Origin IGS: tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc .........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 gattacttttcctattgattttcaatttcgaatactcctcgtttcgtctacatcattgctcgcaacccagtaataaccttgccaagacagaaagctaagcgaaactgcaaatcaactatgatttgaataggttttcgaagagtattaatcaaaatccccaatcacatgactggggaatggttca Mask Tandem Repeat Region ================================================ tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc Find is-nt database================================================ Query_seq: SSA_0914:SSA_0915|SSA_0914:SSA_0915:Phenylalanyl-tRNA synthetase beta chain, putative:hypothetical protein:->->:927498..927681 184 tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0914:SSA_0915|SSA_0914:SSA_0915:Phenylalanyl-tRNA synthetase beta chain, putative:hypothetical protein:->->:927498..927681 184 tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0914:SSA_0915|SSA_0914:SSA_0915:Phenylalanyl-tRNA synthetase beta chain, putative:hypothetical protein:->->:927498..927681 184 tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 24 End: 134 ....................... M G I L I N T L R K P I Q I I V D L Q F R L A F C L G K V I T G L R A M M .................................................. Protein_Len: 33 Strand: - Start: 62 End: 160 ............................................................. I M T S K C N R K A K Q R P L T I V P N R A I I Y V F R P T N S M ........................ tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc 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================================================ PromScan Matrix: RpoN Strand: + Score: 81 Start: 100 End: 116 ...................................................................................................TTGGCAAGGTTATTACT.................................................................... tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0914:SSA_0915|SSA_0914:SSA_0915:Phenylalanyl-tRNA synthetase beta chain, putative:hypothetical protein:->->:927498..927681 184 tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: NC_009009_SSA_0914_SSA_0915|Phenylalanyl-tRNA synthetase beta chain, putative:hypothetical protein|POSITIVE:POSITIVE|[927498,927681]|184 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc tgaaccattccccagtcatgtgattggggattttgattaatactcttcgaaaacctattcaaatcatagttgatttgcagtttcgcttagctttctgtcttggcaaggttattactgggttgcgagcaatgatgtagacgaaacgaggagtattcgaaattgaaaatcaataggaaaagtaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACCAUUCCCCAGUCAUGUGAUUGGGGAUUUUGAUUAAUACUCUUCGAAAACCUAUUCAAAUCAUAGUUGAUUUGCAGUUUCGCUUAGCUUUCUGUCUUGGCAAGGUUAUUACUGGGUUGCGAGCAAUGAUGUAGACGAAACGAGGAGUAUUCGAAAUUGAAAAUCAAUAGGAAAAGUAAUC ....((..(((((((((....)))))))))(((..((((((((((((((..(((((...(((((((....))))))).......(((.(((.....).)).))).))))).((((...((((....))))...))))......)))))))))))...)))..))).......)).......... (-51.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUACUUUUCCUAUUGAUUUUCAAUUUCGAAUACUCCUCGUUUCGUCUACAUCAUUGCUCGCAACCCAGUAAUAACCUUGCCAAGACAGAAAGCUAAGCGAAACUGCAAAUCAACUAUGAUUUGAAUAGGUUUUCGAAGAGUAUUAAUCAAAAUCCCCAAUCACAUGACUGGGGAAUGGUUCA ..........((..((((((.....(((((((....(((.((((((..((.....(((((.((((.............))))..)).))).....))..))))))..(((((((....)))))))...)))..)))))))......))))))..((((((.((....)).))))))..)).... (-40.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 128 82 228 182 NC_009009:SSA_2138|5end_RNA-binding_protein,_Jag_family,_putative_2139487..2139717_NEGATIVE 330 118 71 173 113 NC_009009:SSA_1445|5end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447886..1448116_NEGATIVE 329 135 97 191 150 NC_009009:SSA_1640|5end_hypothetical_protein_1642530..1642760_NEGATIVE 315 104 67 230 192 NC_009009:SSA_0187|5end_Competence_protein_ComYD,_putative_190350..190580_POSITIVE 314 125 83 179 137 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 311 140 91 176 131 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 308 129 81 207 148 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 305 109 62 204 135 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 305 124 81 158 102 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 304 128 84 210 161 NC_009009:SSA_0493|5end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_492868..493098_POSITIVE 299 139 91 152 105 NC_009009:SSA_0804|5end_Phosphoglucomutase/phosphomannomutase_family_protein,_putative_785995..786225_POSITIVE 299 127 85 221 173 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 293 128 84 148 93 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 291 127 81 190 146 NC_009009:SSA_1653|5end_hypothetical_protein_1651371..1651601_NEGATIVE 290 108 74 208 176 NC_009009:SSA_1470|5end_3-dehydroquinate_dehydratase,_putative_1476984..1477214_NEGATIVE 289 109 62 171 127 NC_009009:SSA_0093|5end_V-type_sodium_ATPase,_subunit_D,_putative_94286..94516_POSITIVE 286 60 11 204 162 NC_009009:SSA_1196|5end_Acetyltransferase,_GNAT_family,_putative_1222052..1222282_NEGATIVE 284 100 59 197 147 NC_009009:SSA_2263|5end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2261176..2261406_NEGATIVE 283 137 92 198 148 NC_009009:SSA_1430|5end_Ribonuclease_Z,_putative_1438036..1438266_NEGATIVE 282 128 90 57 5 NC_009009:SSA_1902|5end_tRNA_(guanine-N(7)-)-methyltransferase,_putative_1897391..1897621_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 46 9 103 61 NC_009009:SSA_0914|3end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_927437..927587_POSITIVE 299 139 91 57 10 NC_009009:SSA_0803|3end_hypothetical_protein_785980..786130_POSITIVE 284 100 59 134 84 NC_009009:SSA_2264|3end_hypothetical_protein_2261239..2261389_NEGATIVE 282 128 90 60 8 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 281 99 67 52 17 NC_009009:SSA_2329|3end_hypothetical_protein_2333169..2333319_POSITIVE 281 108 63 118 68 NC_009009:SSA_0587|3end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_579761..579911_POSITIVE 277 128 81 137 89 NC_009009:SSA_1327|3end_hypothetical_protein_1343750..1343900_NEGATIVE 275 127 81 79 22 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 274 127 83 131 79 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 273 119 74 87 29 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 272 127 81 83 29 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 270 127 94 62 20 NC_009009:SSA_2200|3end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201109..2201259_NEGATIVE 270 150 101 54 1 NC_009009:SSA_1946|3end_Oligopeptide_transport_system_permease_protein,_putative_1937698..1937848_NEGATIVE 270 127 84 150 100 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 268 128 85 145 102 NC_009009:SSA_1498|3end_50S_ribosomal_protein_L20,_putative_1503753..1503903_NEGATIVE 267 127 89 151 119 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 266 126 84 139 98 NC_009009:SSA_0091|3end_V-type_sodium_ATPase,_subunit_A,_putative_92988..93138_POSITIVE 263 128 84 148 101 NC_009009:SSA_1829|3end_RNA_methyltransferase,_putative_1818959..1819109_NEGATIVE 260 124 84 46 3 NC_009009:SSA_2045|3end_Reductase,_putative_2048427..2048577_NEGATIVE 260 117 78 72 25 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE