Origin IGS: aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatatattttatatcattctttaaattttagcaaccaaaattaattaaaaatctaatataaaattttttttaaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtcactttcaatatctccttttatattctatttttaaaatgaccgtgcagtcattgaccgtgtggtcaattctatcaaaaaatataatttaagtcaagttttttaaaaaaaattttatattagatttttaattaattttggttgctaaaatttaaagaatgatataaaatatattgaagtttttacataaaggagttaaagaaaaaatgaaaattttacactatctaaaaagatttatattgttt Mask Tandem Repeat Region ================================================ aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatatattttatatcattctttaaattttagcaaccaaaattaattaaaaatctaatataaaattttttttaaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac Find is-nt database================================================ Query_seq: FN1271:FN1272|FN1271:FN1272:Protease IV:Transcriptional regulator, TetR family:<-->:1928533..1928777 245 aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatatattttatatcattctttaaattttagcaaccaaaattaattaaaaatctaatataaaattttttttaaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1271:FN1272|FN1271:FN1272:Protease IV:Transcriptional regulator, TetR family:<-->:1928533..1928777 245 aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatatattttatatcattctttaaattttagcaaccaaaattaattaaaaatctaatataaaattttttttaaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1271:FN1272|FN1271:FN1272:Protease IV:Transcriptional regulator, TetR family:<-->:1928533..1928777 245 aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatatattttatatcattctttaaattttagcaaccaaaattaattaaaaatctaatataaaattttttttaaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatatattttatatcattctttaaattttagcaaccaaaattaattaaaaatctaatataaaattttttttaaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac Predict ORF larger than 30AA ================================================ aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatatattttatatcattctttaaattttagcaaccaaaattaattaaaaatctaatataaaattttttttaaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac 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: 89 Start: 148 End: 177 ...................................................................................................................................................CTTGACTTAAATTATATTTTTTGATAGAAT.................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 76 End: 105 ...........................................................................GTTGCTAAAATTTAAAGAATGATATAAAAT............................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatatattttatatcattctttaaattttagcaaccaaaattaattaaaaatctaatataaaattttttttaaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1271:FN1272|FN1271:FN1272:Protease IV:Transcriptional regulator, TetR family:<-->:1928533..1928777 245 aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatatattttatatcattctttaaattttagcaaccaaaattaattaaaaatctaatataaaattttttttaaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: NC_003454_FN1271_FN1272|Protease IV:Transcriptional regulator, TetR family|NEGATIVE:POSITIVE|[1928533,1928777]|245 HSP 1 e-value: 3.0E-52 bit: 206.0 Len: 104 Query Start:142 Query End:245 Subject Strand: POSITIVE Subject Start: 142 Subject End: 245 .............................................................................................................................................aaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac .............................................................................................................................................aaaaaacttgacttaaattatattttttgatagaattgaccacacggtcaatgactgcacggtcattttaaaaatagaatataaaaggagatattgaaagtgac HSP 2 e-value: 5.0E-35 bit: 149.0 Len: 75 Query Start:1 Query End:75 Subject Strand: POSITIVE Subject Start: 1 Subject End: 75 aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatat.......................................................................................................................................................................... aaacaatataaatctttttagatagtgtaaaattttcattttttctttaactcctttatgtaaaaacttcaatat.......................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAAUAUAAAUCUUUUUAGAUAGUGUAAAAUUUUCAUUUUUUCUUUAACUCCUUUAUGUAAAAACUUCAAUAUAUUUUAUAUCAUUCUUUAAAUUUUAGCAACCAAAAUUAAUUAAAAAUCUAAUAUAAAAUUUUUUUUAAAAAACUUGACUUAAAUUAUAUUUUUUGAUAGAAUUGACCACACGGUCAAUGACUGCACGGUCAUUUUAAAAAUAGAAUAUAAAAGGAGAUAUUGAAAGUGAC ......((((.((((....))))..))))......((((((((....((.(((((((((((.........((((((.((((..(((.......((((((.......))))))..(((((((...(((.....))).)))))))......)))