Origin IGS: actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta .........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 taaaggtcacaacataattgtccgccttatttcaaacgccatattttataaacaacaactattcaacaaaataacattaaacaagcatcacgtattgtccgcctgaaaatttcaccgcaccgcctgttcaagctatttttgtcgtaccgattgaaactaattccaaatgttataacattaaaaacaatgaaagt Mask Tandem Repeat Region ================================================ actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta Find is-nt database================================================ Query_seq: TF0011:TF0012|TF0011:TF0012:conserved hypothetical protein:conserved hypothetical protein:->->:5458..5651 194 actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0011:TF0012|TF0011:TF0012:conserved hypothetical protein:conserved hypothetical protein:->->:5458..5651 194 actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0011:TF0012|TF0011:TF0012:conserved hypothetical protein:conserved hypothetical protein:->->:5458..5651 194 actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 7 End: 129 ...... M V F N V I T F G I S F N R Y D K N S L N R R C G E I F R R T I R D A C L M L F C ................................................................. Protein_Len: 30 Strand: - Start: 92 End: 181 ........................................................................................... A S L V H H K N L T I K N F L Q Q K Y F I A N S I L R V I M ............. Protein_Len: 44 Strand: - Start: 3 End: 134 .. K M T K L T I V N P I L K L R Y S L F L K F L R H P S I K L R V I R S A Q K I N N Q Q M ............................................................ Protein_Len: 36 Strand: - Start: 1 End: 108 S E N N K I N Y C K S N T E I P V V F I A Q V P P A T F N E P P C Y T M ...................................................................................... actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta 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================================================ actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0011:TF0012|TF0011:TF0012:conserved hypothetical protein:conserved hypothetical protein:->->:5458..5651 194 actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: tfor_TF0011_TF0012|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[5458,5651]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta actttcattgtttttaatgttataacatttggaattagtttcaatcggtacgacaaaaatagcttgaacaggcggtgcggtgaaattttcaggcggacaatacgtgatgcttgtttaatgttattttgttgaatagttgttgtttataaaatatggcgtttgaaataaggcggacaattatgttgtgaccttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUCAUUGUUUUUAAUGUUAUAACAUUUGGAAUUAGUUUCAAUCGGUACGACAAAAAUAGCUUGAACAGGCGGUGCGGUGAAAUUUUCAGGCGGACAAUACGUGAUGCUUGUUUAAUGUUAUUUUGUUGAAUAGUUGUUGUUUAUAAAAUAUGGCGUUUGAAAUAAGGCGGACAAUUAUGUUGUGACCUUUA ..................(((((((((((((...((.(((((((.((...((((((((.(((((((((((((((..(((.((.....(((....)))))...)))..))))))))))).))))))))))))......((((........))))...)).))))))).)).....)))..))))))))))..... (-42.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGGUCACAACAUAAUUGUCCGCCUUAUUUCAAACGCCAUAUUUUAUAAACAACAACUAUUCAACAAAAUAACAUUAAACAAGCAUCACGUAUUGUCCGCCUGAAAAUUUCACCGCACCGCCUGUUCAAGCUAUUUUUGUCGUACCGAUUGAAACUAAUUCCAAAUGUUAUAACAUUAAAAACAAUGAAAGU ..(((((.((((.....))))..))))).(((((.....................(((.....(.((((((.....((.((((.((...((.....))..((.(((.....)))..))...)).)))).)).....)))))).)......)))............(((((....)))))........))))).. (-17.