Origin IGS: ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctttctatgtttttatttgtttgacaatcatgaatcatatttttcttttcgagcaagcaaatgtatcgaccgcaagactttttgtacaatctatttgacgaaccccctatctgcttttgacgaatggcactcttcttctctttttcccgtccgttatatcgttaactttgcgcc Mask Tandem Repeat Region ================================================ ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag Find is-nt database================================================ Query_seq: TF1164:TF1165|TF1164:TF1165:two-component system sensor histidine kinase:conserved hypothetical protein:->->:1244839..1245012 174 ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1164:TF1165|TF1164:TF1165:two-component system sensor histidine kinase:conserved hypothetical protein:->->:1244839..1245012 174 ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1164:TF1165|TF1164:TF1165:two-component system sensor histidine kinase:conserved hypothetical protein:->->:1244839..1245012 174 ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 50 End: 172 ................................................. M R Q K Q I G G S S N R L Y K K S C G R Y I C L L E K K N M I H D C Q T N K N I E .. Protein_Len: 52 Strand: - Start: 3 End: 158 .. A F N V I Y R V P F L S S S H W E D F A S L P N T L Y I T C F T K R D I C K S A R F S F Y S E H N D F M ................ ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag 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================================================ ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1164:TF1165|TF1164:TF1165:two-component system sensor histidine kinase:conserved hypothetical protein:->->:1244839..1245012 174 ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: tfor_TF1164_TF1165|two-component system sensor histidine kinase:conserved hypothetical protein|POSITIVE:POSITIVE|[1244839,1245012]|174 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag ggcgcaaagttaacgatataacggacgggaaaaagagaagaagagtgccattcgtcaaaagcagatagggggttcgtcaaatagattgtacaaaaagtcttgcggtcgatacatttgcttgctcgaaaagaaaaatatgattcatgattgtcaaacaaataaaaacatagaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCGCAAAGUUAACGAUAUAACGGACGGGAAAAAGAGAAGAAGAGUGCCAUUCGUCAAAAGCAGAUAGGGGGUUCGUCAAAUAGAUUGUACAAAAAGUCUUGCGGUCGAUACAUUUGCUUGCUCGAAAAGAAAAAUAUGAUUCAUGAUUGUCAAACAAAUAAAAACAUAGAAAG (((((...((((......))))...(........).........))))).((((....((((((((.(.....(((.(....(((((........)))))....).)))..)))))))))...))))..........((((........))))..................... (-28.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUCUAUGUUUUUAUUUGUUUGACAAUCAUGAAUCAUAUUUUUCUUUUCGAGCAAGCAAAUGUAUCGACCGCAAGACUUUUUGUACAAUCUAUUUGACGAACCCCCUAUCUGCUUUUGACGAAUGGCACUCUUCUUCUCUUUUUCCCGUCCGUUAUAUCGUUAACUUUGCGCC .............((((((((((........(((........)))........)))))))))).......((((((....(((((.(((.....))))))))..............(((((((((((.((..................))))))....))))))).)))))).. (-25.