..)))).))))))((((((....(((((((....)))))))((((....))))...)))))).....)))).))))))).))..)))))))). (-36.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCACUUUCAAUAUCUCCUUUUAUAUUCUAUUUUUAAAAUGACCGUGCAGUCAUUGACCGUGUGGUCAAUUCUAUCAAAAAAUAUAAUUUAAGUCAAGUUUUUUAAAAAAAAUUUUAUAUUAGAUUUUUAAUUAAUUUUGGUUGCUAAAAUUUAAAGAAUGAUAUAAAAUAUAUUGAAGUUUUUACAUAAAGGAGUUAAAGAAAAAAUGAAAAUUUUACACUAUCUAAAAAGAUUUAUAUUGUUU ........(((((((((((((..................((((((..(.(((...))).)..))))))......((((.........((((((........))))))....(((((((((((..(((((((...(((((((...)))))))))))))).)))))))))))...))))...........)))))))........(((((....)))))...................))))))... (-39.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 643 70 21 161 112 NC_003454:FN1271|5end_Protease_IV_1928442..1928672_NEGATIVE 267 107 75 182 148 NC_003454:FN0089|5end_Ethanolamine_permease_725222..725452_POSITIVE 253 88 42 140 91 NC_003454:FN0646|5end_Glutamyl-tRNA_reductase_1303289..1303519_NEGATIVE 219 70 24 124 70 NC_003454:FN0987|5end_Amidophosphoribosyltransferase_1640210..1640440_NEGATIVE 216 56 14 157 111 NC_003454:FN0689|5end_hypothetical_protein_1344658..1344888_POSITIVE 215 64 33 112 85 NC_003454:FN0731|5end_hypothetical_protein_1387720..1387950_POSITIVE 207 79 31 115 65 NC_003454:FN0543|5end_Lipopolysaccharide_heptosyltransferase-1_1195986..1196216_POSITIVE 205 63 31 108 66 NC_003454:FN1408|5end_Aminoacyl-histidine_dipeptidase_2067395..2067625_POSITIVE 205 68 23 118 79 NC_003454:FN0117|5end_O6-methylguanine-DNA_methyltransferase_750338..750568_POSITIVE 204 72 33 185 139 NC_003454:FN0764|5end_Transporter,_LysE_family_1420327..1420557_POSITIVE 202 70 22 126 75 NC_003454:FN0908|5end_Tpl_protein_1566935..1567165_NEGATIVE 200 69 21 124 66 NC_003454:FN1579|5end_Cysteinyl-tRNA_synthetase_90205..90435_NEGATIVE 197 80 31 135 83 NC_003454:FN1313|5end_Oligopeptide-binding_protein_oppA_1967053..1967283_POSITIVE 190 78 36 70 24 NC_003454:FN1303|5end_Adenosylcobalamin-dependent_DIOL_dehydratase_gamma_subunit_1960284..1960514_NEGATIVE 190 54 22 164 121 NC_003454:FN1229|5end_hypothetical_protein_1886700..1886930_NEGATIVE 190 66 22 117 60 NC_003454:FN0891|5end_DNAse_I_homologous_protein_DHP2_precursor_1552926..1553156_NEGATIVE 188 55 15 207 163 NC_003454:FN1635|5end_LSU_ribosomal_protein_L14P_136572..136802_NEGATIVE 187 195 159 158 110 NC_003454:FN1518|5end_RNA_polymerase_sigma-70_factor_24077..24307_NEGATIVE 186 57 12 52 10 NC_003454:FN1039|5end_Branched-chain_amino_acid_transport_protein_azlC_1690997..1691227_POSITIVE 182 58 15 113 63 NC_003454:FN0423|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1066328..1066558_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 70 24 79 25 NC_003454:FN0988|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1640255..1640405_NEGATIVE 215 64 33 83 56 NC_003454:FN0730|3end_Phosphoglycerate_mutase_1387771..1387921_POSITIVE 207 79 31 143 93 NC_003454:FN0542|3end_Beta_1,4_glucosyltransferase_1196094..1196244_POSITIVE 202 70 22 105 54 NC_003454:FN0909|3end_DNA_repair_protein_radC_1566956..1567106_NEGATIVE 200 69 21 105 47 NC_003454:FN1580|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90224..90374_NEGATIVE 194 88 53 39 1 NC_003454:FN0647|3end_Hypothetical_cytosolic_protein_1303390..1303540_NEGATIVE 190 78 36 55 9 NC_003454:FN1304|3end_Single-strand_DNA_binding_protein_1960299..1960449_NEGATIVE 187 195 159 147 99 NC_003454:FN1519|3end_23S_rRNA_methyltransferase_24088..24238_NEGATIVE 180 55 11 100 53 NC_003454:FN1104|3end_Holliday_junction_DNA_helicase_ruvA_1750117..1750267_POSITIVE 180 77 33 108 72 NC_003454:FN1672|3end_Membrane-bound_O-acyltransferase_169833..169983_NEGATIVE 178 58 13 139 79 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 176 53 13 140 97 NC_003454:FN0805|3end_hypothetical_protein_1464832..1464982_NEGATIVE 174 58 13 93 48 NC_003454:FN1342|3end_Holo-[acyl-carrier_protein]_synthase_1996091..1996241_NEGATIVE 174 69 35 90 63 NC_003454:FN0698|3end_DNA_integration/recombination/invertion_protein_1357107..1357257_POSITIVE 172 58 11 131 73 NC_003454:FN0717|3end_Ribosomal_small_subunit_pseudouridine_synthase_A_1375673..1375823_POSITIVE 170 66 33 34 6 NC_003454:FN1145|3end_Oligoendopeptidase_F_1794252..1794402_NEGATIVE 170 55 19 44 12 NC_003454:FN2098|3end_MRP-family_nucleotide-binding_protein_607373..607523_NEGATIVE 169 52 15 145 101 NC_003454:FN1633|3end_LSU_ribosomal_protein_L24P_135838..135988_NEGATIVE 168 57 12 91 51 NC_003454:FN0779|3end_Putative_GTPase_(G3E_family)_1436096..1436246_NEGATIVE 168 71 32 103 66 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE