Origin IGS: taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaattaaacattcttccgcaaaagagatcgaattcaaaaaaacacctccgaaggccgtagaacgtccccctcggaggtatctaattacttatttttttttaaaagaatctttctgttta Mask Tandem Repeat Region ================================================ taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc Find is-nt database================================================ Query_seq: TF3120:TF3121|TF3120:TF3121:HD superfamily hydrolase:nicotinate phosphoribosyltransferase:->->:3354836..3354954 119 taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3120:TF3121|TF3120:TF3121:HD superfamily hydrolase:nicotinate phosphoribosyltransferase:->->:3354836..3354954 119 taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3120:TF3121|TF3120:TF3121:HD superfamily hydrolase:nicotinate phosphoribosyltransferase:->->:3354836..3354954 119 taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 1 End: 117 L C F S E K L F F Y T I L Y R R P P R E V A K P P T K K F E I E K A S S H K M .. taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc 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================================================ taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -5.2 Tail_Score: -5.53288 Start: 41 End: 77 Full_Region: AAATAAGTAATTAGA TACCTCCGAGGGGGACGT TCT ACGGCCTTCGGAGGTG TTTTTTTGAATTCGA ........................................TACCTCCGAGGGGGACGTTCTACGGCCTTCGGAGGTG.......................................... TransTerm Strand: + Conf: 70 HP_score: -5.6 Tail_Score: -4.40173 Start: 43 End: 75 Full_Region: ATAAGTAATTAGATA CCTCCGAGGGGGACGT TCT ACGGCCTTCGGAGG TGTTTTTTTGAATTC ..........................................CCTCCGAGGGGGACGTTCTACGGCCTTCGGAGG............................................ Find igs database================================================ Query_seq: TF3120:TF3121|TF3120:TF3121:HD superfamily hydrolase:nicotinate phosphoribosyltransferase:->->:3354836..3354954 119 taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: tfor_TF3120_TF3121|HD superfamily hydrolase:nicotinate phosphoribosyltransferase|POSITIVE:POSITIVE|[3354836, 3354954]|119 HSP 1 e-value: 6.0E-33 bit: 141.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 taaacagaaagattcttttnnnnnnnnntaagtaattagatacctccgagggggacgttctacggccttcggaggtgnnnnnnngaattcgatctcttttgcggaagaatgtttaattc taaacagaaagattcttttaaaaaaaaataagtaattagatacctccgagggggacgttctacggccttcggaggtgtttttttgaattcgatctcttttgcggaagaatgtttaattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAGAAAGAUUCUUUUAAAAAAAAAUAAGUAAUUAGAUACCUCCGAGGGGGACGUUCUACGGCCUUCGGAGGUGUUUUUUUGAAUUCGAUCUCUUUUGCGGAAGAAUGUUUAAUUC ((((((...(((((..(((((((((...(((....))).(((((((((((((...((.....)).))))))))))))))))))))))...)))))......(....)..)))))).... (-34.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUUAAACAUUCUUCCGCAAAAGAGAUCGAAUUCAAAAAAACACCUCCGAAGGCCGUAGAACGUCCCCCUCGGAGGUAUCUAAUUACUUAUUUUUUUUUAAAAGAAUCUUUCUGUUUA ((((.(((.((((((....(((((((((.(....)........((((((((.((.((.....))...)).))))))))............)))))))))...)))))).)))..)))). (-22.