Origin IGS: ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttatctagcgaattttccacttaacggtgggaaattaaaaactagcgttgtaattgaagatgttatctcaaagtctagtaaaaccctacctttgggatacttacaaagaagtaagatatattaatcaagaaaaataggagaactattcaa Mask Tandem Repeat Region ================================================ ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa Find is-nt database================================================ Query_seq: SSA_2314:SSA_2315|SSA_2314:SSA_2315:hypothetical protein:Conserved uncharacterized protein:<-<-:2316426..2316576 151 ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2314:SSA_2315|SSA_2314:SSA_2315:hypothetical protein:Conserved uncharacterized protein:<-<-:2316426..2316576 151 ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2314:SSA_2315|SSA_2314:SSA_2315:hypothetical protein:Conserved uncharacterized protein:<-<-:2316426..2316576 151 ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 34 End: 147 ................................. M L L L C K Y P K G R V L L D F E I T S S I T T L V F N F P P L S G K F A R * .... ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa 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================================================ ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2314:SSA_2315|SSA_2314:SSA_2315:hypothetical protein:Conserved uncharacterized protein:<-<-:2316426..2316576 151 ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: NC_009009_SSA_2314_SSA_2315|hypothetical protein:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2316426,2316576]|151 HSP 1 e-value: 1.0E-80 bit: 299.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa ttgaatagttctcctatttttcttgattaatatatcttacttctttgtaagtatcccaaaggtagggttttactagactttgagataacatcttcaattacaacgctagtttttaatttcccaccgttaagtggaaaattcgctagataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAAUAGUUCUCCUAUUUUUCUUGAUUAAUAUAUCUUACUUCUUUGUAAGUAUCCCAAAGGUAGGGUUUUACUAGACUUUGAGAUAACAUCUUCAAUUACAACGCUAGUUUUUAAUUUCCCACCGUUAAGUGGAAAAUUCGCUAGAUAAA ..((((((.....))))))...((((......(((((((..(((..(((((...(((.......))).))))).)))...)))))))......))))........(((((....(((((.((((......)))).))))).)))))..... (-27.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUCUAGCGAAUUUUCCACUUAACGGUGGGAAAUUAAAAACUAGCGUUGUAAUUGAAGAUGUUAUCUCAAAGUCUAGUAAAACCCUACCUUUGGGAUACUUACAAAGAAGUAAGAUAUAUUAAUCAAGAAAAAUAGGAGAACUAUUCAA .....((((..(((((((((((....))))))))))).....))))........((((......((((((((((..(((.......))).))))))))))(((((......))))).........))))....(((((.....)))))... (-31.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 828 110 61 201 152 NC_009009:SSA_2314|5end_hypothetical_protein_2316335..2316565_NEGATIVE 271 92 54 55 1 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 259 93 53 216 166 NC_009009:SSA_1579|5end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1582851..1583081_POSITIVE 257 149 103 82 22 NC_009009:SSA_0540|5end_Glycerol_uptake_facilitator_protein,_putative_534955..535185_POSITIVE 253 95 57 46 2 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 245 137 95 216 170 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 239 49 1 147 85 NC_009009:SSA_0416|5end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_411890..412120_POSITIVE 237 80 33 203 146 NC_009009:SSA_2307|5end_hypothetical_protein_2309909..2310139_NEGATIVE 237 65 22 136 93 NC_009009:SSA_0802|5end_hypothetical_protein_784300..784530_POSITIVE 237 79 33 134 88 NC_009009:SSA_0202|5end_hypothetical_protein_200534..200764_POSITIVE 235 94 51 82 43 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 233 96 56 90 33 NC_009009:SSA_0330|5end_hypothetical_protein_323799..324029_POSITIVE 230 71 40 86 47 NC_009009:SSA_0869|5end_Peptide_chain_release_factor_2,_putative_861914..862144_POSITIVE 229 80 40 225 185 NC_009009:SSA_1240|5end_Orotate_phosphoribosyltransferase,_putative_1265430..1265660_NEGATIVE 224 150 105 210 166 NC_009009:SSA_2125|5end_Small_primase-like_protein_(Toprim_domain),_putative_2130019..2130249_NEGATIVE 223 147 105 67 32 NC_009009:SSA_0356|5end_Dipeptidase,_putative_349259..349489_POSITIVE 222 146 102 72 38 NC_009009:SSA_0463|5end_Cobyrinic_acid_A,C-diamide_synthase,_putative_466865..467095_POSITIVE 219 148 103 75 36 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 219 149 105 202 161 NC_009009:SSA_1602|5end_Exoribonuclease,_VacB/Rnb_family,_putative_1609370..1609600_NEGATIVE 219 128 81 86 36 NC_009009:SSA_0172|5end_Transcriptional_regulator,_XRE_family,_putative_169140..169370_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 92 53 62 7 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 253 95 57 53 9 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 244 91 54 45 1 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 237 79 33 132 86 NC_009009:SSA_0201|3end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_200612..200762_POSITIVE 235 94 51 143 104 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 235 147 108 70 37 NC_009009:SSA_0363|3end_D-alanine/glycine/Na_permease,_putative_355275..355425_POSITIVE 231 76 43 150 113 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 229 80 40 146 106 NC_009009:SSA_1241|3end_Orotidine-5'-phosphate_decarboxylase,_putative_1265509..1265659_NEGATIVE 220 143 104 64 17 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 219 148 103 49 10 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 217 147 105 149 103 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 214 113 76 63 23 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 212 99 59 146 101 NC_009009:SSA_1837|3end_hypothetical_protein_1832955..1833105_POSITIVE 212 148 105 61 11 NC_009009:SSA_0061|3end_Tagatose_1,6-diphosphate_aldolase,_putative_63787..63937_POSITIVE 211 56 13 89 45 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 211 95 56 58 16 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE 211 81 41 99 62 NC_009009:SSA_0587|3end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_579761..579911_POSITIVE 209 76 32 121 79 NC_009009:SSA_0398|3end_hypothetical_protein_394674..394824_NEGATIVE 208 96 51 84 40 NC_009009:SSA_2179|3end_Conserved_uncharacterized_protein_2178104..2178254_NEGATIVE 208 58 11 52 8 NC_009009:SSA_1635|3end_hypothetical_protein_1637152..1637302_NEGATIVE