Origin IGS: aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatgctccatacatcgtatgcatccgcaaagcatgcacacataccgtatgccccacgcccgtaacggcggaaaatatccgccgcgaaaaagcaattattcagcgtaaaatataggcagtttcaattttttagtatcttt Mask Tandem Repeat Region ================================================ aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta Find is-nt database================================================ Query_seq: TF2374:TF2375|TF2374:TF2375:UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt ransferase:conserved hypothetical protein:->->:2540953..2541092 140 aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2374:TF2375|TF2374:TF2375:UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt ransferase:conserved hypothetical protein:->->:2540953..2541092 140 aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2374:TF2375|TF2374:TF2375:UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt ransferase:conserved hypothetical protein:->->:2540953..2541092 140 aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 46 End: 138 ............................................. M L F R G G Y F P P L R A W G I R Y V C M L C G C I R C M E H .. Protein_Len: 34 Strand: + Start: 38 End: 139 ..................................... M N N C F F A A D I F R R Y G R G A Y G M C A C F A D A Y D V W S I . Protein_Len: 33 Strand: + Start: 42 End: 140 ......................................... M I A F S R R I F S A V T G V G H T V C V H A L R M H T M Y G A L Protein_Len: 32 Strand: - Start: 36 End: 131 ................................... A S Y N S K R P P Y K G G N R A H P M R Y T H M S Q P H M R H M ......... Protein_Len: 33 Strand: - Start: 29 End: 127 ............................ I K R Q I I A K E R R I N E A T V P T P C V T H T C A K R I C V M ............. aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta 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================================================ aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2374:TF2375|TF2374:TF2375:UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt ransferase:conserved hypothetical protein:->->:2540953..2541092 140 aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: tfor_TF2374_TF2375|UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N- acylt ransferase:conserved hypothetical protein|POSITIVE:POSITIVE|[2540953,2541092]|140 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta aaagatactaaaaaattgaaactgcctatattttacgctgaataattgctttttcgcggcggatattttccgccgttacgggcgtggggcatacggtatgtgtgcatgctttgcggatgcatacgatgtatggagcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAUACUAAAAAAUUGAAACUGCCUAUAUUUUACGCUGAAUAAUUGCUUUUUCGCGGCGGAUAUUUUCCGCCGUUACGGGCGUGGGGCAUACGGUAUGUGUGCAUGCUUUGCGGAUGCAUACGAUGUAUGGAGCAUUA ......................(((......(((((((((((..........))).(((((((.....))))))).....)))))))).((((((...(((((((((.(.....).))))))))).))))))..)))... (-40.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGCUCCAUACAUCGUAUGCAUCCGCAAAGCAUGCACACAUACCGUAUGCCCCACGCCCGUAACGGCGGAAAAUAUCCGCCGCGAAAAAGCAAUUAUUCAGCGUAAAAUAUAGGCAGUUUCAAUUUUUUAGUAUCUUU ...((((.(((((...((.(((((.(.....).))))).)).....)))))....((((......(((((((.....))))))).(((.((....)).))).))))........))))...................... (-30.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 516 109 71 230 191 tfor:TF1536|5end_hypothetical_protein_1643245..1643475_POSITIVE 455 90 48 221 179 tfor:TF2329|5end_conserved_hypothetical_protein_2488324..2488554_POSITIVE 446 120 72 137 67 tfor:TF1735|5end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_1860127..1860357_POSITIVE 446 90 42 175 113 tfor:TF1714|5end_hypothetical_protein_1834125..1834355_POSITIVE 444 97 55 57 12 tfor:TF0987|5end_DNA_repair_protein_1043090..1043320_POSITIVE 441 96 53 48 5 tfor:TF1464|5end_conserved_hypothetical_protein_1553467..1553697_POSITIVE 440 119 71 164 107 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 436 96 54 53 3 tfor:TF1723|5end_alpha-rhamnosidase_1848496..1848726_POSITIVE 433 120 71 196 143 tfor:TF2535|5end_histidyl-tRNA_synthetase_2717740..2717970_POSITIVE 422 96 56 164 117 tfor:TF1401|5end_Holliday_junction_DNA_helicase_1476502..1476732_POSITIVE 421 98 53 76 42 tfor:TF0799|5end_conserved_hypothetical_protein_855191..855421_POSITIVE 418 99 52 217 158 tfor:TF1246|5end_protease,_with_chaperone_function_1329390..1329620_POSITIVE 417 119 72 148 103 tfor:TF0744|5end_DNA_polymerase_III_subunit,_gamma/tau_791095..791325_POSITIVE 416 120 71 71 15 tfor:TF0888|5end_transfer_region-related_protein,_TraN_938392..938622_POSITIVE 415 120 71 214 147 tfor:TF0584|5end_phosphopantetheinyl_transferase_613755..613985_POSITIVE 414 90 46 81 21 tfor:TF1293|5end_ATPase,_possible_AAA_superfamily_1374579..1374809_POSITIVE 413 110 69 118 81 tfor:TF0841|5end_NADH_dehydrogenase/NAD(P)H_nitroreductase_892165..892395_POSITIVE 410 123 81 212 157 tfor:TF2238|5end_conserved_hypothetical_protein_2414098..2414328_POSITIVE 410 116 71 219 172 tfor:TF2083|5end_conserved_hypothetical_protein_2250834..2251064_POSITIVE 409 120 72 133 80 tfor:TF3067|5end_conserved_hypothetical_protein_3292432..3292662_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 490 116 71 50 1 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 440 119 71 135 78 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 430 114 73 146 110 tfor:TF3064|3end_oxidoreductase,_aldo/keto_reductase_family_3290984..3291134_POSITIVE 421 98 53 40 6 tfor:TF0798|3end_conserved_hypothetical_protein;_possible_lactoylglutathione_lyase_855235..855385_POSITIVE 417 119 72 47 2 tfor:TF0745|3end_conserved_hypothetical_protein_791074..791224_POSITIVE 415 100 56 150 108 tfor:TF1400|3end_polysaccharide_biosynthesis_protein;_membrane_protein_1476573..1476723_POSITIVE 408 116 71 68 10 tfor:TF1680|3end_peptide_chain_release_factor_3_1794969..1795119_POSITIVE 398 120 72 61 12 tfor:TF2593|3end_amino_acid_transport_protein_2764242..2764392_POSITIVE 394 90 43 149 84 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 392 98 56 57 13 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 388 100 54 86 21 tfor:TF0583|3end_possible_gliding_motility-related_protein_613829..613979_POSITIVE 383 115 73 49 1 tfor:TF2673|3end_conserved_hypothetical_protein_2848272..2848422_POSITIVE 383 118 72 99 51 tfor:TF1498|3end_GTP-binding_protein_1598490..1598640_POSITIVE 380 116 71 103 41 tfor:TF2344|3end_ATP/GTP_binding_protein_2508434..2508584_POSITIVE 378 120 72 139 86 tfor:TF2328|3end_conserved_hypothetical_protein_2488349..2488499_POSITIVE 378 97 56 62 20 tfor:TF1597|3end_TatD_family_protein_1713418..1713568_POSITIVE 377 96 56 61 22 tfor:TF1247|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330928..1331078_POSITIVE 375 89 48 142 104 tfor:TF0061|3end_hypothetical_protein_65006..65156_POSITIVE 373 119 79 37 4 tfor:TF0512|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_538264..538414_POSITIVE 373 128 81 75 18 tfor:TF0248|3end_hypothetical_protein_278895..279045_POSITIVE