Origin IGS: atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat .........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 attcgtttctcctcttatgtttagtttatatatttatgtctgttgttacttgatgattagacctgattttaccgctaaagtttaatgtctgtctgtctttattacgatataaaacgcattttttgaaagcaaacatacggtttttccgtattccaagcaaatgaattagaatatttaacataatccattgagatacggttttataagtatgatgcaaaagaggaataaat Mask Tandem Repeat Region ================================================ atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat Find is-nt database================================================ Query_seq: TF1442:TF1443|TF1442:TF1443:hypothetical protein:hypothetical protein:->->:1526669..1526898 230 atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1442:TF1443|TF1442:TF1443:hypothetical protein:hypothetical protein:->->:1526669..1526898 230 atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1442:TF1443|TF1442:TF1443:hypothetical protein:hypothetical protein:->->:1526669..1526898 230 atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 37 End: 126 .................................... M S M D Y V K Y S N S F A W N T E K P Y V C F Q K M R F I S ........................................................................................................ Protein_Len: 60 Strand: + Start: 5 End: 202 .... M P L L H H T Y K T V S Q W I M L N I L I H L L G I R K N R M F A F K K C V L Y R N K D R Q T L N F S G K I R S N H Q V ............................ Protein_Len: 33 Strand: - Start: 70 End: 168 ..................................................................... K S P I R F F R I N A K L F H T K Y R L L S L C V N F K L P L I M .............................................................. atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat 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================================================ atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -3.1 Tail_Score: -4.05788 Start: 79 End: 97 Full_Region: AATTCATTTGCTTGG AATACGG AAAAA CCGTATG TTTGCTTTCAAAAAA ..............................................................................AATACGGAAAAACCGTATG..................................................................................................................................... Find igs database================================================ Query_seq: TF1442:TF1443|TF1442:TF1443:hypothetical protein:hypothetical protein:->->:1526669..1526898 230 atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat Intra-Species Hit: Count: 1 Min: 1 Max: 230 Len: 230 Subject: tfor_TF1442_TF1443|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1526669,1526898]|230 HSP 1 e-value: 1.0E-127 bit: 456.0 Len: 230 Query Start:1 Query End:230 Subject Strand: POSITIVE Subject Start: 1 Subject End: 230 atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat atttattcctcttttgcatcatacttataaaaccgtatctcaatggattatgttaaatattctaattcatttgcttggaatacggaaaaaccgtatgtttgctttcaaaaaatgcgttttatatcgtaataaagacagacagacattaaactttagcggtaaaatcaggtctaatcatcaagtaacaacagacataaatatataaactaaacataagaggagaaacgaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAUUCCUCUUUUGCAUCAUACUUAUAAAACCGUAUCUCAAUGGAUUAUGUUAAAUAUUCUAAUUCAUUUGCUUGGAAUACGGAAAAACCGUAUGUUUGCUUUCAAAAAAUGCGUUUUAUAUCGUAAUAAAGACAGACAGACAUUAAACUUUAGCGGUAAAAUCAGGUCUAAUCAUCAAGUAACAACAGACAUAAAUAUAUAAACUAAACAUAAGAGGAGAAACGAAU .....((((((((.((.........((((...((((((..((((((((((.(........).)))))))).....))..))))))....((((((((((((((.((......((((........)))).....)).)).))))))).........)))))........((((.................)))).....)))).........)).))))))))........ (-40.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCGUUUCUCCUCUUAUGUUUAGUUUAUAUAUUUAUGUCUGUUGUUACUUGAUGAUUAGACCUGAUUUUACCGCUAAAGUUUAAUGUCUGUCUGUCUUUAUUACGAUAUAAAACGCAUUUUUUGAAAGCAAACAUACGGUUUUUCCGUAUUCCAAGCAAAUGAAUUAGAAUAUUUAACAUAAUCCAUUGAGAUACGGUUUUAUAAGUAUGAUGCAAAAGAGGAAUAAAU .........