Origin IGS: ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaatgatttggccggtcggctggtgaaccaatcgggataaagagagtgtagtatctttatcccatcccgataagcgaacgtttgttaaacccgagtttaacacaaaaccccggttggaaggatgggctgtgatgaatgataacagtgtattgatttgattttcaaaatatattaaaa Mask Tandem Repeat Region ================================================ ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta Find is-nt database================================================ Query_seq: TF2459:TF2460|TF2459:TF2460:conserved hypothetical protein:outer membrane protein, possibly involved in nutrient binding:->->:2636719..2636896 178 ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2459:TF2460|TF2459:TF2460:conserved hypothetical protein:outer membrane protein, possibly involved in nutrient binding:->->:2636719..2636896 178 ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2459:TF2460|TF2459:TF2460:conserved hypothetical protein:outer membrane protein, possibly involved in nutrient binding:->->:2636719..2636896 178 ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 6 End: 176 ..... M Y F E N Q I N T L L S F I T A H P S N R G F V L N S G L T N V R L S G W D K D T T L S L S R L V H Q P T G Q I I .. ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta 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================================================ ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -3.2 Tail_Score: -3.33696 Start: 113 End: 146 Full_Region: CGTTCGCTTATCGGG ATGGGATAAAGATA CTACAC TCTCTTTATCCCGA TTGGTTCACCAGCCG ................................................................................................................ATGGGATAAAGATACTACACTCTCTTTATCCCGA................................ TransTerm Strand: + Conf: 56 HP_score: -6.7 Tail_Score: -2.60075 Start: 114 End: 145 Full_Region: GTTCGCTTATCGGGA TGGGATAAAGATA CTACAC TCTCTTTATCCCG ATTGGTTCACCAGCC .................................................................................................................TGGGATAAAGATACTACACTCTCTTTATCCCG................................. Find igs database================================================ Query_seq: TF2459:TF2460|TF2459:TF2460:conserved hypothetical protein:outer membrane protein, possibly involved in nutrient binding:->->:2636719..2636896 178 ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: tfor_TF2459_TF2460|conserved hypothetical protein:outer membrane protein, possibly involved in nutrient binding|POSITIVE:POSITIVE|[2636719,2636896]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta ttttaatatattttgaaaatcaaatcaatacactgttatcattcatcacagcccatccttccaaccggggttttgtgttaaactcgggtttaacaaacgttcgcttatcgggatgggataaagatactacactctctttatcccgattggttcaccagccgaccggccaaatcattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAUAUAUUUUGAAAAUCAAAUCAAUACACUGUUAUCAUUCAUCACAGCCCAUCCUUCCAACCGGGGUUUUGUGUUAAACUCGGGUUUAACAAACGUUCGCUUAUCGGGAUGGGAUAAAGAUACUACACUCUCUUUAUCCCGAUUGGUUCACCAGCCGACCGGCCAAAUCAUUUA ...(((((....((((........)))).....)))))........((.(((((.............))))).))((((((((....)))))))).......(((..((((..(((((((((((..........)))))))))))..(((....))).))))..)))........... (-37.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUGAUUUGGCCGGUCGGCUGGUGAACCAAUCGGGAUAAAGAGAGUGUAGUAUCUUUAUCCCAUCCCGAUAAGCGAACGUUUGUUAAACCCGAGUUUAACACAAAACCCCGGUUGGAAGGAUGGGCUGUGAUGAAUGAUAACAGUGUAUUGAUUUGAUUUUCAAAAUAUAUUAAAA .......((..(((((((((.(((....)))...((((((((((..........))))))))))...))))............((((((((....)))))))).......)))))..))..((((.(((((...........))))).))))..((((.....))))........... (-49.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 120 71 159 110 tfor:TF0278|5end_conserved_hypothetical_protein_305570..305800_POSITIVE 349 168 122 64 7 tfor:TF1797|5end_SNF_family_transporter_1937136..1937366_POSITIVE 343 168 130 127 89 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 337 169 140 86 55 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 334 87 43 205 164 tfor:TF1850|5end_Na+/H+-exchanging_protein_1998542..1998772_POSITIVE 321 75 41 218 190 tfor:TF1619|5end_riboflavin_synthase,_beta_subunit_1733948..1734178_POSITIVE 319 170 134 192 154 tfor:TF2484|5end_hypothetical_protein_2660005..2660235_POSITIVE 319 169 143 82 48 tfor:TF1735|5end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_1860127..1860357_POSITIVE 315 166 129 182 140 tfor:TF0344|5end_hypothetical_protein_366722..366952_POSITIVE 313 127 83 161 117 tfor:TF3127|5end_acetyltransferase,_possible_GNAT_family_3361627..3361857_POSITIVE 307 77 44 222 184 tfor:TF3003|5end_hypothetical_protein_3220382..3220612_POSITIVE 307 169 128 57 11 tfor:TF1455|5end_conserved_hypothetical_protein_1540688..1540918_POSITIVE 306 168 132 62 28 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 306 168 132 217 183 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 306 168 132 217 183 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 305 110 62 185 129 tfor:TF2572|5end_50S_ribosomal_protein_L30_2743081..2743311_POSITIVE 305 169 123 51 11 tfor:TF1955|5end_amino_acid_exporter,_possible_threonine_efflux_protein_2106952..2107182_POSITIVE 305 77 31 218 173 tfor:TF0685|5end_hypothetical_protein_730852..731082_POSITIVE 302 118 73 62 5 tfor:TF0832|5end_conserved_hypothetical_protein_888466..888696_POSITIVE 301 117 71 90 34 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 168 122 64 7 tfor:TF1796|3end_ABC_transporter,_ATP-binding_protein_1937216..1937366_POSITIVE 343 168 130 127 89 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 333 110 63 146 99 tfor:TF0277|3end_outer_membrane_protein_305647..305797_POSITIVE 319 170 134 129 91 tfor:TF2483|3end_hypothetical_protein_2660022..2660172_POSITIVE 313 127 83 139 95 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 305 166 130 150 103 tfor:TF1657|3end_lauroyl/myristoyl_acyltransferase_1773407..1773557_POSITIVE 303 168 135 44 10 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 301 167 125 139 85 tfor:TF0752|3end_nucleotide-binding_protein;_MAF-like_protein_801713..801863_POSITIVE 299 110 61 128 91 tfor:TF3012|3end_possible_outer_membrane_protein_3236238..3236388_POSITIVE 295 108 61 56 9 tfor:TF2631|3end_conserved_hypothetical_protein_2802088..2802238_POSITIVE 286 110 66 142 92 tfor:TF0764|3end_conserved_hypothetical_protein;_possible_exopolyphosphatase-related_protein_811371..811521_POSITIVE 283 149 102 77 28 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 281 168 128 88 49 tfor:TF1090|3end_hypothetical_protein_1159360..1159510_POSITIVE 280 67 21 86 29 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 280 149 102 66 14 tfor:TF0810|3end_possible_outer_membrane_efflux_protein_869696..869846_POSITIVE 278 88 42 74 23 tfor:TF2819|3end_N-acetyl-gamma-glutamylphosphate_reductase_3009956..3010106_POSITIVE 278 99 53 120 77 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 278 69 33 144 107 tfor:TF0595|3end_hypothetical_protein_628073..628223_POSITIVE 276 79 52 85 57 tfor:TF2480|3end_hypothetical_protein_2657708..2657858_POSITIVE 276 167 136 65 38 tfor:TF2132|3end_TIM-barrel_protein,_NifR3_family_2308769..2308919_POSITIVE