Origin IGS: ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaaagtagtattgcgaaaagttgttgtgcgtgctataatattgctagaaaaataggatttgtctggaaattcctataagttgtttttccagattttttaggaggataatcaacc Mask Tandem Repeat Region ================================================ ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa Find is-nt database================================================ Query_seq: SSA_2156:SSA_2157|SSA_2156:SSA_2157:Conserved uncharacterized protein:ATP-dependent serine protease, putative:<-<-:2157023..2157137 115 ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2156:SSA_2157|SSA_2156:SSA_2157:Conserved uncharacterized protein:ATP-dependent serine protease, putative:<-<-:2157023..2157137 115 ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2156:SSA_2157|SSA_2156:SSA_2157:Conserved uncharacterized protein:ATP-dependent serine protease, putative:<-<-:2157023..2157137 115 ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa Predict ORF larger than 30AA ================================================ ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa 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: 89 Start: 76 End: 105 ...........................................................................ATTGCGAAAAGTTGTTGTGCGTGCTATAAT.......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2156:SSA_2157|SSA_2156:SSA_2157:Conserved uncharacterized protein:ATP-dependent serine protease, putative:<-<-:2157023..2157137 115 ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_009009_SSA_2156_SSA_2157|Conserved uncharacterized protein:ATP-dependent serine protease, putative|NEGATIVE:NEGATIVE|[2157023,2157137]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa ggttgattatcctcctaaaaaatctggaaaaacaacttataggaatttccagacaaatcctatttttctagcaatattatagcacgcacaacaacttttcgcaatactactttaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUGAUUAUCCUCCUAAAAAAUCUGGAAAAACAACUUAUAGGAAUUUCCAGACAAAUCCUAUUUUUCUAGCAAUAUUAUAGCACGCACAACAACUUUUCGCAAUACUACUUUAA .((((.................((((((((..(........)...)))))))).................((.........)).....))))....................... (-12.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAGUAGUAUUGCGAAAAGUUGUUGUGCGUGCUAUAAUAUUGCUAGAAAAAUAGGAUUUGUCUGGAAAUUCCUAUAAGUUGUUUUUCCAGAUUUUUUAGGAGGAUAAUCAACC ....((((((((((((....((......)).)))...)))))))))......((((((.((.......)).))))))..((((.((((((.((....)).))))))....)))). (-21.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 819 90 41 181 132 NC_009009:SSA_2156|5end_Conserved_uncharacterized_protein_2156932..2157162_NEGATIVE 253 100 58 147 99 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 251 96 51 193 143 NC_009009:SSA_0666|5end_hypothetical_protein_649788..650018_NEGATIVE 240 86 41 216 172 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 238 100 58 105 62 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 232 94 51 142 96 NC_009009:SSA_0802|5end_hypothetical_protein_784300..784530_POSITIVE 227 88 41 138 97 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 224 100 51 140 86 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 220 90 46 142 101 NC_009009:SSA_2078|5end_hypothetical_protein_2083837..2084067_NEGATIVE 219 83 46 197 163 NC_009009:SSA_1698|5end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690648..1690878_NEGATIVE 216 60 14 67 12 NC_009009:SSA_2153|5end_ABC-type_transporter_(uncharacterized),_permease_component,_putative_2154664..2154894_NEGATIVE 215 86 64 119 97 NC_009009:SSA_0018|5end_Cell-shape_determining_protein_MreD,_putative_23628..23858_POSITIVE 213 107 67 180 143 NC_009009:SSA_2112|5end_hypothetical_protein_2116091..2116321_NEGATIVE 212 85 41 131 78 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 211 88 41 142 92 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 210 69 22 111 59 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 210 106 71 188 140 NC_009009:SSA_1316|5end_Nicotinamide_mononucleotide_transporter,_putative_1332948..1333178_NEGATIVE 209 24 1 112 82 NC_009009:SSA_0046|5end_Adenylosuccinate_lyase,_putative_50894..51124_POSITIVE 208 88 41 128 81 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 208 70 36 144 109 NC_009009:SSA_1803|5end_GTP-binding_protein,_putative_1787909..1788139_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 86 42 80 29 NC_009009:SSA_1964|3end_conserved_uncharacterized_protein_1960996..1961146_NEGATIVE 240 86 41 70 26 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 238 100 58 112 69 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 227 88 41 145 104 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 215 86 64 117 95 NC_009009:SSA_0017|3end_Cell_shape_determining_protein_MreC,_putative_23706..23856_POSITIVE 213 107 67 43 6 NC_009009:SSA_2113|3end_hypothetical_protein_2116228..2116378_NEGATIVE 210 69 22 53 1 NC_009009:SSA_2237|3end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2235508..2235658_NEGATIVE 209 24 1 87 57 NC_009009:SSA_0045|3end_hypothetical_protein_50949..51099_POSITIVE 208 70 36 101 66 NC_009009:SSA_1804|3end_NADPH-flavin_oxidoreductase,_putative_1787952..1788102_NEGATIVE 205 102 73 101 72 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE 202 100 53 64 6 NC_009009:SSA_1810|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1794707..1794857_NEGATIVE 202 63 25 94 56 NC_009009:SSA_0103|3end_Integral_membrane_protein,_putative_104630..104780_NEGATIVE 195 79 39 93 55 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 189 85 46 71 35 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 188 87 41 132 93 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 187 86 46 67 27 NC_009009:SSA_1783|3end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1768102..1768252_NEGATIVE 186 62 29 72 39 NC_009009:SSA_0102|3end_Kinase,_putative_104627..104777_POSITIVE 185 87 41 107 53 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 183 47 10 101 54 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 181 67 24 92 61 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE