Origin IGS: ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccttattcttgattaaattggtataccttattctactataaaatttatattatttcaagtcaaaatataatttttttgtattaatatcaattttactattgatatatttaaaaattttaattaaacttat Mask Tandem Repeat Region ================================================ ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga Find is-nt database================================================ Query_seq: FN1137:FN1138|FN1137:FN1138:Phosphonates transport system permease protein phnE:Hypothetical cytosolic protein:->->:1785478..1785608 131 ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1137:FN1138|FN1137:FN1138:Phosphonates transport system permease protein phnE:Hypothetical cytosolic protein:->->:1785478..1785608 131 ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1137:FN1138|FN1137:FN1138:Phosphonates transport system permease protein phnE:Hypothetical cytosolic protein:->->:1785478..1785608 131 ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga Predict ORF larger than 30AA ================================================ ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga 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: 87 Start: 72 End: 101 .......................................................................CTTGAAATAATATAAATTTTATAGTAGAAT.............................. PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 67 End: 96 ..................................................................TTTGACTTGAAATAATATAAATTTTATAGT................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 4 End: 33 ...ATTGATATATTTAAAAATTTTAATTAAACT.................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1137:FN1138|FN1137:FN1138:Phosphonates transport system permease protein phnE:Hypothetical cytosolic protein:->->:1785478..1785608 131 ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_003454_FN1137_FN1138|Phosphonates transport system permease protein phnE:Hypothetical cytosolic protein|POSITIVE:POSITIVE|[1785478,1785608]|131 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacnnnnnnnttatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga ataagtttaattaaaatttttaaatatatcaatagtaaaattgatattaatacaaaaaaattatattttgacttgaaataatataaattttatagtagaataaggtataccaatttaatcaagaataagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGUUUAAUUAAAAUUUUUAAAUAUAUCAAUAGUAAAAUUGAUAUUAAUACAAAAAAAUUAUAUUUUGACUUGAAAUAAUAUAAAUUUUAUAGUAGAAUAAGGUAUACCAAUUUAAUCAAGAAUAAGGA .((((((.((.((.(((((((....((((((((......))))))))........))))))).)).)).))))))............................((....)).................... (-12.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUAUUCUUGAUUAAAUUGGUAUACCUUAUUCUACUAUAAAAUUUAUAUUAUUUCAAGUCAAAAUAUAAUUUUUUUGUAUUAAUAUCAAUUUUACUAUUGAUAUAUUUAAAAAUUUUAAUUAAACUUAU .........(((((((((..((....)).........(((((((.(((((((............)))))))...)))))))...((((((((......))))))))..........)))))))))...... (-15.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 164 99 60 51 17 NC_003454:FN0479|5end_RNA_polymerase_sigma-E_factor_1127003..1127233_POSITIVE 163 97 55 217 176 NC_003454:FN1313|5end_Oligopeptide-binding_protein_oppA_1967053..1967283_POSITIVE 163 109 63 203 161 NC_003454:FN0635|5end_tRNA_pseudouridine_synthase_B_1294993..1295223_NEGATIVE 163 120 71 123 74 NC_003454:FN1953|5end_Na(+)-linked_D-alanine_glycine_permease_459499..459729_NEGATIVE 162 49 29 26 6 NC_003454:FN0400|5end_Dipeptide_transport_ATP-binding_protein_dppF_1038658..1038888_POSITIVE 156 130 87 201 151 NC_003454:FN0421|5end_carbamoyl-phosphate_synthase_small_subunit_1061936..1062166_POSITIVE 153 114 94 85 68 NC_003454:FN0728|5end_hypothetical_protein_1386120..1386350_NEGATIVE 150 124 92 68 30 NC_003454:FN1311|5end_Biopolymer_transport_exbD_protein_1966250..1966480_NEGATIVE 147 122 85 70 35 NC_003454:FN1486|5end_Integral_membrane_protein_with_CBS_domains_2169299..2169529_NEGATIVE 146 59 19 165 120 NC_003454:FN1081|5end_hypothetical_protein_1727534..1727764_NEGATIVE 144 124 100 112 90 NC_003454:FN0691|5end_hypothetical_protein_1346372..1346602_NEGATIVE 143 130 82 215 155 NC_003454:FN0315|5end_Transcriptional_regulator,_AraC_family_951934..952164_POSITIVE 137 128 88 170 123 NC_003454:FN0437|5end_Allophanate_hydrolase_1079642..1079872_NEGATIVE 133 97 56 200 158 NC_003454:FN0900|5end_Metal_dependent_hydrolase_1559180..1559410_POSITIVE 131 130 91 195 153 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 129 111 75 140 97 NC_003454:FN0300|5end_Iron(III)_dicitrate-binding_protein_934679..934909_POSITIVE 126 109 68 215 176 NC_003454:FN1411|5end_Threonine_dehydratase_2070730..2070960_POSITIVE 125 107 61 196 140 NC_003454:FN1424|5end_ACYL-COA_dehydrogenase,_short-chain_specific_2092005..2092235_NEGATIVE 124 100 65 185 152 NC_003454:FN0738|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1395846..1396076_POSITIVE 124 111 80 205 176 NC_003454:FN2126|5end_DNA_gyrase_subunit_B_638225..638455_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 171 126 82 120 74 NC_003454:FN1721|3end_hypothetical_protein_219661..219811_NEGATIVE 162 49 29 21 1 NC_003454:FN0399|3end_Dipeptide_transport_ATP-binding_protein_dppD_1038733..1038883_POSITIVE 145 109 62 115 68 NC_003454:FN1615|3end_Integral_membrane_protein_125756..125906_POSITIVE 144 40 11 69 40 NC_003454:FN1616|3end_transcription_antitermination_protein_NusB_125976..126126_NEGATIVE 143 130 82 132 72 NC_003454:FN0314|3end_Caffeoyl-CoA_O-methyltransferase_951931..952081_POSITIVE 140 108 61 54 5 NC_003454:FN0967|3end_CbiD_protein_1619923..1620073_NEGATIVE 131 105 65 58 23 NC_003454:FN1175|3end_hypothetical_protein_1836557..1836707_NEGATIVE 127 121 92 140 109 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 124 59 15 136 93 NC_003454:FN0674|3end_Transporter_1330401..1330551_POSITIVE 122 42 6 38 2 NC_003454:FN0473|3end_Regulatory_protein_betI_1118941..1119091_POSITIVE 120 129 93 103 57 NC_003454:FN0144|3end_hypothetical_protein_774165..774315_NEGATIVE 117 24 1 144 122 NC_003454:FN1383|3end_DNA_polymerase_III_alpha_subunit_2034455..2034605_NEGATIVE 117 96 51 72 20 NC_003454:FN1833|3end_Biopolymer_transport_exbD_protein_322222..322372_NEGATIVE 116 128 92 54 19 NC_003454:FN1672|3end_Membrane-bound_O-acyltransferase_169833..169983_NEGATIVE 115 37 4 109 76 NC_003454:FN1940|3end_Na+_driven_multidrug_efflux_pump_439585..439735_NEGATIVE 114 122 88 108 77 NC_003454:FN1160|3end_SWF/SNF_family_helicase_1819185..1819335_POSITIVE 114 61 36 28 1 NC_003454:FN0532|3end_Hypothetical_membrane-spanning_protein_1186524..1186674_NEGATIVE 113 96 59 68 25 NC_003454:FN1345|3end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase_1998130..1998280_NEGATIVE 111 128 90 64 31 NC_003454:FN1154|3end_Ribonuclease_BN_1809502..1809652_POSITIVE 111 129 91 68 22 NC_003454:FN0349|3end_D-tyrosyl-tRNA_deacylase_982336..982486_POSITIVE