Origin IGS: accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattgccttccggtggaactctttgacgaagggcaggaatttgtccctgcaggctcgatgaaacatacaaggtcttccggcagtcgcagacgcaagggcgaccttttcaaacaggtagaatacatggt Mask Tandem Repeat Region ================================================ accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta Find is-nt database================================================ Query_seq: TF1197:TF1198|TF1197:TF1198:transcriptional regulator:conserved hypothetical protein:->->:1281475..1281603 129 accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1197:TF1198|TF1197:TF1198:transcriptional regulator:conserved hypothetical protein:->->:1281475..1281603 129 accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1197:TF1198|TF1197:TF1198:transcriptional regulator:conserved hypothetical protein:->->:1281475..1281603 129 accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 15 End: 128 .............. M F E K V A L A S A T A G R P C M F H R A C R D K F L P F V K E F H R K A I . Protein_Len: 42 Strand: + Start: 4 End: 129 ... M Y S T C L K R S P L R L R L P E D L V C F I E P A G T N S C P S S K S S T G R Q L Protein_Len: 38 Strand: - Start: 3 End: 116 .. M Y E V Q K F L D G K R R R S G S S R T H K M S G A P V F E Q G E D F L E M ............. Protein_Len: 30 Strand: - Start: 1 End: 90 G H I R G T Q F P R G Q T Q S Q R F V K Y T E D L R C P C M ....................................... accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta 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================================================ accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1197:TF1198|TF1197:TF1198:transcriptional regulator:conserved hypothetical protein:->->:1281475..1281603 129 accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: tfor_TF1197_TF1198|transcriptional regulator:conserved hypothetical protein|POSITIVE:POSITIVE|[1281475,1281603]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta accatgtattctacctgtttgaaaaggtcgcccttgcgtctgcgactgccggaagaccttgtatgtttcatcgagcctgcagggacaaattcctgcccttcgtcaaagagttccaccggaaggcaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAUGUAUUCUACCUGUUUGAAAAGGUCGCCCUUGCGUCUGCGACUGCCGGAAGACCUUGUAUGUUUCAUCGAGCCUGCAGGGACAAAUUCCUGCCCUUCGUCAAAGAGUUCCACCGGAAGGCAAUUA ..............((.(((((...((((((..........))))))((.((((..(((((((.((((....)))).))))))).....)))).))......))))).)).....((....))...... (-32.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUGCCUUCCGGUGGAACUCUUUGACGAAGGGCAGGAAUUUGUCCCUGCAGGCUCGAUGAAACAUACAAGGUCUUCCGGCAGUCGCAGACGCAAGGGCGACCUUUUCAAACAGGUAGAAUACAUGGU ...((((((...(.(((((..(((((.(....)(((((........))))).................)))))..))))).).(((((...(....).)))))..........)))))).......... (-35.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 450 80 31 49 1 tfor:TF2322|5end_conserved_hypothetical_protein;_possible_lipoprotein_2482743..2482973_POSITIVE 426 80 31 78 23 tfor:TF1474|5end_6-phosphogluconolactonase_1567342..1567572_POSITIVE 398 56 17 53 9 tfor:TF2645|5end_conserved_hypothetical_protein_2813799..2814029_POSITIVE 395 63 26 210 162 tfor:TF2830|5end_ABC_transporter,_ATP-binding_protein_3020581..3020811_POSITIVE 392 108 68 206 167 tfor:TF0685|5end_hypothetical_protein_730852..731082_POSITIVE 387 80 32 64 9 tfor:TF2573|5end_50S_ribosomal_protein_L15_2743310..2743540_POSITIVE 381 58 16 208 165 tfor:TF2611|5end_conserved_hypothetical_protein_2787204..2787434_POSITIVE 378 70 25 193 151 tfor:TF2295|5end_hypothetical_protein_2448164..2448394_POSITIVE 372 58 25 162 125 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 370 84 43 204 166 tfor:TF0472|5end_multidrug_resistance_protein,_AcrB/AcrD/AcrF_family_(cation_efflux_pump)_487813..488043_POSITIVE 369 115 71 101 45 tfor:TF1484|5end_penicillin_binding_protein_1579559..1579789_POSITIVE 367 78 31 68 17 tfor:TF2310|5end_dehydrogenase,_possible_3-oxoacyl-[acyl-carrier-protein]_reductase_2470481..2470711_POSITIVE 363 79 31 96 35 tfor:TF2336|5end_conserved_hypothetical_protein_2496169..2496399_POSITIVE 363 120 74 182 138 tfor:TF1432|5end_possible_hemolysin_A_1515936..1516166_POSITIVE 357 119 71 230 159 tfor:TF3096|5end_conserved_hypothetical_protein_3327963..3328193_POSITIVE 357 59 11 185 140 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 355 70 27 41 1 tfor:TF2294|5end_hypothetical_protein_2448012..2448242_POSITIVE 354 49 14 62 20 tfor:TF0096|5end_tRNA-guanine_transglycosylase_(queuine_tRNA-ribosyltransferase)_106971..107201_POSITIVE 353 59 13 230 182 tfor:TF3112|5end_Na+/H+_anitporter_3346775..3347005_POSITIVE 353 59 13 56 8 tfor:TF3111|5end_hypothetical_protein_3346601..3346831_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 80 37 151 93 tfor:TF1968|3end_conserved_hypothetical_protein_2115959..2116109_POSITIVE 362 80 31 147 84 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 357 80 31 79 25 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 352 59 15 131 58 tfor:TF0970|3end_2-keto-3-deoxygluconate_kinase_1021540..1021690_POSITIVE 349 79 31 118 61 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 347 79 35 131 84 tfor:TF2314|3end_conserved_hypothetical_protein_2474044..2474194_POSITIVE 347 86 41 73 21 tfor:TF1771|3end_prolipoprotein_diacylglyceryl_transferase_1910607..1910757_POSITIVE 344 58 17 58 12 tfor:TF0960|3end_beta-galactosidase_1010506..1010656_POSITIVE 341 47 1 59 5 tfor:TF2768|3end_ferredoxin_oxidoreductase,_beta_subunit_2955169..2955319_POSITIVE 341 102 65 46 16 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 341 58 14 120 58 tfor:TF2588|3end_coproporphryninogen_III_oxidase_2753432..2753582_POSITIVE 340 85 42 59 17 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 339 68 26 59 2 tfor:TF2247|3end_transfer_region-related_protein,_TraA_2422625..2422775_POSITIVE 337 58 15 142 79 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 337 80 31 70 14 tfor:TF1931|3end_ATPase/GTPase_2078622..2078772_POSITIVE 336 59 16 51 11 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE 335 60 17 140 99 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 334 78 32 71 22 tfor:TF0460|3end_hypothetical_protein_477070..477220_POSITIVE 333 60 24 149 105 tfor:TF1200|3end_conserved_hypothetical_protein_1283798..1283948_POSITIVE 333 69 24 80 32 tfor:TF1177|3end_conserved_hypothetical_protein;_possible_ribosomal_protein_S1_1264773..1264923_POSITIVE