Origin IGS: ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataccagaaaagcatgataaactctagtctgacaagggaaataaacactcgaaatatgagattgcaaaacttcaatcagctttttcttctgtgtaaaagacaagtaaaaaactcttagtgataaccaagagttttgcaataa Mask Tandem Repeat Region ================================================ ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata Find is-nt database================================================ Query_seq: SSA_1165:SSA_1166|SSA_1165:SSA_1166:Transcriptional regulator, GntR family, putative:hypothetical protein:->->:1191926..1192068 143 ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1165:SSA_1166|SSA_1165:SSA_1166:Transcriptional regulator, GntR family, putative:hypothetical protein:->->:1191926..1192068 143 ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1165:SSA_1166|SSA_1165:SSA_1166:Transcriptional regulator, GntR family, putative:hypothetical protein:->->:1191926..1192068 143 ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 4 End: 141 ... M Q N S W L S L R V F Y L S F T Q K K K L I E V L Q S H I S S V Y F P C Q T R V Y H A F L V .. Protein_Len: 34 Strand: - Start: 28 End: 129 ........................... S N K V Q R K C L L F L Q N F N Q L R M N R T N I E R T L S S N I M .............. ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata 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================================================ ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1165:SSA_1166|SSA_1165:SSA_1166:Transcriptional regulator, GntR family, putative:hypothetical protein:->->:1191926..1192068 143 ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata Intra-Species Hit: Count: 1 Min: 1 Max: 143 Len: 143 Subject: NC_009009_SSA_1165_SSA_1166|Transcriptional regulator, GntR family, putative:hypothetical protein|POSITIVE:POSITIVE|[1191926,1192068]|143 HSP 1 e-value: 8.0E-76 bit: 283.0 Len: 143 Query Start:1 Query End:143 Subject Strand: POSITIVE Subject Start: 1 Subject End: 143 ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata ttattgcaaaactcttggttatcactaagagttttttacttgtcttttacacagaagaaaaagctgattgaagttttgcaatctcatatttcgagtgtttatttcccttgtcagactagagtttatcatgcttttctggtata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUGCAAAACUCUUGGUUAUCACUAAGAGUUUUUUACUUGUCUUUUACACAGAAGAAAAAGCUGAUUGAAGUUUUGCAAUCUCAUAUUUCGAGUGUUUAUUUCCCUUGUCAGACUAGAGUUUAUCAUGCUUUUCUGGUAUA .......((((((((((((....))))))))))))............(((.(((((((...(((((((.(((((...(((..(((.......))))))..)))))....))))).)).((.....))....)))))))))).. (-31.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUACCAGAAAAGCAUGAUAAACUCUAGUCUGACAAGGGAAAUAAACACUCGAAAUAUGAGAUUGCAAAACUUCAAUCAGCUUUUUCUUCUGUGUAAAAGACAAGUAAAAAACUCUUAGUGAUAACCAAGAGUUUUGCAAUAA ..((((((((((((.((((...((((.(.....).)))).........((((.....))))..............))))))))....))))).)))........(((((..((((((.((....)).)))))))))))..... (-26.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 140 91 220 161 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 293 140 93 110 64 NC_009009:SSA_1863|5end_NH(3)-dependent_NAD(+)_synthetase,_putative_1859413..1859643_NEGATIVE 281 133 91 85 42 NC_009009:SSA_0734|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_716895..717125_POSITIVE 280 138 91 61 3 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 274 120 72 165 116 NC_009009:SSA_1790|5end_SpoU_rRNA_Methylase_family_protein,_putative_1773641..1773871_NEGATIVE 273 130 92 179 139 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 270 138 92 136 91 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 268 67 27 148 106 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 265 139 103 190 150 NC_009009:SSA_1978|5end_Dihydroxyacetone_kinase_family_protein_(Dak2_domain),_putative_1973933..1974163_NEGATIVE 262 139 99 186 138 NC_009009:SSA_1341|5end_Carbamoyl-phosphate_synthase_large_chain,_putative_1359827..1360057_NEGATIVE 262 118 72 190 139 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 254 139 95 136 92 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 252 140 99 133 96 NC_009009:SSA_1789|5end_Metal-dependent_phosphohydrolase,_HD_superfamily,_putative_1772856..1773086_NEGATIVE 252 138 98 81 35 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 241 140 91 220 183 NC_009009:SSA_0039|5end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_45833..46063_POSITIVE 240 55 12 41 2 NC_009009:SSA_1218|5end_DNA_repair_protein_radC,_putative_1240459..1240689_NEGATIVE 239 138 93 106 67 NC_009009:SSA_2174|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2172689..2172919_NEGATIVE 239 140 94 128 83 NC_009009:SSA_0555|5end_Conserved_hypothetical_cytosolic_protein_549615..549845_POSITIVE 239 131 92 63 25 NC_009009:SSA_0118|5end_50S_ribosomal_protein_L24,_putative_113363..113593_POSITIVE 238 139 92 213 156 NC_009009:SSA_0975|5end_2-isopropylmalate_synthase,_putative_980971..981201_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 140 93 113 67 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 281 133 91 47 4 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 260 138 106 60 27 NC_009009:SSA_0387|3end_Transcriptional_regulator,_GntR_family,_putative_381702..381852_NEGATIVE 254 133 92 98 55 NC_009009:SSA_0915|3end_hypothetical_protein_928014..928164_POSITIVE 254 139 95 143 99 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 252 140 99 88 51 NC_009009:SSA_1790|3end_SpoU_rRNA_Methylase_family_protein,_putative_1772901..1773051_NEGATIVE 252 138 98 84 38 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE 244 115 74 98 50 NC_009009:SSA_1103|3end_hypothetical_protein_1124539..1124689_POSITIVE 243 137 92 151 107 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 239 140 94 125 80 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 238 138 95 144 95 NC_009009:SSA_1652|3end_Acetyltransferases,_putative_1649955..1650105_NEGATIVE 238 80 38 40 1 NC_009009:SSA_1624|3end_hypothetical_protein_1626497..1626647_POSITIVE 238 138 103 148 118 NC_009009:SSA_0310|3end_hypothetical_protein_305973..306123_POSITIVE 236 117 75 114 65 NC_009009:SSA_2099|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103621..2103771_NEGATIVE 231 137 92 90 36 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE 228 110 71 82 39 NC_009009:SSA_1592|3end_hypothetical_protein_1595576..1595726_NEGATIVE 227 139 91 76 8 NC_009009:SSA_1047|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_1062845..1062995_POSITIVE 223 130 102 150 114 NC_009009:SSA_1799|3end_Acetyltransferase,_putative_1780513..1780663_NEGATIVE 222 139 92 117 68 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 221 80 36 140 99 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE