Origin IGS: ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaatattttttttataaattca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaatttataaaaaaaatattgaaatataatattttttcttgacattaaagaatttttatagtagaatgcgaaagaaaggtagagaaattaacttctcttgttcaaaatatttaacttttataaaatatatggaggtatttaa Mask Tandem Repeat Region ================================================ ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaatattttttttataaattca Find is-nt database================================================ Query_seq: FN1024:FN1025|FN1024:FN1025:DNA-binding protein HU:Guanine-hypoxanthine permease:<-<-:1678571..1678713 143 ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaatattttttttataaattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1024:FN1025|FN1024:FN1025:DNA-binding protein HU:Guanine-hypoxanthine permease:<-<-:1678571..1678713 143 ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaatattttttttataaattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1024:FN1025|FN1024:FN1025:DNA-binding protein HU:Guanine-hypoxanthine permease:<-<-:1678571..1678713 143 ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaatattttttttataaattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaatattttttttataaattca Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 3 End: 104 .. F V E M Y K I F T L Y K S C S F N I E R G K K R M R S Y F N K L T M ....................................... ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaatattttttttataaattca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 90 Start: 76 End: 105 ...........................................................................CTTGACATTAAAGAATTTTTATAGTAGAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaatattttttttataaattca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 48 HP_score: -3.3 Tail_Score: -3.65603 Start: 46 End: 61 Full_Region: tgcgaaagaaaggta gagaa attaac ttctc ttgttcaaaatattt .............................................gagaaattaacttctc.................................................................................. Find igs database================================================ Query_seq: FN1024:FN1025|FN1024:FN1025:DNA-binding protein HU:Guanine-hypoxanthine permease:<-<-:1678571..1678713 143 ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaatattttttttataaattca Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_003454_FN1024_FN1025|DNA-binding protein HU:Guanine-hypoxanthine permease|NEGATIVE:NEGATIVE|[1678571,1678713]|143 HSP 1 e-value: 1.0E-65 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaata................. ttaaatacctccatatattttataaaagttaaatattttgaacaagagaagttaatttctctacctttctttcgcattctactataaaaattctttaatgtcaagaaaaaatattatatttcaata................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAUACCUCCAUAUAUUUUAUAAAAGUUAAAUAUUUUGAACAAGAGAAGUUAAUUUCUCUACCUUUCUUUCGCAUUCUACUAUAAAAAUUCUUUAAUGUCAAGAAAAAAUAUUAUAUUUCAAUA .....................................(((((..(((((((....)))))))...((((((..(((((..................))))).))))))...........))))).. (-11.57) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUGAAAUAUAAUAUUUUUUCUUGACAUUAAAGAAUUUUUAUAGUAGAAUGCGAAAGAAAGGUAGAGAAAUUAACUUCUCUUGUUCAAAAUAUUUAACUUUUAUAAAAUAUAUGGAGGUAUUUAA ..(((...(((.(((....(((((.......)))))....))).))).....)))..(((....((((((......))))))..)))..........(((((((((.....)))))))))...... (-17.