Origin IGS: taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaagcttaccgtacctaaagaaaatggttcaagatgtttcttggttatttcccgaaataaaatgattaagacggaagccgccaatgcagcctccgcctttgtcaaaaattaatcttccgatattttta Mask Tandem Repeat Region ================================================ taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta Find is-nt database================================================ Query_seq: TF0079:TF0080|TF0079:TF0080:conserved hypothetical protein:phosphate ABC transporter, periplasmic phosphate-binding protein:->->:86334..86464 131 taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0079:TF0080|TF0079:TF0080:conserved hypothetical protein:phosphate ABC transporter, periplasmic phosphate-binding protein:->->:86334..86464 131 taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0079:TF0080|TF0079:TF0080:conserved hypothetical protein:phosphate ABC transporter, periplasmic phosphate-binding protein:->->:86334..86464 131 taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 8 End: 97 ....... M G R L I F D K G G G C I G G F R L N H F I S G N N Q E T S .................................. Protein_Len: 36 Strand: + Start: 24 End: 131 ....................... M T K A E A A L A A S V L I I L F R E I T K K H L E P F S L G T V S F L taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta 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================================================ taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.3 Tail_Score: -4.86731 Start: 25 End: 66 Full_Region: CGGAAGATTAATTTT TGACAAAGGCGGAGGCTGC ATTG GCGGCTTCCGTCTTAATCA TTTTATTTCGGGAAA ........................TGACAAAGGCGGAGGCTGCATTGGCGGCTTCCGTCTTAATCA................................................................. Find igs database================================================ Query_seq: TF0079:TF0080|TF0079:TF0080:conserved hypothetical protein:phosphate ABC transporter, periplasmic phosphate-binding protein:->->:86334..86464 131 taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: tfor_TF0079_TF0080|conserved hypothetical protein:phosphate ABC transporter, periplasmic phosphate-binding protein|POSITIVE:POSITIVE|[86334,86464]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta taaaaatatcggaagattaatttttgacaaaggcggaggctgcattggcggcttccgtcttaatcattttatttcgggaaataaccaagaaacatcttgaaccattttctttaggtacggtaagcttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUAUCGGAAGAUUAAUUUUUGACAAAGGCGGAGGCUGCAUUGGCGGCUUCCGUCUUAAUCAUUUUAUUUCGGGAAAUAACCAAGAAACAUCUUGAACCAUUUUCUUUAGGUACGGUAAGCUUCUUA ((((((((((....)))..)))))))...((((((((((((((....))))))))))))))....((..(((((..(((((....(((((....)))))......)))))..)))))..)).......... (-39.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAGCUUACCGUACCUAAAGAAAAUGGUUCAAGAUGUUUCUUGGUUAUUUCCCGAAAUAAAAUGAUUAAGACGGAAGCCGCCAAUGCAGCCUCCGCCUUUGUCAAAAAUUAAUCUUCCGAUAUUUUUA ((((((((.......(((..........))).......)))))))).((((((....))))))..((((.(((.((((.((.((....)).)).)))).))).))))........................ (-26.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 478 80 31 183 124 tfor:TF0431|5end_hypothetical_protein_452178..452408_POSITIVE 478 80 31 168 109 tfor:TF0430|5end_hypothetical_protein_452163..452393_POSITIVE 389 60 11 60 1 tfor:TF3070|5end_conserved_hypothetical_protein_3294380..3294610_POSITIVE 379 79 31 65 22 tfor:TF1603|5end_RNA_polymerase_ECF-type_sigma_factor_1717176..1717406_POSITIVE 369 58 11 230 178 tfor:TF0281|5end_hypothetical_protein_308909..309139_POSITIVE 369 58 11 128 76 tfor:TF0280|5end_hypothetical_protein_308807..309037_POSITIVE 369 76 31 182 131 tfor:TF0140|5end_exodeoxyribonuclease_VII,_small_subunit_148203..148433_POSITIVE 359 56 11 193 143 tfor:TF0793|5end_conserved_hypothetical_protein;_possible_AAA_superfamily_ATPase_850036..850266_POSITIVE 358 77 31 55 6 tfor:TF1776|5end_urocanate_hydratase_1914660..1914890_POSITIVE 352 80 31 210 151 tfor:TF0338|5end_alkaline_phosphatase_361788..362018_POSITIVE 349 58 20 137 94 tfor:TF2047|5end_hypothetical_protein_2210057..2210287_POSITIVE 349 57 11 77 29 tfor:TF0136|5end_transposase_element_145627..145857_POSITIVE 348 58 30 199 170 tfor:TF2835|5end_stationary-phase_survival_protein_SurE_3025113..3025343_POSITIVE 346 78 31 70 18 tfor:TF1800|5end_conserved_hypothetical_protein_1941214..1941444_POSITIVE 345 78 31 189 131 tfor:TF0759|5end_heat_shock_protein_15,_RNA-binding_domain_S4_805870..806100_POSITIVE 344 79 33 98 53 tfor:TF2542|5end_DNA_topoisomerase_III_2725544..2725774_POSITIVE 343 80 32 114 59 tfor:TF2435|5end_DNA_repair_protein_radC_2614352..2614582_POSITIVE 340 79 32 59 4 tfor:TF1084|5end_transposase_1153310..1153540_POSITIVE 335 70 23 68 21 tfor:TF2233|5end_conserved_hypothetical_protein_2406755..2406985_POSITIVE 333 78 31 226 157 tfor:TF2004|5end_thymidylate_synthase_2156372..2156602_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 482 66 25 66 25 tfor:TF0079|3end_conserved_hypothetical_protein_86273..86423_POSITIVE 469 79 31 151 93 tfor:TF0429|3end_ABC_transporter,_ATP-binding_protein_452227..452377_POSITIVE 359 77 32 79 30 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 359 56 11 150 100 tfor:TF0792|3end_pyruvate_ferredoxin;_flavodoxin_oxidoreductase_850073..850223_POSITIVE 346 78 31 70 18 tfor:TF1799|3end_quinolinate_synthetase_1941294..1941444_POSITIVE 338 52 20 144 106 tfor:TF0139|3end_4-diphosphocytidyl-2c-methyl-D-erythritol_synthase_(MEP_cytidylyltransferase)_(MCT)_148269..148419_POSITIVE 333 57 20 151 109 tfor:TF2046|3end_polyribonucleotide_nucleotidyltransferase_2210152..2210302_POSITIVE 332 61 24 36 2 tfor:TF2044|3end_excinuclease_ABC,_subunit_A_2206163..2206313_POSITIVE 331 78 32 128 85 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 328 50 5 126 70 tfor:TF2243|3end_possible_mobilization_protein_2419470..2419620_POSITIVE 327 78 31 76 26 tfor:TF2267|3end_lysozyme-related_protein_2435473..2435623_POSITIVE 326 59 12 141 99 tfor:TF2271|3end_conserved_hypothetical_protein_2436187..2436337_POSITIVE 326 75 32 73 14 tfor:TF1908|3end_possible_phosphoglycerate_mutase_2063299..2063449_POSITIVE 325 59 32 139 107 tfor:TF2578|3end_30S_ribosomal_protein_S11_2747164..2747314_POSITIVE 322 61 23 87 50 tfor:TF1026|3end_beta-N-acetylglucosaminidase;_beta_lactamase_1085639..1085789_POSITIVE 321 79 31 106 56 tfor:TF2394|3end_integrase/recombinase_XerD_2566590..2566740_POSITIVE 320 80 32 69 8 tfor:TF2770|3end_conserved_hypothetical_protein_2956639..2956789_POSITIVE 319 68 25 66 7 tfor:TF0811|3end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_870724..870874_POSITIVE 316 61 29 62 15 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 315 48 8 140 99 tfor:TF1788|3end_conserved_hypothetical_protein_1930119..1930269_POSITIVE