Origin IGS: aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt .........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 aatagaaactcagctgtcatggctgggttttcttatttttaaatttaatataacaattttttttgcaaaaataggtatataccatttacaaataaaaaagaaagagttataatatagtcaagaaaactcagagattcaaaagcgggagttagaaagcagctatagaaagatgctagatctatcacagaattccgttttgaatggccgagaatatagcattcaagaacaagggaggcagtctt Mask Tandem Repeat Region ================================================ aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt Find is-nt database================================================ Query_seq: SSA_1893:SSA_1895|SSA_1893:SSA_1895:N-acetylglucosamine-6-phosphate deacetylase, putative:Ribosome-binding factor A, putative:<-<-:1890663..1890904 242 aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1893:SSA_1895|SSA_1893:SSA_1895:N-acetylglucosamine-6-phosphate deacetylase, putative:Ribosome-binding factor A, putative:<-<-:1890663..1890904 242 aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1893:SSA_1895|SSA_1893:SSA_1895:N-acetylglucosamine-6-phosphate deacetylase, putative:Ribosome-binding factor A, putative:<-<-:1890663..1890904 242 aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 31 End: 195 .............................. M L G H S K R N S V I D L A S F Y S C F L T P A F E S L S F L D Y I I T L S F L F V N G I Y L F L Q K K L L Y ............................................... Protein_Len: 36 Strand: - Start: 134 End: 241 ..................................................................................................................................... L E K K K I Q L H Y I G I K A F F I T I N F K F I L F G L W S L Q T E M . Protein_Len: 36 Strand: - Start: 2 End: 109 . S Q R G Q E Q I S Y E R G N L V S N Q S L D L M K R Y S S E L E R K Q M ..................................................................................................................................... aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt 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: 90 Start: 130 End: 159 .................................................................................................................................ATTTACAAATAAAAAAGAAAGAGTTATAAT................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 103 End: 132 ......................................................................................................TTTGAATCTCTGAGTTTTCTTGACTATATT.............................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1893:SSA_1895|SSA_1893:SSA_1895:N-acetylglucosamine-6-phosphate deacetylase, putative:Ribosome-binding factor A, putative:<-<-:1890663..1890904 242 aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt Intra-Species Hit: Count: 1 Min: 1 Max: 242 Len: 242 Subject: NC_009009_SSA_1893_SSA_1895|N-acetylglucosamine-6-phosphate deacetylase, putative:Ribosome-binding factor A, putative|NEGATIVE:NEGATIVE|[1890663,1890904]|242 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 242 Query Start:1 Query End:242 Subject Strand: POSITIVE Subject Start: 1 Subject End: 242 aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcnnnnnnnnttgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt aagactgcctcccttgttcttgaatgctatattctcggccattcaaaacggaattctgtgatagatctagcatctttctatagctgctttctaactcccgcttttgaatctctgagttttcttgactatattataactctttcttttttatttgtaaatggtatatacctatttttgcaaaaaaaattgttatattaaatttaaaaataagaaaacccagccatgacagctgagtttctatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGACUGCCUCCCUUGUUCUUGAAUGCUAUAUUCUCGGCCAUUCAAAACGGAAUUCUGUGAUAGAUCUAGCAUCUUUCUAUAGCUGCUUUCUAACUCCCGCUUUUGAAUCUCUGAGUUUUCUUGACUAUAUUAUAACUCUUUCUUUUUUAUUUGUAAAUGGUAUAUACCUAUUUUUGCAAAAAAAAUUGUUAUAUUAAAUUUAAAAAUAAGAAAACCCAGCCAUGACAGCUGAGUUUCUAUU ............((((((.((((((........(((((..(((((((((((......(.(.((((...((((.((......)).)))).)))).).)))).))))))))..)))))............((.((((((.......(((((.((((((((.(((....)))....)))))))))))))..)))))).)).)))))).)))))).((((.((((.......)))).))))..... (-45.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGAAACUCAGCUGUCAUGGCUGGGUUUUCUUAUUUUUAAAUUUAAUAUAACAAUUUUUUUUGCAAAAAUAGGUAUAUACCAUUUACAAAUAAAAAAGAAAGAGUUAUAAUAUAGUCAAGAAAACUCAGAGAUUCAAAAGCGGGAGUUAGAAAGCAGCUAUAGAAAGAUGCUAGAUCUAUCACAGAAUUCCGUUUUGAAUGGCCGAGAAUAUAGCAUUCAAGAACAAGGGAGGCAGUCUU .((((((((((.(((.......(((((((((((((((........((.((((((..((((((((....((((.(((....)))))))........))))))))..)))))).)).))).)))))))))))).........)))..)))))....((((.((......)).))))...)))))....(..((((.(((((((((.............)))))))))....))))..)...... (-50.11) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 922 50 1 141 92 NC_009009:SSA_1893|5end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1890572..1890802_NEGATIVE 356 41 1 218 173 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 347 45 2 215 175 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 320 110 66 205 165 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 315 43 3 139 92 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 315 113 72 125 83 NC_009009:SSA_0895|5end_ATP-binding_cassette_transporter-like_protein,_putative_886466..886696_POSITIVE 303 113 71 162 113 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 292 88 49 65 14 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 291 118 71 155 109 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 291 58 12 189 143 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 291 239 200 142 101 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 289 41 10 45 3 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 288 117 72 174 126 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 288 127 83 83 35 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 283 125 83 132 85 NC_009009:SSA_0242|5end_hypothetical_protein_234978..235208_POSITIVE 282 77 35 61 16 NC_009009:SSA_2299|5end_hypothetical_protein_2301545..2301775_NEGATIVE 281 104 71 58 23 NC_009009:SSA_0972|5end_hypothetical_protein_979973..980203_POSITIVE 280 78 32 65 27 NC_009009:SSA_0200|5end_Bifunctional_folate_synthesis_protein,_putative_198918..199148_POSITIVE 280 44 5 93 43 NC_009009:SSA_0068|5end_Alcohol-acetaldehyde_dehydrogenase,_putative_70114..70344_POSITIVE 279 75 32 209 165 NC_009009:SSA_2154|5end_Conserved_uncharacterized_protein_2155259..2155489_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 41 7 48 1 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 325 110 66 146 98 NC_009009:SSA_2141|3end_Argininosuccinate_lyase,_putative_2140819..2140969_NEGATIVE 315 43 3 142 95 NC_009009:SSA_1722|3end_Thymidylate_kinase,_putative_1708025..1708175_NEGATIVE 315 113 72 112 70 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 300 59 11 132 72 NC_009009:SSA_1972|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1967811..1967961_NEGATIVE 298 106 65 145 83 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 291 118 71 145 99 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 291 239 200 67 26 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 288 127 83 71 23 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 287 126 83 138 76 NC_009009:SSA_1803|3end_GTP-binding_protein,_putative_1786599..1786749_NEGATIVE 283 125 83 131 84 NC_009009:SSA_0241|3end_Ribosomal_protein_L11_methyltransferase,_putative_235057..235207_POSITIVE 281 104 71 74 39 NC_009009:SSA_0971|3end_Conserved_uncharacterized_protein_980069..980219_POSITIVE 279 75 32 61 17 NC_009009:SSA_2155|3end_hypothetical_protein_2155407..2155557_NEGATIVE 275 38 1 94 49 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE 274 56 11 122 63 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 271 127 81 62 21 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 269 40 9 142 112 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 267 118 71 113 64 NC_009009:SSA_2199|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2198679..2198829_NEGATIVE 267 79 32 147 106 NC_009009:SSA_1493|3end_hypothetical_protein_1498929..1499079_NEGATIVE 266 236 214 82 58 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE