Origin IGS: atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcaaatattaaataaagtttaaaagtgtagttattatattagctacacttttaattttctaacttgctaacactgttagaatatgttagcatatgttagaaaaagatagaatat Mask Tandem Repeat Region ================================================ atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga Find is-nt database================================================ Query_seq: FN1870:FN1871|FN1870:FN1871:hypothetical protein:hypothetical protein:<-<-:362273..362386 114 atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1870:FN1871|FN1870:FN1871:hypothetical protein:hypothetical protein:<-<-:362273..362386 114 atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1870:FN1871|FN1870:FN1871:hypothetical protein:hypothetical protein:<-<-:362273..362386 114 atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga Predict ORF larger than 30AA ================================================ atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga 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: 84 Start: 23 End: 52 ......................CTTGCTAACACTGTTAGAATATGTTAGCAT.............................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 53 End: 82 ....................................................TTAGAAAATTAAAAGTGTAGCTAATATAAT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 56 HP_score: -2.3 Tail_Score: -4.59293 Start: 59 End: 98 Full_Region: GTTAGCAAGTTAGAA AATTAAAAGTGTAGCTA ATATAA TAACTACACTTTTAAAC TTTATTTAATATTTG ..........................................................AATTAAAAGTGTAGCTAATATAATAACTACACTTTTAAAC................ TransTerm Strand: + Conf: 57 HP_score: -5.8 Tail_Score: -3.33949 Start: 60 End: 97 Full_Region: TTAGCAAGTTAGAAA ATTAAAAGTGTAGCTA ATATAA TAACTACACTTTTAAA CTTTATTTAATATTT ...........................................................ATTAAAAGTGTAGCTAATATAATAACTACACTTTTAAA................. TransTerm Strand: + Conf: 75 HP_score: -9.3 Tail_Score: -2.58743 Start: 61 End: 96 Full_Region: TAGCAAGTTAGAAAA TTAAAAGTGTAGCTA ATATAA TAACTACACTTTTAA ACTTTATTTAATATT ............................................................TTAAAAGTGTAGCTAATATAATAACTACACTTTTAA.................. TransTerm Strand: + Conf: 58 HP_score: -3.9 Tail_Score: -4.287 Start: 67 End: 90 Full_Region: GTTAGAAAATTAAAA GTGTAGCTA ATATAA TAACTACAC TTTTAAACTTTATTT ..................................................................GTGTAGCTAATATAATAACTACAC........................ Find igs database================================================ Query_seq: FN1870:FN1871|FN1870:FN1871:hypothetical protein:hypothetical protein:<-<-:362273..362386 114 atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_003454_FN1870_FN1871|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[362273,362386]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga atattctatctttttctaacatatgctaacatattctaacagtgttagcaagttagaaaattaaaagtgtagctaatataataactacacttttaaactttatttaatatttga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUCUAUCUUUUUCUAACAUAUGCUAACAUAUUCUAACAGUGUUAGCAAGUUAGAAAAUUAAAAGUGUAGCUAAUAUAAUAACUACACUUUUAAACUUUAUUUAAUAUUUGA ...........(((((((((...(((((((((.........))))))))).)))))))))((((((((((((.((......)).)))))))))))).................. (-29.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAUAUUAAAUAAAGUUUAAAAGUGUAGUUAUUAUAUUAGCUACACUUUUAAUUUUCUAACUUGCUAACACUGUUAGAAUAUGUUAGCAUAUGUUAGAAAAAGAUAGAAUAU ....(((((.........(((((((((((((((......)))))))))))))))(((((((((.((((((((.(((....)))))))))))...)))))))))......))))) (-35.