Origin IGS: agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaatagcggataaaaacaggattttattcttttgatctgttttaaaatcagtaagttggaaaataatcaatcttttttttcaaaaaagtgtattatttcaaataaaacctatatct Mask Tandem Repeat Region ================================================ agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc Find is-nt database================================================ Query_seq: TF0579:TF0580|TF0579:TF0580:DNA-binding protein HU:A/G-specific adenine glycosylase:->->:610185..610301 117 agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0579:TF0580|TF0579:TF0580:DNA-binding protein HU:A/G-specific adenine glycosylase:->->:610185..610301 117 agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0579:TF0580|TF0579:TF0580:DNA-binding protein HU:A/G-specific adenine glycosylase:->->:610185..610301 117 agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 2 End: 91 . I Y T K N S I I C K K S F F S Q N N E L K S I K F C I L L M .......................... agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc 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================================================ agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0579:TF0580|TF0579:TF0580:DNA-binding protein HU:A/G-specific adenine glycosylase:->->:610185..610301 117 agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: tfor_TF0579_TF0580|DNA-binding protein HU:A/G-specific adenine glycosylase|POSITIVE:POSITIVE|[610185,610301]|117 HSP 1 e-value: 4.0E-46 bit: 184.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 agatataggttttatttgaaataatacacttttttgnnnnnnnngattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc agatataggttttatttgaaataatacacttttttgaaaaaaaagattgattattttccaacttactgattttaaaacagatcaaaagaataaaatcctgtttttatccgctatttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUAUAGGUUUUAUUUGAAAUAAUACACUUUUUUGAAAAAAAAGAUUGAUUAUUUUCCAACUUACUGAUUUUAAAACAGAUCAAAAGAAUAAAAUCCUGUUUUUAUCCGCUAUUUC (((.(((((((((((((((((((((.((.((((((.....)))))).)))))))))).........((((((......))))))...)))))))).))))).)))............ (-18.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUAGCGGAUAAAAACAGGAUUUUAUUCUUUUGAUCUGUUUUAAAAUCAGUAAGUUGGAAAAUAAUCAAUCUUUUUUUUCAAAAAAGUGUAUUAUUUCAAAUAAAACCUAUAUCU (((((((.((((((((......))))))))..(((((.((((((..(((......)))..))))))))))).((((((.....))))))....)))))))................. (-14.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 208 110 85 65 38 tfor:TF1008|5end_rod_shape-determining_protein_MreC_1063446..1063676_POSITIVE 197 104 61 185 136 tfor:TF2541|5end_transposase_2723914..2724144_POSITIVE 189 73 46 87 62 tfor:TF1758|5end_conserved_hypothetical_protein_1894769..1894999_POSITIVE 181 73 31 87 54 tfor:TF2757|5end_hypothetical_protein_2942022..2942252_POSITIVE 170 109 66 168 134 tfor:TF2636|5end_glutaminase_2806096..2806326_POSITIVE 165 50 2 94 37 tfor:TF0411|5end_methyltransferase_428917..429147_POSITIVE 164 107 77 91 57 tfor:TF1801|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_1944213..1944443_POSITIVE 163 110 77 125 100 tfor:TF1718|5end_conserved_hypothetical_protein_1840462..1840692_POSITIVE 162 36 3 222 190 tfor:TF2337|5end_conserved_hypothetical_protein_2497997..2498227_POSITIVE 162 110 78 160 129 tfor:TF1001|5end_penicillin-binding_protein_1A_1054097..1054327_POSITIVE 161 109 78 93 56 tfor:TF2844|5end_possible_phosphatase_or_hydrolase_3033680..3033910_POSITIVE 160 110 75 73 41 tfor:TF3088|5end_conserved_hypothetical_protein_3322512..3322742_POSITIVE 160 82 43 63 32 tfor:TF0133|5end_transposase_element_145174..145404_POSITIVE 158 43 3 185 143 tfor:TF1997|5end_ROK_family_transcriptional_regulator_2151638..2151868_POSITIVE 158 62 28 218 180 tfor:TF0990|5end_hypothetical_protein_1045395..1045625_POSITIVE 158 69 24 183 125 tfor:TF0650|5end_serine/threonine-protein_kinase_691442..691672_POSITIVE 157 62 28 163 125 tfor:TF0988|5end_conserved_hypothetical_protein;_possible_nucleotidyltransferase_1044463..1044693_POSITIVE 156 48 3 119 75 tfor:TF2168|5end_hypothetical_protein_2343916..2344146_POSITIVE 155 110 61 201 158 tfor:TF2920|5end_conserved_hypothetical_protein_3115903..3116133_POSITIVE 154 71 45 96 65 tfor:TF2865|5end_conserved_hypothetical_protein;_possible_Rhs_family_protein_3057184..3057414_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 189 73 46 63 38 tfor:TF1757|3end_chromosome_partitioning_protein_1894825..1894975_POSITIVE 170 109 66 93 59 tfor:TF2635|3end_ABC_transporter,_ATP-binding_protein/permease_component_2806101..2806251_POSITIVE 170 99 53 82 39 tfor:TF0428|3end_methylmalonyl-CoA_mutase,_beta_subunit_450033..450183_POSITIVE 164 73 43 30 3 tfor:TF2756|3end_conserved_hypothetical_protein_2942045..2942195_POSITIVE 164 107 77 49 15 tfor:TF1800|3end_conserved_hypothetical_protein_1944251..1944401_POSITIVE 163 110 77 77 52 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 161 109 78 93 56 tfor:TF2843|3end_conserved_hypothetical_protein;_possible_lipoprotein_3033760..3033910_POSITIVE 160 110 75 63 31 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 158 43 3 58 16 tfor:TF1996|3end_ATP-dependent_exonuclease_SbcC_2151591..2151741_POSITIVE 158 69 24 99 41 tfor:TF0649|3end_protein_serine/threonine_phosphatase_691438..691588_POSITIVE 157 109 67 124 92 tfor:TF2597|3end_outer_membrane_receptor_protein;_possible_TonB_dependent_receptor_2770851..2771001_POSITIVE 156 48 3 102 58 tfor:TF2167|3end_hypothetical_protein_2343979..2344129_POSITIVE 154 71 45 32 1 tfor:TF2864|3end_conserved_hypothetical_protein_3057200..3057350_POSITIVE 154 109 64 142 100 tfor:TF2235|3end_tetracycline_resistance_protein_related_to_CtnDOT_tetQ_2410260..2410410_POSITIVE 144 73 43 99 67 tfor:TF1682|3end_hydrolase_1797343..1797493_POSITIVE 140 106 82 63 37 tfor:TF1877|3end_hypothetical_protein_2030665..2030815_POSITIVE 139 108 64 51 18 tfor:TF1767|3end_3-dehydroquinate_synthase_1906624..1906774_POSITIVE 139 99 58 67 21 tfor:TF1754|3end_conserved_hypothetical_protein_1891847..1891997_POSITIVE 138 68 27 49 8 tfor:TF1428|3end_conserved_hypothetical_protein_1513996..1514146_POSITIVE 137 68 47 55 33 tfor:TF3102|3end_hypothetical_protein_3332969..3333119_POSITIVE