Origin IGS: ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttacattctccttttgctcctgaatttcttacagactcaccttcaccttattatacaacagttccagcatataaacaaagatttgtgaatttttttattttaaatagctgatatgttgaattttaatgtcgaaattagttgaaatactttgaatcctgttctacagcaaaaacaccaagaactgttcacagcagaaataagggggctataatttactttgataaacaggactgcttcaatcagcatgattaaggaaactacattggctcatacttatatttctgcaggactgagaataagaagttttattgaacaaacaaaaagagagaacttgcattctctctcgacgctaaaattgccgccaactctaattagctatctacc Mask Tandem Repeat Region ================================================ ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa Find is-nt database================================================ Query_seq: SSA_0706:SSA_0707|SSA_0706:SSA_0707:RNA helicase, putative:Lactose phosphotransferase system transcriptional repressor, putative:->->:692970..693354 385 ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0706:SSA_0707|SSA_0706:SSA_0707:RNA helicase, putative:Lactose phosphotransferase system transcriptional repressor, putative:->->:692970..693354 385 ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0706:SSA_0707|SSA_0706:SSA_0707:RNA helicase, putative:Lactose phosphotransferase system transcriptional repressor, putative:->->:692970..693354 385 ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 13 End: 108 ............ M R V G G N F S V E R E C K F S L F V C S I K L L I L S P A E I ..................................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 48 End: 146 ............................................... M Q V L S F C L F N K T S Y S Q S C R N I S M S Q C S F L N H A D ............................................................................................................................................................................................................................................... Protein_Len: 49 Strand: + Start: 136 End: 282 ....................................................................................................................................... M M L I E A V L F I K V N Y S P L I S A V N S S W C F C C R T G F K V F Q L I S T L K F N I S A I ....................................................................................................... Protein_Len: 37 Strand: - Start: 136 End: 246 ....................................................................................................................................... D H Q N F C D Q K D F Y I I A G K N R S H V T R P T K A T S C S E F Y K M ........................................................................................................................................... Protein_Len: 55 Strand: - Start: 3 End: 167 .. L Y S I L T P P L K L T S L S H L N E R K T Q E I F S R I R L G A S I Y T H A L T T E K I M S I S A T R N I M .......................................................................................................................................................................................................................... ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa 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: 306 End: 335 .................................................................................................................................................................................................................................................................................................................TTTGTTTATATGCTGGAACTGTTGTATAAT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -7.2 Tail_Score: -5.47159 Start: 42 End: 61 Full_Region: CAATTTTAGCGTCGA GAGAGAAT GCAA GTTCTCTC TTTTTGTTTGTTCAA .........................................GAGAGAATGCAAGTTCTCTC.................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0706:SSA_0707|SSA_0706:SSA_0707:RNA helicase, putative:Lactose phosphotransferase system transcriptional repressor, putative:->->:692970..693354 385 ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 385 Len: 385 Subject: NC_009009_SSA_0706_SSA_0707|RNA helicase, putative:Lactose phosphotransferase system transcriptional repressor, putative|POSITIVE:POSITIVE|[692970,693354]|385 HSP 1 e-value: 0.0 bit: 722.0 Len: 385 Query Start:1 Query End:385 Subject Strand: POSITIVE Subject Start: 1 Subject End: 385 ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaatnnnnnnnttcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa ggtagatagctaattagagttggcggcaattttagcgtcgagagagaatgcaagttctctctttttgtttgttcaataaaacttcttattctcagtcctgcagaaatataagtatgagccaatgtagtttccttaatcatgctgattgaagcagtcctgtttatcaaagtaaattatagcccccttatttctgctgtgaacagttcttggtgtttttgctgtagaacaggattcaaagtatttcaactaatttcgacattaaaattcaacatatcagctatttaaaataaaaaaattcacaaatctttgtttatatgctggaactgttgtataataaggtgaaggtgagtctgtaagaaattcaggagcaaaaggagaatgtaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAGAUAGCUAAUUAGAGUUGGCGGCAAUUUUAGCGUCGAGAGAGAAUGCAAGUUCUCUCUUUUUGUUUGUUCAAUAAAACUUCUUAUUCUCAGUCCUGCAGAAAUAUAAGUAUGAGCCAAUGUAGUUUCCUUAAUCAUGCUGAUUGAAGCAGUCCUGUUUAUCAAAGUAAAUUAUAGCCCCCUUAUUUCUGCUGUGAACAGUUCUUGGUGUUUUUGCUGUAGAACAGGAUUCAAAGUAUUUCAACUAAUUUCGACAUUAAAAUUCAACAUAUCAGCUAUUUAAAAUAAAAAAAUUCACAAAUCUUUGUUUAUAUGCUGGAACUGUUGUAUAAUAAGGUGAAGGUGAGUCUGUAAGAAAUUCAGGAGCAAAAGGAGAAUGUAAA ........((((((....)))))).(((.((((.(((..((((((((((....))))))))))..)))((((((........(((((((.((((........(((((((.(((((((...................)))))))..((((....(((((((((............((((((.....((((...((((....))))....)))).....))))))))))))))))))).)))))))......(((((...(((.....(((((..((((((((...(((((((..............)))))))))).)))))...))))).....)))..))))).))))...)))))))......))))))...)))).)))... (-82.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACAUUCUCCUUUUGCUCCUGAAUUUCUUACAGACUCACCUUCACCUUAUUAUACAACAGUUCCAGCAUAUAAACAAAGAUUUGUGAAUUUUUUUAUUUUAAAUAGCUGAUAUGUUGAAUUUUAAUGUCGAAAUUAGUUGAAAUACUUUGAAUCCUGUUCUACAGCAAAAACACCAAGAACUGUUCACAGCAGAAAUAAGGGGGCUAUAAUUUACUUUGAUAAACAGGACUGCUUCAAUCAGCAUGAUUAAGGAAACUACAUUGGCUCAUACUUAUAUUUCUGCAGGACUGAGAAUAAGAAGUUUUAUUGAACAAACAAAAAGAGAGAACUUGCAUUCUCUCUCGACGCUAAAAUUGCCGCCAACUCUAAUUAGCUAUCUACC .............((((.((..((((((((((....((((((...............((((((((((((((((............(((((....)))))............))))))))..((((..(((.(((.....(..((....))..)......))).)))..)))).......))))))))....(((((((((((.((((((.......................((((......))))......((....))....))))))...))..))))))))).))..))))..))))))))))....)).)))).....((((((((......))))))))....(((((..................)))))........ (-71.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 41 4 55 22 NC_009009:SSA_1357|5end_hypothetical_protein_1373024..1373254_NEGATIVE 302 158 115 209 164 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 296 66 21 109 60 NC_009009:SSA_0656|5end_Cell_division_protein_FtsZ,_putative_640159..640389_POSITIVE 296 230 184 162 111 NC_009009:SSA_0544|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase,_putative_539819..540049_POSITIVE 287 57 22 61 26 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 283 70 21 74 26 NC_009009:SSA_0731|5end_Integral_membrane_protein,_putative_715065..715295_POSITIVE 282 370 325 66 1 NC_009009:SSA_1315|5end_hypothetical_protein_1332052..1332282_NEGATIVE 280 41 1 72 30 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 280 70 25 130 78 NC_009009:SSA_0722|5end_hypothetical_protein_706875..707105_POSITIVE 279 223 181 142 100 NC_009009:SSA_0993|5end_hypothetical_protein_994064..994294_POSITIVE 278 223 181 51 7 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 276 54 17 143 111 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 275 38 1 210 170 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 275 60 15 101 50 NC_009009:SSA_0012|5end_Beta-lactamase_class_A,_putative_9916..10146_POSITIVE 274 62 21 160 121 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 273 41 1 229 183 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 272 100 51 112 62 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 272 221 183 139 101 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 270 161 127 137 104 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 269 105 69 200 160 NC_009009:SSA_0830|5end_Glycosyltransferase,_putative_812430..812660_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 219 177 122 78 NC_009009:SSA_2287|3end_50S_ribosomal_protein_L32,_putative_2290083..2290233_POSITIVE 309 100 52 116 72 NC_009009:SSA_1373|3end_ATPase_components_of_ABC_transporters_with_duplicated_ATPase_domains,_multidrug_transport_system,_putative_1391313..1391463_POSITIVE 296 66 21 92 43 NC_009009:SSA_0655|3end_Cell_division_protein_FtsA,_putative_640222..640372_POSITIVE 296 230 184 141 90 NC_009009:SSA_0543|3end_SecA,_putative_539878..540028_POSITIVE 295 230 184 133 90 NC_009009:SSA_0596|3end_hypothetical_protein_587352..587502_POSITIVE 294 360 316 90 45 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 287 159 119 121 70 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE 284 54 16 121 66 NC_009009:SSA_0207|3end_hypothetical_protein_204944..205094_POSITIVE 283 70 21 96 48 NC_009009:SSA_0730|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_715167..715317_POSITIVE 280 41 1 60 18 NC_009009:SSA_1416|3end_hypothetical_protein_1426520..1426670_NEGATIVE 280 70 25 75 23 NC_009009:SSA_0721|3end_Mn/Fe-dependent_superoxide_dismutase,_putative_706900..707050_POSITIVE 279 223 181 145 103 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 278 223 181 50 6 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 276 104 61 124 83 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE 276 54 17 138 106 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 275 60 15 108 57 NC_009009:SSA_0011|3end_hypothetical_protein_10003..10153_POSITIVE 273 379 338 52 3 NC_009009:SSA_0608|3end_Macrolide-efflux_protein,_putative_596901..597051_NEGATIVE 272 221 183 142 104 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 271 76 38 119 81 NC_009009:SSA_2296|3end_Transcriptional_regulator,_XRE_family,_putative_2298549..2298699_NEGATIVE 270 230 182 145 88 NC_009009:SSA_0967|3end_hypothetical_protein_976620..976770_POSITIVE