Origin IGS: tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt .........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 aagaacatctcttttctttattattcattaataaacactttgaaatctattctatttggatattttgcttattttttgttatcaactacagtatagcacaaggtcgtgaaaatgtaaacgctttatattttctttgacaaaatagcctgctttcaaaaccaaaagcagactattgaaatgcactcgattatttttgatttgagaaagatgcgataagtactcttatctctgca Mask Tandem Repeat Region ================================================ tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt Find is-nt database================================================ Query_seq: SSA_0263:SSA_0264|SSA_0263:SSA_0264:Zinc metalloproteinase in scaA 5'region, putative:PEP phosphonomutase-like protein, putative:->->:258307..258539 233 tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0263:SSA_0264|SSA_0263:SSA_0264:Zinc metalloproteinase in scaA 5'region, putative:PEP phosphonomutase-like protein, putative:->->:258307..258539 233 tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0263:SSA_0264|SSA_0263:SSA_0264:Zinc metalloproteinase in scaA 5'region, putative:PEP phosphonomutase-like protein, putative:->->:258307..258539 233 tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 36 End: 149 ................................... M K N N R V H F N S L L L V L K A G Y F V K E N I K R L H F H D L V L Y C S .................................................................................... Protein_Len: 36 Strand: - Start: 100 End: 207 ................................................................................................... L F Y L A N V N E R G Q A I S Y N I V F F L C F I W I S Y I E F H K N M .......................... tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt 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: 87 Start: 115 End: 144 ..................................................................................................................GTTTACATTTTCACGACCTTGTGCTATACT......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -8.7 Tail_Score: -4.36914 Start: 62 End: 91 Full_Region: TCGAGTGCATTTCAA TAGTCTGCTTTTG GTTT TGAAAGCAGGCTA TTTTGTCAAAGAAAA .............................................................TAGTCTGCTTTTGGTTTTGAAAGCAGGCTA.............................................................................................................................................. TransTerm Strand: - Conf: 74 HP_score: -8.1 Tail_Score: -3.54424 Start: 102 End: 126 Full_Region: atagcacaaggtcgt gaaaatgtaaa cgc tttatattttc tttgacaaaatagcc .....................................................................................................gaaaatgtaaacgctttatattttc........................................................................................................... Find igs database================================================ Query_seq: SSA_0263:SSA_0264|SSA_0263:SSA_0264:Zinc metalloproteinase in scaA 5'region, putative:PEP phosphonomutase-like protein, putative:->->:258307..258539 233 tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: NC_009009_SSA_0263_SSA_0264|Zinc metalloproteinase in scaA 5'region, putative:PEP phosphonomutase-like protein, putative|POSITIVE:POSITIVE|[258307,258539]|233 HSP 1 e-value: 1.0E-129 bit: 462.0 Len: 233 Query Start:1 Query End:233 Subject Strand: POSITIVE Subject Start: 1 Subject End: 233 tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt tgcagagataagagtacttatcgcatctttctcaaatcaaaaataatcgagtgcatttcaatagtctgcttttggttttgaaagcaggctattttgtcaaagaaaatataaagcgtttacattttcacgaccttgtgctatactgtagttgataacaaaaaataagcaaaatatccaaatagaatagatttcaaagtgtttattaatgaataataaagaaaagagatgttctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAGAGAUAAGAGUACUUAUCGCAUCUUUCUCAAAUCAAAAAUAAUCGAGUGCAUUUCAAUAGUCUGCUUUUGGUUUUGAAAGCAGGCUAUUUUGUCAAAGAAAAUAUAAAGCGUUUACAUUUUCACGACCUUGUGCUAUACUGUAGUUGAUAACAAAAAAUAAGCAAAAUAUCCAAAUAGAAUAGAUUUCAAAGUGUUUAUUAAUGAAUAAUAAAGAAAAGAGAUGUUCUU (((.((((.((((((.......)).))))))))..(((((..(((....((..((....((((((((((((((......))))))))))))))..(((...((((((.(((.....))).))))))..)))..))..))....)))..)))))............)))............(((((..(((((....(.(((((((.....))))))).)...)))))))))). (-48.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAACAUCUCUUUUCUUUAUUAUUCAUUAAUAAACACUUUGAAAUCUAUUCUAUUUGGAUAUUUUGCUUAUUUUUUGUUAUCAACUACAGUAUAGCACAAGGUCGUGAAAAUGUAAACGCUUUAUAUUUUCUUUGACAAAAUAGCCUGCUUUCAAAACCAAAAGCAGACUAUUGAAAUGCACUCGAUUAUUUUUGAUUUGAGAAAGAUGCGAUAAGUACUCUUAUCUCUGCA .....(((((...(((((......(((..(((((.(........(((((.......)))))....(((........((((((..((....))))))))....((((.((((((((((.....))))))))))..))))..(((((.(((((((........))))))).))))).....)))...).)))))..)))...)))))))))).((((((....))))))...... (-45.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 90 49 204 153 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 286 98 51 161 124 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 285 89 49 146 112 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 283 98 52 56 4 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 277 90 46 42 3 NC_009009:SSA_1356|5end_Helicase_subunit_of_the_DNA_excision_repair_complex,_subunit_B,_putative_1371915..1372145_NEGATIVE 269 98 51 167 122 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 268 70 21 191 147 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 267 98 58 57 12 NC_009009:SSA_1001|5end_Arabinose_(multiple_sugar_metabolism)_operon_transcriptional_regulator,_putative_1001689..1001919_NEGATIVE 266 95 53 170 124 NC_009009:SSA_1343|5end_Aspartate_carbamoyltransferase,_putative_1361959..1362189_NEGATIVE 266 70 22 205 158 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 258 103 61 46 3 NC_009009:SSA_1122|5end_Thioredoxin_family_protein,_putative_1147871..1148101_POSITIVE 255 99 54 183 135 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 252 90 46 138 73 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 250 89 47 165 116 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 247 89 52 198 154 NC_009009:SSA_1860|5end_Penicillin-binding_protein_1A,_putative_1854299..1854529_POSITIVE 247 99 52 192 144 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 247 103 61 187 133 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 246 98 53 137 88 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 246 103 63 51 13 NC_009009:SSA_1116|5end_hypothetical_protein_1142352..1142582_POSITIVE 238 97 52 202 159 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 95 53 60 14 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 258 100 52 128 59 NC_009009:SSA_0541|3end_Acetate_kinase,_putative_537082..537232_POSITIVE 253 129 84 147 111 NC_009009:SSA_1625|3end_Lactoylglutathione_lyase,_putative_1626577..1626727_NEGATIVE 246 98 53 134 85 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 244 92 51 147 105 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE 236 90 47 104 62 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 235 87 48 149 101 NC_009009:SSA_1829|3end_RNA_methyltransferase,_putative_1818959..1819109_NEGATIVE 232 97 55 63 4 NC_009009:SSA_1035|3end_Pyrimidine_nucleoside_phosphorylase,_putative_1051531..1051681_POSITIVE 232 204 175 60 29 NC_009009:SSA_0750|3end_hypothetical_protein_732255..732405_POSITIVE 232 90 48 85 52 NC_009009:SSA_0106|3end_30S_ribosomal_protein_S10,_putative_108160..108310_POSITIVE 231 100 56 143 104 NC_009009:SSA_1583|3end_6-O-methylguanine-DNA_methyltransferase,_putative_1585523..1585673_NEGATIVE 228 98 57 95 51 NC_009009:SSA_1213|3end_Pyridoxal-phosphate_dependent_aminotransferase,_putative_1237560..1237710_POSITIVE 226 85 43 117 69 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 225 97 64 61 18 NC_009009:SSA_0638|3end_Tryptophan_synthase_alpha_chain,_putative_627794..627944_POSITIVE 223 75 47 147 123 NC_009009:SSA_0278|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_272382..272532_POSITIVE 222 90 53 143 104 NC_009009:SSA_1810|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1794707..1794857_NEGATIVE 222 103 65 31 1 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 221 99 64 143 100 NC_009009:SSA_1003|3end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1005214..1005364_POSITIVE 220 100 51 105 57 NC_009009:SSA_2078|3end_hypothetical_protein_2082176..2082326_NEGATIVE 220 128 81 73 27 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE