protein_267071..267301_POSITIVE 238 109 63 135 92 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 238 159 113 200 147 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 237 100 55 56 2 NC_009009:SSA_0108|5end_50S_ribosomal_protein_L4,_putative_108816..109046_POSITIVE 236 138 94 192 144 NC_009009:SSA_1571|5end_Threonyl-tRNA_synthetase,_putative_1575154..1575384_NEGATIVE 236 119 71 161 100 NC_009009:SSA_1049|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064085..1064315_POSITIVE 236 135 95 98 59 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 235 117 72 141 97 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 136 92 66 29 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 284 140 93 148 87 NC_009009:SSA_2243|3end_Conserved_uncharacterized_protein_2238769..2238919_NEGATIVE 282 100 53 58 6 NC_009009:SSA_1198|3end_ATPase_(PilT_family),_putative_1222703..1222853_NEGATIVE 278 96 51 127 69 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 265 116 71 77 21 NC_009009:SSA_1004|3end_ABC_transporter_membrane-spanning_permease-multiple_sugars,_putative_1006094..1006244_POSITIVE 256 114 73 148 96 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 255 140 91 84 23 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 253 135 94 126 87 NC_009009:SSA_0249|3end_hypothetical_protein_242115..242265_POSITIVE 247 118 71 122 74 NC_009009:SSA_1331|3end_Conserved_uncharacterized_protein_1346473..1346623_NEGATIVE 242 119 73 130 84 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 238 109 63 125 82 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 236 129 85 151 89 NC_009009:SSA_2141|3end_Argininosuccinate_lyase,_putative_2140819..2140969_NEGATIVE 236 135 95 78 39 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 233 105 64 134 95 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 232 123 83 98 39 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 232 140 91 126 84 NC_009009:SSA_1528|3end_Phosphoglycerate_mutase,_putative_1535850..1536000_POSITIVE 229 137 92 76 24 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 229 136 92 103 55 NC_009009:SSA_0656|3end_Cell_division_protein_FtsZ,_putative_641516..641666_POSITIVE 228 115 91 136 111 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 227 37 8 141 104 NC_009009:SSA_0618|3end_hypothetical_protein_611680..611830_NEGATIVE