Origin IGS: aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atggataagaataaaaaattaagttatataactacttatgtactattaacagttctatattttatactattctctttgataagttcaggtttcataagtagatatcaagttggaattttaatt Mask Tandem Repeat Region ================================================ aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat Find is-nt database================================================ Query_seq: FN1430:FN1431|FN1430:FN1431:Branched-chain amino acid transport system permease protein livM:Branched-chain amino acid transport system permease protein livH:<-<-:2099293..2099415 123 aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1430:FN1431|FN1430:FN1431:Branched-chain amino acid transport system permease protein livM:Branched-chain amino acid transport system permease protein livH:<-<-:2099293..2099415 123 aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1430:FN1431|FN1430:FN1431:Branched-chain amino acid transport system permease protein livM:Branched-chain amino acid transport system permease protein livH:<-<-:2099293..2099415 123 aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 1 End: 123 I L I G V Q Y R S I F G S S I L S F L I F Y L V T L L V Y T T I Y S L K K N K D M aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat 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================================================ aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1430:FN1431|FN1430:FN1431:Branched-chain amino acid transport system permease protein livM:Branched-chain amino acid transport system permease protein livH:<-<-:2099293..2099415 123 aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: NC_003454_FN1430_FN1431|Branched-chain amino acid transport system permease protein livM:Branched-chain amino acid transport system permease protein livH|NEGATIVE:NEGATIVE|[2099293,2099415]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat aattaaaattccaacttgatatctacttatgaaacctgaacttatcaaagagaatagtataaaatatagaactgttaatagtacataagtagttatataacttaattttttattcttatccat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAAAUUCCAACUUGAUAUCUACUUAUGAAACCUGAACUUAUCAAAGAGAAUAGUAUAAAAUAUAGAACUGUUAAUAGUACAUAAGUAGUUAUAUAACUUAAUUUUUUAUUCUUAUCCAU ...(((((..........(((.(((((((((.....(((.....))).....((((((............)))))).......))))))))).)))...........)))))........... (-14.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGAUAAGAAUAAAAAAUUAAGUUAUAUAACUACUUAUGUACUAUUAACAGUUCUAUAUUUUAUACUAUUCUCUUUGAUAAGUUCAGGUUUCAUAAGUAGAUAUCAAGUUGGAAUUUUAAUU ...........(((((..((((.((((((..(((((((((.(((...(((...((......................))...)))..)))..))))))))))))).)).))))..)))))... (-13.05) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 767 60 11 151 102 NC_003454:FN1430|5end_Branched-chain_amino_acid_transport_system_permease_protein_livM_2099202..2099432_NEGATIVE 196 91 55 210 174 NC_003454:FN1979|5end_SSU_ribosomal_protein_S15P_481736..481966_POSITIVE 180 116 72 113 67 NC_003454:FN1085|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme_1728934..1729164_POSITIVE 180 70 21 213 163 NC_003454:FN0363|5end_ATP_synthase_C_chain,_sodium_ion_specific_993703..993933_NEGATIVE 179 59 15 90 36 NC_003454:FN1314|5end_hypothetical_protein_1968682..1968912_NEGATIVE 179 83 46 126 89 NC_003454:FN0558|5end_TraT_complement_resistance_protein_precursor_1210682..1210912_POSITIVE 179 58 13 200 166 NC_003454:FN0547|5end_recombinase_A_1199643..1199873_POSITIVE 179 73 35 76 43 NC_003454:FN2071|5end_hypothetical_protein_582375..582605_NEGATIVE 178 117 71 87 33 NC_003454:FN0967|5end_CbiD_protein_1621050..1621280_NEGATIVE 178 59 11 153 97 NC_003454:FN0664|5end_2-nitropropane_dioxygenase_1319758..1319988_POSITIVE 178 69 23 51 10 NC_003454:FN1502|5end_Nickel_transport_system_permease_protein_nikC_7522..7752_NEGATIVE 177 36 8 122 90 NC_003454:FN0492|5end_hypothetical_protein_1137651..1137881_NEGATIVE 175 51 15 77 44 NC_003454:FN1694|5end_UDP-N-acetyl-D-quinovosamine_4-epimerase_190169..190399_NEGATIVE 172 69 22 66 11 NC_003454:FN1021|5end_Calcium-transporting_ATPase_1674588..1674818_POSITIVE 170 48 10 165 119 NC_003454:FN1410|5end_Transporter_2069934..2070164_POSITIVE 168 94 51 205 164 NC_003454:FN1133|5end_N-acetylglucosamine-6-phosphate_deacetylase_1781429..1781659_NEGATIVE 168 44 7 179 149 NC_003454:FN1859|5end_Major_outer_membrane_protein_349655..349885_NEGATIVE 165 100 54 179 132 NC_003454:FN1786|5end_ADP-heptose_synthase_266770..267000_POSITIVE 163 52 11 220 176 NC_003454:FN0707|5end_FMN_adenylyltransferase_1365737..1365967_POSITIVE 161 80 48 42 9 NC_003454:FN1031|5end_Hypothetical_membrane-spanning_protein_1685800..1686030_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 196 91 55 97 61 NC_003454:FN1978|3end_Cell_division_protein_ftsH_481703..481853_POSITIVE 183 59 13 49 1 NC_003454:FN0511|3end_D-lactate_dehydrogenase_1161372..1161522_POSITIVE 180 116 72 97 51 NC_003454:FN1084|3end_hypothetical_protein_1728998..1729148_POSITIVE 178 117 71 71 17 NC_003454:FN0968|3end_hypothetical_protein_1621066..1621216_NEGATIVE 178 59 11 112 56 NC_003454:FN0663|3end_hypothetical_protein_1319797..1319947_POSITIVE 178 69 23 70 29 NC_003454:FN1503|3end_Nickel_transport_system_permease_protein_nikB_7503..7653_NEGATIVE 177 36 8 150 118 NC_003454:FN0493|3end_hypothetical_protein_1137623..1137773_NEGATIVE 175 51 15 77 44 NC_003454:FN1695|3end_Probable_quinovosaminephosphotransferae_190169..190319_NEGATIVE 172 58 14 147 102 NC_003454:FN0364|3end_ATP_synthase_A_chain,_sodium_ion_specific_993757..993907_NEGATIVE 165 81 47 61 26 NC_003454:FN0905|3end_hypothetical_protein_1563781..1563931_NEGATIVE 161 97 56 75 38 NC_003454:FN1081|3end_hypothetical_protein_1727325..1727475_NEGATIVE 161 75 34 73 24 NC_003454:FN0543|3end_Lipopolysaccharide_heptosyltransferase-1_1197103..1197253_POSITIVE 161 120 71 91 36 NC_003454:FN0172|3end_RNA_binding_protein_797805..797955_POSITIVE 160 42 11 112 75 NC_003454:FN0997|3end_hypothetical_protein_1651384..1651534_NEGATIVE 160 95 69 32 11 NC_003454:FN1529|3end_hypothetical_protein_42993..43143_NEGATIVE 156 100 55 49 6 NC_003454:FN0316|3end_hypothetical_protein_953234..953384_NEGATIVE 155 32 7 35 8 NC_003454:FN1191|3end_hypothetical_protein_1854729..1854879_POSITIVE 155 56 14 73 22 NC_003454:FN0138|3end_Transposase_771440..771590_POSITIVE 154 77 49 140 113 NC_003454:FN1402|3end_Hypothetical_membrane-spanning_protein_2061700..2061850_POSITIVE 152 80 49 33 1 NC_003454:FN1032|3end_hypothetical_protein_1685809..1685959_NEGATIVE