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 398 113 74 135 99 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 366 112 73 80 47 tfor:TF1204|5end_possible_metal-dependent_membrane_protease_1286359..1286589_POSITIVE 349 108 61 133 77 tfor:TF2689|5end_hypothetical_protein_2864824..2865054_POSITIVE 331 110 69 209 161 tfor:TF1653|5end_hypothetical_protein_1766201..1766431_POSITIVE 331 110 69 209 161 tfor:TF0979|5end_hypothetical_protein_1032838..1033068_POSITIVE 329 103 65 219 171 tfor:TF0522|5end_hypothetical_protein_547638..547868_POSITIVE 329 103 65 211 163 tfor:TF0521|5end_hypothetical_protein_547630..547860_POSITIVE 326 107 62 225 186 tfor:TF1974|5end_glyoxalase_I_related_protein_(lactoylglutathione_lyase)_2120950..2121180_POSITIVE 325 110 61 46 6 tfor:TF2266|5end_transfer_region-related_protein,_TraQ_2434369..2434599_POSITIVE 322 110 63 218 167 tfor:TF2318|5end_conserved_hypothetical_protein_2475603..2475833_POSITIVE 322 107 62 184 131 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 316 109 63 110 55 tfor:TF3131|5end_uracil-DNA_glycosylase_3364467..3364697_POSITIVE 316 105 61 225 180 tfor:TF2353|5end_conserved_hypothetical_protein_2517758..2517988_POSITIVE 316 109 62 70 25 tfor:TF1549|5end_conserved_hypothetical_protein_1653993..1654223_POSITIVE 313 110 61 177 121 tfor:TF2279|5end_hypothetical_protein_2438895..2439125_POSITIVE 312 108 62 223 168 tfor:TF2455|5end_conserved_hypothetical_protein;_possible_membrane_protein_2631959..2632189_POSITIVE 312 110 62 61 6 tfor:TF1402|5end_cation_efflux_system_protein_1477922..1478152_POSITIVE 311 97 62 112 61 tfor:TF0657|5end_conserved_hypothetical_protein_702893..703123_POSITIVE 310 107 65 135 92 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 310 107 65 95 52 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 81 41 60 23 tfor:TF1058|3end_N-acetylglucosamine_kinase_1126848..1126998_POSITIVE 320 82 42 67 16 tfor:TF1247|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330928..1331078_POSITIVE 319 110 71 48 2 tfor:TF1252|3end_phosphofructokinase;_pyrophosphate-fructose_6-phosphate_1-phosphotransferase_(probable_beta_subunit)_1336084..1336234_POSITIVE 312 110 62 84 29 tfor:TF1403|3end_hypothetical_protein_1478025..1478175_POSITIVE 311 97 62 112 61 tfor:TF0656|3end_acetyltransferase,_possible_GNAT_family_702973..703123_POSITIVE 310 107 65 123 80 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 306 110 68 59 6 tfor:TF1179|3end_two-component_sensor_histidine_kinase_1267447..1267597_POSITIVE 305 110 63 53 8 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE 304 114 72 131 88 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 303 115 71 68 23 tfor:TF2263|3end_transfer_region-related_protein,_TraN_2432964..2433114_POSITIVE 301 100 51 50 1 tfor:TF3039|3end_ABC_transporter,_ATP-binding_protein_3267697..3267847_POSITIVE 301 109 62 96 42 tfor:TF1197|3end_transcriptional_regulator_1281414..1281564_POSITIVE 300 116 71 65 6 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 298 117 73 122 83 tfor:TF2778|3end_outer_membrane_protein,__TonB_dependent_receptor_2964251..2964401_POSITIVE 296 107 62 68 21 tfor:TF0480|3end_ornithine_carbamoyltransferase_499589..499739_POSITIVE 295 97 51 60 12 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 295 116 71 77 40 tfor:TF1948|3end_conserved_hypothetical_protein_2096795..2096945_POSITIVE 294 97 54 118 75 tfor:TF2279|3end_hypothetical_protein_2439187..2439337_POSITIVE 294 188 143 87 35 tfor:TF1563|3end_glycerophosphoryl_diester_phosphodiesterase_1671291..1671441_POSITIVE 291 110 61 97 34 tfor:TF0703|3end_conserved_hypothetical_protein_747955..748105_POSITIVE