Origin IGS: taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatccccattcccaataaagtgaaccctttgtttaaagggttcgttttttatccttcgattttctacatctaaaaacgctgtaaaaaatcaccgcactttta Mask Tandem Repeat Region ================================================ taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta Find is-nt database================================================ Query_seq: AA00212:AA00213|AA00212:AA00213:ribokinase:cold shock protein (negative regulator of cspA transcription):->->:147108..147210 103 taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00212:AA00213|AA00212:AA00213:ribokinase:cold shock protein (negative regulator of cspA transcription):->->:147108..147210 103 taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00212:AA00213|AA00212:AA00213:ribokinase:cold shock protein (negative regulator of cspA transcription):->->:147108..147210 103 taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta Predict ORF larger than 30AA ================================================ taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta 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================================================ taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00212:AA00213|AA00212:AA00213:ribokinase:cold shock protein (negative regulator of cspA transcription):->->:147108..147210 103 taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: aact_AA00212_AA00213|ribokinase:cold shock protein (negative regulator of cspA transcription)|POSITIVE:POSITIVE|[147108,147210]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta taaaagtgcggtgattttttacagcgtttttagatgtagaaaatcgaaggataaaaaacgaaccctttaaacaaagggttcactttattgggaatggggatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGUGCGGUGAUUUUUUACAGCGUUUUUAGAUGUAGAAAAUCGAAGGAUAAAAAACGAACCCUUUAAACAAAGGGUUCACUUUAUUGGGAAUGGGGAUUA .....((.(..((((((((((((.(.......).))))))))))))..).)).......(((((((((....))))))))).((((((.....)))))).... (-27.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCCCCAUUCCCAAUAAAGUGAACCCUUUGUUUAAAGGGUUCGUUUUUUAUCCUUCGAUUUUCUACAUCUAAAAACGCUGUAAAAAAUCACCGCACUUUUA .................((((((((((((((....)))))))))..............((((((.((((.(.......).)))).)))))).....))))).. (-19.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 453 47 3 159 104 aact:AA02706|5end_2-oxoglutarate_dehydrogenase_E1_component_(decarboxylase_component)_1886843..1887073_POSITIVE 414 45 2 157 111 aact:AA02597|5end_ribonuclease_D_1807124..1807354_POSITIVE 404 45 2 138 94 aact:AA00854|5end_arginine_transport_system_permease_protein_588898..589128_POSITIVE 381 42 2 105 66 aact:AA00587|5end_hypothetical_protein_399975..400205_POSITIVE 373 50 1 174 125 aact:AA02836|5end_colicin_transport_protein_1991777..1992007_POSITIVE 373 50 1 98 49 aact:AA02835|5end_hypothetical_protein_1991701..1991931_POSITIVE 368 46 2 148 102 aact:AA01954|5end_excinuclease_ABC,_subunit_C_1320468..1320698_POSITIVE 351 42 1 134 92 aact:AA02673|5end_gluconate_utilization_operon_repressor_1858913..1859143_POSITIVE 347 31 1 159 129 aact:AA00691|5end_conserved_hypothetical_protein_(possible_multidrug/sugar_efflux_transporter)_472038..472268_POSITIVE 334 40 2 217 177 aact:AA01883|5end_recycling_protein;_permease_1269821..1270051_POSITIVE 334 45 2 162 116 aact:AA01666|5end_penicillin-binding_protein_4;_D-alanyl-D-alanine_carboxypeptidase;_D-alanyl-D-alanine-endopeptidase_1128231..1128461_POSITIVE 331 30 2 86 58 aact:AA01338|5end_hypothetical_protein_904967..905197_POSITIVE 328 32 2 138 108 aact:AA00410|5end_peptide_deformylase_(PDF)_(Polypeptide_deformylase)_274633..274863_POSITIVE 327 46 2 69 24 aact:AA02518|5end_hypothetical_protein_1749707..1749937_POSITIVE 327 34 1 173 140 aact:AA00511|5end_nicotinamide_mononucleotide_transporter_353884..354114_POSITIVE 325 50 2 147 94 aact:AA01673|5end_riboflavin_synthase,_alpha_chain_1131477..1131707_POSITIVE 324 42 2 229 189 aact:AA02519|5end_DNA_gyrase_A_1749872..1750102_POSITIVE 315 50 3 148 99 aact:AA00467|5end_hypothetical_protein_324565..324795_POSITIVE 312 50 2 135 82 aact:AA02832|5end_outer_membrane_integrity_protein_1990044..1990274_POSITIVE 311 50 4 84 37 aact:AA00582|5end_conserved_hypothetical_protein_397904..398134_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 46 3 151 109 aact:AA02705|3end_hypothetical_protein_1886928..1887078_POSITIVE 414 45 2 63 17 aact:AA02595|3end_cytochrome_c_peroxidase_1807110..1807260_POSITIVE 381 42 2 76 37 aact:AA00586|3end_glycerol-3-phosphate_regulon_repressor_400026..400176_POSITIVE 373 50 1 85 36 aact:AA02834|3end_colicin_transport_protein_1991768..1991918_POSITIVE 351 42 1 58 16 aact:AA02671|3end_gluconokinase_1858917..1859067_POSITIVE 347 31 1 83 53 aact:AA00689|3end_GTP-binding_protein_472042..472192_POSITIVE 334 40 2 81 41 aact:AA01881|3end_adenylate_kinase_1269765..1269915_POSITIVE 334 45 2 55 9 aact:AA01663|3end_GTP_cyclohydrolase_I_1128204..1128354_POSITIVE 331 30 2 70 42 aact:AA01337|3end_cell_division_protein_N_905031..905181_POSITIVE 328 32 2 69 39 aact:AA00409|3end_methionyl-tRNA_formyltransferase_274644..274794_POSITIVE 327 46 2 63 18 aact:AA02516|3end_ferric_uptake_regulation_protein_1749781..1749931_POSITIVE 327 34 1 92 59 aact:AA00508|3end_SAM-dependent_methyltransferase_353883..354033_POSITIVE 325 50 2 108 55 aact:AA01672|3end_conserved_hypothetical_protein_1131518..1131668_POSITIVE 315 50 3 103 54 aact:AA00465|3end_hypothetical_protein_324600..324750_POSITIVE 312 50 2 97 44 aact:AA02830|3end_colicin_tolerance_protein_1990086..1990236_POSITIVE 311 50 4 66 19 aact:AA00581|3end_thiosulfate_sulfurtransferase_(rhodanese)_397966..398116_POSITIVE 307 32 3 90 61 aact:AA01462|3end_xylose_operon_regulatory_protein_982779..982929_POSITIVE 305 48 2 71 16 aact:AA00081|3end_fatty_acid_metabolism_regulator_protein_60767..60917_POSITIVE 300 32 2 131 100 aact:AA02824|3end_conserved_hypothetical_protein_1986399..1986549_POSITIVE 300 45 3 60 14 aact:AA01057|3end_DnaJ-like_protein_djlA_735047..735197_POSITIVE