Origin IGS: agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggaaatctcctttaaattttttcatgctttatcattatatacgtaaatagcccgctccgcaagatttttaacttttcacagtaggttggtttaaaatcaaaaacaatacatcgaattaaatcgaataatttatcaatggtttttagcaaaatcatcacttttccacagatttaaggcttattttaaattattttagaataatacaaataaatttgttttaaatcgtatttatataacttcactattacctatctttttaaaagtttccttactttaaatatatatgctctactgtttctgaatgcgagaaaaatacaatattgtccttccagatccaaaacaaaataaaagagatttttcatagtaaaaaggttgagacatcctatctcaaccttttaaaaatggctataaatcatttagcattct Mask Tandem Repeat Region ================================================ agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc Find is-nt database================================================ Query_seq: SSA_1110:SSA_1111|SSA_1110:SSA_1111:hypothetical protein:Branched-chain amino acid transport system II carrier protein, putative:->->:1136246..1136671 426 agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1110:SSA_1111|SSA_1110:SSA_1111:hypothetical protein:Branched-chain amino acid transport system II carrier protein, putative:->->:1136246..1136671 426 agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1110:SSA_1111|SSA_1110:SSA_1111:hypothetical protein:Branched-chain amino acid transport system II carrier protein, putative:->->:1136246..1136671 426 agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 46 End: 135 ............................................. M S Q P F Y Y E K S L L F C F G S G R T I L Y F S R I Q K Q ................................................................................................................................................................................................................................................................................................... Protein_Len: 45 Strand: + Start: 41 End: 175 ........................................ M G C L N L F T M K N L F Y F V L D L E G Q Y C I F L A F R N S R A Y I F K V R K L L K R ........................................................................................................................................................................................................................................................... Protein_Len: 52 Strand: + Start: 257 End: 412 ................................................................................................................................................................................................................................................................ M C G K V M I L L K T I D K L F D L I R C I V F D F K P T Y C E K L K I L R S G L F T Y I M I K H E K I .............. Protein_Len: 45 Strand: - Start: 82 End: 216 ................................................................................. K T K S R S P C Y Q I K R A N L F L L A Y I N L T L F S K F L Y T I T F N Y L Y S K F C M .................................................................................................................................................................................................................. Protein_Len: 48 Strand: - Start: 2 End: 145 . F A L H N I A M K L L N L Y S T E V K K S H F I E K I K N Q I Q F S L I T N K E C E S V T S C M ......................................................................................................................................................................................................................................................................................... agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc 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: 84 Start: 364 End: 393 ...........................................................................................................................................................................................................................................................................................................................................................................CTTGCGGAGCGGGCTATTTACGTATATAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 84 HP_score: -9.2 Tail_Score: -4.11692 Start: 34 End: 56 Full_Region: ttttcatagtaaaaa ggttgagaca tcc tatctcaacc ttttaaaaatggcta .................................ggttgagacatcctatctcaacc.................................................................................................................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_1110:SSA_1111|SSA_1110:SSA_1111:hypothetical protein:Branched-chain amino acid transport system II carrier protein, putative:->->:1136246..1136671 426 agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc Intra-Species Hit: Count: 1 Min: 1 Max: 426 Len: 426 Subject: NC_009009_SSA_1110_SSA_1111|hypothetical protein:Branched-chain amino acid transport system II carrier protein, putative|POSITIVE:POSITIVE|[1136246,1136671]|426 HSP 1 e-value: 0.0 bit: 844.0 Len: 426 Query Start:1 Query End:426 Subject Strand: POSITIVE Subject Start: 1 Subject End: 426 agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc agaatgctaaatgatttatagccatttttaaaaggttgagataggatgtctcaacctttttactatgaaaaatctcttttattttgttttggatctggaaggacaatattgtatttttctcgcattcagaaacagtagagcatatatatttaaagtaaggaaacttttaaaaagataggtaatagtgaagttatataaatacgatttaaaacaaatttatttgtattattctaaaataatttaaaataagccttaaatctgtggaaaagtgatgattttgctaaaaaccattgataaattattcgatttaattcgatgtattgtttttgattttaaaccaacctactgtgaaaagttaaaaatcttgcggagcgggctatttacgtatataatgataaagcatgaaaaaatttaaaggagatttcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUGCUAAAUGAUUUAUAGCCAUUUUUAAAAGGUUGAGAUAGGAUGUCUCAACCUUUUUACUAUGAAAAAUCUCUUUUAUUUUGUUUUGGAUCUGGAAGGACAAUAUUGUAUUUUUCUCGCAUUCAGAAACAGUAGAGCAUAUAUAUUUAAAGUAAGGAAACUUUUAAAAAGAUAGGUAAUAGUGAAGUUAUAUAAAUACGAUUUAAAACAAAUUUAUUUGUAUUAUUCUAAAAUAAUUUAAAAUAAGCCUUAAAUCUGUGGAAAAGUGAUGAUUUUGCUAAAAACCAUUGAUAAAUUAUUCGAUUUAAUUCGAUGUAUUGUUUUUGAUUUUAAACCAACCUACUGUGAAAAGUUAAAAAUCUUGCGGAGCGGGCUAUUUACGUAUAUAAUGAUAAAGCAUGAAAAAAUUUAAAGGAGAUUUCC .....((((.........))))(((....(((((((((((((.....)))))))))))))....)))..((((((((((((..(((((((.........))))))).......((((((..((..((((((((((((...........((((((...((....))))))))......(((..(((..(((((((.....((((((((((......(((((((..((((((....))))))...)))))))..))))))).)))........)))))))..)))...))).............((((......))))..)))))))))))).............(((.(((((.((((.....((.....))...)))).))))))))............))..))))))...)))))))))))).. (-86.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAUCUCCUUUAAAUUUUUUCAUGCUUUAUCAUUAUAUACGUAAAUAGCCCGCUCCGCAAGAUUUUUAACUUUUCACAGUAGGUUGGUUUAAAAUCAAAAACAAUACAUCGAAUUAAAUCGAAUAAUUUAUCAAUGGUUUUUAGCAAAAUCAUCACUUUUCCACAGAUUUAAGGCUUAUUUUAAAUUAUUUUAGAAUAAUACAAAUAAAUUUGUUUUAAAUCGUAUUUAUAUAACUUCACUAUUACCUAUCUUUUUAAAAGUUUCCUUACUUUAAAUAUAUAUGCUCUACUGUUUCUGAAUGCGAGAAAAAUACAAUAUUGUCCUUCCAGAUCCAAAACAAAAUAAAAGAGAUUUUUCAUAGUAAAAAGGUUGAGACAUCCUAUCUCAACCUUUUAAAAAUGGCUAUAAAUCAUUUAGCAUUCU (((....))).............(((((..............((((((..............((((((.((((..((......))..)))).))))))............((((......))))...)))))).((((((((.((((....................((((((((((((((((((((....)))))))))).............))))))))))................(((((.....((((((((.(((((......))))).................((..((((...(.((.((..........)).)))...))))..))..........)))))))).....))))).((((((((((((.......)))))))))))).......)))).)))))))).)))))... (-71.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 58 20 176 132 NC_009009:SSA_0325|5end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_317603..317833_POSITIVE 298 375 339 160 117 NC_009009:SSA_2086|5end_hypothetical_protein_2091428..2091658_NEGATIVE 297 49 4 150 101 NC_009009:SSA_1239|5end_hypothetical_protein_1264689..1264919_NEGATIVE 292 59 30 225 196 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 275 80 32 87 45 NC_009009:SSA_1095|5end_Peptidoglycan_hydrolase,_putative_1112310..1112540_POSITIVE 261 402 365 194 148 NC_009009:SSA_1343|5end_Aspartate_carbamoyltransferase,_putative_1361959..1362189_NEGATIVE 259 403 361 96 49 NC_009009:SSA_1386|5end_NADPH-dependent_FMN_reductase,_putative_1402800..1403030_POSITIVE 254 69 24 183 135 NC_009009:SSA_2096|5end_ATP-dependent_protease,_ATP-binding_subunit,_putative_2101695..2101925_NEGATIVE 253 391 352 49 11 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 253 396 364 193 155 NC_009009:SSA_0895|5end_ATP-binding_cassette_transporter-like_protein,_putative_886466..886696_POSITIVE 250 80 31 154 108 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 248 380 351 37 9 NC_009009:SSA_1022|5end_Glycosyl_transferase,_group_1,_putative_1037283..1037513_POSITIVE 248 57 16 136 88 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 245 378 338 227 182 NC_009009:SSA_1364|5end_hypothetical_protein_1381297..1381527_NEGATIVE 242 138 92 61 14 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 241 385 341 207 151 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 236 383 361 22 1 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 236 376 348 193 165 NC_009009:SSA_1653|5end_hypothetical_protein_1651371..1651601_NEGATIVE 235 374 335 66 22 NC_009009:SSA_1018|5end_Zinc_metalloprotease_zmpC_precursor,_putative_1023346..1023576_POSITIVE 234 68 21 195 150 NC_009009:SSA_2016|5end_Phosphoglycerate_mutase,_putative_2016293..2016523_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 58 20 86 42 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 350 66 23 94 48 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 323 60 15 61 22 NC_009009:SSA_1110|3end_hypothetical_protein_1136185..1136335_POSITIVE 318 60 11 82 35 NC_009009:SSA_1834|3end_30S_ribosomal_interface_protein_S30EA,_putative_1829652..1829802_NEGATIVE 292 59 30 42 13 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 285 49 13 38 3 NC_009009:SSA_1240|3end_Orotate_phosphoribosyltransferase,_putative_1264801..1264951_NEGATIVE 280 58 32 83 57 NC_009009:SSA_0844|3end_hypothetical_protein_828491..828641_NEGATIVE 274 61 35 28 1 NC_009009:SSA_0396|3end_hypothetical_protein_392648..392798_NEGATIVE 262 376 355 27 4 NC_009009:SSA_2001|3end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1997450..1997600_NEGATIVE 261 402 365 84 38 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 254 61 21 75 33 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 253 391 352 52 14 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 250 378 335 62 11 NC_009009:SSA_1529|3end_Lysyl-tRNA_synthetase,_putative_1537441..1537591_POSITIVE 250 80 31 106 60 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 250 378 338 84 38 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 248 62 33 93 63 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 248 57 16 83 35 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 242 62 30 71 36 NC_009009:SSA_0955|3end_Aminopeptidase_N,_putative_961139..961289_POSITIVE 242 138 92 64 17 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE 241 58 11 76 22 NC_009009:SSA_2075|3end_Transketolase,_putative_2077113..2077263_NEGATIVE