Origin IGS: ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttaatagtttttatatgatattattaaatggtagaggtgtctattatgaaaaaaattatattacttattacaatgctttttttattaatatcatgctctaataataactatattaaaaaaggtttttctcaaaatgaaaaacaagaa Mask Tandem Repeat Region ================================================ ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa Find is-nt database================================================ Query_seq: FN1916:FN1917|FN1916:FN1917:hypothetical protein:tRNA delta(2)-isopentenylpyrophosphate transferase:<-<-:412787..412934 148 ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1916:FN1917|FN1916:FN1917:hypothetical protein:tRNA delta(2)-isopentenylpyrophosphate transferase:<-<-:412787..412934 148 ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1916:FN1917|FN1916:FN1917:hypothetical protein:tRNA delta(2)-isopentenylpyrophosphate transferase:<-<-:412787..412934 148 ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 1 End: 120 E Q K E N Q S F G K K I Y N N N S C S I L L F L M T I L L I I K K M I S V E V M ............................ ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa 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: 104 End: 133 .......................................................................................................ATAGACACCTCTACCATTTAATAATATCAT............... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 74 End: 103 .........................................................................TATGAAAAAAATTATATTACTTATTACAAT............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1916:FN1917|FN1916:FN1917:hypothetical protein:tRNA delta(2)-isopentenylpyrophosphate transferase:<-<-:412787..412934 148 ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa Intra-Species Hit: Count: 1 Min: 1 Max: 148 Len: 148 Subject: NC_003454_FN1916_FN1917|hypothetical protein:tRNA delta(2)-isopentenylpyrophosphate transferase|NEGATIVE:NEGATIVE|[412787,412934]|148 HSP 1 e-value: 9.0E-54 bit: 210.0 Len: 148 Query Start:1 Query End:148 Subject Strand: POSITIVE Subject Start: 1 Subject End: 148 ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaatnnnnnnngcattgtaataagtaatataannnnnnncataatagacacctctaccatttaataatatcatataaaaactattaaa ttcttgtttttcattttgagaaaaaccttttttaatatagttattattagagcatgatattaataaaaaaagcattgtaataagtaatataatttttttcataatagacacctctaccatttaataatatcatataaaaactattaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUGUUUUUCAUUUUGAGAAAAACCUUUUUUAAUAUAGUUAUUAUUAGAGCAUGAUAUUAAUAAAAAAAGCAUUGUAAUAAGUAAUAUAAUUUUUUUCAUAAUAGACACCUCUACCAUUUAAUAAUAUCAUAUAAAAACUAUUAAA .....(((((((.......)))))))..........((((((.((((......(((((((((.(((((((((.((((((........)))))).))))).....((((....))))...)))).))))))))))))).)))))).... (-18.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAUAGUUUUUAUAUGAUAUUAUUAAAUGGUAGAGGUGUCUAUUAUGAAAAAAAUUAUAUUACUUAUUACAAUGCUUUUUUUAUUAAUAUCAUGCUCUAAUAAUAACUAUAUUAAAAAAGGUUUUUCUCAAAAUGAAAAACAAGAA ....((((((.(((((((((((((.((((.((((..((((..((.(((((......))))).))..))))....))))...)))).)))))))))......)))).))))))..........(((((((.......)))))))..... (-24.