Origin IGS: cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct .........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 agctattcccttctattctgagttgaattgtttttattttctcacaattcagactttttttcaagctattttggaacgtgaaaacggatttagttcttccaaatgaaaaatccctttcggactcctcaaaatggcggacttatgatagaatataagtactaaagaaggcggaggtcagaag Mask Tandem Repeat Region ================================================ cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct Find is-nt database================================================ Query_seq: SSA_2284:SSA_2285|SSA_2284:SSA_2285:Histidyl-tRNA synthetase, putative:hypothetical protein:<-->:2287363..2287543 181 cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2284:SSA_2285|SSA_2284:SSA_2285:Histidyl-tRNA synthetase, putative:hypothetical protein:<-->:2287363..2287543 181 cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2284:SSA_2285|SSA_2284:SSA_2285:Histidyl-tRNA synthetase, putative:hypothetical protein:<-->:2287363..2287543 181 cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 29 End: 118 ............................ M F Y H K S A I L R S P K G I F H L E E L N P F S R S K I A ............................................................... Protein_Len: 33 Strand: - Start: 79 End: 177 .............................................................................. K S S S F G N E R E L I A Q F F T Q I T L F Y F C N L E S Y F P M .... Protein_Len: 42 Strand: - Start: 30 End: 155 ............................. I R D Y T R W K S S D S L S K E N P L V L D T K V N W F L K F F L R F Q S F I F V M .......................... cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct 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: 82 Start: 117 End: 146 ....................................................................................................................CTTGAAAAAAAGTCTGAATTGTGAGAAAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -3.6 Tail_Score: -3.53811 Start: 54 End: 78 Full_Region: ATAAGTCCGCCATTT TGAGGAGTCC GAAAG GGATTTTTCA TTTGGAAGAACTAAA .....................................................TGAGGAGTCCGAAAGGGATTTTTCA....................................................................................................... Find igs database================================================ Query_seq: SSA_2284:SSA_2285|SSA_2284:SSA_2285:Histidyl-tRNA synthetase, putative:hypothetical protein:<-->:2287363..2287543 181 cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_009009_SSA_2284_SSA_2285|Histidyl-tRNA synthetase, putative:hypothetical protein|NEGATIVE:POSITIVE|[2287363,2287543]|181 HSP 1 e-value: 7.0E-86 bit: 317.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgnnnnnnngtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct cttctgacctccgccttctttagtacttatattctatcataagtccgccattttgaggagtccgaaagggatttttcatttggaagaactaaatccgttttcacgttccaaaatagcttgaaaaaaagtctgaattgtgagaaaataaaaacaattcaactcagaatagaagggaatagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUGACCUCCGCCUUCUUUAGUACUUAUAUUCUAUCAUAAGUCCGCCAUUUUGAGGAGUCCGAAAGGGAUUUUUCAUUUGGAAGAACUAAAUCCGUUUUCACGUUCCAAAAUAGCUUGAAAAAAAGUCUGAAUUGUGAGAAAAUAAAAACAAUUCAACUCAGAAUAGAAGGGAAUAGCU .............(((((((((((((((((........))))))...(((...((((((((((.....))))))))))..)))....))))).....((((((.(((.......))).))))))..(((.((((((((............)))))))))))......))))))........ (-37.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUAUUCCCUUCUAUUCUGAGUUGAAUUGUUUUUAUUUUCUCACAAUUCAGACUUUUUUUCAAGCUAUUUUGGAACGUGAAAACGGAUUUAGUUCUUCCAAAUGAAAAAUCCCUUUCGGACUCCUCAAAAUGGCGGACUUAUGAUAGAAUAUAAGUACUAAAGAAGGCGGAGGUCAGAAG .(((.(((((((((..(((((((((...................)))))))))...........(((((((((((...(((((..((((((..(((........))))))))).)))))...)))..))))))))..(((((((......))))))).....)))))).))))))...... (-39.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 908 50 1 141 92 NC_009009:SSA_2284|5end_Histidyl-tRNA_synthetase,_putative_2287272..2287502_NEGATIVE 358 52 14 137 100 NC_009009:SSA_1557|5end_SRPR,_signal_recognition_particle-docking_protein,_putative_1560040..1560270_NEGATIVE 320 50 3 90 52 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 310 50 3 142 82 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 304 86 41 193 132 NC_009009:SSA_0697|5end_hypothetical_protein_680083..680313_POSITIVE 293 90 42 173 127 NC_009009:SSA_2333|5end_Integral_membrane_protein,_putative_2336460..2336690_NEGATIVE 286 71 45 206 177 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 285 67 29 119 80 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 281 47 1 134 79 NC_009009:SSA_0523|5end_Aldehyde_dehydrogenase,_putative_521637..521867_POSITIVE 278 86 42 76 41 NC_009009:SSA_0021|5end_hypothetical_protein_26842..27072_POSITIVE 276 83 43 226 186 NC_009009:SSA_0522|5end_Ethanolamine_utilization_protein,_putative_521067..521297_POSITIVE 269 72 32 144 101 NC_009009:SSA_1480|5end_hypothetical_protein_1484811..1485041_NEGATIVE 269 49 4 177 126 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 268 72 35 146 106 NC_009009:SSA_0397|5end_hypothetical_protein_394657..394887_NEGATIVE 267 50 1 62 19 NC_009009:SSA_0572|5end_Dehydrogenase,_putative_567426..567656_POSITIVE 266 50 3 63 10 NC_009009:SSA_0046|5end_Adenylosuccinate_lyase,_putative_50894..51124_POSITIVE 265 71 35 192 154 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 264 71 42 53 18 NC_009009:SSA_0780|5end_Acid_phosphatase_(PAP2_family),_putative_764748..764978_POSITIVE 263 50 1 163 96 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 263 49 5 47 1 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 52 14 133 96 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 310 50 3 139 79 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 291 77 42 82 41 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 285 67 29 66 27 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 281 47 1 127 72 NC_009009:SSA_0522|3end_Ethanolamine_utilization_protein,_putative_521710..521860_POSITIVE 277 82 41 63 11 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 269 72 32 129 86 NC_009009:SSA_1481|3end_FmtA-like_protein,_putative_1484826..1484976_NEGATIVE 268 72 35 129 89 NC_009009:SSA_0398|3end_hypothetical_protein_394674..394824_NEGATIVE 265 71 35 127 89 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 259 79 36 57 12 NC_009009:SSA_1782|3end_hypothetical_protein_1767602..1767752_NEGATIVE 258 84 44 86 29 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 258 83 42 98 53 NC_009009:SSA_0036|3end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_42050..42200_NEGATIVE 256 78 44 113 82 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 249 98 52 49 9 NC_009009:SSA_1540|3end_hypothetical_protein_1544915..1545065_NEGATIVE 247 70 38 79 38 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 247 72 36 129 90 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 247 49 13 112 76 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE 246 78 42 64 26 NC_009009:SSA_2255|3end_Transcriptional_regulator,_XRE_family,_putative_2250730..2250880_POSITIVE 244 50 4 110 59 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 244 69 27 60 22 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE