Origin IGS: cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaagttttttcaagtgttttaggtaaaaaattttttataattagaaattttattataattcttgaatttattttaataaaatgtaattcttacatttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa .........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 tttctaatccccctactaaaatttacttaatattataaattttactttatctaaataaaaaattcaagatatagtttaaattgtaatgtagaatagaaatgtaagaattacattttattaaaataaattcaagaattataataaaatttctaattataaaaaattttttacctaaaacacttgaaaaaacttgtaatatatgatataaaatattgtgtattctatatgtgagtgtatttttttattaggaggaaggatagaag Mask Tandem Repeat Region ================================================ cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaagttttttcaagtgttttaggtaaaaaattttttataattagaaattttattataattcttgaatttattttaataaaatgtaattcttacatttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa Find is-nt database================================================ Query_seq: FN0818:FN0819|FN0818:FN0819:DNA-binding protein HU:Tetratricopeptide repeat family protein:<-->:1477125..1477387 263 cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaagttttttcaagtgttttaggtaaaaaattttttataattagaaattttattataattcttgaatttattttaataaaatgtaattcttacatttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0818:FN0819|FN0818:FN0819:DNA-binding protein HU:Tetratricopeptide repeat family protein:<-->:1477125..1477387 263 cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaagttttttcaagtgttttaggtaaaaaattttttataattagaaattttattataattcttgaatttattttaataaaatgtaattcttacatttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0818:FN0819|FN0818:FN0819:DNA-binding protein HU:Tetratricopeptide repeat family protein:<-->:1477125..1477387 263 cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaagttttttcaagtgttttaggtaaaaaattttttataattagaaattttattataattcttgaatttattttaataaaatgtaattcttacatttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaagttttttcaagtgttttaggtaaaaaattttttataattagaaattttattataattcttgaatttattttaataaaatgtaattcttacatttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 44 End: 214 ........................................... M H N I L Y H I L Q V F S S V L G K K F F I I R N F I I I L E F I L I K C N S Y I S I L H Y N L N Y I L N F L F R ................................................. cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaagttttttcaagtgttttaggtaaaaaattttttataattagaaattttattataattcttgaatttattttaataaaatgtaattcttacatttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa 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: 85 Start: 55 End: 84 ......................................................CTTGAAAAAACTTGTAATATATGATATAAA................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 196 End: 225 ...................................................................................................................................................................................................CTTGAATTTTTTATTTAGATAAAGTAAAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaagttttttcaagtgttttaggtaaaaaattttttataattagaaattttattataattcttgaatttattttaataaaatgtaattcttacatttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 36 HP_score: -2.9 Tail_Score: -2.75528 Start: 38 End: 60 Full_Region: AAAAATACACTCACA TATAGAATA CACAA TATTTTATA TCATATATTACAAGT .....................................TATAGAATACACAATATTTTATA........................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN0818:FN0819|FN0818:FN0819:DNA-binding protein HU:Tetratricopeptide repeat family protein:<-->:1477125..1477387 263 cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaagttttttcaagtgttttaggtaaaaaattttttataattagaaattttattataattcttgaatttattttaataaaatgtaattcttacatttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 263 Len: 263 Subject: NC_003454_FN0818_FN0819|DNA-binding protein HU:Tetratricopeptide repeat family protein|NEGATIVE:POSITIVE|[1477125,1477387]|263 HSP 1 e-value: 2.0E-50 bit: 200.0 Len: 101 Query Start:163 Query End:263 Subject Strand: POSITIVE Subject Start: 163 Subject End: 263 ..................................................................................................................................................................catttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa ..................................................................................................................................................................catttctattctacattacaatttaaactatatcttgaattttttatttagataaagtaaaatttataatattaagtaaattttagtagggggattagaaa HSP 2 e-value: 8.0E-22 bit: 105.0 Len: 74 Query Start:1 Query End:74 Subject Strand: POSITIVE Subject Start: 1 Subject End: 74 cttctatccttcctcctaatnnnnnnntacactcacatatagaatacacaatattttatatcatatattacaag............................................................................................................................................................................................. cttctatccttcctcctaataaaaaaatacactcacatatagaatacacaatattttatatcatatattacaag............................