Origin IGS: agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagctcccttgctttactttagtacttggttaatgcaaaaataaaactaagacatcagcctgccattggaaagaattgctttttatagtaaaataaagaaagtaacaaggagatact Mask Tandem Repeat Region ================================================ agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt Find is-nt database================================================ Query_seq: SSA_1440:SSA_1441|SSA_1440:SSA_1441:Phosphoribosyl-ATP pyrophosphohydrolase, putative:Phosphoribosyl-AMP cyclohydrolase, putative:<-<-:1444812..1444928 117 agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1440:SSA_1441|SSA_1440:SSA_1441:Phosphoribosyl-ATP pyrophosphohydrolase, putative:Phosphoribosyl-AMP cyclohydrolase, putative:<-<-:1444812..1444928 117 agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1440:SSA_1441|SSA_1440:SSA_1441:Phosphoribosyl-ATP pyrophosphohydrolase, putative:Phosphoribosyl-AMP cyclohydrolase, putative:<-<-:1444812..1444928 117 agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt Predict ORF larger than 30AA ================================================ agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt 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: 24 End: 53 .......................ATTGGAAAGAATTGCTTTTTATAGTAAAAT................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1440:SSA_1441|SSA_1440:SSA_1441:Phosphoribosyl-ATP pyrophosphohydrolase, putative:Phosphoribosyl-AMP cyclohydrolase, putative:<-<-:1444812..1444928 117 agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_009009_SSA_1440_SSA_1441|Phosphoribosyl-ATP pyrophosphohydrolase, putative:Phosphoribosyl-AMP cyclohydrolase, putative|NEGATIVE:NEGATIVE|[1444812,1444928]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt agtatctccttgttactttctttattttactataaaaagcaattctttccaatggcaggctgatgtcttagttttatttttgcattaaccaagtactaaagtaaagcaagggagctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUCUCCUUGUUACUUUCUUUAUUUUACUAUAAAAAGCAAUUCUUUCCAAUGGCAGGCUGAUGUCUUAGUUUUAUUUUUGCAUUAACCAAGUACUAAAGUAAAGCAAGGGAGCUU (((.((.(((((.......((((((((((.(((.....((.(((......))).)).((.((((((...((......))..)))))).))..))).)))))))))))))))))))). (-20.01) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCUCCCUUGCUUUACUUUAGUACUUGGUUAAUGCAAAAAUAAAACUAAGACAUCAGCCUGCCAUUGGAAAGAAUUGCUUUUUAUAGUAAAAUAAAGAAAGUAACAAGGAGAUACU ...((((.(((((((.(((((.((((.((((.((((..............).))).))))......(((((((.....))))))).))))...))))))))))))...))))..... (-22.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 801 90 41 181 132 NC_009009:SSA_1440|5end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444721..1444951_NEGATIVE 259 89 45 76 31 NC_009009:SSA_0041|5end_hypothetical_protein_47662..47892_POSITIVE 258 94 55 62 13 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 257 76 36 68 33 NC_009009:SSA_1098|5end_Formate-nitrate_transporter,_putative_1114134..1114364_POSITIVE 250 80 37 82 30 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 249 59 13 192 138 NC_009009:SSA_1735|5end_UreX,_putative_1721072..1721302_NEGATIVE 246 80 33 181 127 NC_009009:SSA_0325|5end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_317603..317833_POSITIVE 245 83 43 98 53 NC_009009:SSA_1144|5end_Beta-N-acetylhexosaminidase,_putative_1175610..1175840_NEGATIVE 244 71 38 63 30 NC_009009:SSA_1777|5end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1765155..1765385_NEGATIVE 239 69 21 169 118 NC_009009:SSA_0809|5end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791146..791376_POSITIVE 239 66 39 134 95 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 237 81 43 147 107 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 236 59 16 140 92 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 235 77 38 183 147 NC_009009:SSA_2004|5end_Zinc_metalloprotease_zmpB_precursor,_putative_2004930..2005160_NEGATIVE 234 72 39 174 136 NC_009009:SSA_2188|5end_Conserved_uncharacterized_protein_2188896..2189126_POSITIVE 231 84 43 147 101 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 231 90 43 43 3 NC_009009:SSA_0254|5end_hypothetical_protein_247492..247722_NEGATIVE 230 76 54 204 180 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 227 40 5 139 98 NC_009009:SSA_0670|5end_Conserved_uncharacterized_protein_653920..654150_POSITIVE 225 84 56 228 200 NC_009009:SSA_2369|5end_hypothetical_protein_2371093..2371323_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 94 55 69 20 NC_009009:SSA_1526|3end_hypothetical_protein_1534674..1534824_POSITIVE 258 69 21 130 70 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 246 80 33 91 37 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 244 80 35 97 42 NC_009009:SSA_2080|3end_hypothetical_protein_2084598..2084748_NEGATIVE 244 71 38 76 43 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 239 66 39 134 95 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 234 72 39 149 111 NC_009009:SSA_2187|3end_Conserved_hypothetical_membrane_associated_protein_2188951..2189101_POSITIVE 231 74 35 88 37 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 231 84 43 113 67 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 231 90 43 50 10 NC_009009:SSA_0255|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247485..247635_NEGATIVE 222 93 54 81 41 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 220 83 42 131 93 NC_009009:SSA_2369|3end_hypothetical_protein_2370239..2370389_NEGATIVE 219 83 49 101 61 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 217 85 46 102 65 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 216 81 48 91 52 NC_009009:SSA_2155|3end_hypothetical_protein_2155407..2155557_NEGATIVE 216 84 46 137 96 NC_009009:SSA_1446|3end_Histidinol_dehydrogenase,_putative_1447898..1448048_NEGATIVE 214 85 47 94 57 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 213 71 31 125 76 NC_009009:SSA_1254|3end_hypothetical_protein_1281242..1281392_NEGATIVE 213 94 53 83 42 NC_009009:SSA_0129|3end_Translation_initiation_factor_IF-1,_putative_120255..120405_POSITIVE 212 109 61 64 14 NC_009009:SSA_2210|3end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2211454..2211604_POSITIVE