Origin IGS: gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa .........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 ttagagttcctcctattcgaatttcattctagcacaagaaaaaaacttttgcacaattctgctacgctttaaaaaagtttatgaaatagtggaaagtttaactttattttctcagaaaaatcgtttacatgactttatcgatggattgggctatcttttgcttctctcttgtgttatactagataggttgcaaagaaaacagtacttttcttttgtggaaaagaagcaacacgattttatatccagtatatgaaaatacgtcataaaaagaaaagtataaactaagtcctatagggtggcttcgcaccacctttagaaagaagaataac Mask Tandem Repeat Region ================================================ gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa Find is-nt database================================================ Query_seq: SMT_933:SMT_934|SMT_933:SMT_934:ATP-dependent RNA helicase:pyridine nucleotide-disulfide oxidoreductase:<-->:885722..886050 329 gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_933:SMT_934|SMT_933:SMT_934:ATP-dependent RNA helicase:pyridine nucleotide-disulfide oxidoreductase:<-->:885722..886050 329 gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_933:SMT_934|SMT_933:SMT_934:ATP-dependent RNA helicase:pyridine nucleotide-disulfide oxidoreductase:<-->:885722..886050 329 gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 20 End: 148 ................... M V R S H P I G L S L Y F S F Y D V F S Y T G Y K I V L L L F H K R K V L F S L Q P I ..................................................................................................................................................................................... Protein_Len: 37 Strand: + Start: 66 End: 176 ................................................................. M T Y F H I L D I K S C C F F S T K E K Y C F L C N L S S I T Q E R S K R ......................................................................................................................................................... Protein_Len: 60 Strand: - Start: 80 End: 304 ............................................................................... Y Q K R Q L R D L I V C S L L L L Y G L G D I F D H L R N K Q S F L T L S E V I E Y V K K F R L L I T C F N K E Q A L M ......................... gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa 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================================================ gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_933:SMT_934|SMT_933:SMT_934:ATP-dependent RNA helicase:pyridine nucleotide-disulfide oxidoreductase:<-->:885722..886050 329 gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa Intra-Species Hit: Count: 1 Min: 1 Max: 329 Len: 329 Subject: smit_SMT_933_SMT_934|ATP-dependent RNA helicase:pyridine nucleotide-disulfide oxidoreductase|NEGATIVE:POSITIVE|[885722,886050]|329 HSP 1 e-value: 1.0E-174 bit: 611.0 Len: 329 Query Start:1 Query End:329 Subject Strand: POSITIVE Subject Start: 1 Subject End: 329 gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagnnnnnnncttgtgctagaatgaaattcgaataggaggaactctaa gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatatactggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagcccaatccatcgataaagtcatgtaaacgatttttctgagaaaataaagttaaactttccactatttcataaacttttttaaagcgtagcagaattgtgcaaaagtttttttcttgtgctagaatgaaattcgaataggaggaactctaa Inter-species Hit: Count: 3 Min: 1 Max: 182 Len: 182 Subject: NC_008533_SPD_1413_SPD_1414|ATP-dependent RNA helicase, putative:oxalate:formate antiporter|NEGATIVE:NEGATIVE|[1432894,1433091]|198 HSP 1 e-value: 3.0E-80 bit: 299.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatat-actggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagccc................................................................................................................................................... gttattcttctttctaaaggtggtgcgaagccaccctatagggcttagtttatacttttctttttatgacgtattttcatataactagatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagaccagagcaaaagatagccc................................................................................................................................................... Subject: NC_003098_spr1440_spr1441|hypothetical protein:Major facilitator:Oxalate:Formate Antiporter|NEGATIVE:NEGATIVE|[1425363,1425560]|198 HSP 1 e-value: 3.0E-80 bit: 299.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatat-actggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagccc................................................................................................................................................... gttattcttctttctaaaggtggtgcgaagccaccctatagggcttagtttatacttttctttttatgacgtattttcatataactagatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagaccagagcaaaagatagccc................................................................................................................................................... Subject: NC_003028_SP_1586_SP_1587|ATP-dependent RNA helicase, putative:oxalate:formate antiporter|NEGATIVE:NEGATIVE|[1491341,1491538]|198 HSP 1 e-value: 3.0E-80 bit: 299.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 gttattcttctttctaaaggtggtgcgaagccaccctataggacttagtttatacttttctttttatgacgtattttcatat-actggatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagagagaagcaaaagatagccc................................................................................................................................................... gttattcttctttctaaaggtggtgcgaagccaccctatagggcttagtttatacttttctttttatgacgtattttcatataactagatataaaatcgtgttgcttcttttccacaaaagaaaagtactgttttctttgcaacctatctagtataacacaagaccagagcaaaagatagccc................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAUUCUUCUUUCUAAAGGUGGUGCGAAGCCACCCUAUAGGACUUAGUUUAUACUUUUCUUUUUAUGACGUAUUUUCAUAUACUGGAUAUAAAAUCGUGUUGCUUCUUUUCCACAAAAGAAAAGUACUGUUUUCUUUGCAACCUAUCUAGUAUAACACAAGAGAGAAGCAAAAGAUAGCCC (((((((((((((((...((((((.....)))))).(((((((...(((....))).....)))))))...........(((((((((((.......(.(((((............((((((((......))))))))))))))))))))))))).....))))))))).....)))))).. (-41.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGCUAUCUUUUGCUUCUCUCUUGUGUUAUACUAGAUAGGUUGCAAAGAAAACAGUACUUUUCUUUUGUGGAAAAGAAGCAACACGAUUUUAUAUCCAGUAUAUGAAAAUACGUCAUAAAAAGAAAAGUAUAAACUAAGUCCUAUAGGGUGGCUUCGCACCACCUUUAGAAAGAAGAAUAAC (((((...((((((.(((.(((.(((...))).))).)))..))))))......((((((((((((((((............)))..((((((((.....))))))))..........)))))))))))))......)))))...(((((((.......)))))))................ (-40.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 50 1 141 92 smit:SMT_933|5end_ATP-dependent_RNA_helicase_885631..885861_NEGATIVE 283 37 2 138 88 smit:SMT_1199|5end_lactococcin_A_ABC_transporter_permease_protein_1161063..1161293_NEGATIVE 281 50 4 156 96 smit:SMT_1680|5end_hypothetical_protein_1663494..1663724_POSITIVE 273 70 21 54 1 smit:SMT_1867|5end_peptide_chain_release_factor_1_1828218..1828448_NEGATIVE 270 64 21 202 158 smit:SMT_537|5end_oxidoreductase,_aldo/keto_reductase_family_454773..455003_POSITIVE 266 53 16 186 141 smit:SMT_335|5end_glutamine_synthetase_273753..273983_POSITIVE 259 45 10 135 104 smit:SMT_448|5end_K03707_transcriptional_activator_TenA_386789..387019_POSITIVE 253 58 14 170 129 smit:SMT_2009|5end_GtrA_family_protein_1928973..1929203_POSITIVE 244 136 95 38 2 smit:SMT_630|5end_phosphoserine_phosphatase_535459..535689_POSITIVE 241 35 1 133 87 smit:SMT_1013|5end_galactose-1-phosphate_uridylyltransferase_950626..950856_NEGATIVE 240 160 112 108 56 smit:SMT_662|5end_A/G-specific_adenine_glycosylase_573827..574057_NEGATIVE 239 46 4 178 133 smit:SMT_568|5end_hypothetical_protein_485674..485904_POSITIVE 239 168 124 119 71 smit:SMT_407|5end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_351365..351595_POSITIVE 239 35 7 92 64 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 236 69 25 108 54 smit:SMT_1631|5end_phosphopantothenoylcysteine_synthase/decarboxylase_1618359..1618589_NEGATIVE 236 166 121 181 130 smit:SMT_1359|5end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1338003..1338233_NEGATIVE 236 70 28 109 65 smit:SMT_1092|5end_transcription_antitermination_factor_1033696..1033926_NEGATIVE 235 49 5 152 96 smit:SMT_817|5end_aminotransferase_728699..728929_NEGATIVE 234 50 2 207 155 smit:SMT_1184|5end_phosphotransferase_system,_mannose/fructose/N-acetylgalactosamine-specific_component_IIB_1142037..1142267_NEGATIVE 231 73 31 205 159 smit:SMT_1554|5end_isoleucyl-tRNA_synthetase_1537040..1537270_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 41 16 66 38 smit:SMT_999|3end_hypothetical_protein_predicted_by_Glimmer/Critica_941496..941646_NEGATIVE 283 37 2 125 75 smit:SMT_1200|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1161076..1161226_NEGATIVE 275 71 31 116 71 smit:SMT_1833|3end_tagatose_1,6-diphosphate_aldolase_1802429..1802579_POSITIVE 273 70 21 57 4 smit:SMT_1868|3end_thymidine_kinase_1828215..1828365_NEGATIVE 270 64 21 92 48 smit:SMT_536|3end_oxidoreductase,_aldo/keto_reductase_family_454743..454893_POSITIVE 266 53 16 149 104 smit:SMT_334|3end_K03713_MerR_family_transcriptional_regulator,_glutamine_synthetase_repressor_273796..273946_POSITIVE 247 179 139 52 5 smit:SMT_1848|3end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1812694..1812844_NEGATIVE 243 50 8 54 2 smit:SMT_1641|3end_arginyl-tRNA_synthetase_1626562..1626712_NEGATIVE 241 35 1 114 68 smit:SMT_1014|3end_galactokinase_950645..950795_NEGATIVE 237 42 6 119 79 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 236 69 25 96 42 smit:SMT_1632|3end_hypothetical_protein_1618371..1618521_NEGATIVE 236 70 28 55 11 smit:SMT_1093|3end_K03073_preprotein_translocase_SecE_subunit_1033750..1033900_NEGATIVE 236 37 5 85 48 smit:SMT_699|3end_K03106_signal_recognition_particle,_subunit_SRP54_609941..610091_NEGATIVE 235 49 5 144 88 smit:SMT_818|3end_cystathionine_gamma-synthase_728707..728857_NEGATIVE 235 50 15 86 50 smit:SMT_721|3end_Tn5252,_relaxase_626892..627042_NEGATIVE 233 35 2 122 91 smit:SMT_365|3end_hypothetical_protein_301747..301897_POSITIVE 230 140 97 46 3 smit:SMT_593|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_510317..510467_POSITIVE 229 56 16 47 6 smit:SMT_83|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_14543..14693_NEGATIVE 228 62 27 92 58 smit:SMT_1742|3end_sodium-dependent_phosphate_transporter_1724991..1725141_POSITIVE 225 35 5 77 35 smit:SMT_1785|3end_phenylalanyl-tRNA_synthetase_beta_chain_1762327..1762477_NEGATIVE