Origin IGS: tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta .........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 tagcgcaaggaaagggaaaaagaacctatggaaaagtcattaccataggttctttctttatcattgctgtcgtccgtaaaattttcccctatgaccgatgtaggaaaaaacgactttaaaacgatgatttgttgaattattcactccttattcgtttttatctcataaagacaagagattcaactctacttctatttctttggcctgctcgatatccgggacggtgatacgcgaagaatgtgctcaagcccgggtttcctttgctgtttttca Mask Tandem Repeat Region ================================================ tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta Find is-nt database================================================ Query_seq: TF0038:TF0039|TF0038:TF0039:conserved hypothetical protein:conserved hypothetical protein:->->:41274..41546 273 tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0038:TF0039|TF0038:TF0039:conserved hypothetical protein:conserved hypothetical protein:->->:41274..41546 273 tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0038:TF0039|TF0038:TF0039:conserved hypothetical protein:conserved hypothetical protein:->->:41274..41546 273 tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 134 End: 271 ..................................................................................................................................... M I Q Q I I V L K S F F P T S V I G E N F T D D S N D K E R T Y G N D F S I G S F S L S L R .. Protein_Len: 32 Strand: - Start: 50 End: 145 ................................................. R G P Y R A P W L F L L L T S D R T K I L Y F R I L L S Y N L M ................................................................................................................................ Protein_Len: 32 Strand: - Start: 1 End: 96 S F C C L F G P S S C M R R T D G D R I D L L G F F Y F Y L Q M ................................................................................................................................................................................. tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta 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================================================ tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -11.3 Tail_Score: -4.83759 Start: 222 End: 252 Full_Region: GCAATGATAAAGAAA GAACCTATGGTAA TGACT TTTCCATAGGTTC TTTTTCCCTTTCCTT .............................................................................................................................................................................................................................GAACCTATGGTAATGACTTTTCCATAGGTTC..................... Find igs database================================================ Query_seq: TF0038:TF0039|TF0038:TF0039:conserved hypothetical protein:conserved hypothetical protein:->->:41274..41546 273 tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta Intra-Species Hit: Count: 1 Min: 1 Max: 273 Len: 273 Subject: tfor_TF0038_TF0039|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[41274,41546]|273 HSP 1 e-value: 1.0E-153 bit: 541.0 Len: 273 Query Start:1 Query End:273 Subject Strand: POSITIVE Subject Start: 1 Subject End: 273 tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta tgaaaaacagcaaaggaaacccgggcttgagcacattcttcgcgtatcaccgtcccggatatcgagcaggccaaagaaatagaagtagagttgaatctcttgtctttatgagataaaaacgaataaggagtgaataattcaacaaatcatcgttttaaagtcgttttttcctacatcggtcataggggaaaattttacggacgacagcaatgataaagaaagaacctatggtaatgacttttccataggttctttttccctttccttgcgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAACAGCAAAGGAAACCCGGGCUUGAGCACAUUCUUCGCGUAUCACCGUCCCGGAUAUCGAGCAGGCCAAAGAAAUAGAAGUAGAGUUGAAUCUCUUGUCUUUAUGAGAUAAAAACGAAUAAGGAGUGAAUAAUUCAACAAAUCAUCGUUUUAAAGUCGUUUUUUCCUACAUCGGUCAUAGGGGAAAAUUUUACGGACGACAGCAAUGAUAAAGAAAGAACCUAUGGUAAUGACUUUUCCAUAGGUUCUUUUUCCCUUUCCUUGCGCUA ........(((.(((((((...(((........(((((((((((((......((((..(((((((..(((..((((((...((((.((((......))))...))))....(((.(((((((........(((.....)))........)))))))...))).)))))))))...))))).))..))))......))))..))).)).))))....(((((((((((((((.((.....)).)))))))))))))))))))))))))..))). (-69.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCGCAAGGAAAGGGAAAAAGAACCUAUGGAAAAGUCAUUACCAUAGGUUCUUUCUUUAUCAUUGCUGUCGUCCGUAAAAUUUUCCCCUAUGACCGAUGUAGGAAAAAACGACUUUAAAACGAUGAUUUGUUGAAUUAUUCACUCCUUAUUCGUUUUUAUCUCAUAAAGACAAGAGAUUCAACUCUACUUCUAUUUCUUUGGCCUGCUCGAUAUCCGGGACGGUGAUACGCGAAGAAUGUGCUCAAGCCCGGGUUUCCUUUGCUGUUUUUCA (((((.