Origin IGS: ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctgatagaataagtaaaaaaatgaattttcttttcattaaaattctcctaaaattaaatttatgttaaagattataccataattctattattttttaaaatttaa Mask Tandem Repeat Region ================================================ ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct Find is-nt database================================================ Query_seq: FN0609:FN0610|FN0609:FN0610:SsrA-binding protein:hypothetical protein:->->:1264848..1264954 107 ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0609:FN0610|FN0609:FN0610:SsrA-binding protein:hypothetical protein:->->:1264848..1264954 107 ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0609:FN0610|FN0609:FN0610:SsrA-binding protein:hypothetical protein:->->:1264848..1264954 107 ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct Predict ORF larger than 30AA ================================================ ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct 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: 85 Start: 6 End: 35 .....TTTTAAAAAATAATAGAATTATGGTATAAT........................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 52 End: 81 ...................................................ATTTTCTTTTCATTAAAATTCTCCTAAAAT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0609:FN0610|FN0609:FN0610:SsrA-binding protein:hypothetical protein:->->:1264848..1264954 107 ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_003454_FN0609_FN0610|SsrA-binding protein:hypothetical protein|POSITIVE:POSITIVE|[1264848,1264954]|107 HSP 1 e-value: 6.0E-42 bit: 170.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcannnnnnnacttattctatcagct ttaaattttaaaaaataatagaattatggtataatctttaacataaatttaattttaggagaattttaatgaaaagaaaattcatttttttacttattctatcagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAUUUUAAAAAAUAAUAGAAUUAUGGUAUAAUCUUUAACAUAAAUUUAAUUUUAGGAGAAUUUUAAUGAAAAGAAAAUUCAUUUUUUUACUUAUUCUAUCAGCU .................(((((((...((((...(((((....((((......))))))))).....((((((.......))))))....)))).)))))))..... (-10.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGAUAGAAUAAGUAAAAAAAUGAAUUUUCUUUUCAUUAAAAUUCUCCUAAAAUUAAAUUUAUGUUAAAGAUUAUACCAUAAUUCUAUUAUUUUUUAAAAUUUAA ...(((((((((.........((((((.......))))))......................((((........)))).....)))))))))............... ( -9.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 170 65 28 59 26 NC_003454:FN0880|5end_ABC_transporter_ATP-binding_protein_1541978..1542208_NEGATIVE 170 40 15 44 21 NC_003454:FN0365|5end_ATP_synthase_protein_I,_sodium_ion_specific_994859..995089_NEGATIVE 170 94 57 216 178 NC_003454:FN0222|5end_Melibiose_carrier_protein_846812..847042_POSITIVE 165 67 22 154 109 NC_003454:FN0493|5end_hypothetical_protein_1138552..1138782_NEGATIVE 148 100 52 198 138 NC_003454:FN0646|5end_Glutamyl-tRNA_reductase_1303289..1303519_NEGATIVE 148 68 27 207 168 NC_003454:FN1728|5end_Pyrrolidone-carboxylate_peptidase_228366..228596_NEGATIVE 147 92 51 226 179 NC_003454:FN0122|5end_hypothetical_protein_753401..753631_POSITIVE 145 96 63 198 165 NC_003454:FN1866|5end_Lysine_2,3-aminomutase_358440..358670_NEGATIVE 142 100 67 94 61 NC_003454:FN1068|5end_Smf_protein_1713811..1714041_POSITIVE 139 68 24 139 97 NC_003454:FN0275|5end_Transposase_901560..901790_NEGATIVE 138 87 45 220 183 NC_003454:FN0920|5end_Protease_HTPX_1575547..1575777_NEGATIVE 137 87 56 195 161 NC_003454:FN1158|5end_hypothetical_protein_1814420..1814650_POSITIVE 137 100 52 109 57 NC_003454:FN0283|5end_tRNA_(Guanine-N1)_-methyltransferase_913405..913635_NEGATIVE 135 58 15 201 159 NC_003454:FN1554|5end_Fusobacterium_outer_membrane_protein_family_73467..73697_NEGATIVE 134 77 31 64 8 NC_003454:FN0261|5end_Pyruvate_formate-lyase_activating_enzyme_887510..887740_NEGATIVE 132 61 27 117 86 NC_003454:FN0255|5end_Hypothetical_cytosolic_protein_881870..882100_POSITIVE 132 89 47 182 138 NC_003454:FN1602|5end_Hypothetical_cytosolic_protein_111492..111722_NEGATIVE 131 100 70 71 43 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 128 85 46 145 110 NC_003454:FN0848|5end_hypothetical_protein_1507069..1507299_POSITIVE 127 77 43 230 194 NC_003454:FN0917|5end_hypothetical_protein_1572595..1572825_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 170 65 28 78 45 NC_003454:FN0881|3end_ABC_transporter_integral_membrane_protein_1541959..1542109_NEGATIVE 148 100 52 97 37 NC_003454:FN0647|3end_Hypothetical_cytosolic_protein_1303390..1303540_NEGATIVE 145 96 63 78 45 NC_003454:FN1867|3end_Zn-dependent_alcohol_dehydrogenase_and_related_dehydrogenase_358560..358710_NEGATIVE 143 91 51 134 95 NC_003454:FN0555|3end_Transcriptional_regulator,_MerR_family_1208332..1208482_POSITIVE 142 100 67 82 49 NC_003454:FN1067|3end_Tetratricopeptide_repeat_family_protein_1713879..1714029_POSITIVE 137 100 51 53 6 NC_003454:FN0556|3end_hypothetical_protein_1208380..1208530_NEGATIVE 137 100 52 112 60 NC_003454:FN0284|3end_16S_rRNA_processing_protein_rimM_913402..913552_NEGATIVE 132 100 55 66 14 NC_003454:FN0274|3end_Transposase_900285..900435_NEGATIVE 132 89 47 64 20 NC_003454:FN1603|3end_2',3'-cyclic_nucleotide_3'-phosphodiesterase_111610..111760_NEGATIVE 128 85 46 128 93 NC_003454:FN0847|3end_TPR-repeat-containing_proteins_1507132..1507282_POSITIVE 127 57 27 87 61 NC_003454:FN0076|3end_Ethanolamine_two-component_response_regulator_714784..714934_POSITIVE 125 79 54 47 23 NC_003454:FN0047|3end_Exodeoxyribonuclease_III_685268..685418_POSITIVE 123 100 78 91 69 NC_003454:FN1484|3end_Tetratricopeptide_repeat_family_protein_2166538..2166688_NEGATIVE 123 100 57 53 14 NC_003454:FN1754|3end_thiazole_synthase_250344..250494_NEGATIVE 123 100 58 85 34 NC_003454:FN1666|3end_hypothetical_protein_163257..163407_POSITIVE 122 100 80 87 68 NC_003454:FN1853|3end_methylaspartate_mutase_subunit_S_342607..342757_POSITIVE 121 100 55 105 47 NC_003454:FN0812|3end_Hypothetical_cytosolic_protein_1471397..1471547_POSITIVE 120 70 26 95 59 NC_003454:FN0413|3end_hypothetical_protein_1049257..1049407_NEGATIVE 118 100 62 85 50 NC_003454:FN0668|3end_High-affinity_zinc_uptake_system_protein_znuA_precursor_1324987..1325137_POSITIVE 118 100 55 66 13 NC_003454:FN0599|3end_Transposase_1255199..1255349_POSITIVE