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUAUCCUUCCUCCUAAUAAAAAAAUACACUCACAUAUAGAAUACACAAUAUUUUAUAUCAUAUAUUACAAGUUUUUUCAAGUGUUUUAGGUAAAAAAUUUUUUAUAAUUAGAAAUUUUAUUAUAAUUCUUGAAUUUAUUUUAAUAAAAUGUAAUUCUUACAUUUCUAUUCUACAUUACAAUUUAAACUAUAUCUUGAAUUUUUUAUUUAGAUAAAGUAAAAUUUAUAAUAUUAAGUAAAUUUUAGUAGGGGGAUUAGAAA .(((((....((((((((.(((((...(((......((((((((((.....))))))))))...((((((.(((((((((((((.(((.(((....(((((((((.......))))))))).))).))).))))))........(((((((((((.....))))))).))))................(((.(((((.((((.....))))))))).)))))))))).))))))...)))..))))).)))))))).))))). (-44.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUAAUCCCCCUACUAAAAUUUACUUAAUAUUAUAAAUUUUACUUUAUCUAAAUAAAAAAUUCAAGAUAUAGUUUAAAUUGUAAUGUAGAAUAGAAAUGUAAGAAUUACAUUUUAUUAAAAUAAAUUCAAGAAUUAUAAUAAAAUUUCUAAUUAUAAAAAAUUUUUUACCUAAAACACUUGAAAAAACUUGUAAUAUAUGAUAUAAAAUAUUGUGUAUUCUAUAUGUGAGUGUAUUUUUUUAUUAGGAGGAAGGAUAGAAG .(((((.(((.((((.(((((..(((...(((((((((.((..(((.(((((..............))))).)))..)).)))))))))......((((((((.....))))))))...........((((((..(((((((..........)))))))....((((......))))..))))))...(((..((.((((.((((((........)))))).))))))..))))))...))))).)))).)))....))))). (-43.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 766 50 1 141 92 NC_003454:FN0818|5end_DNA-binding_protein_HU_1477034..1477264_NEGATIVE 223 86 49 191 150 NC_003454:FN0411|5end_hypothetical_protein_1048240..1048470_POSITIVE 212 259 211 225 170 NC_003454:FN0320|5end_Hypothetical_cytosolic_protein_956940..957170_POSITIVE 211 258 212 146 106 NC_003454:FN1021|5end_Calcium-transporting_ATPase_1674588..1674818_POSITIVE 206 100 54 68 14 NC_003454:FN1010|5end_Hypothetical_cytosolic_protein_1664608..1664838_NEGATIVE 201 46 11 79 38 NC_003454:FN0383|5end_Lipopolysaccharide_N-acetylglucosaminyltransferase_1014148..1014378_POSITIVE 196 42 2 108 59 NC_003454:FN0864|5end_hypothetical_protein_1522900..1523130_NEGATIVE 192 21 3 110 94 NC_003454:FN1862|5end_L-beta-lysine_5,6-aminomutase_beta_subunit_353122..353352_NEGATIVE 191 46 7 132 97 NC_003454:FN0212|5end_hypothetical_protein_838125..838355_NEGATIVE 190 89 45 158 106 NC_003454:FN1617|5end_Prolipoprotein_diacylglyceryltransferase_126666..126896_NEGATIVE 190 90 47 160 114 NC_003454:FN1580|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90919..91149_NEGATIVE 188 78 37 170 128 NC_003454:FN1195|5end_hypothetical_protein_1856239..1856469_NEGATIVE 187 159 112 167 126 NC_003454:FN1701|5end_ABC_transporter_ATP-binding_protein_197138..197368_NEGATIVE 183 257 213 199 158 NC_003454:FN0042|5end_Rod_shape-determining_protein_rodA_682129..682359_NEGATIVE 182 175 131 114 51 NC_003454:FN0219|5end_Autolysin_response_regulator_843316..843546_NEGATIVE 180 186 153 215 176 NC_003454:FN0863|5end_hypothetical_protein_1522574..1522804_NEGATIVE 175 28 1 144 108 NC_003454:FN0573|5end_hypothetical_protein_1222518..1222748_POSITIVE 172 89 50 163 117 NC_003454:FN1250|5end_Guanine-hypoxanthine_permease_1907832..1908062_NEGATIVE 171 42 2 127 83 NC_003454:FN1448|5end_Hypothetical_cytosolic_protein_2118428..2118658_NEGATIVE 170 185 152 47 8 NC_003454:FN0556|5end_hypothetical_protein_1209000..1209230_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 201 46 11 75 34 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 192 21 3 110 94 NC_003454:FN1863|3end_L-beta-lysine_5,6-aminomutase_alpha_subunit_353122..353272_NEGATIVE 191 46 7 105 70 NC_003454:FN0213|3end_N-acylneuraminate-9-phosphatase_838152..838302_NEGATIVE 187 159 112 141 100 NC_003454:FN1702|3end_undecaprenyl_pyrophosphate_phosphatase_197164..197314_NEGATIVE 182 175 131 121 58 NC_003454:FN0220|3end_Autolysin_sensor_kinase_843309..843459_NEGATIVE 174 176 150 119 95 NC_003454:FN1449|3end_Fusobacterium_outer_membrane_protein_family_2118612..2118762_NEGATIVE 169 29 2 43 12 NC_003454:FN1420|3end_NA+/H+_antiporter_NHAC_2083316..2083466_POSITIVE 168 19 4 94 76 NC_003454:FN1126|3end_Acetyltransferase_1769820..1769970_NEGATIVE 166 110 61 67 25 NC_003454:FN1759|3end_Hydroxymethylpyrimidine_kinase_253896..254046_NEGATIVE 165 206 164 135 87 NC_003454:FN1096|3end_hypothetical_protein_1741911..1742061_POSITIVE 164 48 1 151 101 NC_003454:FN1897|3end_ABC_transporter_integral_membrane_protein_383965..384115_NEGATIVE 163 17 1 87 71 NC_003454:FN1368|3end_COMF_operon_protein_3_2018157..2018307_NEGATIVE 163 17 1 100 82 NC_003454:FN1188|3end_hypothetical_protein_1851357..1851507_POSITIVE 163 37 2 105 68 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE 162 180 143 98 63 NC_003454:FN0923|3end_Cardiolipin_synthetase_1577538..1577688_NEGATIVE 162 17 1 134 120 NC_003454:FN2114|3end_hypothetical_protein_624010..624160_NEGATIVE 162 194 157 123 83 NC_003454:FN2016|3end_ATP-dependent_Clp_protease_proteolytic_subunit_518267..518417_NEGATIVE 161 191 152 84 42 NC_003454:FN0008|3end_quinolinate_synthetase_648986..649136_POSITIVE 159 92 68 128 105 NC_003454:FN1431|3end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2099326..2099476_NEGATIVE 159 42 4 107 69 NC_003454:FN0205|3end_Sodium/glutamate_symport_carrier_protein_832808..832958_POSITIVE