Origin IGS: aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcaaaagtacctccataaatttcgatttgatccctctgagcacagaggtaacaattataagtcagactaattcattgtatcactacttgtcaaatattgcaagcaggaaaaacgctt Mask Tandem Repeat Region ================================================ aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc Find is-nt database================================================ Query_seq: SSA_0128:SSA_0129|SSA_0128:SSA_0129:Adenylate kinase, putative:Translation initiation factor IF-1, putative:->->:119980..120096 117 aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0128:SSA_0129|SSA_0128:SSA_0129:Adenylate kinase, putative:Translation initiation factor IF-1, putative:->->:119980..120096 117 aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0128:SSA_0129|SSA_0128:SSA_0129:Adenylate kinase, putative:Translation initiation factor IF-1, putative:->->:119980..120096 117 aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 2 End: 103 . A N K R S A I N S L Y H Y L S N T Q S I I T V E T S L P I L D F N M .............. aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc 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: 86 Start: 15 End: 44 ..............CTTGCAATATTTGACAAGTAGTGATACAAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0128:SSA_0129|SSA_0128:SSA_0129:Adenylate kinase, putative:Translation initiation factor IF-1, putative:->->:119980..120096 117 aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_009009_SSA_0128_SSA_0129|Adenylate kinase, putative:Translation initiation factor IF-1, putative|POSITIVE:POSITIVE|[119980,120096]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc aagcgtttttcctgcttgcaatatttgacaagtagtgatacaatgaattagtctgacttataattgttacctctgtgctcagagggatcaaatcgaaatttatggaggtacttttgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCGUUUUUCCUGCUUGCAAUAUUUGACAAGUAGUGAUACAAUGAAUUAGUCUGACUUAUAAUUGUUACCUCUGUGCUCAGAGGGAUCAAAUCGAAAUUUAUGGAGGUACUUUUGC ..(((....(((((((((((.....)).))))))).))(((.(((((((....((((........))))((((((....))))))...........)))))))....)))....))) (-23.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAAAGUACCUCCAUAAAUUUCGAUUUGAUCCCUCUGAGCACAGAGGUAACAAUUAUAAGUCAGACUAAUUCAUUGUAUCACUACUUGUCAAAUAUUGCAAGCAGGAAAAACGCUU ......((...(((..........(((((((.((((((....))))))..(((((.((.((.....)).))..)))))..........)))))))..........)))...)).... (-17.25) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 87 50 35 3 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 255 45 1 75 30 NC_009009:SSA_0157|5end_hypothetical_protein_153513..153743_POSITIVE 251 34 4 52 25 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 245 109 73 64 14 NC_009009:SSA_1399|5end_hypothetical_protein_1412225..1412455_NEGATIVE 243 110 70 230 192 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 242 84 50 228 194 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 241 110 70 148 108 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 240 108 73 77 46 NC_009009:SSA_0243|5end_Cyclo-nucleotide_phosphodiesterase,_putative_238235..238465_NEGATIVE 238 79 34 229 186 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 238 90 43 162 120 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 234 110 64 226 181 NC_009009:SSA_1971|5end_hypothetical_protein_1967167..1967397_POSITIVE 234 78 34 188 145 NC_009009:SSA_1330|5end_hypothetical_protein_1346368..1346598_NEGATIVE 231 86 50 220 179 NC_009009:SSA_0842|5end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827330..827560_POSITIVE 227 46 1 42 5 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 225 58 11 59 10 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 225 85 50 223 195 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 222 108 63 228 179 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 222 110 66 153 98 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 222 110 69 38 2 NC_009009:SSA_0463|5end_Cobyrinic_acid_A,C-diamide_synthase,_putative_466865..467095_POSITIVE 221 107 80 70 40 NC_009009:SSA_1882|5end_Subtilisin-like_serine_proteases,_putative_1880797..1881027_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 86 49 143 99 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 273 41 2 129 80 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 253 90 43 52 1 NC_009009:SSA_1400|3end_Pyridoxal_kinase,_putative_1412206..1412356_NEGATIVE 251 34 4 55 28 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 248 85 48 61 14 NC_009009:SSA_1753|3end_Transcriptional_regulator,_GntR_family_(repressor_of_trehalose_operon),_putative_1742740..1742890_POSITIVE 246 97 51 90 55 NC_009009:SSA_1520|3end_Elongation_factor_Tu,_putative_1526385..1526535_NEGATIVE 241 110 70 148 108 NC_009009:SSA_1531|3end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1538778..1538928_NEGATIVE 234 78 34 83 40 NC_009009:SSA_1331|3end_Conserved_uncharacterized_protein_1346473..1346623_NEGATIVE 231 86 50 46 5 NC_009009:SSA_0841|3end_hypothetical_protein_827236..827386_POSITIVE 221 109 64 141 88 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 218 42 3 138 96 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 215 110 70 139 82 NC_009009:SSA_0291|3end_Oxidoreductase,_putative_286269..286419_POSITIVE 213 80 32 148 100 NC_009009:SSA_1852|3end_Metal_dependent_phosphohydrolase_(HD_motif),_putative_1846869..1847019_NEGATIVE 213 41 2 64 36 NC_009009:SSA_0110|3end_50S_ribosomal_protein_L2,_putative_110666..110816_POSITIVE 212 109 63 143 98 NC_009009:SSA_0148|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_143467..143617_POSITIVE 210 39 2 91 43 NC_009009:SSA_2165|3end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2163787..2163937_POSITIVE 210 95 76 148 129 NC_009009:SSA_1470|3end_3-dehydroquinate_dehydratase,_putative_1476307..1476457_NEGATIVE 208 108 63 65 25 NC_009009:SSA_0433|3end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435028..435178_NEGATIVE 207 90 55 127 94 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 206 105 62 151 112 NC_009009:SSA_0019|3end_Secreted_antigen_GbpB/SagA;_peptidoglycan_hydrolase;_PcsB_protein_precursor,_putative_25519..25669_POSITIVE