Origin IGS: ctattattgcctccttaccttcttctttatttctgactttataaaaatagcataaacatttgctatacttaaaaaatatataagtaaaaaatgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagtgatcttagaagcacttaatgaacttgttcatttagagcttcttacagatagcgaatttgcagcaaattcttgatttttatcattaagaaatttagctagtaatgaagcattttttactctataaactaagaagtgaataaatatctattt .........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 aaatagatatttattcacttcttagtttatagagtaaaaaatgcttcattactagctaaatttcttaatgataaaaatcaagaatttgctgcaaattcgctatctgtaagaagctctaaatgaacaagttcattaagtgcttctaagatcacttcgttcaaacatagcgagatttgctcggctcattctatttgactttttatctaaaatttagaatgtaattctctcattttttacttatatattttttaagtatagcaaatgtttatgctatttttataaagtcagaaataaagaagaaggtaaggaggcaataatag Mask Tandem Repeat Region ================================================ ctattattgcctccttaccttcttctttatttctgactttataaaaatagcataaacatttgctatacttaaaaaatatataagtaaaaaatgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagtgatcttagaagcacttaatgaacttgttcatttagagcttcttacagatagcgaatttgcagcaaattcttgatttttatcattaagaaatttagctagtaatgaagcattttttactctataaactaagaagtgaataaatatctattt Find is-nt database================================================ Query_seq: FN0358:FN0359|FN0358:FN0359:ATP synthase subunit B:ATP synthase gamma chain, sodium ion specific:<-<-:989765..990084 320 ctattattgcctccttaccttcttctttatttctgactttataaaaatagcataaacatttgctatacttaaaaaatatataagtaaaaaatgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagtgatcttagaagcacttaatgaacttgttcatttagagcttcttacagatagcgaatttgcagcaaattcttgatttttatcattaagaaatttagctagtaatgaagcattttttactctataaactaagaagtgaataaatatctattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0358:FN0359|FN0358:FN0359:ATP synthase subunit B:ATP synthase gamma chain, sodium ion specific:<-<-:989765..990084 320 ctattattgcctccttaccttcttctttatttctgactttataaaaatagcataaacatttgctatacttaaaaaatatataagtaaaaaatgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagtgatcttagaagcacttaatgaacttgttcatttagagcttcttacagatagcgaatttgcagcaaattcttgatttttatcattaagaaatttagctagtaatgaagcattttttactctataaactaagaagtgaataaatatctattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0358:FN0359|FN0358:FN0359:ATP synthase subunit B:ATP synthase gamma chain, sodium ion specific:<-<-:989765..990084 320 ctattattgcctccttaccttcttctttatttctgactttataaaaatagcataaacatttgctatacttaaaaaatatataagtaaaaaatgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagtgatcttagaagcacttaatgaacttgttcatttagagcttcttacagatagcgaatttgcagcaaattcttgatttttatcattaagaaatttagctagtaatgaagcattttttactctataaactaagaagtgaataaatatctattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 172 Max: 285 Len: 114 Subject: UniRef90_Q7P6T5 Cluster: Hypothetical protein FNV1606; n=1; Fusobacterium nucleatum subsp. vincentii ATCC 49256|Rep: Hypothetical protein FNV1606 - Fusobacterium nucleatum subsp. vincentii ATCC 49256 HSP 1 e-value: 4.0E-9 bit: 62.8 Len: 114 Query Start:172 Query End:285 Subject Strand: null Subject Start: 9 Subject End: 46 ........................................................................................................................................................................... I L E A L N E L V H L E L L T D S E F A A N S * F L S L R N L A S N E A F F ................................... ........................................................................................................................................................................... I L E A I N E L V H L E L L T D A E F A A N V N F S S L R N L A S N E L F F ................................... ctattattgcctccttaccttcttctttatttctgactttataaaaatagcataaacatttgctatacttaaaaaatatataagtaaaaaatgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactctataaactaagaagtgaataaatatctattt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 148 End: 240 ................................................................................................................................................... M S L C L N E V I L E A L N E L V H L E L L T D S E F A A N S ................................................................................ Protein_Len: 38 Strand: - Start: 201 End: 314 ........................................................................................................................................................................................................ K S S R V S L S N A A F E Q N K D N L F K A L L S A N K V R Y V L F H I F M ...... Protein_Len: 33 Strand: - Start: 2 End: 100 . I I A E K G E E K N R V K Y F Y C L C K S Y K F F I Y T F F S L M ............................................................................................................................................................................................................................ ctattattgcctccttaccttcttctttatttctgactttataaaaatagcataaacatttgctatacttaaaaaatatataagtaaaaaatgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactctataaactaagaagtgaataaatatctattt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctattattgcctccttaccttcttctttatttctgactttataaaaatagcataaacatttgctatacttaaaaaatatataagtaaaaaatgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactctataaactaagaagtgaataaatatctattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 78 HP_score: -8.1 Tail_Score: -3.90511 Start: 223 End: 239 Full_Region: CTTCTTACAGATAGC GAATTTG CAG CAAATTC TTGATTTTTATCATT ..............................................................................................................................................................................................................................GAATTTGCAGCAAATTC................................................................................. Find igs database================================================ Query_seq: FN0358:FN0359|FN0358:FN0359:ATP synthase subunit B:ATP synthase gamma chain, sodium ion specific:<-<-:989765..990084 320 ctattattgcctccttaccttcttctttatttctgactttataaaaatagcataaacatttgctatacttaaaaaatatataagtaaaaaatgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactctataaactaagaagtgaataaatatctattt Intra-Species Hit: Count: 1 Min: 1 Max: 320 Len: 320 Subject: NC_003454_FN0358_FN0359|ATP synthase subunit B:ATP synthase gamma chain, sodium ion specific|NEGATIVE:NEGATIVE|[989765,990084]|320 HSP 1 e-value: 3.0E-37 bit: 157.0 Len: 79 Query Start:92 Query End:170 Subject Strand: POSITIVE Subject Start: 92 Subject End: 170 ...........................................................................................tgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagt...................................................................................................................................................... ...........................................................................................tgagagaattacattctaaattttagataaaaagtcaaatagaatgagccgagcaaatctcgctatgtttgaacgaagt...................................................................................................................................................... HSP 2 e-value: 2.0E-13 bit: 77.8 Len: 39 Query Start:1 Query End:39 Subject Strand: POSITIVE Subject Start: 1 Subject End: 39 ctattattgcctccttaccttcttctttatttctgactt......................................................................................................................................................................................................................................................................................... ctattattgcctccttaccttcttctttatttctgactt......................................................................................................................................................................................................................................................................................... HSP 3 e-value: 5.0E-11 bit: 69.9 Len: 35 Query Start:286 Query End:320 Subject Strand: POSITIVE Subject Start: 286 Subject End: 320 .............................................................................................................................................................................................................................................................................................actctataaactaagaagtgaataaatatctattt .............................................................................................................................................................................................................................................................................................actctataaactaagaagtgaataaatatctattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUAUUGCCUCCUUACCUUCUUCUUUAUUUCUGACUUUAUAAAAAUAGCAUAAACAUUUGCUAUACUUAAAAAAUAUAUAAGUAAAAAAUGAGAGAAUUACAUUCUAAAUUUUAGAUAAAAAGUCAAAUAGAAUGAGCCGAGCAAAUCUCGCUAUGUUUGAACGAAGUGAUCUUAGAAGCACUUAAUGAACUUGUUCAUUUAGAGCUUCUUACAGAUAGCGAAUUUGCAGCAAAUUCUUGAUUUUUAUCAUUAAGAAAUUUAGCUAGUAAUGAAGCAUUUUUUACUCUAUAAACUAAGAAGUGAAUAAAUAUCUAUUU .........................(((((((((...((((((...((((((........))))))................(((((((((((.....(((((...(((((((((.((((((((.(((...(((((..((...((((((.(((((..(((((....(((....))).(((((.((.((((((....)))))).)).)))))...)))))))))))))))).))..)))))))))))))))).....)))))))))...)))))....))))))))))).))))))...)))))))))............. (-75.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAGAUAUUUAUUCACUUCUUAGUUUAUAGAGUAAAAAAUGCUUCAUUACUAGCUAAAUUUCUUAAUGAUAAAAAUCAAGAAUUUGCUGCAAAUUCGCUAUCUGUAAGAAGCUCUAAAUGAACAAGUUCAUUAAGUGCUUCUAAGAUCACUUCGUUCAAACAUAGCGAGAUUUGCUCGGCUCAUUCUAUUUGACUUUUUAUCUAAAAUUUAGAAUGUAAUUCUCUCAUUUUUUACUUAUAUAUUUUUUAAGUAUAGCAAAUGUUUAUGCUAUUUUUAUAAAGUCAGAAAUAAAGAAGAAGGUAAGGAGGCAAUAAUAG ..........(((((..(((((((.(((...((((((((((((....(((((...((((((((......((((((((((((((((..((((((((((((((((.....((((((.((.((((((....)))))).)).))))))..((.....))........))))))).))))))..)))..)))))...))).))))))))..))))))))...))))).....))))))))))))....(((((.((((.((((((........)))))).)))).)))))..............))).)))))))..)))))... (-81.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 735 50 1 141 92 NC_003454:FN0358|5end_ATP_synthase_subunit_B_989674..989904_NEGATIVE 634 159 111 216 168 NC_003454:FN0070|5end_Glycyl-tRNA_synthetase_beta_chain_708902..709132_POSITIVE 612 170 121 207 158 NC_003454:FN2095|5end_General_secretion_pathway_protein_E_606080..606310_NEGATIVE 582 178 132 215 167 NC_003454:FN2006|5end_Cobalt_transport_protein_cbiQ_506079..506309_POSITIVE 581 160 111 215 166 NC_003454:FN1486|5end_Integral_membrane_protein_with_CBS_domains_2169299..2169529_NEGATIVE 539 172 136 226 190 NC_003454:FN1217|5end_Holliday_junction_DNA_helicase_ruvB_1877597..1877827_NEGATIVE 535 150 101 195 146 NC_003454:FN0906|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1565131..1565361_NEGATIVE 510 150 101 201 152 NC_003454:FN0392|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1029624..1029854_POSITIVE 481 150 101 206 157 NC_003454:FN1819|5end_Export_ABC_transporter_307519..307749_POSITIVE 477 269 223 88 41 NC_003454:FN0797|5end_hypothetical_protein_1455799..1456029_NEGATIVE 472 150 101 220 170 NC_003454:FN0117|5end_O6-methylguanine-DNA_methyltransferase_750338..750568_POSITIVE 457 164 121 220 177 NC_003454:FN1835|5end_hypothetical_protein_323680..323910_NEGATIVE 455 155 111 217 172 NC_003454:FN0988|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1640968..1641198_NEGATIVE 433 140 91 231 182 NC_003454:FN0484|5end_Lipase_1129470..1129700_POSITIVE 429 149 101 231 183 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 425 167 121 208 160 NC_003454:FN1822|5end_Flavodoxin_311148..311378_POSITIVE 425 167 121 91 43 NC_003454:FN1821|5end_Hypothetical_cytosolic_protein_311031..311261_POSITIVE 421 150 104 198 152 NC_003454:FN0047|5end_Exodeoxyribonuclease_III_684427..684657_POSITIVE 401 149 103 218 172 NC_003454:FN2036|5end_DNA-directed_RNA_polymerase_beta_chain_546371..546601_NEGATIVE 393 270 222 86 37 NC_003454:FN0171|5end_Hypothetical_cytosolic_protein_796548..796778_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 688 150 103 134 87 NC_003454:FN0797|3end_hypothetical_protein_1455668..1455818_NEGATIVE 589 250 203 57 10 NC_003454:FN1809|3end_Iron/zinc/copper-binding_protein_290180..290330_NEGATIVE 556 270 221 64 14 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 498 250 201 50 1 NC_003454:FN0084|3end_Acetaldehyde_dehydrogenase_[acetylating]_723094..723244_POSITIVE 494 270 223 78 30 NC_003454:FN0391|3end_Hydrolase_(HAD_superfamily)_1029496..1029646_POSITIVE 488 270 221 70 20 NC_003454:FN0483|3end_Uracil_phosphoribosyltransferase_1129301..1129451_POSITIVE 484 270 222 68 19 NC_003454:FN1836|3end_Tetratricopeptide_repeat_family_protein_323904..324054_NEGATIVE 484 276 235 45 3 NC_003454:FN1826|3end_Protease_314654..314804_NEGATIVE 476 270 222 68 19 NC_003454:FN1461|3end_Histidinol-phosphatase_2141603..2141753_NEGATIVE 474 270 223 78 30 NC_003454:FN2096|3end_hypothetical_protein_606267..606417_NEGATIVE 408 286 244 82 40 NC_003454:FN1218|3end_hypothetical_protein_1877812..1877962_NEGATIVE 400 270 222 63 14 NC_003454:FN1820|3end_Export_ABC_transporter_311016..311166_POSITIVE 393 270 222 71 22 NC_003454:FN0170|3end_GTP-binding_protein_796613..796763_POSITIVE 392 269 223 80 34 NC_003454:FN2005|3end_Cobalt_transport_ATP-binding_protein_cbiO_505976..506126_POSITIVE 367 279 232 78 31 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE 356 289 244 89 41 NC_003454:FN1811|3end_Manganese_transport_system_ATP-binding_protein_mntA_292161..292311_NEGATIVE 349 288 244 58 14 NC_003454:FN0046|3end_3-dehydroquinate_dehydratase_684265..684415_POSITIVE 342 276 237 41 1 NC_003454:FN0116|3end_Chaperone_protein_dnaK_750156..750306_POSITIVE 338 276 235 85 43 NC_003454:FN0907|3end_Ribosomal_RNA_small_subunit_methyltransferase_C_1565324..1565474_NEGATIVE 328 269 223 47 1 NC_003454:FN0129|3end_Urease_accessory_protein_ureG_758370..758520_POSITIVE