((((((((((..(((((((((((((...........))))))))))))).....((.(((((((((.(((........((((..(((..(((.(((((..(((..((....(((((((........(((.....)))........)))))))....))....(((..((((......))))...))).....)))..)))))))).)))..)))))))))))).)))).))...........)))...))))))))))))....... (-70.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 76 33 57 11 tfor:TF2385|5end_conserved_hypothetical_protein;_possible_MazG_family_protein_2550676..2550906_POSITIVE 383 70 22 224 173 tfor:TF1409|5end_outer_membrane_protein_TolC_1485479..1485709_POSITIVE 380 69 22 191 139 tfor:TF2402|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2574582..2574812_POSITIVE 374 70 21 196 128 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 368 58 18 191 154 tfor:TF2368|5end_uridine_phosphorylase_2533666..2533896_POSITIVE 356 79 33 172 126 tfor:TF2837|5end_conserved_hypothetical_protein_3027939..3028169_POSITIVE 355 68 21 78 25 tfor:TF2830|5end_ABC_transporter,_ATP-binding_protein_3020581..3020811_POSITIVE 351 68 28 191 140 tfor:TF2661|5end_hypothetical_protein_2833509..2833739_POSITIVE 350 69 23 186 131 tfor:TF1916|5end_conserved_hypothetical_protein;_possible_ATPase_2068530..2068760_POSITIVE 348 70 23 54 8 tfor:TF2724|5end_anti-sigma_factor_2898193..2898423_POSITIVE 348 72 35 213 171 tfor:TF0299|5end_hypothetical_protein_324821..325051_POSITIVE 346 69 22 196 136 tfor:TF0890|5end_transfer_region-related_protein,_TraQ_940014..940244_POSITIVE 346 69 21 49 2 tfor:TF0710|5end_two_component_system_histidine_kinase_757250..757480_POSITIVE 342 73 31 60 16 tfor:TF1928|5end_conserved_hypothetical_protein_2075529..2075759_POSITIVE 338 57 19 47 12 tfor:TF1252|5end_phosphofructokinase;_pyrophosphate-fructose_6-phosphate_1-phosphotransferase_(probable_beta_subunit)_1334361..1334591_POSITIVE 338 76 31 68 22 tfor:TF0644|5end_pyruvate_phosphate_dikinase_685784..686014_POSITIVE 337 69 22 146 99 tfor:TF1287|5end_hypothetical_protein_1369545..1369775_POSITIVE 336 60 19 229 181 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 336 70 21 100 53 tfor:TF0690|5end_preprotein_translocase_subunit_735243..735473_POSITIVE 335 70 21 50 3 tfor:TF1237|5end_possible_L-fuculose_kinase_1322041..1322271_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 76 33 57 11 tfor:TF2384|3end_thiol:disulfide_interchange_protein_2550756..2550906_POSITIVE 380 68 22 140 78 tfor:TF2500|3end_ABC_transporter,_ATP-binding_protein_2675302..2675452_POSITIVE 367 70 21 66 23 tfor:TF0073|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_82051..82201_POSITIVE 355 68 21 78 25 tfor:TF2829|3end_conserved_hypothetical_protein_3020661..3020811_POSITIVE 351 68 28 142 91 tfor:TF2660|3end_hypothetical_protein_2833540..2833690_POSITIVE 350 69 23 65 10 tfor:TF1915|3end_NAD-dependent_protein_deacetylase,_SIR2_family_2068489..2068639_POSITIVE 350 60 12 141 82 tfor:TF0186|3end_ribonucleotide_reductase,_alpha_subunit_201812..201962_POSITIVE 342 73 31 53 9 tfor:TF1927|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2075602..2075752_POSITIVE 331 189 144 104 68 tfor:TF1814|3end_conserved_hypothetical_protein;_possible_biotin_synthase_related_domain_containing_protein_1956670..1956820_POSITIVE 329 58 14 138 94 tfor:TF2653|3end_hypothetical_protein_2822460..2822610_POSITIVE 329 55 19 58 14 tfor:TF2575|3end_methionine_aminopeptidase_2745985..2746135_POSITIVE 326 58 20 53 8 tfor:TF2498|3end_electron_transfer_flavoprotein,_alpha_subunit_2673885..2674035_POSITIVE 325 67 22 147 77 tfor:TF0535|3end_surface_antigen_BspA_561701..561851_POSITIVE 324 48 7 149 121 tfor:TF0022|3end_two-component_system_sensor_histidine_kinase_19522..19672_POSITIVE 323 70 21 132 79 tfor:TF3154|3end_conserved_hypothetical_protein_3390489..3390639_POSITIVE 323 70 23 121 79 tfor:TF1011|3end_cell_division_protein;_rod_shape-determining_protein_1068169..1068319_POSITIVE 323 70 22 117 59 tfor:TF0478|3end_conserved_hypothetical_protein_498627..498777_POSITIVE 323 68 21 104 27 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 321 72 31 53 10 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 315 70 21 145 91 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE