Origin IGS: gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattcctctttcagttctgatactgctgcggtgctaatatcgcagacagggggggccaagctagaacattatcaaatacttcaagcggttccctgcattaatcttc Mask Tandem Repeat Region ================================================ gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt Find is-nt database================================================ Query_seq: SSA_0548:SSA_0549|SSA_0548:SSA_0549:Alanine racemase, putative:ATP-dependent DNA helicase recG, transcription-repair coupling factor, putative:->->:543590..543695 106 gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0548:SSA_0549|SSA_0548:SSA_0549:Alanine racemase, putative:ATP-dependent DNA helicase recG, transcription-repair coupling factor, putative:->->:543590..543695 106 gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0548:SSA_0549|SSA_0548:SSA_0549:Alanine racemase, putative:ATP-dependent DNA helicase recG, transcription-repair coupling factor, putative:->->:543590..543695 106 gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt Predict ORF larger than 30AA ================================================ gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt 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================================================ gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0548:SSA_0549|SSA_0548:SSA_0549:Alanine racemase, putative:ATP-dependent DNA helicase recG, transcription-repair coupling factor, putative:->->:543590..543695 106 gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: NC_009009_SSA_0548_SSA_0549|Alanine racemase, putative:ATP-dependent DNA helicase recG, transcription-repair coupling factor, putative|POSITIVE:POSITIVE|[543590,543695]|106 HSP 1 e-value: 2.0E-41 bit: 168.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggnnnnnnntgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt gaagattaatgcagggaaccgcttgaagtatttgataatgttctagcttggccccccctgtctgcgatattagcaccgcagcagtatcagaactgaaagaggaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGAUUAAUGCAGGGAACCGCUUGAAGUAUUUGAUAAUGUUCUAGCUUGGCCCCCCCUGUCUGCGAUAUUAGCACCGCAGCAGUAUCAGAACUGAAAGAGGAAUU ..........((((((..(((((.(((.((((....))))))).)))..))....))))))(((((..........)))))((((......))))........... (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCCUCUUUCAGUUCUGAUACUGCUGCGGUGCUAAUAUCGCAGACAGGGGGGGCCAAGCUAGAACAUUAUCAAAUACUUCAAGCGGUUCCCUGCAUUAAUCUUC ..........(((....)))..(((((((((((....)))))))).))).(((((((..(((.(((.............))).))))))))))............. (-28.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 87 42 221 185 NC_009009:SSA_1306|5end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324910..1325140_NEGATIVE 348 96 51 57 4 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 346 90 42 77 24 NC_009009:SSA_0576|5end_Conserved_GTPase,_putative_570039..570269_POSITIVE 336 79 37 221 174 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 333 89 49 74 31 NC_009009:SSA_1262|5end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1287782..1288012_POSITIVE 333 83 42 71 28 NC_009009:SSA_1182|5end_Gid-like_protein,_putative_1210866..1211096_NEGATIVE 329 60 11 70 20 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 324 84 41 231 177 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 322 90 43 88 21 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 316 99 56 52 8 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 316 59 13 228 187 NC_009009:SSA_2198|5end_hypothetical_protein_2198585..2198815_NEGATIVE 315 90 43 174 121 NC_009009:SSA_1131|5end_High-affinity_Fe_2+/Pb2+_permease,_putative_1157183..1157413_POSITIVE 314 90 48 64 24 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 312 82 51 144 98 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 308 68 21 82 21 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 306 79 36 137 94 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 303 89 45 171 119 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 303 89 43 56 11 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 302 69 48 231 204 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 301 56 11 222 171 NC_009009:SSA_0709|5end_hypothetical_protein_695895..696125_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 90 42 74 21 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 336 58 18 151 115 NC_009009:SSA_1810|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1794707..1794857_NEGATIVE 329 60 11 85 35 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 319 84 43 57 3 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 316 59 13 134 93 NC_009009:SSA_2199|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2198679..2198829_NEGATIVE 308 68 21 82 21 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 306 79 36 135 92 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 303 89 45 137 85 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 303 89 43 69 24 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 298 96 51 86 22 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 297 89 46 145 98 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 296 97 55 55 14 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 295 93 51 135 82 NC_009009:SSA_1139|3end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1167934..1168084_POSITIVE 294 91 52 50 4 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 293 90 46 140 83 NC_009009:SSA_2090|3end_Hexulose-6-phosphate_synthase,_putative_2094343..2094493_NEGATIVE 293 70 21 137 86 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 290 97 63 88 50 NC_009009:SSA_1794|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1776345..1776495_NEGATIVE 289 83 45 151 115 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE 282 80 43 86 40 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 282 73 45 145 115 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE