Origin IGS: gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaattgcattctaaattttagatgaaaaattaaagcaagtgagccgagcaaatttcggtgtgtttgaagctaatttattggcaagtttaccgaatttgcagcgaacattaattttttatcattaaaaaatttagctagcaataaactatttttaagatattaaaaattatttataatagtatcctaatatagttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaatattattctttgatattaaaaaaataataggcactcttggaaatttggagtgcctttttgccaactttacaggttagatagttgatcttttggaagtaaatgagccttgtttcttacaaaagactaactatattaggatactattataaataatttttaatatcttaaaaatagtttattgctagctaaattttttaatgataaaaaattaatgttcgctgcaaattcggtaaacttgccaataaattagcttcaaacacaccgaaatttgctcggctcacttgctttaatttttcatctaaaatttagaatgcaattcacttatttttagttttatttaactaattactttataatagctaattgtaccaatatttttaaggagagtgaaac Mask Tandem Repeat Region ================================================ gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaattgcattctaaattttagatgaaaaattaaagcaagtgagccgagcaaatttcggtgtgtttgaagctaatttattggcaagtttaccgaatttgcagcgaacattaattttttatcattaaaaaatttagctagcaataaactatttttaagatattaaaaattatttataatagtatcctaatatagttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa Find is-nt database================================================ Query_seq: FN2036:FN2037|FN2036:FN2037:DNA-directed RNA polymerase beta chain:LSU ribosomal protein L12P (L7/L12):<-<-:546462..546858 397 gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaattgcattctaaattttagatgaaaaattaaagcaagtgagccgagcaaatttcggtgtgtttgaagctaatttattggcaagtttaccgaatttgcagcgaacattaattttttatcattaaaaaatttagctagcaataaactatttttaagatattaaaaattatttataatagtatcctaatatagttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2036:FN2037|FN2036:FN2037:DNA-directed RNA polymerase beta chain:LSU ribosomal protein L12P (L7/L12):<-<-:546462..546858 397 gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaattgcattctaaattttagatgaaaaattaaagcaagtgagccgagcaaatttcggtgtgtttgaagctaatttattggcaagtttaccgaatttgcagcgaacattaattttttatcattaaaaaatttagctagcaataaactatttttaagatattaaaaattatttataatagtatcctaatatagttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2036:FN2037|FN2036:FN2037:DNA-directed RNA polymerase beta chain:LSU ribosomal protein L12P (L7/L12):<-<-:546462..546858 397 gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaattgcattctaaattttagatgaaaaattaaagcaagtgagccgagcaaatttcggtgtgtttgaagctaatttattggcaagtttaccgaatttgcagcgaacattaattttttatcattaaaaaatttagctagcaataaactatttttaagatattaaaaattatttataatagtatcctaatatagttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 78 Max: 264 Len: 187 Subject: UniRef90_Q7P652 Cluster: Hypothetical protein FNV1211; n=1; Fusobacterium nucleatum subsp. vincentii ATCC 49256|Rep: Hypothetical protein FNV1211 - Fusobacterium nucleatum subsp. vincentii ATCC 49256 HSP 1 e-value: 5.0E-13 bit: 75.5 Len: 153 Query Start:78 Query End:230 Subject Strand: null Subject Start: 4 Subject End: 54 ............................................................................. L K N S L L L A K F F N D K K L M F A A N S V N L P I N * L Q T H R N L L G S L A L I F H L K F R M Q ....................................................................................................................................................................... ............................................................................. V K N S S L L A K F L N D K K L T F A A N S V N L P T S W L Q T H R D L L G S F P S I F Y L K F R I Q ....................................................................................................................................................................... Subject: UniRef90_Q7P3S4 Cluster: Hypothetical protein FNV0127; n=1; Fusobacterium nucleatum subsp. vincentii ATCC 49256|Rep: Hypothetical protein FNV0127 - Fusobacterium nucleatum subsp. vincentii ATCC 49256 HSP 1 e-value: 7.0E-8 bit: 40.0 Len: 72 Query Start:159 Query End:230 Subject Strand: null Subject Start: 23 Subject End: 46 .............................................................................................................................................................. L K N S L L L A K F F N D K K L M F A A N S V N ....................................................................................................................................................................... .............................................................................................................................................................. L K N S S L L A K F L N D E K L T F A A N S L N ....................................................................................................................................................................... HSP 2 e-value: 7.0E-8 bit: 38.5 Len: 66 Query Start:88 Query End:153 Subject Strand: null Subject Start: 46 Subject End: 67 ....................................................................................... N K L A S N T P K F A R L T C F N F S S K I .................................................................................................................................................................................................................................................... ....................................................................................... N S F H S N T A R F A R L T C F N F S S K I .................................................................................................................................................................................................................................................... Subject: UniRef90_Q8RDP9 Cluster: Hypothetical cytosolic protein; n=1; Fusobacterium nucleatum subsp. nucleatum|Rep: Hypothetical cytosolic protein - Fusobacterium nucleatum subsp. nucleatum HSP 1 e-value: 3.0E-7 bit: 47.0 Len: 81 Query Start:113 Query End:193 Subject Strand: null Subject Start: 1 Subject End: 27 ................................................................................................................ V S R A N F G V F E A N L L A S L P N L Q R T L I F Y ............................................................................................................................................................................................................ ................................................................................................................ M S R V N F G M F E A N L L A S L P N L Q R I L N F Y ............................................................................................................................................................................................................ HSP 2 e-value: 3.0E-7 bit: 29.3 Len: 84 Query Start:181 Query End:264 Subject Strand: null Subject Start: 24 Subject End: 48 .................................................................................................................................................................................... I N F L S L K N L A S N K L F L R Y * K L F I I V S * Y ..................................................................................................................................... .................................................................................................................................................................................... L N F Y S L R N L A S N E L F L - - - L I F M I V L L Y ..................................................................................................................................... gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 89 End: 196 ........................................................................................ M L D E K L K Q V S R A N F G V F E A N L L A S L P N L Q R T L I F Y H ......................................................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 293 End: 388 .................................................................................................................................................................................................................................................................................................... M Y F Q K I N Y L T C K V G K K A L Q I S K S A Y Y F F N I K E ......... Protein_Len: 33 Strand: - Start: 88 End: 186 ....................................................................................... I K S S F N F C T L R A F K P T N S A L K N A L K G F K C R V N M ................................................................................................................................................................................................................... gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa 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: 82 Start: 2 End: 31 .TTTCACTCTCCTTAAAAATATTGGTACAAT.............................................................................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 12 End: 41 ...........CTTAAAAATATTGGTACAATTAGCTATTAT.................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 350 End: 379 .............................................................................................................................................................................................................................................................................................................................................................ATTTCCAAGAGTGCCTATTATTTTTTTAAT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -3.5 Tail_Score: -3.25204 Start: 118 End: 132 Full_Region: ATTAAAGCAAGTGAG CCGAG CAAAT TTCGG TGTGTTTGAAGCTAA .....................................................................................................................CCGAGCAAATTTCGG......................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN2036:FN2037|FN2036:FN2037:DNA-directed RNA polymerase beta chain:LSU ribosomal protein L12P (L7/L12):<-<-:546462..546858 397 gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa Intra-Species Hit: Count: 1 Min: 1 Max: 397 Len: 397 Subject: NC_003454_FN2036_FN2037|DNA-directed RNA polymerase beta chain:LSU ribosomal protein L12P (L7/L12)|NEGATIVE:NEGATIVE|[546462,546858]|397 HSP 1 e-value: 7.0E-57 bit: 222.0 Len: 133 Query Start:265 Query End:397 Subject Strand: POSITIVE Subject Start: 265 Subject End: 397 ........................................................................................................................................................................................................................................................................agttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattannnnnnnaatatcaaagaataatattaa ........................................................................................................................................................................................................................................................................agttagtcttttgtaagaaacaaggctcatttacttccaaaagatcaactatctaacctgtaaagttggcaaaaaggcactccaaatttccaagagtgcctattatttttttaatatcaaagaataatattaa HSP 2 e-value: 6.0E-36 bit: 153.0 Len: 77 Query Start:1 Query End:77 Subject Strand: POSITIVE Subject Start: 1 Subject End: 77 gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaa................................................................................................................................................................................................................................................................................................................................ gtttcactctccttaaaaatattggtacaattagctattataaagtaattagttaaataaaactaaaaataagtgaa................................................................................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUCACUCUCCUUAAAAAUAUUGGUACAAUUAGCUAUUAUAAAGUAAUUAGUUAAAUAAAACUAAAAAUAAGUGAAUUGCAUUCUAAAUUUUAGAUGAAAAAUUAAAGCAAGUGAGCCGAGCAAAUUUCGGUGUGUUUGAAGCUAAUUUAUUGGCAAGUUUACCGAAUUUGCAGCGAACAUUAAUUUUUUAUCAUUAAAAAAUUUAGCUAGCAAUAAACUAUUUUUAAGAUAUUAAAAAUUAUUUAUAAUAGUAUCCUAAUAUAGUUAGUCUUUUGUAAGAAACAAGGCUCAUUUACUUCCAAAAGAUCAACUAUCUAACCUGUAAAGUUGGCAAAAAGGCACUCCAAAUUUCCAAGAGUGCCUAUUAUUUUUUUAAUAUCAAAGAAUAAUAUUAA ...................(((.(((.......(((((((((((....((((((......)))))).....(((..(((((...(((((((((.(((((((((((((.....((..((...(((((((.(((((..(((...(((((....))))))))..)))))))))))).))..)).))))))))))))).....)))))))))...)))))..))).(((((((....)))))))...)))))))))))........((((((.((((((((.((((((.........))).))).)))))))).))))))...))).)))............((((((((...........))))))))((((((((((.......))))))))))..... (-85.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUAUUAUUCUUUGAUAUUAAAAAAAUAAUAGGCACUCUUGGAAAUUUGGAGUGCCUUUUUGCCAACUUUACAGGUUAGAUAGUUGAUCUUUUGGAAGUAAAUGAGCCUUGUUUCUUACAAAAGACUAACUAUAUUAGGAUACUAUUAUAAAUAAUUUUUAAUAUCUUAAAAAUAGUUUAUUGCUAGCUAAAUUUUUUAAUGAUAAAAAAUUAAUGUUCGCUGCAAAUUCGGUAAACUUGCCAAUAAAUUAGCUUCAAACACACCGAAAUUUGCUCGGCUCACUUGCUUUAAUUUUUCAUCUAAAAUUUAGAAUGCAAUUCACUUAUUUUUAGUUUUAUUUAACUAAUUACUUUAUAAUAGCUAAUUGUACCAAUAUUUUUAAGGAGAGUGAAAC ......(((((((((....(((((((......(((((((((.........)))))))))............(((((.(((((((((((.(((((((.(((.(((..(...)..)))))).))))))).))))))).........(((((((((((((((...((((..(((((((((((..(((((...(((((((((.....(((.(((((((((.((..((((((((((((((......((..........)).........)))).)))))))..)))......)).))))))))).))).)))))))))...)))))..)).)))))))))...)))).....))))).)))))))))))))))))))......))))))))))))))))... (-88.56) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 817 140 91 231 182 NC_003454:FN2036|5end_DNA-directed_RNA_polymerase_beta_chain_546371..546601_NEGATIVE 808 160 113 221 174 NC_003454:FN1822|5end_Flavodoxin_311148..311378_POSITIVE 808 160 113 104 57 NC_003454:FN1821|5end_Hypothetical_cytosolic_protein_311031..311261_POSITIVE 733 120 71 189 140 NC_003454:FN1810|5end_Manganese_transport_system_membrane_protein_mntB_291953..292183_NEGATIVE 727 130 81 189 140 NC_003454:FN2006|5end_Cobalt_transport_protein_cbiQ_506079..506309_POSITIVE 651 130 82 200 152 NC_003454:FN0047|5end_Exodeoxyribonuclease_III_684427..684657_POSITIVE 594 130 81 206 157 NC_003454:FN1217|5end_Holliday_junction_DNA_helicase_ruvB_1877597..1877827_NEGATIVE 567 140 91 219 170 NC_003454:FN0070|5end_Glycyl-tRNA_synthetase_beta_chain_708902..709132_POSITIVE 555 150 101 227 178 NC_003454:FN1486|5end_Integral_membrane_protein_with_CBS_domains_2169299..2169529_NEGATIVE 553 140 91 199 150 NC_003454:FN2095|5end_General_secretion_pathway_protein_E_606080..606310_NEGATIVE 542 159 112 231 185 NC_003454:FN0392|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1029624..1029854_POSITIVE 525 179 133 54 8 NC_003454:FN0797|5end_hypothetical_protein_1455799..1456029_NEGATIVE 490 150 101 227 179 NC_003454:FN1819|5end_Export_ABC_transporter_307519..307749_POSITIVE 458 179 135 51 7 NC_003454:FN0171|5end_Hypothetical_cytosolic_protein_796548..796778_POSITIVE 446 150 101 228 184 NC_003454:FN0988|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1640968..1641198_NEGATIVE 434 158 112 228 183 NC_003454:FN0085|5end_Ethanolamine_utilization_cobalamin_adenosyltransferase_723270..723500_POSITIVE 433 129 81 196 148 NC_003454:FN0906|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1565131..1565361_NEGATIVE 430 150 101 228 179 NC_003454:FN1835|5end_hypothetical_protein_323680..323910_NEGATIVE 412 100 57 231 189 NC_003454:FN0130|5end_ABC_transporter_ATP-binding_protein_758586..758816_POSITIVE 396 140 91 231 182 NC_003454:FN0117|5end_O6-methylguanine-DNA_methyltransferase_750338..750568_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 576 130 81 136 87 NC_003454:FN0797|3end_hypothetical_protein_1455668..1455818_NEGATIVE 507 220 171 73 24 NC_003454:FN1218|3end_hypothetical_protein_1877812..1877962_NEGATIVE 475 220 171 55 6 NC_003454:FN0129|3end_Urease_accessory_protein_ureG_758370..758520_POSITIVE 471 190 147 45 1 NC_003454:FN1461|3end_Histidinol-phosphatase_2141603..2141753_NEGATIVE 446 220 171 88 39 NC_003454:FN2005|3end_Cobalt_transport_ATP-binding_protein_cbiO_505976..506126_POSITIVE 430 216 171 70 24 NC_003454:FN1811|3end_Manganese_transport_system_ATP-binding_protein_mntA_292161..292311_NEGATIVE 402 192 152 45 4 NC_003454:FN0989|3end_phosphoribosylaminoimidazole_carboxylase_catalytic_subunit_1641194..1641344_NEGATIVE 398 190 152 40 1 NC_003454:FN1820|3end_Export_ABC_transporter_311016..311166_POSITIVE 385 199 152 57 9 NC_003454:FN0170|3end_GTP-binding_protein_796613..796763_POSITIVE 364 179 136 43 1 NC_003454:FN0391|3end_Hydrolase_(HAD_superfamily)_1029496..1029646_POSITIVE 335 194 152 48 6 NC_003454:FN1836|3end_Tetratricopeptide_repeat_family_protein_323904..324054_NEGATIVE 316 220 174 47 1 NC_003454:FN0046|3end_3-dehydroquinate_dehydratase_684265..684415_POSITIVE 309 227 185 53 11 NC_003454:FN1826|3end_Protease_314654..314804_NEGATIVE 302 194 158 50 14 NC_003454:FN0483|3end_Uracil_phosphoribosyltransferase_1129301..1129451_POSITIVE 298 108 64 150 106 NC_003454:FN1821|3end_Hypothetical_cytosolic_protein_311209..311359_POSITIVE 297 194 158 58 22 NC_003454:FN2096|3end_hypothetical_protein_606267..606417_NEGATIVE 294 210 165 61 15 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 260 94 58 43 8 NC_003454:FN1919|3end_Methyltransferase_415133..415283_NEGATIVE 234 210 164 68 21 NC_003454:FN0084|3end_Acetaldehyde_dehydrogenase_[acetylating]_723094..723244_POSITIVE 231 104 63 47 5 NC_003454:FN1348|3end_ABC_transporter_ATP-binding_protein_2000470..2000620_NEGATIVE