(((((((.(((...((((.....((((((((.((.((.....((((..(((((..(((((((....)))))))....)))))..))))...)).))))))))))...((.....)).))))...(((((.......((((((..(((.........(((((...))))).........)))..))))))........)))))..))).)))))))...... (-42.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 119 73 227 182 tfor:TF2348|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2511088..2511318_POSITIVE 280 194 153 68 27 tfor:TF1196|5end_acetyl-coenzyme_A_synthetase_1279064..1279294_POSITIVE 275 107 68 109 68 tfor:TF1987|5end_hypothetical_protein_2137359..2137589_POSITIVE 269 38 1 133 94 tfor:TF3155|5end_glycosyltransferase,_group_2_family_protein_3390417..3390647_POSITIVE 261 128 83 82 49 tfor:TF1241|5end_prolyl-tRNA_synthetase_1324711..1324941_POSITIVE 258 116 73 221 172 tfor:TF0968|5end_hypothetical_protein_1018908..1019138_POSITIVE 257 110 68 100 52 tfor:TF2333|5end_signal_peptidase_I_2492560..2492790_POSITIVE 249 117 73 71 31 tfor:TF0775|5end_ABC_transporter,_permease_component_823664..823894_POSITIVE 245 117 71 156 107 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 245 107 62 146 91 tfor:TF0558|5end_conserved_hypothetical_protein_590116..590346_POSITIVE 244 117 73 69 31 tfor:TF2152|5end_uronate_isomerase_2326575..2326805_POSITIVE 238 117 75 203 156 tfor:TF0401|5end_hypothetical_protein_421343..421573_POSITIVE 237 105 61 80 32 tfor:TF2604|5end_possible_membrane_transport_protein_2777407..2777637_POSITIVE 236 140 91 86 46 tfor:TF2097|5end_glucose_inhibited_division_protein_A_2269137..2269367_POSITIVE 235 106 68 197 153 tfor:TF2673|5end_conserved_hypothetical_protein_2846987..2847217_POSITIVE 234 120 72 77 9 tfor:TF2516|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2692071..2692301_POSITIVE 234 117 71 170 134 tfor:TF0590|5end_hypothetical_protein_625134..625364_POSITIVE 232 169 131 157 128 tfor:TF2528|5end_anti-sigma_factor_2708961..2709191_POSITIVE 232 98 57 109 63 tfor:TF1887|5end_hypothetical_protein_2040301..2040531_POSITIVE 230 120 71 84 29 tfor:TF1360|5end_conserved_hypothetical_protein_1440059..1440289_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 119 73 151 106 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 275 107 68 151 110 tfor:TF1988|3end_hypothetical_protein_2137481..2137631_POSITIVE 269 38 1 125 86 tfor:TF3154|3end_conserved_hypothetical_protein_3390489..3390639_POSITIVE 258 116 73 105 56 tfor:TF0967|3end_alpha_glycan_phosphorylase_1018872..1019022_POSITIVE 257 110 68 73 25 tfor:TF2332|3end_signal_peptidase_I_2492613..2492763_POSITIVE 257 120 71 84 29 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 253 102 61 126 82 tfor:TF1539|3end_conserved_hypothetical_protein_1644341..1644491_POSITIVE 249 117 73 57 17 tfor:TF0774|3end_membrane-fusion_protein;_36_kDa_antigen_823730..823880_POSITIVE 245 107 62 136 81 tfor:TF0557|3end_conserved_hypothetical_protein_590186..590336_POSITIVE 244 117 73 69 31 tfor:TF2150|3end_Na+/phosphate_symporter_2326655..2326805_POSITIVE 244 116 83 147 110 tfor:TF0986|3end_50S_ribosomal_protein_L31_1041757..1041907_POSITIVE 235 106 68 144 100 tfor:TF2672|3end_lipoic_acid_synthetase_2847014..2847164_POSITIVE 232 169 131 123 94 tfor:TF2526|3end_outer_membrane_protein,_TonB_dependent_receptor_2709007..2709157_POSITIVE 232 98 57 69 23 tfor:TF1886|3end_auxin-regulated_protein_2040341..2040491_POSITIVE 228 103 69 117 90 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 224 102 70 53 17 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 221 188 152 74 43 tfor:TF0534|3end_hypothetical_protein_559768..559918_POSITIVE 220 108 64 122 78 tfor:TF1120|3end_conserved_hypothetical_protein_1195256..1195406_POSITIVE 220 127 83 48 3 tfor:TF0858|3end_conserved_hypothetical_protein_911833..911983_POSITIVE 219 120 77 149 105 tfor:TF2949|3end_dihydroxynaphthoate_synthase_(naphthoate_synthase)_3157479..3157629_POSITIVE