Origin IGS: taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatcgggcgtaacagtcaataaacgtagcgatagtagctgttatgggggcttccgccttcggaagattctgtgacaacttcaaaaagaggagggggatcaaaacaaaatgtttggcccccttttttacacattgccactttgggttta Mask Tandem Repeat Region ================================================ taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta Find is-nt database================================================ Query_seq: TF1532:TF1534|TF1532:TF1534:potassium uptake system protein:conserved hypothetical protein:->->:1639476..1639624 149 taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1532:TF1534|TF1532:TF1534:potassium uptake system protein:conserved hypothetical protein:->->:1639476..1639624 149 taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1532:TF1534|TF1532:TF1534:potassium uptake system protein:conserved hypothetical protein:->->:1639476..1639624 149 taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 11 End: 130 .......... M A M C K K G G Q T F C F D P P P L F E V V T E S S E G G S P H N S Y Y R Y V Y ................... Protein_Len: 34 Strand: + Start: 48 End: 149 ............................................... M I P L L F L K L S Q N L P K A E A P I T A T I A T F I D C Y A R L Protein_Len: 43 Strand: - Start: 2 End: 130 . F G F H C H T F F P A L C K T K I G R R K K F N D C F R G F A S A G M V A V I A V N M ................... Protein_Len: 37 Strand: - Start: 1 End: 111 L G L T A I H L F P P W V N Q K S G G G R K S T T V S D E S P P L G W L M ...................................... taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta 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================================================ taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -5.6 Tail_Score: -5.055 Start: 29 End: 56 Full_Region: cttcaaaaagaggag ggggatcaaaaca aaa tgtttggccccc ttttttacacattgc ............................ggggatcaaaacaaaatgtttggccccc............................................................................................. Find igs database================================================ Query_seq: TF1532:TF1534|TF1532:TF1534:potassium uptake system protein:conserved hypothetical protein:->->:1639476..1639624 149 taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: tfor_TF1532_TF1534|potassium uptake system protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1639476,1639624]|149 HSP 1 e-value: 2.0E-79 bit: 295.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta taaacccaaagtggcaatgtgtaaaaaagggggccaaacattttgttttgatccccctcctctttttgaagttgtcacagaatcttccgaaggcggaagcccccataacagctactatcgctacgtttattgactgttacgcccgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACCCAAAGUGGCAAUGUGUAAAAAAGGGGGCCAAACAUUUUGUUUUGAUCCCCCUCCUCUUUUUGAAGUUGUCACAGAAUCUUCCGAAGGCGGAAGCCCCCAUAACAGCUACUAUCGCUACGUUUAUUGACUGUUACGCCCGAUUA ..........((((((((...((((((((((((..((((.....))))....))))))....))))))..))))))))..((((.......(((....)))....(((((((......((...))......).)))))).....)))). (-38.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCGGGCGUAACAGUCAAUAAACGUAGCGAUAGUAGCUGUUAUGGGGGCUUCCGCCUUCGGAAGAUUCUGUGACAACUUCAAAAAGAGGAGGGGGAUCAAAACAAAAUGUUUGGCCCCCUUUUUUACACAUUGCCACUUUGGGUUUA .((((.(((......))).......((.(((((.(.((.((((((((((.((((((....)))))).)))))))))).)).)....(((((((((((.(((((........))))))))))))))))....))))).))....)))).. (-46.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 62 27 159 122 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 383 119 78 199 163 tfor:TF1875|5end_conserved_hypothetical_protein_2028752..2028982_POSITIVE 369 120 72 219 165 tfor:TF3112|5end_Na+/H+_anitporter_3346775..3347005_POSITIVE 365 128 81 216 158 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 364 99 51 83 39 tfor:TF0190|5end_cell_division_protein_FtsH_204029..204259_POSITIVE 356 67 26 166 116 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 333 80 32 186 150 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 333 125 85 165 128 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 330 106 67 111 61 tfor:TF2807|5end_possible_chloride_channel_protein_2996637..2996867_POSITIVE 323 68 23 178 134 tfor:TF1708|5end_transcriptional_regulator_1829185..1829415_POSITIVE 323 95 51 66 5 tfor:TF0016|5end_hypothetical_protein_10292..10522_POSITIVE 322 59 13 226 174 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 320 59 12 227 182 tfor:TF1260|5end_chaperone_protein_DnaJ_1345325..1345555_POSITIVE 319 95 55 53 8 tfor:TF1912|5end_transcriptional_regulator,_TetR_family_2065970..2066200_POSITIVE 318 100 54 146 101 tfor:TF2135|5end_conserved_hypothetical_protein_2311316..2311546_POSITIVE 316 63 26 78 35 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 313 100 54 147 101 tfor:TF2145|5end_conserved_hypothetical_protein;_possible_rhodanese-domain_protein_2319764..2319994_POSITIVE 311 99 51 48 6 tfor:TF1167|5end_hypothetical_protein_1248559..1248789_POSITIVE 310 119 71 56 1 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 306 70 27 207 157 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 99 51 64 20 tfor:TF0189|3end_phosphatidate_cytidylytransferase_(CDP-diglyceride_synthetase)_204090..204240_POSITIVE 333 125 85 101 64 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 330 106 67 59 9 tfor:TF2805|3end_zinc_protease_2996665..2996815_POSITIVE 326 125 81 121 77 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 323 70 25 62 9 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 322 59 13 63 11 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 318 100 54 112 67 tfor:TF2133|3end_aspartate-semialdehyde_dehydrogenase_2311362..2311512_POSITIVE 316 63 26 65 22 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 313 128 86 42 6 tfor:TF0072|3end_hypothetical_protein_81070..81220_POSITIVE 306 70 27 68 18 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 303 121 90 58 30 tfor:TF0079|3end_conserved_hypothetical_protein_86273..86423_POSITIVE 302 121 81 114 72 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 296 137 92 101 41 tfor:TF2315|3end_thioesterase_2474498..2474648_POSITIVE 294 126 87 59 11 tfor:TF2762|3end_conserved_hypothetical_protein_2946134..2946284_POSITIVE 294 121 88 75 46 tfor:TF2657|3end_conserved_hypothetical_protein_2830873..2831023_POSITIVE 291 71 31 70 22 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 290 99 51 58 10 tfor:TF2687|3end_iron-regulated_ABC-type_transporter_membrane_component_2864962..2865112_POSITIVE 288 128 88 95 53 tfor:TF2394|3end_integrase/recombinase_XerD_2566590..2566740_POSITIVE 288 129 88 132 91 tfor:TF0429|3end_ABC_transporter,_ATP-binding_protein_452227..452377_POSITIVE 288 101 68 150 119 tfor:TF0283|3end_possible_nicotinamide_mononucleotide_transporter_312074..312224_POSITIVE