Origin IGS: tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggaacaaaggtaatcacatctttccgaatcttcaaaatcgaagttttttgttgcaatagtactttttttctttccccaccgaaatagcgggcggatacgttgttttccgtccaagacatttggttacatccttccaaacatttacctttgggcattgttttttgatgtttttagcgaaa Mask Tandem Repeat Region ================================================ tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc Find is-nt database================================================ Query_seq: TF0613:TF0614|TF0613:TF0614:conserved hypothetical protein:UDP-glucose 6-dehydrogenase/UDP-N-acetyl-D-mannosaminuronate dehydrogenase:->->:647482..647660 179 tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0613:TF0614|TF0613:TF0614:conserved hypothetical protein:UDP-glucose 6-dehydrogenase/UDP-N-acetyl-D-mannosaminuronate dehydrogenase:->->:647482..647660 179 tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0613:TF0614|TF0613:TF0614:conserved hypothetical protein:UDP-glucose 6-dehydrogenase/UDP-N-acetyl-D-mannosaminuronate dehydrogenase:->->:647482..647660 179 tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 14 End: 145 ............. M K K Q C P K V N V W K D V T K C L G R K T T Y P P A I S V G K E K K Y Y C N K K L R F .................................. Protein_Len: 51 Strand: + Start: 25 End: 177 ........................ M P K G K C L E G C N Q M S W T E N N V S A R Y F G G E R K K V L L Q Q K T S I L K I R K D V I T F V .. Protein_Len: 38 Strand: + Start: 66 End: 179 ................................................................. M D G K Q R I R P L F R W G K K K S T I A T K N F D F E D S E R C D Y L C S Protein_Len: 41 Strand: - Start: 2 End: 124 . E S F V D F F L A W L Y I N P L I Y G F T K S P F C R I R G S N R H P F F F L V M ....................................................... Protein_Len: 32 Strand: - Start: 1 End: 96 K A L F M L F C H G F T F T Q F S T V L H R P R F V V Y G G A M ................................................................................... tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc 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================================================ tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0613:TF0614|TF0613:TF0614:conserved hypothetical protein:UDP-glucose 6-dehydrogenase/UDP-N-acetyl-D-mannosaminuronate dehydrogenase:->->:647482..647660 179 tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: tfor_TF0613_TF0614|conserved hypothetical protein:UDP-glucose 6-dehydrogenase/UDP-N-acetyl-D-mannosaminuronate dehydrogenase|POSITIVE:POSITIVE|[647482,647660]|179 HSP 1 e-value: 1.0E-84 bit: 313.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagnnnnnnngtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc tttcgctaaaaacatcaaaaaacaatgcccaaaggtaaatgtttggaaggatgtaaccaaatgtcttggacggaaaacaacgtatccgcccgctatttcggtggggaaagaaaaaaagtactattgcaacaaaaaacttcgattttgaagattcggaaagatgtgattacctttgttcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCGCUAAAAACAUCAAAAAACAAUGCCCAAAGGUAAAUGUUUGGAAGGAUGUAACCAAAUGUCUUGGACGGAAAACAACGUAUCCGCCCGCUAUUUCGGUGGGGAAAGAAAAAAAGUACUAUUGCAACAAAAAACUUCGAUUUUGAAGAUUCGGAAAGAUGUGAUUACCUUUGUUCC .............................(((((((((...((((..(((((((......)))))))...)))).....((((.((((((((((.....))))))...............................(((((....)))))...))))...))))..))))))))).... (-34.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAACAAAGGUAAUCACAUCUUUCCGAAUCUUCAAAAUCGAAGUUUUUUGUUGCAAUAGUACUUUUUUUCUUUCCCCACCGAAAUAGCGGGCGGAUACGUUGUUUUCCGUCCAAGACAUUUGGUUACAUCCUUCCAAACAUUUACCUUUGGGCAUUGUUUUUUGAUGUUUUUAGCGAAA ((((.(((((((............((((.((((......))))...)))).........))))))).)))).........(((((((((........))))))))).(((..((((((((..(..(((....((((((........))))))...)))..)..))))))))..)))... (-33.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 108 61 203 154 tfor:TF1246|5end_protease,_with_chaperone_function_1329390..1329620_POSITIVE 374 108 61 183 127 tfor:TF2922|5end_surface_antigen_BspA_3119122..3119352_POSITIVE 362 110 64 118 70 tfor:TF3055|5end_hypothetical_protein_3278775..3279005_POSITIVE 355 102 63 179 141 tfor:TF1048|5end_permease_1109241..1109471_POSITIVE 354 110 69 222 179 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 346 107 65 148 102 tfor:TF2079|5end_permease_2245585..2245815_POSITIVE 337 107 61 189 142 tfor:TF0193|5end_conserved_hypothetical_protein;_possible_internalin-like_protein_(LPXTG_motif)_207955..208185_POSITIVE 334 104 62 181 138 tfor:TF1440|5end_hypothetical_protein_1524599..1524829_POSITIVE 334 105 65 65 19 tfor:TF1289|5end_ribosomal_protein_L11_methyltransferase_1370302..1370532_POSITIVE 328 119 71 228 178 tfor:TF1435|5end_acetate_coenzyme_A_transferase_1519574..1519804_POSITIVE 326 108 71 181 130 tfor:TF1481|5end_ABC_transporter,_ATP-binding_protein_1574783..1575013_POSITIVE 320 100 51 187 144 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 319 107 64 69 22 tfor:TF3094|5end_translation_elongation_factor_Ts_3326122..3326352_POSITIVE 314 100 56 163 119 tfor:TF0414|5end_N-ethylammeline_chlorohydrolase_431789..432019_POSITIVE 313 107 67 105 66 tfor:TF1866|5end_conserved_hypothetical_protein;_possible_transposase_2022272..2022502_POSITIVE 311 114 71 60 12 tfor:TF2519|5end_membrane_protein,_metallopeptidase_M23/M37_family_2697676..2697906_POSITIVE 306 110 63 62 15 tfor:TF1472|5end_acyl-ACP_thioesterase_1565475..1565705_POSITIVE 303 107 64 156 115 tfor:TF2475|5end_GTP_pyrophosphokinase,_(p)ppGpp_synthetase_2651925..2652155_POSITIVE 303 105 67 133 96 tfor:TF2271|5end_conserved_hypothetical_protein_2435802..2436032_POSITIVE 302 90 45 228 157 tfor:TF3039|5end_ABC_transporter,_ATP-binding_protein_3265731..3265961_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 110 69 58 15 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE 337 107 61 138 91 tfor:TF0192|3end_hypothetical_protein_207984..208134_POSITIVE 333 109 64 151 104 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 324 108 62 98 51 tfor:TF0880|3end_conserved_hypothetical_protein_934371..934521_POSITIVE 319 107 64 48 1 tfor:TF3093|3end_30S_ribosomal_protein_S2_3326181..3326331_POSITIVE 302 106 66 131 77 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 302 106 67 148 92 tfor:TF0200|3end_2-nitropropane_dioxygenase_226082..226232_POSITIVE 301 160 119 137 86 tfor:TF2214|3end_peptidyl-prolyl_cis-trans_isomerase_2387564..2387714_POSITIVE 300 106 61 121 69 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 299 106 64 79 40 tfor:TF2466|3end_pyruvate_kinase_2645907..2646057_POSITIVE 298 110 61 146 85 tfor:TF0134|3end_transposase_element_146044..146194_POSITIVE 294 104 62 105 50 tfor:TF2394|3end_integrase/recombinase_XerD_2566590..2566740_POSITIVE 294 106 65 79 41 tfor:TF1342|3end_possible_lipoprotein_1424620..1424770_POSITIVE 292 99 55 94 37 tfor:TF2991|3end_conserved_hypothetical_protein_3209107..3209257_POSITIVE 291 127 81 94 50 tfor:TF2007|3end_uracil_phosphoribosyltransferase_2159327..2159477_POSITIVE 289 116 71 72 25 tfor:TF2971|3end_possible_transposase_3179354..3179504_POSITIVE 289 107 72 137 93 tfor:TF1784|3end_conserved_hypothetical_protein;_possible_formiminotransferase-cyclodeaminase_1924556..1924706_POSITIVE 289 116 71 72 25 tfor:TF1770|3end_hypothetical_protein_1908812..1908962_POSITIVE 288 104 62 131 86 tfor:TF1145|3end_anaerobic_C4-dicarboxylate_membrane_transporter_1227180..1227330_POSITIVE 286 108 67 57 20 tfor:TF2274|3end_conserved_hypothetical_protein_2436986..2437136_POSITIVE