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 77 39 46 4 tfor:TF2514|5end_conserved_hypothetical_protein_2691632..2691862_POSITIVE 383 81 41 172 117 tfor:TF3033|5end_S1_RNA_binding_domain_protein,_S1_ribosomal_protein_3256786..3257016_POSITIVE 382 77 35 211 151 tfor:TF1681|5end_dTDP-4-keto-L-rhamnose_reductase_1794904..1795134_POSITIVE 375 108 61 54 11 tfor:TF1039|5end_conserved_hypothetical_protein_1100608..1100838_POSITIVE 352 86 42 224 183 tfor:TF0885|5end_conjugative_transposon_protein_fragment_937754..937984_POSITIVE 352 86 42 73 32 tfor:TF0884|5end_hypothetical_protein_937603..937833_POSITIVE 350 82 43 229 191 tfor:TF2557|5end_30S_ribosomal_protein_S19_2737170..2737400_POSITIVE 336 86 46 203 155 tfor:TF2215|5end_conserved_hypothetical_protein_2387501..2387731_POSITIVE 336 84 46 197 155 tfor:TF1327|5end_L-fucose_permease_1405790..1406020_POSITIVE 333 88 43 223 165 tfor:TF0379|5end_conserved_hypothetical_protein,_nif3_family_399458..399688_POSITIVE 326 86 43 208 162 tfor:TF2512|5end_possible_abortive_infection_protein_2690247..2690477_POSITIVE 326 75 45 207 167 tfor:TF0685|5end_hypothetical_protein_730852..731082_POSITIVE 324 98 52 225 177 tfor:TF2761|5end_thioredoxin_2945390..2945620_POSITIVE 324 89 50 228 187 tfor:TF2341|5end_hypothetical_protein_2505735..2505965_POSITIVE 323 88 43 62 18 tfor:TF2636|5end_glutaminase_2806096..2806326_POSITIVE 323 88 45 185 143 tfor:TF0950|5end_ribosomal_large_subunit_pseudouridine_synthase_D_(pseudouridylate_synthase)_(uracil_hydrolyase)_994630..994860_POSITIVE 322 90 44 164 107 tfor:TF1003|5end_conserved_hypothetical_protein;_possible_secreted_glycosylhydrolase_1058177..1058407_POSITIVE 320 79 36 84 28 tfor:TF2547|5end_hypothetical_protein_2730664..2730894_POSITIVE 320 89 41 92 48 tfor:TF2358|5end_possible_small-conductance_mechanosensitive_channel_2523829..2524059_POSITIVE 320 73 39 43 4 tfor:TF1600|5end_uroporphyrinogen-III_synthase_1713964..1714194_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 554 80 38 53 11 tfor:TF3120|3end_HD_superfamily_hydrolase_3354775..3354925_POSITIVE 383 81 41 144 89 tfor:TF3032|3end_thiamin_biosynthesis_protein_3256838..3256988_POSITIVE 351 79 38 67 20 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 350 82 43 74 36 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 326 86 43 113 67 tfor:TF2511|3end_RNA_binding_protein_2690232..2690382_POSITIVE 323 80 38 147 93 tfor:TF0684|3end_conserved_hypothetical_protein_730564..730714_POSITIVE 322 90 44 139 82 tfor:TF1002|3end_replicative_DNA_helicase_1058232..1058382_POSITIVE 320 89 41 83 39 tfor:TF2357|3end_collagenase_2523900..2524050_POSITIVE 320 77 43 46 6 tfor:TF2172|3end_hypothetical_protein_2346135..2346285_POSITIVE 320 73 39 53 14 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 319 85 48 121 76 tfor:TF2876|3end_cytosine_deaminase_3065664..3065814_POSITIVE 319 85 47 72 22 tfor:TF0279|3end_conserved_hypothetical_protein_308679..308829_POSITIVE 318 85 42 106 41 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 316 87 47 47 4 tfor:TF0746|3end_possible_DNA_polymerase_III_792910..793060_POSITIVE 311 75 46 56 28 tfor:TF2466|3end_pyruvate_kinase_2645907..2646057_POSITIVE 311 87 43 104 64 tfor:TF0939|3end_ISPg1_transposase,_IS1106-related_transposase_981115..981265_POSITIVE 311 75 47 122 91 tfor:TF0429|3end_ABC_transporter,_ATP-binding_protein_452227..452377_POSITIVE 310 80 39 110 70 tfor:TF3018|3end_polyphosphate_kinase_3242241..3242391_POSITIVE 309 76 37 66 23 tfor:TF1857|3end_conserved_hypothetical_protein_2015168..2015318_POSITIVE 308 84 41 143 93 tfor:TF1690|3end_chaperone_protein_dnaK_1808721..1808871_POSITIVE