Origin IGS: aatagcttgttaaaattataaatataataaaaacagttcattgctagctaaattttttaacactgaaaaattaacgttcgctgcaaattcgctaaacttgctgacaagtcagcttcaaacacaccgagatttgctcggctcacttgctttaatttttcatctaaaatttagaatgcaatttcacttgtttttatttatattgtaaaacttgcttattttattgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt .........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 aaggtcaaagtccatttcatctaattcattattgtctatactcatttcctctccttaatctgtacctatgaacaataaaataagcaagttttacaatataaataaaaacaagtgaaattgcattctaaattttagatgaaaaattaaagcaagtgagccgagcaaatctcggtgtgtttgaagctgacttgtcagcaagtttagcgaatttgcagcgaacgttaatttttcagtgttaaaaaatttagctagcaatgaactgtttttattatatttataattttaacaagctatt Mask Tandem Repeat Region ================================================ aatagcttgttaaaattataaatataataaaaacagttcattgctagctaaattttttaacactgaaaaattaacgttcgctgcaaattcgctaaacttgctgacaagtcagcttcaaacacaccgagatttgctcggctcacttgctttaatttttcatctaaaatttagaatgcaatttcacttgtttttatttatattgtaaaacttgcttattttattgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt Find is-nt database================================================ Query_seq: FN0129:FN0130|FN0129:FN0130:Urease accessory protein ureG:ABC transporter ATP-binding protein:->->:758431..758725 295 aatagcttgttaaaattataaatataataaaaacagttcattgctagctaaattttttaacactgaaaaattaacgttcgctgcaaattcgctaaacttgctgacaagtcagcttcaaacacaccgagatttgctcggctcacttgctttaatttttcatctaaaatttagaatgcaatttcacttgtttttatttatattgtaaaacttgcttattttattgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0129:FN0130|FN0129:FN0130:Urease accessory protein ureG:ABC transporter ATP-binding protein:->->:758431..758725 295 aatagcttgttaaaattataaatataataaaaacagttcattgctagctaaattttttaacactgaaaaattaacgttcgctgcaaattcgctaaacttgctgacaagtcagcttcaaacacaccgagatttgctcggctcacttgctttaatttttcatctaaaatttagaatgcaatttcacttgtttttatttatattgtaaaacttgcttattttattgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0129:FN0130|FN0129:FN0130:Urease accessory protein ureG:ABC transporter ATP-binding protein:->->:758431..758725 295 aatagcttgttaaaattataaatataataaaaacagttcattgctagctaaattttttaacactgaaaaattaacgttcgctgcaaattcgctaaacttgctgacaagtcagcttcaaacacaccgagatttgctcggctcacttgctttaatttttcatctaaaatttagaatgcaatttcacttgtttttatttatattgtaaaacttgcttattttattgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 29 Max: 219 Len: 191 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: 4.0E-14 bit: 79.3 Len: 156 Query Start:29 Query End:184 Subject Strand: null Subject Start: 5 Subject End: 56 ............................ K N S S L L A K F F N T E K L T F A A N S L N L L T S Q L Q T H R D L L G S L A L I F H L K F R M Q F H ............................................................................................................... ............................ 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 V H ............................................................................................................... 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: 1.0E-8 bit: 43.1 Len: 69 Query Start:29 Query End:97 Subject Strand: null Subject Start: 24 Subject End: 46 ............................ K N S S L L A K F F N T E K L T F A A N S L N ...................................................................................................................................................................................................... ............................ 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: 1.0E-8 bit: 38.1 Len: 54 Query Start:115 Query End:168 Subject Strand: null Subject Start: 50 Subject End: 67 .................................................................................................................. S N T P R F A R L T C F N F S S K I ............................................................................................................................... .................................................................................................................. S N T A R F A R L T C F N F S S K I ............................................................................................................................... Subject: UniRef90_Q8RGV6 Cluster: Hypothetical cytosolic protein; n=1; Fusobacterium nucleatum subsp. nucleatum|Rep: Hypothetical cytosolic protein - Fusobacterium nucleatum subsp. nucleatum HSP 1 e-value: 2.0E-6 bit: 53.9 Len: 153 Query Start:67 Query End:219 Subject Strand: null Subject Start: 11 Subject End: 60 .................................................................. K I N V R C K F A K L A D K S A S N T P R F A R L T C F N F S S K I * N A I S L V F I Y I V K L A Y F ............................................................................ .................................................................. K L R I R C K F D K L A D K S A S N K S R F A W L I L F N F L S K I Y I R N S L I F - Y L I S I N F Y ............................................................................ aatagcttgttaaaattataaatataatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnattgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 70 End: 168 ..................................................................... M N V R C K F A K L A D K S A S N T P R F A R L T C F N F S S K I ............................................................................................................................... Protein_Len: 54 Strand: + Start: 41 End: 202 ........................................ M L A K F F N T E K L T F A A N S L N L L T S Q L Q T H R D L L G S L A L I F H L K F R M Q F H L F L F I L ............................................................................................. Protein_Len: 36 Strand: - Start: 60 End: 167 ........................................................... C Q F I L T R Q L N A L S A S L D A E F V G L N A R S V Q K L K E D L M ................................................................................................................................ aatagcttgttaaaattataaatataatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnattgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt 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================================================ aatagcttgttaaaattataaatataatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnattgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -2.3 Tail_Score: -3.36694 Start: 122 End: 140 Full_Region: aaattaaagcaagtg agccgag caaat ctcggtg tgtttgaagctgact .........................................................................................................................agccgagcaaatctcggtg........................................................................................................................................................... Find igs database================================================ Query_seq: FN0129:FN0130|FN0129:FN0130:Urease accessory protein ureG:ABC transporter ATP-binding protein:->->:758431..758725 295 aatagcttgttaaaattataaatataatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnattgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt Intra-Species Hit: Count: 1 Min: 1 Max: 295 Len: 295 Subject: NC_003454_FN0129_FN0130|Urease accessory protein ureG:ABC transporter ATP-binding protein|POSITIVE:POSITIVE|[758431,758725]|295 HSP 1 e-value: 2.0E-35 bit: 151.0 Len: 76 Query Start:220 Query End:295 Subject Strand: POSITIVE Subject Start: 220 Subject End: 295 ...........................................................................................................................................................................................................................attgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt ...........................................................................................................................................................................................................................attgttcataggtacagattaaggagaggaaatgagtatagacaataatgaattagatgaaatggactttgacctt HSP 2 e-value: 7.0E-7 bit: 56.0 Len: 28 Query Start:1 Query End:28 Subject Strand: POSITIVE Subject Start: 1 Subject End: 28 aatagcttgttaaaattataaatataat........................................................................................................................................................................................................................................................................... aatagcttgttaaaattataaatataat........................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGCUUGUUAAAAUUAUAAAUAUAAUAAAAACAGUUCAUUGCUAGCUAAAUUUUUUAACACUGAAAAAUUAACGUUCGCUGCAAAUUCGCUAAACUUGCUGACAAGUCAGCUUCAAACACACCGAGAUUUGCUCGGCUCACUUGCUUUAAUUUUUCAUCUAAAAUUUAGAAUGCAAUUUCACUUGUUUUUAUUUAUAUUGUAAAACUUGCUUAUUUUAUUGUUCAUAGGUACAGAUUAAGGAGAGGAAAUGAGUAUAGACAAUAAUGAAUUAGAUGAAAUGGACUUUGACCUU ........((((((...........((((((((((((..(((((...(((((((((.......(((((((((((.((..((((((((((((........(((((....)))))...........))).))))))..)))......)).)))))))))))...)))))))))...)))))...)).))))))))))..((((((......((((((((((.((.(((.(((.......))).))).))))))))))))...))))))....................))))))... (-58.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGUCAAAGUCCAUUUCAUCUAAUUCAUUAUUGUCUAUACUCAUUUCCUCUCCUUAAUCUGUACCUAUGAACAAUAAAAUAAGCAAGUUUUACAAUAUAAAUAAAAACAAGUGAAAUUGCAUUCUAAAUUUUAGAUGAAAAAUUAAAGCAAGUGAGCCGAGCAAAUCUCGGUGUGUUUGAAGCUGACUUGUCAGCAAGUUUAGCGAAUUUGCAGCGAACGUUAAUUUUUCAGUGUUAAAAAAUUUAGCUAGCAAUGAACUGUUUUUAUUAUAUUUAUAAUUUUAACAAGCUAUU .((((.(((.....))).))))......(((((((.((((..........................)))).)))))))....(((..(((....(((((((.((((((((.((...(((((...(((((((((((.(((((((((((.((((((.(((((((((.((....)).))))))..))).))))))..((((((((...))))))))........)))))))))))...)))..))))))))...)))))..))))))))))))))))).........)))..)))... (-58.99) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 682 140 93 88 41 NC_003454:FN1460|5end_Hypothetical_cytosolic_protein_2141429..2141659_POSITIVE 664 140 91 124 76 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 522 80 31 225 175 NC_003454:FN1603|5end_2',3'-cyclic_nucleotide_3'-phosphodiesterase_113661..113891_NEGATIVE 434 90 41 227 177 NC_003454:FN0798|5end_Fructose-1,6-bisphosphatase_1455835..1456065_POSITIVE 394 98 52 190 143 NC_003454:FN0714|5end_NADH_oxidase_1372062..1372292_POSITIVE 389 140 92 230 188 NC_003454:FN1651|5end_Oligopeptide_transport_system_permease_protein_oppB_145799..146029_NEGATIVE 381 170 121 152 101 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 375 72 35 156 119 NC_003454:FN0081|5end_Ethanolamine_utilization_protein_eutL_720035..720265_POSITIVE 267 169 124 65 12 NC_003454:FN0093|5end_Thioredoxin_729169..729399_POSITIVE 254 120 75 231 190 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 251 273 237 104 59 NC_003454:FN0572|5end_hypothetical_protein_1222555..1222785_NEGATIVE 247 135 105 62 29 NC_003454:FN1518|5end_RNA_polymerase_sigma-70_factor_24077..24307_NEGATIVE 242 149 105 41 1 NC_003454:FN1253|5end_hypothetical_protein_1910405..1910635_NEGATIVE 240 131 91 71 24 NC_003454:FN0182|5end_Sarcosine_oxidase_alpha_subunit_807066..807296_NEGATIVE 239 109 81 224 195 NC_003454:FN1643|5end_LSU_ribosomal_protein_L23P_140017..140247_NEGATIVE 237 68 21 168 123 NC_003454:FN0367|5end_Integral_membrane_protein_996901..997131_NEGATIVE 236 138 95 204 149 NC_003454:FN0532|5end_Hypothetical_membrane-spanning_protein_1187579..1187809_NEGATIVE 234 135 95 207 172 NC_003454:FN0094|5end_hypothetical_protein_729740..729970_NEGATIVE 230 140 97 223 176 NC_003454:FN1856|5end_Butyrate-acetoacetate_CoA-transferase_subunit_B_346146..346376_NEGATIVE 229 116 80 67 39 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 461 200 152 66 17 NC_003454:FN0796|3end_pyruvate_phosphate_dikinase_1455643..1455793_POSITIVE 381 170 121 59 8 NC_003454:FN1506|3end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_12060..12210_POSITIVE 375 72 35 49 12 NC_003454:FN0080|3end_ethanolamine_ammonia-lyase_small_subunit_720008..720158_POSITIVE 329 62 21 44 4 NC_003454:FN0454|3end_Aldehyde_dehydrogenase_B_1101022..1101172_POSITIVE 315 157 116 42 1 NC_003454:FN0713|3end_Chromate_transport_protein_1371943..1372093_POSITIVE 247 135 105 51 18 NC_003454:FN1519|3end_23S_rRNA_methyltransferase_24088..24238_NEGATIVE 240 131 91 59 12 NC_003454:FN0183|3end_Glycerol-3-phosphate_dehydrogenase_807078..807228_NEGATIVE 235 196 168 42 14 NC_003454:FN1825|3end_hypothetical_protein_314511..314661_POSITIVE 218 50 1 53 1 NC_003454:FN0453|3end_Xaa-Pro_aminopeptidase_1099381..1099531_POSITIVE 210 176 134 119 68 NC_003454:FN0087|3end_Ethanolamine_utilization_protein_eutN_724954..725104_POSITIVE 209 146 107 52 15 NC_003454:FN0679|3end_GTPase_1335533..1335683_POSITIVE 208 140 92 53 7 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 199 160 113 149 105 NC_003454:FN1875|3end_Peptidyl-prolyl_cis-trans_isomerase_363906..364056_NEGATIVE 198 251 216 151 118 NC_003454:FN0204|3end_Glutaconyl-CoA_decarboxylase_A_subunit_831406..831556_POSITIVE 196 182 143 150 110 NC_003454:FN0765|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_1421960..1422110_POSITIVE 195 65 21 66 17 NC_003454:FN1439|3end_Transcriptional_regulator,_DeoR_family_2107245..2107395_POSITIVE 195 226 183 99 54 NC_003454:FN0129|3end_Urease_accessory_protein_ureG_758370..758520_POSITIVE 193 169 136 55 19 NC_003454:FN1938|3end_hypothetical_protein_437949..438099_NEGATIVE 192 139 98 64 9 NC_003454:FN1630|3end_SSU_ribosomal_protein_S8P_134533..134683_NEGATIVE 190 180 133 142 95 NC_003454:FN0294|3end_Transketolase_subunit_A_928041..928191_POSITIVE