Origin IGS: gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 atctaatgatggatttactcaattatgatgagaatcttactcaattctacttgcaaaagtactcaattttctctgttcgcacaaataaaatcgctgtaaacttcaggtaatagacaagttagaaggtgagacatctccttttttatcctcccaccgccgtgggcgggaggagaggtttttatcgtcggcctatcgcgtcatgcccgtttcgggcaaggcaaattttatgggcggacgggcagcaccgtgaacccgtagtagcggttggtgttgtaaagtc Mask Tandem Repeat Region ================================================ gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat Find is-nt database================================================ Query_seq: TF2895:TF2896|TF2895:TF2896:hypothetical protein:conserved hypothetical protein; possible ATPase, AAA superfamily:->->:3084253..3084532 280 gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2895:TF2896|TF2895:TF2896:hypothetical protein:conserved hypothetical protein; possible ATPase, AAA superfamily:->->:3084253..3084532 280 gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2895:TF2896|TF2895:TF2896:hypothetical protein:conserved hypothetical protein; possible ATPase, AAA superfamily:->->:3084253..3084532 280 gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 99 End: 215 .................................................................................................. M K T S P P A H G G G R I K K E M S H L L T C L L P E V Y S D F I C A N R E N ................................................................. Protein_Len: 34 Strand: - Start: 174 End: 275 ............................................................................................................................................................................. R F N V A I K N T R V S F I S Y K Q L Y F Q T L N E D Y N L L D M M ..... Protein_Len: 46 Strand: - Start: 34 End: 171 ................................. P A A R G G M F N A K G S V P M V R Y A S S L F R E E R G R R H S S L F P S T E G E L K D M ............................................................................................................. Protein_Len: 41 Strand: - Start: 26 End: 148 ......................... P N V T S G T R G Y F K G Q G F R A H R S L G V I F V E G G A W P P P L I F F S M .................................................................................................................................... Protein_Len: 51 Strand: - Start: 3 End: 155 .. K V V G V A V V P E R H Q G D A W L I Q R A R F P C S A I P R R Y F G R R G G V A T P P Y F L L H R M ............................................................................................................................. gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat 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================================================ gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 85 HP_score: -7.4 Tail_Score: -4.91109 Start: 106 End: 134 Full_Region: catctccttttttat cctcccaccgcc gtg ggcgggaggagagg tttttatcgtcggcc .........................................................................................................cctcccaccgccgtgggcgggaggagagg.................................................................................................................................................. TransTerm Strand: - Conf: 77 HP_score: -2.9 Tail_Score: -5.31275 Start: 143 End: 159 Full_Region: gtaatagacaagtta gaaggtg aga catctcc ttttttatcctccca ..............................................................................................................................................gaaggtgagacatctcc......................................................................................................................... Find igs database================================================ Query_seq: TF2895:TF2896|TF2895:TF2896:hypothetical protein:conserved hypothetical protein; possible ATPase, AAA superfamily:->->:3084253..3084532 280 gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat Intra-Species Hit: Count: 1 Min: 1 Max: 280 Len: 280 Subject: tfor_TF2895_TF2896|hypothetical protein:conserved hypothetical protein; possible ATPase, AAA superfamily|POSITIVE:POSITIVE|[3084253,3084532]|280 HSP 1 e-value: 1.0E-157 bit: 555.0 Len: 280 Query Start:1 Query End:280 Subject Strand: POSITIVE Subject Start: 1 Subject End: 280 gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat gactttacaacaccaaccgctactacgggttcacggtgctgcccgtccgcccataaaatttgccttgcccgaaacgggcatgacgcgataggccgacgataaaaacctctcctcccgcccacggcggtgggaggataaaaaaggagatgtctcaccttctaacttgtctattacctgaagtttacagcgattttatttgtgcgaacagagaaaattgagtacttttgcaagtagaattgagtaagattctcatcataattgagtaaatccatcattagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUUUACAACACCAACCGCUACUACGGGUUCACGGUGCUGCCCGUCCGCCCAUAAAAUUUGCCUUGCCCGAAACGGGCAUGACGCGAUAGGCCGACGAUAAAAACCUCUCCUCCCGCCCACGGCGGUGGGAGGAUAAAAAAGGAGAUGUCUCACCUUCUAACUUGUCUAUUACCUGAAGUUUACAGCGAUUUUAUUUGUGCGAACAGAGAAAAUUGAGUACUUUUGCAAGUAGAAUUGAGUAAGAUUCUCAUCAUAAUUGAGUAAAUCCAUCAUUAGAU ..