Origin IGS: tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc .........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 gaatagcctattcaagatagtattgacagaagcctgaacctcctctggaaagaaaactactatatctttaaattgaggaaatatattatgaaaaccggaaacaaattccggttttttattcttgacgaaagaagccgataggtatcgttgaattttggcctattgacgcagtttaagggcaatcgaaaactatttttttaagtgacaaaaatgtaagtttaaaggctaaa Mask Tandem Repeat Region ================================================ tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc Find is-nt database================================================ Query_seq: SSA_1661:SSA_1662|SSA_1661:SSA_1662:hypothetical protein:NADH-dependent oxidoreductase, putative:<-<-:1658095..1658324 230 tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1661:SSA_1662|SSA_1661:SSA_1662:hypothetical protein:NADH-dependent oxidoreductase, putative:<-<-:1658095..1658324 230 tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1661:SSA_1662|SSA_1661:SSA_1662:hypothetical protein:NADH-dependent oxidoreductase, putative:<-<-:1658095..1658324 230 tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 49 End: 168 ................................................ M P L N C V N R P K F N D T Y R L L S S R I K N R N L F P V F I I Y F L N L K I .............................................................. Protein_Len: 51 Strand: + Start: 78 End: 230 ............................................................................. M Q R Y L S A S F V K N K K P E F V S G F H N I F P Q F K D I V V F F P E E V Q A S V N T I L N R L F Protein_Len: 43 Strand: - Start: 93 End: 221 ............................................................................................ R S R E D L I F F R F K N G T K M I Y K R L K F I Y Y N E K W L L N L S R D I S D Q M ......... tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc 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================================================ tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -8.0 Tail_Score: -5.64873 Start: 120 End: 136 Full_Region: aatatattatgaaaa ccggaa acaaa ttccgg ttttttattcttgac .......................................................................................................................ccggaaacaaattccgg.............................................................................................. Find igs database================================================ Query_seq: SSA_1661:SSA_1662|SSA_1661:SSA_1662:hypothetical protein:NADH-dependent oxidoreductase, putative:<-<-:1658095..1658324 230 tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc Intra-Species Hit: Count: 1 Min: 1 Max: 230 Len: 230 Subject: NC_009009_SSA_1661_SSA_1662|hypothetical protein:NADH-dependent oxidoreductase, putative|NEGATIVE:NEGATIVE|[1658095,1658324]|230 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 230 Query Start:1 Query End:230 Subject Strand: POSITIVE Subject Start: 1 Subject End: 230 tttagcctttaaacttacatttttgtcacttnnnnnnntagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc tttagcctttaaacttacatttttgtcacttaaaaaaatagttttcgattgcccttaaactgcgtcaataggccaaaattcaacgatacctatcggcttctttcgtcaagaataaaaaaccggaatttgtttccggttttcataatatatttcctcaatttaaagatatagtagttttctttccagaggaggttcaggcttctgtcaatactatcttgaataggctattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGCCUUUAAACUUACAUUUUUGUCACUUAAAAAAAUAGUUUUCGAUUGCCCUUAAACUGCGUCAAUAGGCCAAAAUUCAACGAUACCUAUCGGCUUCUUUCGUCAAGAAUAAAAAACCGGAAUUUGUUUCCGGUUUUCAUAAUAUAUUUCCUCAAUUUAAAGAUAUAGUAGUUUUCUUUCCAGAGGAGGUUCAGGCUUCUGUCAAUACUAUCUUGAAUAGGCUAUUC ..((((((..(((((....((((((.....))))))...)))))...................(((.(((((................))))).)))........((((((....((((((((((.....))))))))))........((((((((.....(((((...........)))))...))))))))...(((....))).......))))))..))))))... (-46.39) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUAGCCUAUUCAAGAUAGUAUUGACAGAAGCCUGAACCUCCUCUGGAAAGAAAACUACUAUAUCUUUAAAUUGAGGAAAUAUAUUAUGAAAACCGGAAACAAAUUCCGGUUUUUUAUUCUUGACGAAAGAAGCCGAUAGGUAUCGUUGAAUUUUGGCCUAUUGACGCAGUUUAAGGGCAAUCGAAAACUAUUUUUUUAAGUGACAAAAAUGUAAGUUUAAAGGCUAAA ...((((((....((((((((.(..((.((.(((((....(((((...(((((...........))))).....)))))..........(((((((((((.....)))))))))))..(((((.....))))).....))))).))))..)......((((...(((...)))...))))........))))))))........(((....)))........)))))).. (-52.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 937 100 51 191 142 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 349 98 51 74 29 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 342 225 181 177 134 NC_009009:SSA_1864|5end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1860870..1861100_NEGATIVE 328 100 51 65 3 NC_009009:SSA_1406|5end_Histone_acetyltransferase_HPA2,_putative_1420315..1420545_NEGATIVE 293 100 51 98 50 NC_009009:SSA_0418|5end_AraC-type_DNA-binding_domain-containing_protein,_putative_415256..415486_POSITIVE 292 100 51 174 129 NC_009009:SSA_2222|5end_Tyrosine-protein_kinase_Wze,_putative_2223997..2224227_NEGATIVE 292 90 41 208 160 NC_009009:SSA_1308|5end_hypothetical_protein_1326818..1327048_NEGATIVE 289 226 183 170 124 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 288 226 184 56 11 NC_009009:SSA_1259|5end_Purine_nucleoside_phosphorylase,_putative_1285722..1285952_NEGATIVE 285 219 175 65 9 NC_009009:SSA_0342|5end_Pyruvate_formate-lyase,_putative_337206..337436_NEGATIVE 284 219 179 219 175 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 280 107 62 109 61 NC_009009:SSA_1065|5end_Beta-hexosamidase_A,_putative_1081258..1081488_POSITIVE 279 219 177 47 2 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 279 212 175 144 107 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 278 123 81 231 187 NC_009009:SSA_1486|5end_hypothetical_protein_1492922..1493152_POSITIVE 277 219 171 200 150 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 275 220 177 156 97 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 273 98 52 68 15 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 272 90 41 100 60 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 271 227 184 49 2 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 110 61 52 3 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 342 225 181 69 26 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 313 140 92 84 37 NC_009009:SSA_0027|3end_Acyl_carrier_protein,_putative_31802..31952_POSITIVE 309 213 172 140 92 NC_009009:SSA_2020|3end_hypothetical_protein_2022471..2022621_POSITIVE 299 107 62 52 8 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 289 226 183 112 66 NC_009009:SSA_2237|3end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2235508..2235658_NEGATIVE 286 219 171 129 67 NC_009009:SSA_0922|3end_hypothetical_protein_932225..932375_NEGATIVE 284 219 179 103 59 NC_009009:SSA_2359|3end_Glucose_inhibited_division_protein_A,_putative_2360613..2360763_NEGATIVE 284 203 165 146 109 NC_009009:SSA_1664|3end_Phosphatidylethanolamine_N-methyltransferase,_putative_1664449..1664599_NEGATIVE 282 217 174 113 70 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 279 219 177 50 5 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 276 200 153 147 97 NC_009009:SSA_2284|3end_Histidyl-tRNA_synthetase,_putative_2285992..2286142_NEGATIVE 275 220 177 77 18 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 275 98 53 49 5 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 267 217 172 144 86 NC_009009:SSA_1625|3end_Lactoylglutathione_lyase,_putative_1626577..1626727_NEGATIVE 265 225 181 115 67 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 264 98 52 148 88 NC_009009:SSA_0212|3end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_209079..209229_POSITIVE 263 220 175 52 1 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 261 225 184 55 16 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 260 205 171 150 107 NC_009009:SSA_2315|3end_Conserved_uncharacterized_protein_2316487..2316637_NEGATIVE