Origin IGS: aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaaaatacgatgatcatcataccgtcagccgttttgctacttcctggtctagtcgaaaagaagatgtggaagccttgtgcagagtgattgaggagttataaaaaacggctttgcgccgtttt Mask Tandem Repeat Region ================================================ aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc Find is-nt database================================================ Query_seq: SSA_0292:SSA_0293|SSA_0292:SSA_0293:Transcriptional regulator, AraC family (arabinose operon control), putative:hypothetical protein:-><-:287323..287445 123 aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0292:SSA_0293|SSA_0292:SSA_0293:Transcriptional regulator, AraC family (arabinose operon control), putative:hypothetical protein:-><-:287323..287445 123 aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0292:SSA_0293|SSA_0292:SSA_0293:Transcriptional regulator, AraC family (arabinose operon control), putative:hypothetical protein:-><-:287323..287445 123 aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc Predict ORF larger than 30AA ================================================ aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc 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================================================ aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0292:SSA_0293|SSA_0292:SSA_0293:Transcriptional regulator, AraC family (arabinose operon control), putative:hypothetical protein:-><-:287323..287445 123 aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: NC_009009_SSA_0292_SSA_0293|Transcriptional regulator, AraC family (arabinose operon control), putative:hypothetical protein|POSITIVE:NEGATIVE|[287323,287445]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc aaaacggcgcaaagccgttttttataactcctcaatcactctgcacaaggcttccacatcttcttttcgactagaccaggaagtagcaaaacggctgacggtatgatgatcatcgtatttttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACGGCGCAAAGCCGUUUUUUAUAACUCCUCAAUCACUCUGCACAAGGCUUCCACAUCUUCUUUUCGACUAGACCAGGAAGUAGCAAAACGGCUGACGGUAUGAUGAUCAUCGUAUUUUUC ((((((((.....))))))))........(((((..(....(((.....((((((...(((((.....))..)))...)))))).)))....)..))).))((((((....))))))...... (-26.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAAUACGAUGAUCAUCAUACCGUCAGCCGUUUUGCUACUUCCUGGUCUAGUCGAAAAGAAGAUGUGGAAGCCUUGUGCAGAGUGAUUGAGGAGUUAUAAAAAACGGCUUUGCGCCGUUUU .........(((....)))...((.(((..((((((((..(((((..((((..((.....))))))..)))))......))))))))..)))))........((((((((.....)))))))) (-30.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 88 41 228 180 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 318 100 51 58 7 NC_009009:SSA_2108|5end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2112464..2112694_NEGATIVE 312 80 31 61 17 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 303 80 39 195 141 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 298 100 58 149 100 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 296 79 31 150 98 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 294 78 36 167 122 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 290 115 73 178 128 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 288 88 42 65 7 NC_009009:SSA_1769|5end_hypothetical_protein_1757490..1757720_NEGATIVE 286 81 42 129 85 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 286 88 41 228 177 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 280 116 73 224 189 NC_009009:SSA_1588|5end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1591905..1592135_NEGATIVE 279 56 12 69 14 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 278 78 31 59 13 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 277 80 32 71 18 NC_009009:SSA_2131|5end_DNA-binding_protein,_putative_2133949..2134179_POSITIVE 276 74 31 161 112 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 276 113 77 190 153 NC_009009:SSA_0307|5end_Glutamine_synthetase_type_1,_putative_302987..303217_POSITIVE 275 109 61 79 13 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 275 40 1 214 181 NC_009009:SSA_1269|5end_hypothetical_protein_1293352..1293582_NEGATIVE 275 115 73 208 158 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 110 61 144 88 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 288 88 42 71 13 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 287 43 1 119 70 NC_009009:SSA_0292|3end_Transcriptional_regulator,_AraC_family_(arabinose_operon_control),_putative_287262..287412_POSITIVE 286 81 42 139 95 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 281 79 40 149 113 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 278 43 1 90 52 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 277 80 32 62 9 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 275 40 1 90 57 NC_009009:SSA_1270|3end_Flavodoxin_1293476..1293626_NEGATIVE 273 117 71 77 23 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 270 70 28 61 27 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 269 98 51 149 105 NC_009009:SSA_1173|3end_Lipoate_protein_ligase_A,_putative_1200092..1200242_NEGATIVE 267 110 65 44 5 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 266 89 48 81 42 NC_009009:SSA_1913|3end_Xanthine/uracil_permease_family_protein,_putative_1903245..1903395_NEGATIVE 265 47 6 118 71 NC_009009:SSA_0661|3end_Isoleucyl-tRNA_synthetase,_putative_647748..647898_POSITIVE 264 85 43 55 20 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 262 80 41 86 49 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 261 86 42 66 20 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 261 110 62 147 89 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 260 114 71 55 16 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE 259 87 48 52 10 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE