Origin IGS: gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaacgaggaactaattttcagttgcaaagatacaaacttttttggaaagcgcctactgtttcctgctatatccgtttggttgaaaggttttcccctcgtaaatccctgaacacgc Mask Tandem Repeat Region ================================================ gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt Find is-nt database================================================ Query_seq: TF0499:TF0500|TF0499:TF0500:hypothetical protein:hypothetical protein:->->:526712..526827 116 gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0499:TF0500|TF0499:TF0500:hypothetical protein:hypothetical protein:->->:526712..526827 116 gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0499:TF0500|TF0499:TF0500:hypothetical protein:hypothetical protein:->->:526712..526827 116 gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 10 End: 102 ......... P N V L P F G K L W V S I A P F L L R K G F F N T D K C S F M .............. Protein_Len: 31 Strand: - Start: 2 End: 94 . T N L S K R P S F R E V L R I Y C S V T P A K W F L K Y R Q M ...................... gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt 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================================================ gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0499:TF0500|TF0499:TF0500:hypothetical protein:hypothetical protein:->->:526712..526827 116 gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: tfor_TF0499_TF0500|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[526712,526827]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt gcgtgttcagggatttacgaggggaaaacctttcaaccaaacggatatagcaggaaacagtaggcgctttccaaaaaagtttgtatctttgcaactgaaaattagttcctcgttgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUGUUCAGGGAUUUACGAGGGGAAAACCUUUCAACCAAACGGAUAUAGCAGGAAACAGUAGGCGCUUUCCAAAAAAGUUUGUAUCUUUGCAACUGAAAAUUAGUUCCUCGUUGU ................((((((((......(((((.......(((....((.(....).....))....)))........(((((....))))).))))).....))))))))... (-21.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAACGAGGAACUAAUUUUCAGUUGCAAAGAUACAAACUUUUUUGGAAAGCGCCUACUGUUUCCUGCUAUAUCCGUUUGGUUGAAAGGUUUUCCCCUCGUAAAUCCCUGAACACGC ...((((((......(((((((...((((((........))))))..(((((..((..((.....))..))..)))))..))))))).......))))))................ (-19.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 86 50 208 170 tfor:TF1065|5end_conserved_hypothetical_protein_1135313..1135543_POSITIVE 306 70 22 131 86 tfor:TF0746|5end_possible_DNA_polymerase_III_792261..792491_POSITIVE 302 65 21 207 152 tfor:TF0839|5end_aminopeptidasem_M28_family_890442..890672_POSITIVE 297 44 1 207 167 tfor:TF0708|5end_possible_alkaline_phosphatase_752173..752403_POSITIVE 294 87 42 67 15 tfor:TF2676|5end_conserved_hypothetical_protein_2849645..2849875_POSITIVE 292 49 1 65 2 tfor:TF2526|5end_outer_membrane_protein,_TonB_dependent_receptor_2705547..2705777_POSITIVE 287 73 37 230 195 tfor:TF1921|5end_hypothetical_protein_2070322..2070552_POSITIVE 284 68 29 39 5 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 281 89 42 111 60 tfor:TF0190|5end_cell_division_protein_FtsH_204029..204259_POSITIVE 280 42 1 186 138 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 280 38 2 226 191 tfor:TF1407|5end_hypothetical_protein_1482185..1482415_POSITIVE 277 96 53 205 162 tfor:TF0976|5end_outer_membrane_receptor,_Ton-linked_1024482..1024712_POSITIVE 272 72 31 160 114 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 270 54 19 41 2 tfor:TF0748|5end_ATP-dependent_protease_La_792890..793120_POSITIVE 269 73 31 64 20 tfor:TF0275|5end_outer_membrane_protein_300884..301114_POSITIVE 268 70 37 31 1 tfor:TF2801|5end_outer_membrane_protein,_TonB_dependent_receptor_2986285..2986515_POSITIVE 267 67 22 63 11 tfor:TF2033|5end_conserved_hypothetical_protein_2191529..2191759_POSITIVE 260 45 4 40 7 tfor:TF1908|5end_possible_phosphoglycerate_mutase_2062695..2062925_POSITIVE 259 67 21 231 183 tfor:TF2848|5end_cobalamin_biosynthesis_protein_3036368..3036598_POSITIVE 259 100 60 208 165 tfor:TF1032|5end_possible_internalin-related_protein_1091296..1091526_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 70 22 98 53 tfor:TF0744|3end_DNA_polymerase_III_subunit,_gamma/tau_792308..792458_POSITIVE 287 73 37 72 37 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 284 68 29 39 5 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 281 89 42 92 41 tfor:TF0189|3end_phosphatidate_cytidylytransferase_(CDP-diglyceride_synthetase)_204090..204240_POSITIVE 280 42 1 72 24 tfor:TF2832|3end_possible_proton/sodium:glutamate_symporter_protein_3023939..3024089_POSITIVE 270 99 52 122 64 tfor:TF2647|3end_transcriptional_regulator,_possible_arylsulfatase_regulator_2818135..2818285_POSITIVE 269 73 31 82 38 tfor:TF0276|3end_hypothetical_protein_300982..301132_POSITIVE 256 47 2 85 28 tfor:TF0505|3end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_531103..531253_POSITIVE 255 56 11 111 56 tfor:TF1764|3end_transcriptional_regulator;_possible_MerR_family_1901848..1901998_POSITIVE 250 97 56 51 2 tfor:TF1709|3end_conserved_hypothetical_protein_1829710..1829860_POSITIVE 250 68 21 56 14 tfor:TF1166|3end_ABC_transporter,_permease_component_1248603..1248753_POSITIVE 246 69 21 70 34 tfor:TF3030|3end_16S_rRNA_processing_protein_3254296..3254446_POSITIVE 245 83 41 142 103 tfor:TF2735|3end_hypothetical_protein_2917928..2918078_POSITIVE 244 50 1 88 35 tfor:TF2345|3end_dGTP_triphosphohydrolase_2509774..2509924_POSITIVE 244 71 32 55 4 tfor:TF1321|3end_conserved_hypothetical_protein_1401914..1402064_POSITIVE 244 50 2 71 31 tfor:TF0959|3end_periplasmic_protease_1008540..1008690_POSITIVE 244 66 25 126 90 tfor:TF0663|3end_conserved_hypothetical_protein_709093..709243_POSITIVE 242 70 21 139 93 tfor:TF2893|3end_conserved_hypothetical_protein;_possible_phosphoesterase_3082039..3082189_POSITIVE 242 45 1 145 89 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 242 90 45 88 42 tfor:TF0475|3end_possible_transcriptional_regulator,_AraC_family_494825..494975_POSITIVE