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 738 90 41 181 132 NC_003454:FN1024|5end_DNA-binding_protein_HU_1678480..1678710_NEGATIVE 290 87 49 224 180 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 272 78 57 117 96 NC_003454:FN2034|5end_Protein_yicC_538795..539025_NEGATIVE 250 77 52 227 197 NC_003454:FN0361|5end_ATP_synthase_delta_chain,_sodium_ion_specific_992905..993135_NEGATIVE 233 83 46 101 61 NC_003454:FN0005|5end_Jag_protein_644008..644238_POSITIVE 210 88 41 76 14 NC_003454:FN1922|5end_hypothetical_protein_419435..419665_NEGATIVE 205 103 61 174 131 NC_003454:FN2019|5end_Ribosome-binding_factor_A_522292..522522_NEGATIVE 201 79 39 109 69 NC_003454:FN0149|5end_Malonyl-CoA-[acyl-carrier-protein]_transacylase_777486..777716_POSITIVE 196 100 56 201 155 NC_003454:FN1381|5end_hypothetical_protein_2032434..2032664_NEGATIVE 194 81 58 164 131 NC_003454:FN0428|5end_hypothetical_protein_1070037..1070267_POSITIVE 194 83 41 215 166 NC_003454:FN1498|5end_Integral_membrane_protein_2563..2793_POSITIVE 192 89 55 51 10 NC_003454:FN1432|5end_Leucine-,_isoleucine-,_valine-,_threonine-,_and_alanine-binding_protein_2101580..2101810_NEGATIVE 189 98 54 66 27 NC_003454:FN2107|5end_galactokinase_618150..618380_POSITIVE 188 80 36 46 2 NC_003454:FN1455|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_2136519..2136749_NEGATIVE 188 50 8 127 85 NC_003454:FN0238|5end_hypothetical_protein_863314..863544_NEGATIVE 186 68 47 167 143 NC_003454:FN1341|5end_Bacterial_Peptide_Chain_Release_Factor_2_(RF-2)_1995896..1996126_NEGATIVE 182 96 52 100 58 NC_003454:FN2087|5end_hypothetical_protein_599719..599949_NEGATIVE 181 83 45 107 51 NC_003454:FN0858|5end_4-alpha-glucanotransferase_1520507..1520737_NEGATIVE 181 84 46 72 24 NC_003454:FN0717|5end_Ribosomal_small_subunit_pseudouridine_synthase_A_1374913..1375143_POSITIVE 181 84 50 218 181 NC_003454:FN0133|5end_hypothetical_protein_769121..769351_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 78 57 90 69 NC_003454:FN2035|3end_DNA-directed_RNA_polymerase_beta'_chain_538822..538972_NEGATIVE 208 109 64 90 39 NC_003454:FN0325|3end_50S_ribosomal_protein_L20_960924..961074_NEGATIVE 205 66 33 136 98 NC_003454:FN0495|3end_Acetyl-CoA_acetyltransferase_1140855..1141005_POSITIVE 201 79 39 69 29 NC_003454:FN0148|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_777526..777676_POSITIVE 188 80 36 49 5 NC_003454:FN1456|3end_UDP-N-acetylmuramate--alanine_ligase_2136516..2136666_NEGATIVE 187 97 60 145 113 NC_003454:FN2020|3end_translation_initiation_factor_IF-2_522309..522459_NEGATIVE 182 72 44 71 35 NC_003454:FN0497|3end_Plasmid_addiction_system_poison_protein_1141485..1141635_POSITIVE 181 97 51 142 90 NC_003454:FN1351|3end_15_kDa_lipoprotein_precursor_2002950..2003100_NEGATIVE 181 84 46 72 24 NC_003454:FN0716|3end_Phophatidylinositol-4-phosphate_5-kinase_1374993..1375143_POSITIVE 180 105 61 117 71 NC_003454:FN1105|3end_hypothetical_protein_1750618..1750768_POSITIVE 175 97 56 148 108 NC_003454:FN1154|3end_Ribonuclease_BN_1809502..1809652_POSITIVE 175 50 2 120 74 NC_003454:FN0763|3end_Transporter,_LysE_family_1420440..1420590_POSITIVE 175 96 56 103 57 NC_003454:FN1553|3end_Transporter_67150..67300_NEGATIVE 174 87 62 68 30 NC_003454:FN1606|3end_3-deoxy-D-manno-octulosonic-acid_transferase_115286..115436_NEGATIVE 171 108 61 144 102 NC_003454:FN1085|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme_1729562..1729712_POSITIVE 169 82 45 94 59 NC_003454:FN1455|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_2135674..2135824_NEGATIVE 169 84 44 151 115 NC_003454:FN0255|3end_Hypothetical_cytosolic_protein_882117..882267_POSITIVE 168 90 41 116 67 NC_003454:FN0596|3end_hypothetical_protein_1250884..1251034_POSITIVE 168 96 56 61 17 NC_003454:FN0577|3end_hypothetical_protein_1228042..1228192_POSITIVE 168 71 56 25 10 NC_003454:FN0314|3end_Caffeoyl-CoA_O-methyltransferase_951931..952081_POSITIVE