((((.((.((((((((.(......)))))...)))).))..((((.(((........((((..((((((...))))))....))))..))).))))...........((((((((((......))))))))))....))))..((((........(((.((((.((((((....(((((......(((((((.(((((....))))).)))))))...)))))....))))))...)))).)))..((((.......))))......))))....... (-76.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUAAUGAUGGAUUUACUCAAUUAUGAUGAGAAUCUUACUCAAUUCUACUUGCAAAAGUACUCAAUUUUCUCUGUUCGCACAAAUAAAAUCGCUGUAAACUUCAGGUAAUAGACAAGUUAGAAGGUGAGACAUCUCCUUUUUUAUCCUCCCACCGCCGUGGGCGGGAGGAGAGGUUUUUAUCGUCGGCCUAUCGCGUCAUGCCCGUUUCGGGCAAGGCAAAUUUUAUGGGCGGACGGGCAGCACCGUGAACCCGUAGUAGCGGUUGGUGUUGUAAAGUC ......(((.((((((.((((....))).).))))))...)))....(((((....)))))...........((((((((....(((((((.((((.(((((((................((((((.((....)).))))))...(((((((.((......)).)))))))))))))).......)))).......(((.((((((...)))))).)))..)))))))..))))))))(((((((((.....((((....)))).)))))))))...... (-84.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 496 119 75 230 183 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 463 135 107 164 136 tfor:TF0028|5end_hypothetical_protein_24249..24479_POSITIVE 425 79 33 212 147 tfor:TF2025|5end_hypothetical_protein_2181933..2182163_POSITIVE 413 80 33 208 144 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 407 136 91 174 129 tfor:TF1343|5end_hypothetical_protein_1424630..1424860_POSITIVE 406 104 63 99 56 tfor:TF2341|5end_hypothetical_protein_2505735..2505965_POSITIVE 403 128 81 206 154 tfor:TF2946|5end_conserved_hypothetical_protein;_possible_ATPase_3151750..3151980_POSITIVE 395 50 4 172 113 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 392 85 41 71 5 tfor:TF2256|5end_transfer_region-related_protein,_TraI_2427908..2428138_POSITIVE 391 52 18 49 3 tfor:TF2186|5end_outer_membrane_protein_2360291..2360521_POSITIVE 390 50 6 51 10 tfor:TF2564|5end_50S_ribosomal_protein_L14_2739604..2739834_POSITIVE 386 130 81 169 102 tfor:TF0975|5end_hypothetical_protein_1023994..1024224_POSITIVE 385 126 84 218 170 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 385 150 107 103 59 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 384 85 44 200 159 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 382 52 18 201 158 tfor:TF2249|5end_transfer_region-related_protein,_TraC_2422988..2423218_POSITIVE 382 52 14 202 155 tfor:TF0369|5end_hypothetical_protein_385933..386163_POSITIVE 381 96 62 166 118 tfor:TF2148|5end_conserved_hypothetical_protein_2321756..2321986_POSITIVE 381 54 11 130 89 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 380 79 32 227 177 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 135 107 34 6 tfor:TF0027|3end_conserved_hypothetical_protein_24199..24349_POSITIVE 408 160 116 79 35 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE 407 136 91 84 39 tfor:TF1342|3end_possible_lipoprotein_1424620..1424770_POSITIVE 406 104 63 67 24 tfor:TF2339|3end_hypothetical_protein_2505783..2505933_POSITIVE 395 50 4 150 91 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 391 120 72 114 62 tfor:TF0001|3end_hypothetical_protein_158..308_POSITIVE 390 50 6 46 5 tfor:TF2563|3end_30S_ribosomal_protein_S17_2739679..2739829_POSITIVE 381 54 11 130 89 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 376 131 93 138 100 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 374 98 66 140 114 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 373 90 42 122 52 tfor:TF2406|3end_anti-sigma_factor_2581659..2581809_POSITIVE 372 133 91 49 7 tfor:TF0092|3end_outer_membrane_protein_100549..100699_POSITIVE 369 52 19 55 4 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 369 56 12 125 79 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 364 117 75 65 13 tfor:TF2110|3end_transposase_2280526..2280676_POSITIVE 363 55 13 147 94 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 363 51 17 148 110 tfor:TF0969|3end_oxidoreductase_1020439..1020589_POSITIVE 362 87 43 62 7 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 359 119 77 76 24 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 358 134 94 68 28 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE