Origin IGS: atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggtaaaaaagttgaagtaactgagaaagatgagcatagacatttcaaaaaatttcttttaaaattaggtaaggataaattacaaggattaagtataatagatgtaagggaactat Mask Tandem Repeat Region ================================================ atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt Find is-nt database================================================ Query_seq: FN1602:FN1603|FN1602:FN1603:Hypothetical cytosolic protein:2',3'-cyclic nucleotide 3'-phosphodiesterase:<-<-:111583..111699 117 atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1602:FN1603|FN1602:FN1603:Hypothetical cytosolic protein:2',3'-cyclic nucleotide 3'-phosphodiesterase:<-<-:111583..111699 117 atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1602:FN1603|FN1602:FN1603:Hypothetical cytosolic protein:2',3'-cyclic nucleotide 3'-phosphodiesterase:<-<-:111583..111699 117 atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 18 End: 116 ................. M I L N P C N L S L P N F K R N F L K C L C S S F S V T S T F L P . atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt 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: 87 Start: 52 End: 81 ...................................................ATAGACATTTCAAAAAATTTCTTTTAAAAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1602:FN1603|FN1602:FN1603:Hypothetical cytosolic protein:2',3'-cyclic nucleotide 3'-phosphodiesterase:<-<-:111583..111699 117 atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_003454_FN1602_FN1603|Hypothetical cytosolic protein:2',3'-cyclic nucleotide 3'-phosphodiesterase|NEGATIVE:NEGATIVE|[111583, 111699]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt atagttcccttacatctattatacttaatccttgtaatttatccttacctaattttaaaagaaattttttgaaatgtctatgctcatctttctcagttacttcaacttttttacctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGUUCCCUUACAUCUAUUAUACUUAAUCCUUGUAAUUUAUCCUUACCUAAUUUUAAAAGAAAUUUUUUGAAAUGUCUAUGCUCAUCUUUCUCAGUUACUUCAACUUUUUUACCUU ((((.....(((((...((((....))))...)))))..............((((((((((....))))))))))..)))).................................... ( -7.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGUAAAAAAGUUGAAGUAACUGAGAAAGAUGAGCAUAGACAUUUCAAAAAAUUUCUUUUAAAAUUAGGUAAGGAUAAAUUACAAGGAUUAAGUAUAAUAGAUGUAAGGGAACUAU ............(((((((..(((.(.........).)))..))))))).....((((((((.((((..((((.......))))...))))..............)))))))).... ( -8.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 754 50 1 141 92 NC_003454:FN1602|5end_Hypothetical_cytosolic_protein_111492..111722_NEGATIVE 251 110 65 166 115 NC_003454:FN1697|5end_hypothetical_protein_193685..193915_NEGATIVE 232 90 46 174 123 NC_003454:FN1578|5end_hypothetical_protein_88796..89026_NEGATIVE 228 86 44 143 91 NC_003454:FN1457|5end_UDP-N-acetylglucosamine-N-acetylmuramyl-_Pentapeptide_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_2138976..2139206_NEGATIVE 221 50 1 87 27 NC_003454:FN1025|5end_Guanine-hypoxanthine_permease_1679931..1680161_NEGATIVE 221 102 65 145 108 NC_003454:FN0044|5end_Shikimate_5-dehydrogenase_682701..682931_POSITIVE 208 105 70 33 1 NC_003454:FN0858|5end_4-alpha-glucanotransferase_1520507..1520737_NEGATIVE 206 56 15 111 63 NC_003454:FN1309|5end_hypothetical_protein_1964856..1965086_POSITIVE 206 107 63 77 25 NC_003454:FN0981|5end_phosphoribosylamine--glycine_ligase_1634120..1634350_NEGATIVE 205 90 41 106 38 NC_003454:FN0069|5end_glycyl-tRNA_synthetase_alpha_subunit_707809..708039_POSITIVE 205 103 65 118 81 NC_003454:FN1631|5end_SSU_ribosomal_protein_S14P_135247..135477_NEGATIVE 203 108 65 170 114 NC_003454:FN2008|5end_Glycine_betaine_transport_ATP-binding_protein_508319..508549_NEGATIVE 199 89 41 158 105 NC_003454:FN1618|5end_hypothetical_protein_127205..127435_NEGATIVE 198 81 42 149 114 NC_003454:FN0457|5end_hypothetical_protein_1103298..1103528_POSITIVE 198 108 65 209 164 NC_003454:FN1637|5end_LSU_ribosomal_protein_L29P_137070..137300_NEGATIVE 196 110 67 128 76 NC_003454:FN1626|5end_LSU_ribosomal_protein_L30P_133049..133279_NEGATIVE 193 110 65 197 152 NC_003454:FN1639|5end_SSU_ribosomal_protein_S3P_138163..138393_NEGATIVE 190 109 67 82 50 NC_003454:FN0272|5end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_898704..898934_POSITIVE 189 98 59 50 17 NC_003454:FN0852|5end_Hydrolase_1510224..1510454_POSITIVE 188 50 24 40 12 NC_003454:FN0292|5end_Hemolysin_activator_protein_precursor_926063..926293_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 232 99 65 139 103 NC_003454:FN1698|3end_dTDP-4-dehydrorhamnose_reductase_193697..193847_NEGATIVE 228 86 44 142 90 NC_003454:FN1458|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_2138977..2139127_NEGATIVE 221 50 1 64 4 NC_003454:FN1026|3end_tRNA_pseudouridine_synthase_A_1679954..1680104_NEGATIVE 215 35 1 147 107 NC_003454:FN1164|3end_Glucokinase_1822781..1822931_POSITIVE 212 47 2 72 31 NC_003454:FN1983|3end_Alkyl_hydroperoxide_reductase_C22_protein_485265..485415_POSITIVE 206 107 63 60 8 NC_003454:FN0982|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1634137..1634287_NEGATIVE 205 90 41 102 34 NC_003454:FN0068|3end_Lipoprotein_signal_peptidase_707885..708035_POSITIVE 205 103 65 97 60 NC_003454:FN1632|3end_LSU_ribosomal_protein_L5P_135268..135418_NEGATIVE 199 89 41 87 34 NC_003454:FN1619|3end_Hypothetical_cytosolic_protein_127276..127426_NEGATIVE 198 81 42 113 78 NC_003454:FN0456|3end_Hypothetical_cytosolic_protein_1103342..1103492_POSITIVE 196 110 67 115 63 NC_003454:FN1627|3end_SSU_ribosomal_protein_S5P_133062..133212_NEGATIVE 190 49 2 127 74 NC_003454:FN1114|3end_hypothetical_protein_1758686..1758836_POSITIVE 188 50 24 80 52 NC_003454:FN0293|3end_Hemolysin_activator_protein_precursor_926023..926173_NEGATIVE 187 103 77 114 87 NC_003454:FN0182|3end_Sarcosine_oxidase_alpha_subunit_805801..805951_NEGATIVE 187 61 28 150 112 NC_003454:FN1579|3end_Cysteinyl-tRNA_synthetase_88784..88934_NEGATIVE 186 78 38 141 100 NC_003454:FN0711|3end_Phosphopantothenate--cysteine_ligase_1370863..1371013_POSITIVE 184 99 66 33 2 NC_003454:FN1453|3end_hypothetical_protein_2134073..2134223_NEGATIVE 183 110 68 133 84 NC_003454:FN0063|3end_hypothetical_protein_699394..699544_POSITIVE 182 106 67 37 1 NC_003454:FN0718|3end_hypothetical_protein_1376004..1376154_POSITIVE 181 109 65 99 50 NC_003454:FN1368|3end_COMF_operon_protein_3_2018157..2018307_NEGATIVE