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 65 22 90 40 tfor:TF0064|5end_conserved_hypothetical_protein_68419..68649_POSITIVE 348 49 1 55 5 tfor:TF1571|5end_conserved_hypothetical_protein_1680086..1680316_POSITIVE 345 58 12 75 28 tfor:TF1192|5end_alpha-amylase_1274007..1274237_POSITIVE 341 78 40 52 18 tfor:TF0214|5end_DNA_recombination_and_repair_protein,_RecN_239830..240060_POSITIVE 337 48 2 172 123 tfor:TF1796|5end_ABC_transporter,_ATP-binding_protein_1936492..1936722_POSITIVE 329 109 61 90 42 tfor:TF1464|5end_conserved_hypothetical_protein_1553467..1553697_POSITIVE 328 70 22 66 12 tfor:TF0252|5end_hypothetical_protein_283530..283760_POSITIVE 327 49 1 129 79 tfor:TF0018|5end_hypothetical_protein_11250..11480_POSITIVE 321 78 34 177 133 tfor:TF2380|5end_hemagglutinin_2545012..2545242_POSITIVE 321 108 63 190 145 tfor:TF0245|5end_bacterioferritin_comigratory_protein_275733..275963_POSITIVE 319 56 20 127 100 tfor:TF2079|5end_permease_2245585..2245815_POSITIVE 318 77 40 47 2 tfor:TF2911|5end_hypothetical_protein_3105871..3106101_POSITIVE 311 79 31 190 129 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 308 73 41 99 68 tfor:TF0066|5end_conserved_hypothetical_protein_70729..70959_POSITIVE 306 120 71 193 147 tfor:TF1219|5end_conserved_hypothetical_protein_1304404..1304634_POSITIVE 305 77 39 47 14 tfor:TF0298|5end_dipeptidase_323127..323357_POSITIVE 305 65 22 90 38 tfor:TF0063|5end_conserved_hypothetical_protein_66110..66340_POSITIVE 303 69 23 228 162 tfor:TF1421|5end_UDP-N-acetylmuramate--alanine_ligase_1503465..1503695_POSITIVE 300 70 22 208 158 tfor:TF1266|5end_conserved_hypothetical_protein_1353423..1353653_POSITIVE 298 132 96 72 30 tfor:TF0657|5end_conserved_hypothetical_protein_702893..703123_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 65 22 81 31 tfor:TF0063|3end_conserved_hypothetical_protein_68490..68640_POSITIVE 341 78 40 45 11 tfor:TF0213|3end_conserved_hypothetical_protein_239903..240053_POSITIVE 337 48 2 76 27 tfor:TF1795|3end_conserved_hypothetical_protein_1936476..1936626_POSITIVE 329 109 61 51 3 tfor:TF1462|3end_erythronate-4-phosphate_dehydrogenase_1553508..1553658_POSITIVE 318 77 40 52 7 tfor:TF2909|3end_GTP-binding_protein,_possible_GTP1/OBG_family_3105956..3106106_POSITIVE 311 79 31 87 26 tfor:TF0425|3end_outer_membrane_protein_444705..444855_POSITIVE 308 73 41 90 59 tfor:TF0065|3end_conserved_hypothetical_protein_70800..70950_POSITIVE 306 120 71 92 46 tfor:TF1218|3end_hypothetical_protein_1304383..1304533_POSITIVE 305 65 22 80 28 tfor:TF0062|3end_conserved_hypothetical_protein_66180..66330_POSITIVE 300 70 22 119 69 tfor:TF1265|3end_dihydroorotate_dehydrogenase_1353414..1353564_POSITIVE 300 105 63 150 108 tfor:TF0244|3end_DNA_recombination_protein_275776..275926_POSITIVE 298 132 96 72 30 tfor:TF0656|3end_acetyltransferase,_possible_GNAT_family_702973..703123_POSITIVE 296 74 38 39 10 tfor:TF2589|3end_translation_elongation_factor_G_protein_2755667..2755817_POSITIVE 290 89 42 72 36 tfor:TF1061|3end_glycosyltransferase_1131807..1131957_POSITIVE 289 67 22 43 2 tfor:TF2850|3end_endoribonuclease_L-PSP_3038871..3039021_POSITIVE 288 49 14 48 13 tfor:TF1570|3end_ATP_synthase_subunit_A_1680159..1680309_POSITIVE 286 70 22 63 15 tfor:TF1206|3end_conserved_hypothetical_protein_1290136..1290286_POSITIVE 279 47 3 63 11 tfor:TF1911|3end_conserved_hypothetical_protein_2065933..2066083_POSITIVE 277 54 12 77 38 tfor:TF2391|3end_conserved_hypothetical_protein_2563464..2563614_POSITIVE 276 43 1 130 93 tfor:TF1620|3end_TPR_domain_protein_1735223..1735373_POSITIVE