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 734 50 1 141 92 NC_003454:FN1870|5end_hypothetical_protein_362182..362412_NEGATIVE 335 50 3 80 34 NC_003454:FN1923|5end_Adenine-specific_methyltransferase_421097..421327_NEGATIVE 228 79 32 188 125 NC_003454:FN1926|5end_Nitrogen_regulatory_IIA_protein_425287..425517_NEGATIVE 225 47 1 57 10 NC_003454:FN2126|5end_DNA_gyrase_subunit_B_638225..638455_NEGATIVE 219 72 34 69 34 NC_003454:FN1865|5end_hypothetical_protein_357105..357335_NEGATIVE 213 77 36 68 25 NC_003454:FN0397|5end_Dipeptide_transport_system_permease_protein_dppB_1035822..1036052_POSITIVE 207 50 14 193 162 NC_003454:FN0273|5end_Butyrate-acetoacetate_CoA-transferase_subunit_B_899423..899653_POSITIVE 203 79 31 70 23 NC_003454:FN1305|5end_Hypothetical_cytosolic_protein_1961205..1961435_POSITIVE 203 52 12 153 112 NC_003454:FN0263|5end_Peptidyl-prolyl_cis-trans_isomerase_890064..890294_POSITIVE 198 67 24 229 191 NC_003454:FN1114|5end_hypothetical_protein_1758016..1758246_POSITIVE 198 50 4 68 17 NC_003454:FN1875|5end_Peptidyl-prolyl_cis-trans_isomerase_364400..364630_NEGATIVE 196 78 34 77 23 NC_003454:FN0738|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1395846..1396076_POSITIVE 196 32 2 42 8 NC_003454:FN2098|5end_MRP-family_nucleotide-binding_protein_608146..608376_NEGATIVE 193 54 32 169 150 NC_003454:FN1630|5end_SSU_ribosomal_protein_S8P_134931..135161_NEGATIVE 189 47 4 132 83 NC_003454:FN1810|5end_Manganese_transport_system_membrane_protein_mntB_291953..292183_NEGATIVE 186 43 2 105 56 NC_003454:FN0303|5end_Nitrogenase_iron_protein_937526..937756_POSITIVE 184 49 4 64 20 NC_003454:FN1252|5end_34_kDa_membrane_antigen_precursor_1909368..1909598_POSITIVE 183 99 66 88 58 NC_003454:FN0503|5end_Transcriptional_regulatory_protein,_LYSR_family_1153572..1153802_NEGATIVE 181 60 12 122 68 NC_003454:FN1915|5end_Anti-sigma_B_factor_412320..412550_NEGATIVE 178 49 7 213 174 NC_003454:FN1787|5end_Tetratricopeptide_repeat_family_protein_267762..267992_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 225 47 1 56 9 NC_003454:FN2127|3end_hypothetical_protein_638226..638376_NEGATIVE 221 102 62 45 7 NC_003454:FN0603|3end_Transcriptional_regulatory_protein,_LYSR_family_1257501..1257651_NEGATIVE 220 79 44 60 14 NC_003454:FN1927|3end_DEGV_protein_425415..425565_NEGATIVE 208 47 5 146 94 NC_003454:FN0842|3end_hypothetical_protein_1502822..1502972_NEGATIVE 193 54 32 140 121 NC_003454:FN1631|3end_SSU_ribosomal_protein_S14P_134960..135110_NEGATIVE 186 43 2 77 28 NC_003454:FN0302|3end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_937578..937728_POSITIVE 175 49 10 84 33 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 174 73 43 33 7 NC_003454:FN0170|3end_GTP-binding_protein_796613..796763_POSITIVE 174 73 43 30 4 NC_003454:FN1836|3end_Tetratricopeptide_repeat_family_protein_323904..324054_NEGATIVE 171 46 5 133 90 NC_003454:FN2032|3end_DNA-directed_RNA_polymerase_omega_chain_537121..537271_NEGATIVE 170 108 63 89 33 NC_003454:FN1170|3end_Pyruvate-flavodoxin_oxidoreductase_1828707..1828857_NEGATIVE 169 49 2 108 62 NC_003454:FN0783|3end_Acyl-CoA_dehydrogenase_1440391..1440541_POSITIVE 169 25 5 116 94 NC_003454:FN1863|3end_L-beta-lysine_5,6-aminomutase_alpha_subunit_353122..353272_NEGATIVE 166 39 11 41 14 NC_003454:FN0187|3end_Thiol:disulfide_interchange_protein_tlpA_812299..812449_POSITIVE 163 49 10 40 4 NC_003454:FN0260|3end_Transcriptional_repressor_smtB_886261..886411_NEGATIVE 160 50 2 130 72 NC_003454:FN0376|3end_Iron(III)-transport_ATP-binding_protein_sfuC_1007560..1007710_POSITIVE 160 50 4 136 89 NC_003454:FN0111|3end_hypothetical_protein_746155..746305_NEGATIVE 160 78 34 50 7 NC_003454:FN2118|3end_Hypothetical_exported_24-amino_acid_repeat_protein_626287..626437_NEGATIVE 158 47 1 58 2 NC_003454:FN1829|3end_hypothetical_protein_317717..317867_NEGATIVE 156 72 35 102 60 NC_003454:FN2006|3end_Cobalt_transport_protein_cbiQ_506959..507109_POSITIVE