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 706 120 71 211 162 NC_003454:FN1916|5end_hypothetical_protein_412696..412926_NEGATIVE 251 119 87 132 90 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 237 122 88 109 77 NC_003454:FN1217|5end_Holliday_junction_DNA_helicase_ruvB_1877597..1877827_NEGATIVE 223 128 81 122 76 NC_003454:FN1903|5end_Coenzyme_A_disulfide_reductase/_disulfide_bond_regulator_domain_393104..393334_NEGATIVE 216 50 1 231 182 NC_003454:FN0648|5end_Exoenzyme_regulatory_protein_aepA_precursor_1306061..1306291_NEGATIVE 214 135 92 122 80 NC_003454:FN1444|5end_GMP_synthase_[glutamine-hydrolyzing]_2111585..2111815_POSITIVE 213 130 82 118 68 NC_003454:FN0516|5end_Acriflavin_resistance_protein_E_1168076..1168306_NEGATIVE 210 130 90 196 152 NC_003454:FN1665|5end_Virulence-associated_protein_I_162515..162745_POSITIVE 199 118 79 105 62 NC_003454:FN1529|5end_hypothetical_protein_43364..43594_NEGATIVE 197 116 80 106 66 NC_003454:FN0556|5end_hypothetical_protein_1209000..1209230_NEGATIVE 197 122 89 111 78 NC_003454:FN0151|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_778771..779001_POSITIVE 192 115 71 70 20 NC_003454:FN0113|5end_Heat-inducible_transcription_repressor_hrcA_746557..746787_POSITIVE 190 122 87 196 151 NC_003454:FN0971|5end_Huntington_interacting_Protein_HYPE_1624273..1624503_NEGATIVE 190 116 71 176 131 NC_003454:FN0774|5end_Hypothetical_cytosolic_protein_1429692..1429922_POSITIVE 190 117 71 108 58 NC_003454:FN0613|5end_hypothetical_protein_1270890..1271120_POSITIVE 189 118 71 140 96 NC_003454:FN1504|5end_Nickel-binding_protein_10015..10245_NEGATIVE 188 116 72 107 60 NC_003454:FN0916|5end_hypothetical_protein_1572514..1572744_NEGATIVE 188 85 49 41 3 NC_003454:FN0489|5end_Prolipoprotein_diacylglyceryl_transferase_1135425..1135655_NEGATIVE 186 128 96 116 85 NC_003454:FN0260|5end_Transcriptional_repressor_smtB_886638..886868_NEGATIVE 183 120 72 109 58 NC_003454:FN1037|5end_flavodoxin_1689447..1689677_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 119 87 112 70 NC_003454:FN1127|3end_Hypothetical_membrane-spanning_protein_1770307..1770457_NEGATIVE 213 130 82 108 58 NC_003454:FN0517|3end_Outer_membrane_protein_tolC_1168086..1168236_NEGATIVE 210 136 93 70 24 NC_003454:FN1177|3end_hypothetical_protein_1837789..1837939_NEGATIVE 210 130 90 131 87 NC_003454:FN1664|3end_hypothetical_protein_162530..162680_POSITIVE 189 106 66 115 65 NC_003454:FN1891|3end_Glycerophosphoryl_diester_phosphodiesterase_373509..373659_NEGATIVE 183 41 6 100 70 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 183 120 72 60 9 NC_003454:FN1036|3end_hypothetical_protein_1689478..1689628_POSITIVE 183 118 71 128 95 NC_003454:FN1729|3end_4-amino-4-deoxychorismate_lyase_228338..228488_NEGATIVE 180 116 77 39 2 NC_003454:FN0773|3end_hypothetical_protein_1429635..1429785_POSITIVE 179 118 71 91 48 NC_003454:FN1837|3end_putative_nucleotide-binding_protein_326725..326875_NEGATIVE 178 115 75 123 85 NC_003454:FN2047|3end_Fusobacterium_outer_membrane_protein_family_551491..551641_NEGATIVE 177 116 85 79 48 NC_003454:FN1128|3end_Acylamino-acid-releasing_enzyme_1772153..1772303_NEGATIVE 176 114 78 43 8 NC_003454:FN0163|3end_5-methyltetrahydrofolate--homocysteine_methyltransferase_792327..792477_POSITIVE 174 114 71 88 47 NC_003454:FN1267|3end_hypothetical_protein_1923054..1923204_NEGATIVE 173 115 73 106 59 NC_003454:FN0088|3end_hypothetical_protein_725302..725452_POSITIVE 171 130 83 50 6 NC_003454:FN0914|3end_hypothetical_protein_1570797..1570947_NEGATIVE 169 119 71 151 103 NC_003454:FN0616|3end_hypothetical_protein_1275024..1275174_NEGATIVE 168 119 71 145 97 NC_003454:FN1279|3end_Zinc_metallohydrolase,_glyoxalase_II_family_1937290..1937440_NEGATIVE 168 136 93 110 67 NC_003454:FN0439|3end_hypothetical_protein_1080837..1080987_NEGATIVE 165 120 74 128 82 NC_003454:FN1449|3end_Fusobacterium_outer_membrane_protein_family_2118612..2118762_NEGATIVE