Origin IGS: caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaatttttttattttttttctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag .........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 ctttaatttctcctttattttatattaaaaaaatactatcttaataagtaaaatttgtcaataatattttaaattttagaaaaaaaataaaaaaattttatgaatttactaaaaaatactataaattagatagattttttgctataatataaaataaacttagaatctatgaataaggggaattg Mask Tandem Repeat Region ================================================ caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaatttttttattttttttctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag Find is-nt database================================================ Query_seq: FN1782:FN1783|FN1782:FN1783:Phosphocarrier protein HPr:Ethanolamine utilization protein eutJ:<-->:264581..264765 185 caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaatttttttattttttttctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1782:FN1783|FN1782:FN1783:Phosphocarrier protein HPr:Ethanolamine utilization protein eutJ:<-->:264581..264765 185 caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaatttttttattttttttctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1782:FN1783|FN1782:FN1783:Phosphocarrier protein HPr:Ethanolamine utilization protein eutJ:<-->:264581..264765 185 caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaatttttttattttttttctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaatttttttattttttttctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag Predict ORF larger than 30AA ================================================ caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaatttttttattttttttctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag 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: 124 End: 153 ...........................................................................................................................ATTGACAAATTTTACTTATTAAGATAGTAT................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 38 End: 67 .....................................CTATAAATTAGATAGATTTTTTGCTATAAT...................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaatttttttattttttttctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -3.5 Tail_Score: -5.94713 Start: 86 End: 98 Full_Region: TTTTTAGTAAATTCA TAAAA TTT TTTTA TTTTTTTTCTAAAAT .....................................................................................TAAAATTTTTTTA....................................................................................... Find igs database================================================ Query_seq: FN1782:FN1783|FN1782:FN1783:Phosphocarrier protein HPr:Ethanolamine utilization protein eutJ:<-->:264581..264765 185 caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaatttttttattttttttctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag Intra-Species Hit: Count: 1 Min: 1 Max: 185 Len: 185 Subject: NC_003454_FN1782_FN1783|Phosphocarrier protein HPr:Ethanolamine utilization protein eutJ|NEGATIVE:POSITIVE|[264581,264765]|185 HSP 1 e-value: 4.0E-44 bit: 178.0 Len: 90 Query Start:1 Query End:90 Subject Strand: POSITIVE Subject Start: 1 Subject End: 90 caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaa............................................................................................... caattccccttattcatagattctaagtttattttatattatagcaaaaaatctatctaatttatagtattttttagtaaattcataaaa............................................................................................... HSP 2 e-value: 5.0E-25 bit: 115.0 Len: 79 Query Start:107 Query End:185 Subject Strand: POSITIVE Subject Start: 107 Subject End: 185 ..........................................................................................................ctaaaatttaaaatattattgacaaattttacttattaagatagtannnnnnnaatataaaataaaggagaaattaaag ..........................................................................................................ctaaaatttaaaatattattgacaaattttacttattaagatagtatttttttaatataaaataaaggagaaattaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUUCCCCUUAUUCAUAGAUUCUAAGUUUAUUUUAUAUUAUAGCAAAAAAUCUAUCUAAUUUAUAGUAUUUUUUAGUAAAUUCAUAAAAUUUUUUUAUUUUUUUUCUAAAAUUUAAAAUAUUAUUGACAAAUUUUACUUAUUAAGAUAGUAUUUUUUUAAUAUAAAAUAAAGGAGAAAUUAAAG ................(((.((((...((((((((((((((....((((((((((((((((....((((...(((.((......((((.(((((...(((((......)))))