Origin IGS: tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt .........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 acaattttaatacagtttgttaaaaagaaagtttttttaaactttatttatctaaaatttcgtttattttattgacaaaatcaaagaaaaaaagtatactctaatatataaaaaagttttatcaatttttactcaataaagtataaagggggattttatgaaagcaaagattttattatgctcaatgttaata Mask Tandem Repeat Region ================================================ tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt Find is-nt database================================================ Query_seq: FN2063:FN2064|FN2063:FN2064:hypothetical protein:hypothetical protein:<-<-:575110..575302 193 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2063:FN2064|FN2063:FN2064:hypothetical protein:hypothetical protein:<-<-:575110..575302 193 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2063:FN2064|FN2063:FN2064:hypothetical protein:hypothetical protein:<-<-:575110..575302 193 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt Predict ORF larger than 30AA ================================================ tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt 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: 94 End: 123 .............................................................................................ATTGACAAAATCAAAGAAAAAAAGTATACT...................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN2063:FN2064|FN2063:FN2064:hypothetical protein:hypothetical protein:<-<-:575110..575302 193 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt Intra-Species Hit: Count: 1 Min: 1 Max: 193 Len: 193 Subject: NC_003454_FN2063_FN2064|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[575110,575302]|193 HSP 1 e-value: 2.0E-80 bit: 299.0 Len: 193 Query Start:1 Query End:193 Subject Strand: POSITIVE Subject Start: 1 Subject End: 193 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatacnnnnnnnctttgattttgtcaataaaataaacgaaattttagataaataaagtttnnnnnnnctttctttttaacaaactgtattaaaattgt tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttattgagtaaaaattgataaaacttttttatatattagagtatactttttttctttgattttgtcaataaaataaacgaaattttagataaataaagtttaaaaaaactttctttttaacaaactgtattaaaattgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAACAUUGAGCAUAAUAAAAUCUUUGCUUUCAUAAAAUCCCCCUUUAUACUUUAUUGAGUAAAAAUUGAUAAAACUUUUUUAUAUAUUAGAGUAUACUUUUUUUCUUUGAUUUUGUCAAUAAAAUAAACGAAAUUUUAGAUAAAUAAAGUUUAAAAAAACUUUCUUUUUAACAAACUGUAUUAAAAUUGU .....(((..(((((............)))))...(((((........(((((((((.((.(((((((...........))))))).)).)))))))))...(((.(((..((((((((...........))))))))..))).))).(((((((....)))))))..)))))......)))........... (-22.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAUUUUAAUACAGUUUGUUAAAAAGAAAGUUUUUUUAAACUUUAUUUAUCUAAAAUUUCGUUUAUUUUAUUGACAAAAUCAAAGAAAAAAAGUAUACUCUAAUAUAUAAAAAAGUUUUAUCAAUUUUUACUCAAUAAAGUAUAAAGGGGGAUUUUAUGAAAGCAAAGAUUUUAUUAUGCUCAAUGUUAAUA ......((((((.(((....(((((..(((((((....))))))).....((((((((..(.(((((((((((((..................(((((......)))))..(((((((.....)))))))..)))))))))))...)).)..)))))).)).........)))))....)))...)))))).. (-24.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 732 60 11 151 102 NC_003454:FN2063|5end_hypothetical_protein_575019..575249_NEGATIVE 720 50 1 141 92 NC_003454:FN2052|5end_hypothetical_protein_560943..561173_NEGATIVE 635 49 1 140 92 NC_003454:FN0249|5end_hypothetical_protein_872823..873053_POSITIVE 279 59 20 120 76 NC_003454:FN0371|5end_hypothetical_protein_999993..1000223_POSITIVE 256 66 21 121 78 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 255 60 26 117 78 NC_003454:FN0022|5end_hypothetical_protein_660790..661020_POSITIVE 254 59 11 120 74 NC_003454:FN0972|5end_Cobyrinic_acid_a,c-diamide_synthase_1625607..1625837_NEGATIVE 248 52 16 106 67 NC_003454:FN0897|5end_Hypothetical_cytosolic_protein_1555833..1556063_POSITIVE 248 47 12 102 62 NC_003454:FN1613|5end_hypothetical_protein_123486..123716_NEGATIVE 226 49 8 106 66 NC_003454:FN0718|5end_hypothetical_protein_1375616..1375846_POSITIVE 221 59 20 116 78 NC_003454:FN0556|5end_hypothetical_protein_1209000..1209230_NEGATIVE 216 64 32 117 87 NC_003454:FN1150|5end_hypothetical_protein_1805151..1805381_NEGATIVE 214 47 4 141 86 NC_003454:FN0024|5end_Hypothetical_exported_24-amino_acid_repeat_protein_663051..663281_POSITIVE 207 64 23 124 77 NC_003454:FN1851|5end_Ribonuclease_PH_340179..340409_POSITIVE 206 63 24 125 72 NC_003454:FN0926|5end_GTP_pyrophosphokinase_1580812..1581042_POSITIVE 205 69 28 131 82 NC_003454:FN0978|5end_NA+/H+_antiporter_NHAC_1631965..1632195_NEGATIVE 205 42 7 97 61 NC_003454:FN1922|5end_hypothetical_protein_419435..419665_NEGATIVE 205 47 4 127 86 NC_003454:FN1852|5end_hypothetical_protein_341616..341846_POSITIVE 202 64 36 124 93 NC_003454:FN1855|5end_Methylaspartate_mutase_343949..344179_POSITIVE 196 47 5 106 59 NC_003454:FN0279|5end_Lipoprotein_906479..906709_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 66 21 44 1 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 255 60 26 101 62 NC_003454:FN0021|3end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_660854..661004_POSITIVE 254 59 11 101 55 NC_003454:FN0973|3end_Histidinol-phosphate_aminotransferase_1625626..1625776_NEGATIVE 248 47 12 79 39 NC_003454:FN1614|3end_MG(2+)_chelatase_family_protein_123509..123659_NEGATIVE 226 49 8 83 43 NC_003454:FN0717|3end_Ribosomal_small_subunit_pseudouridine_synthase_A_1375673..1375823_POSITIVE 216 64 32 105 75 NC_003454:FN1151|3end_Na+_driven_multidrug_efflux_pump_1805163..1805313_NEGATIVE 207 64 23 79 32 NC_003454:FN1850|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_340214..340364_POSITIVE 206 63 24 112 59 NC_003454:FN0925|3end_hypothetical_protein_1580879..1581029_POSITIVE 202 64 36 108 77 NC_003454:FN1854|3end_Methylaspartate_mutase_344013..344163_POSITIVE 200 116 78 118 80 NC_003454:FN2047|3end_Fusobacterium_outer_membrane_protein_family_551491..551641_NEGATIVE 197 67 30 146 111 NC_003454:FN1461|3end_Histidinol-phosphatase_2141603..2141753_NEGATIVE 196 47 5 116 69 NC_003454:FN0280|3end_hypothetical_protein_906469..906619_NEGATIVE 195 48 14 52 9 NC_003454:FN1980|3end_Transporter_483252..483402_POSITIVE 189 48 14 105 61 NC_003454:FN0969|3end_hypothetical_protein_1621806..1621956_NEGATIVE 186 56 22 102 67 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 186 89 41 77 31 NC_003454:FN1746|3end_Cystathionine_beta-lyase_245680..245830_POSITIVE 185 61 28 129 87 NC_003454:FN1995|3end_hypothetical_protein_499038..499188_POSITIVE 183 59 30 100 72 NC_003454:FN1527|3end_hypothetical_protein_42183..42333_NEGATIVE 180 46 2 70 29 NC_003454:FN1297|3end_Methionine_aminopeptidase_1954217..1954367_NEGATIVE 180 110 69 106 55 NC_003454:FN1285|3end_30S_ribosomal_protein_S11_1943283..1943433_NEGATIVE