Origin IGS: aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgcaaaaagattaaaaaactaaaacaagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agatttcctactctgtatctaaattttaacttgttattacactacattataccaaatttttatggttttgtgggggaatattcgctaaaatcacagctcaggccaagcgtttcctaaatttaatctgcttgttttagttttttaatctttttgcgcttctttaaaattagatgaaaaagtgtttacatgccgctttttttagctttattggggaaaattttgggaaaaagctggttttcaaagagaaactcagcaaaaaaagattggattttcccaatcttttt Mask Tandem Repeat Region ================================================ aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgcaaaaagattaaaaaactaaaacaagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct Find is-nt database================================================ Query_seq: SSA_0680:SSA_0682|SSA_0680:SSA_0682:Serine/threonine protein phosphatase, putative:Conserved uncharacterized protein:->->:663294..663577 284 aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgcaaaaagattaaaaaactaaaacaagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0680:SSA_0682|SSA_0680:SSA_0682:Serine/threonine protein phosphatase, putative:Conserved uncharacterized protein:->->:663294..663577 284 aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgcaaaaagattaaaaaactaaaacaagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0680:SSA_0682|SSA_0680:SSA_0682:Serine/threonine protein phosphatase, putative:Conserved uncharacterized protein:->->:663294..663577 284 aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgcaaaaagattaaaaaactaaaacaagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgcaaaaagattaaaaaactaaaacaagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 7 End: 99 ...... M G K I Q S F F A E F L F E N Q L F P K I F P N K A K K S G M ......................................................................................................................................................................................... Protein_Len: 36 Strand: + Start: 8 End: 115 ....... M G K S N L F L L S F S L K T S F F P K F S P I K L K K A A C K H F F I ......................................................................................................................................................................... Protein_Len: 34 Strand: - Start: 171 End: 272 .......................................................................................................................................................................... S V S P R L Q S K L S Y E G V F G Y F N P I I Y H L L L N F N L Y M ............ Protein_Len: 33 Strand: - Start: 151 End: 249 ...................................................................................................................................................... F L C I L N L F R K A Q A T I K A F I G G C F W L F K T Y H L T M ................................... Protein_Len: 32 Strand: - Start: 3 End: 98 .. F I P F I W D K K A S N R K S F W S K G L I K G L L A L F L P M .......................................................................................................................................................................................... Protein_Len: 38 Strand: - Start: 1 End: 114 F L N P F D L R K K S L K E K F V L K K G F N E G I F S F F A A H L C K K M .......................................................................................................................................................................... aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgcaaaaagattaaaaaactaaaacaagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct 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================================================ aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgcaaaaagattaaaaaactaaaacaagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0680:SSA_0682|SSA_0680:SSA_0682:Serine/threonine protein phosphatase, putative:Conserved uncharacterized protein:->->:663294..663577 284 aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgcaaaaagattaaaaaactaaaacaagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct Intra-Species Hit: Count: 1 Min: 1 Max: 284 Len: 284 Subject: NC_009009_SSA_0680_SSA_0682|Serine/threonine protein phosphatase, putative:Conserved uncharacterized protein|POSITIVE:POSITIVE|[663294,663577]|284 HSP 1 e-value: 2.0E-68 bit: 260.0 Len: 131 Query Start:154 Query End:284 Subject Strand: POSITIVE Subject Start: 154 Subject End: 284 .........................................................................................................................................................caagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct .........................................................................................................................................................caagcagattaaatttaggaaacgcttggcctgagctgtgattttagcgaatattcccccacaaaaccataaaaatttggtataatgtagtgtaataacaagttaaaatttagatacagagtaggaaatct HSP 2 e-value: 7.0E-44 bit: 178.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 aaaaagattgggaaaatccaatcnnnnnnngctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctnnnnnnngcggcatgtaaacactttttcatctaattttaaagaagcgc........................................................................................................................................................ aaaaagattgggaaaatccaatctttttttgctgagtttctctttgaaaaccagctttttcccaaaattttccccaataaagctaaaaaaagcggcatgtaaacactttttcatctaattttaaagaagcgc........................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGAUUGGGAAAAUCCAAUCUUUUUUUGCUGAGUUUCUCUUUGAAAACCAGCUUUUUCCCAAAAUUUUCCCCAAUAAAGCUAAAAAAAGCGGCAUGUAAACACUUUUUCAUCUAAUUUUAAAGAAGCGCAAAAAGAUUAAAAAACUAAAACAAGCAGAUUAAAUUUAGGAAACGCUUGGCCUGAGCUGUGAUUUUAGCGAAUAUUCCCCCACAAAACCAUAAAAAUUUGGUAUAAUGUAGUGUAAUAACAAGUUAAAAUUUAGAUACAGAGUAGGAAAUCU (((((((((((......)))))))))))..((((..((((.....))))..))))......((((...(((((........(((......))).((.(((......(((((.((((....................)))).)))))......))).))............)))))...))))((((..(((((((((((((...((((.(.(.(((..((((........))))....))).).).))))....))))))))).....))))..))))...... (-54.45) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUUCCUACUCUGUAUCUAAAUUUUAACUUGUUAUUACACUACAUUAUACCAAAUUUUUAUGGUUUUGUGGGGGAAUAUUCGCUAAAAUCACAGCUCAGGCCAAGCGUUUCCUAAAUUUAAUCUGCUUGUUUUAGUUUUUUAAUCUUUUUGCGCUUCUUUAAAAUUAGAUGAAAAAGUGUUUACAUGCCGCUUUUUUUAGCUUUAUUGGGGAAAAUUUUGGGAAAAAGCUGGUUUUCAAAGAGAAACUCAGCAAAAAAAGAUUGGAUUUUCCCAAUCUUUUU ...(((((((..........(((((((..((...((((...(((((....((((........))))..)))))...))))...(((((((....(((...(((((((((................)))))).....................((((((.((((........)))).))))))......))))))..)))))))......))..))))))))))))))..((((..((((.....))))..))))..(((((((((((......))))))))))) (-60.69) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 211 172 89 53 NC_009009:SSA_2258|5end_hypothetical_protein_2254699..2254929_NEGATIVE 307 214 171 47 4 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 304 212 181 180 160 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 302 200 151 58 10 NC_009009:SSA_2059|5end_16S_rRNA_uridine-516_pseudouridylate_synthase,_putative_2061222..2061452_NEGATIVE 293 66 23 117 64 NC_009009:SSA_1933|5end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase,_putative_1921315..1921545_NEGATIVE 285 216 176 68 24 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 282 99 53 92 40 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 268 210 169 72 26 NC_009009:SSA_1588|5end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1591905..1592135_NEGATIVE 267 215 177 57 9 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 265 195 159 217 180 NC_009009:SSA_1184|5end_DNA_topoisomerase_I,_putative_1213605..1213835_NEGATIVE 264 203 170 181 145 NC_009009:SSA_2223|5end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224703..2224933_NEGATIVE 263 133 91 172 132 NC_009009:SSA_1925|5end_Seryl-tRNA_synthetase,_putative_1913508..1913738_POSITIVE 261 202 167 177 145 NC_009009:SSA_1560|5end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1565194..1565424_NEGATIVE 260 210 167 172 127 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 259 212 183 146 109 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 258 214 171 101 52 NC_009009:SSA_0103|5end_Integral_membrane_protein,_putative_105490..105720_NEGATIVE 255 217 172 75 11 NC_009009:SSA_1433|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1440817..1441047_NEGATIVE 255 69 33 44 4 NC_009009:SSA_0484|5end_Glutamyl-tRNA_reductase,_putative_484492..484722_POSITIVE 254 199 153 81 21 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 253 202 175 47 12 NC_009009:SSA_1484|5end_DNA_ligase,_putative_1492188..1492418_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 194 159 67 31 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE 329 211 172 61 25 NC_009009:SSA_2259|3end_hypothetical_protein_2254727..2254877_NEGATIVE 307 214 171 60 17 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 297 200 167 46 12 NC_009009:SSA_2060|3end_Arabinose_efflux_permease,_putative_2061234..2061384_NEGATIVE 293 66 23 120 67 NC_009009:SSA_1934|3end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921312..1921462_NEGATIVE 288 57 17 138 95 NC_009009:SSA_0808|3end_hypothetical_protein_791012..791162_POSITIVE 285 216 176 58 14 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 276 45 1 119 84 NC_009009:SSA_0727|3end_Metal-dependent_membrane_protease,_putative_713639..713789_POSITIVE 268 210 169 70 24 NC_009009:SSA_1589|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1591907..1592057_NEGATIVE 265 195 159 132 95 NC_009009:SSA_1185|3end_DNA_processing_Smf_protein,_putative_1213690..1213840_NEGATIVE 253 203 170 106 73 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 253 201 165 83 45 NC_009009:SSA_1052|3end_hypothetical_protein_1066846..1066996_NEGATIVE 251 222 184 39 8 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 246 45 2 108 61 NC_009009:SSA_1373|3end_ATPase_components_of_ABC_transporters_with_duplicated_ATPase_domains,_multidrug_transport_system,_putative_1391313..1391463_POSITIVE 246 214 177 104 66 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 245 99 53 96 45 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 245 203 170 90 48 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 244 214 171 88 38 NC_009009:SSA_2230|3end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2228963..2229113_NEGATIVE 243 50 7 64 21 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 243 190 146 149 106 NC_009009:SSA_1235|3end_Dihydroorotase,_putative_1259959..1260109_NEGATIVE