..))))).))))..)))))...)))).))).)))))).)))))))))))))))))))))..)))).)))... (-25.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAAUUUCUCCUUUAUUUUAUAUUAAAAAAAUACUAUCUUAAUAAGUAAAAUUUGUCAAUAAUAUUUUAAAUUUUAGAAAAAAAAUAAAAAAAUUUUAUGAAUUUACUAAAAAAUACUAUAAAUUAGAUAGAUUUUUUGCUAUAAUAUAAAAUAAACUUAGAAUCUAUGAAUAAGGGGAAUUG .......(((((((((((((((((((((((((((.((((((.....((((...........(((....)))..((((((.(((...(((((.....)))))...))).))))))..)))).......)))))))))))))....))))))))))))..(.(((...))).)...))))))))... (-27.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 673 50 1 141 92 NC_003454:FN1782|5end_Phosphocarrier_protein_HPr_264490..264720_NEGATIVE 245 42 2 64 22 NC_003454:FN1012|5end_HPr_kinase/phosphorylase_1667527..1667757_NEGATIVE 219 49 3 151 102 NC_003454:FN0592|5end_ATP-dependent_DNA_helicase_pcrA_1245712..1245942_POSITIVE 209 48 4 148 109 NC_003454:FN0768|5end_Hemin_receptor_1423542..1423772_POSITIVE 198 46 4 133 94 NC_003454:FN1209|5end_Hypothetical_RNA_binding_protein_1868914..1869144_NEGATIVE 197 98 55 103 58 NC_003454:FN1709|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_205415..205645_POSITIVE 196 128 88 122 81 NC_003454:FN1306|5end_Methyltransferase_1961674..1961904_POSITIVE 195 43 3 215 171 NC_003454:FN1981|5end_Transposase_483299..483529_POSITIVE 192 100 51 144 98 NC_003454:FN0429|5end_hypothetical_protein_1070949..1071179_POSITIVE 190 109 67 86 36 NC_003454:FN1185|5end_SIR2_family_protein_1848321..1848551_NEGATIVE 190 42 4 132 98 NC_003454:FN0207|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase_alpha-subunit_833618..833848_POSITIVE 188 40 8 113 82 NC_003454:FN1208|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1868601..1868831_NEGATIVE 184 124 83 62 24 NC_003454:FN0356|5end_Lactoylglutathione_lyase_987852..988082_NEGATIVE 182 46 2 142 92 NC_003454:FN1379|5end_Citrate_lyase_beta_chain_2026355..2026585_POSITIVE 181 47 4 128 69 NC_003454:FN0019|5end_Transcription-repair_coupling_factor_656549..656779_POSITIVE 181 137 92 128 84 NC_003454:FN1942|5end_Hypothetical_cytosolic_protein_444689..444919_NEGATIVE 178 108 67 211 172 NC_003454:FN2112|5end_hypothetical_protein_623663..623893_NEGATIVE 177 114 75 150 109 NC_003454:FN0565|5end_hypothetical_protein_1217464..1217694_NEGATIVE 175 68 21 157 101 NC_003454:FN0673|5end_EBSC_protein_1328984..1329214_POSITIVE 174 109 61 212 164 NC_003454:FN0623|5end_Malonate_transporter_1281952..1282182_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 209 48 4 63 24 NC_003454:FN0767|3end_Hemin-binding_periplasmic_protein_hmuT_precursor_1423537..1423687_POSITIVE 198 46 4 107 68 NC_003454:FN1210|3end_Metal_dependent_hydrolase_1868940..1869090_NEGATIVE 198 42 6 39 1 NC_003454:FN1013|3end_hypothetical_protein_1667552..1667702_NEGATIVE 197 98 55 87 42 NC_003454:FN1708|3end_Polyribonucleotide_nucleotidyltransferase_205479..205629_POSITIVE 195 43 3 88 44 NC_003454:FN1980|3end_Transporter_483252..483402_POSITIVE 190 42 4 69 35 NC_003454:FN0206|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_833635..833785_POSITIVE 188 40 8 99 68 NC_003454:FN1209|3end_Hypothetical_RNA_binding_protein_1868615..1868765_NEGATIVE 185 45 4 54 11 NC_003454:FN0950|3end_Precorrin-6X_reductase_1606975..1607125_NEGATIVE 184 124 83 42 4 NC_003454:FN0357|3end_ATP_synthase_epsilon_chain,_sodium_ion_specific_987872..988022_NEGATIVE 182 46 2 133 83 NC_003454:FN1378|3end_Citrate_lyase_acyl_carrier_protein_2026426..2026576_POSITIVE 182 45 7 99 60 NC_003454:FN0549|3end_O-sialoglycoprotein_endopeptidase_1202431..1202581_POSITIVE 180 37 6 116 87 NC_003454:FN1811|3end_Manganese_transport_system_ATP-binding_protein_mntA_292161..292311_NEGATIVE 178 108 67 136 97 NC_003454:FN2113|3end_hypothetical_protein_623738..623888_NEGATIVE 177 114 75 112 71 NC_003454:FN0566|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1217502..1217652_NEGATIVE 175 68 21 135 79 NC_003454:FN0672|3end_ATPase_1329042..1329192_POSITIVE 173 33 1 108 77 NC_003454:FN0109|3end_hypothetical_protein_744333..744483_NEGATIVE 171 43 1 141 92 NC_003454:FN0679|3end_GTPase_1335533..1335683_POSITIVE 169 100 54 132 83 NC_003454:FN0019|3end_Transcription-repair_coupling_factor_659574..659724_POSITIVE 168 177 144 41 7 NC_003454:FN1422|3end_NA+/H+_antiporter_NHAC_2087005..2087155_NEGATIVE 168 117 88 87 57 NC_003454:FN1107|3end_Acetyltransferase_1752367..1752517_POSITIVE