Origin IGS: tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaacttattttttagtatttgttccctcattctttaaaaaatctcctttttttatttattacttttataataactcacctataaacatattttatagatggcaatagttttttaatataacatatgtaatttattttttcaagtataatttttttaaataacaccttcatttttagatttatcttcttaaatagccttttaatctaatattttttaattaatacttaatataaaataaaaagagaattttttaagtttctattcttaaaaaattctctacagtttattt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaataaactgtagagaattttttaagaatagaaacttaaaaaattctctttttattttatattaagtattaattaaaaaatattagattaaaaggctatttaagaagataaatctaaaaatgaaggtgttatttaaaaaaattatacttgaaaaaataaattacatatgttatattaaaaaactattgccatctataaaatatgtttataggtgagttattataaaagtaataaataaaaaaaggagattttttaaagaatgagggaacaaatactaaaaaataagttaatattaatagctttgtcagctgttttacttgtaagttgtgaaggcagtggaagtggaggtggaggaggaagttcaaatgcaccaataaatccaggaaataatgtatcacctacacctaaaaaaccaggaatagaagataaaataaatccgactaatcctgaaagtacagttaatccaagtgtaccaacaccaagtaaaccaactaatcctactaataatgtaaaaagagaatcgcttgaagaacttagggcaaga Mask Tandem Repeat Region ================================================ tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaacttattttttagtatttgttccctcattctttaaaaaatctcctttttttatttattacttttataataactcacctataaacatattttatagatggcaatagttttttaatataacatatgtaatttattttttcaagtataatttttttaaataacaccttcatttttagatttatcttcttaaatagccttttaatctaatattttttaattaatacttaatataaaataaaaagagaattttttaagtttctattcttaaaaaattctctacagtttattt Find is-nt database================================================ Query_seq: FN1950:FN1951|FN1950:FN1951:Serine protease:ATPase associated with chromosome architecture/replication:<-<-:457946..458489 544 tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaacttattttttagtatttgttccctcattctttaaaaaatctcctttttttatttattacttttataataactcacctataaacatattttatagatggcaatagttttttaatataacatatgtaatttattttttcaagtataatttttttaaataacaccttcatttttagatttatcttcttaaatagccttttaatctaatattttttaattaatacttaatataaaataaaaagagaattttttaagtttctattcttaaaaaattctctacagtttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1950:FN1951|FN1950:FN1951:Serine protease:ATPase associated with chromosome architecture/replication:<-<-:457946..458489 544 tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaacttattttttagtatttgttccctcattctttaaaaaatctcctttttttatttattacttttataataactcacctataaacatattttatagatggcaatagttttttaatataacatatgtaatttattttttcaagtataatttttttaaataacaccttcatttttagatttatcttcttaaatagccttttaatctaatattttttaattaatacttaatataaaataaaaagagaattttttaagtttctattcttaaaaaattctctacagtttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1950:FN1951|FN1950:FN1951:Serine protease:ATPase associated with chromosome architecture/replication:<-<-:457946..458489 544 tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaacttattttttagtatttgttccctcattctttaaaaaatctcctttttttatttattacttttataataactcacctataaacatattttatagatggcaatagttttttaatataacatatgtaatttattttttcaagtataatttttttaaataacaccttcatttttagatttatcttcttaaatagccttttaatctaatattttttaattaatacttaatataaaataaaaagagaattttttaagtttctattcttaaaaaattctctacagtttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 263 Max: 419 Len: 157 Subject: UniRef90_Q7P8J2 Cluster: Hypothetical protein FNV2312; n=1; Fusobacterium nucleatum subsp. vincentii ATCC 49256|Rep: Hypothetical protein FNV2312 - Fusobacterium nucleatum subsp. vincentii ATCC 49256 HSP 1 e-value: 9.0E-12 bit: 60.5 Len: 141 Query Start:279 Query End:419 Subject Strand: null Subject Start: 1 Subject End: 48 ...................................................................................................................................................................................................................................................................................... V L F K K I I L E K I N Y I C Y I K K L L P S I K Y V Y R * V I I K V I N K - K R R F F K E * G ............................................................................................................................. ...................................................................................................................................................................................................................................................................................... M L F K K I L L E K I N Y T C Y I K K L L S Y I K Y I Y K C I I I E I T N K I K G E F L K N E G ............................................................................................................................. HSP 2 e-value: 9.0E-12 bit: 32.0 Len: 42 Query Start:263 Query End:304 Subject Strand: null Subject Start: 40 Subject End: 53 ...................................................................................................................................................................................................................................................................... K G D F L K N E G T N T K K ................................................................................................................................................................................................................................................ ...................................................................................................................................................................................................................................................................... K G E F L K N E G T N T K K ................................................................................................................................................................................................................................................ tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaacttannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncttcatttttagatttatcttcttaaatagccttttaatctaatattttttaattaatacttaatataaaataaaaagagaattttttaagtttctattcttaaaaaattctctacagtttattt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 37 End: 147 .................................... M I S R I S W F T W C W Y T W I N C T F R I S R I Y F I F Y S W F F R C R ............................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 59 Strand: + Start: 113 End: 289 ................................................................................................................ M L S S I P G F L G V G D T L F P G F I G A F E L P P P P P L P L P S Q L T S K T A D K A I N I N L F F S I C S L I L ............................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 147 End: 359 .................................................................................................................................................. M I H Y F L D L L V H L N F L L H L H F H C L H N L Q V K Q L T K L L I L T Y F L V F V P S F F K K S P F F I Y Y F Y N ......................................................................................................................................................................................... Protein_Len: 42 Strand: - Start: 333 End: 458 ............................................................................................................................................................................................................................................................................................................................................ R Y V Y K I S P L L K K I Y C I Y N I K E L I I K K F L V K M K L N I K K F L R K M ...................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 285 P N I K D E I G P K K P T P S V N N G P N I P A N S S G G G G G S G S G E C S V L L V A S L A I L I L K N K L I Q E R M ................................................................................................................................................................................................................................................................... tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaacttannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncttcatttttagatttatcttcttaaatagccttttaatctaatattttttaattaatacttaatataaaataaaaagagaattttttaagtttctattcttaaaaaattctctacagtttattt 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: 86 Start: 369 End: 398 ................................................................................................................................................................................................................................................................................................................................................................................CTTGAAAAAATAAATTACATATGTTATATT.................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaacttannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncttcatttttagatttatcttcttaaatagccttttaatctaatattttttaattaatacttaatataaaataaaaagagaattttttaagtttctattcttaaaaaattctctacagtttattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 55 HP_score: -2.3 Tail_Score: -4.48176 Start: 290 End: 309 Full_Region: TGTTCCCTCATTCTT TAAAAAA TCTCCT TTTTTTA TTTATTACTTTTATA .................................................................................................................................................................................................................................................................................................TAAAAAATCTCCTTTTTTTA........................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 48 HP_score: -2.9 Tail_Score: -3.79906 Start: 329 End: 356 Full_Region: attaaaaaactattg ccatctataaa atatg tttataggtgag ttattataaaagtaa ........................................................................................................................................................................................................................................................................................................................................ccatctataaaatatgtttataggtgag............................................................................................................................................................................................ TransTerm Strand: - Conf: 43 HP_score: -3.1 Tail_Score: -2.87622 Start: 330 End: 356 Full_Region: attaaaaaactattg ccatctataaa atatg tttataggtga gttattataaaagta .........................................................................................................................................................................................................................................................................................................................................ccatctataaaatatgtttataggtga............................................................................................................................................................................................ TransTerm Strand: - Conf: 42 HP_score: -3.4 Tail_Score: -2.68806 Start: 333 End: 353 Full_Region: aaaaaactattgcca tctataaa atatg tttatagg tgagttattataaaa ............................................................................................................................................................................................................................................................................................................................................tctataaaatatgtttatagg............................................................................................................................................................................................... TransTerm Strand: + Conf: 50 HP_score: -3.5 Tail_Score: -3.54051 Start: 502 End: 527 Full_Region: AAAATAAAAAGAGAA TTTTTTAAG TTTCTATT CTTAAAAAA TTCTCTACAGTTTAT .....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTTTAAGTTTCTATTCTTAAAAAA................. Find igs database================================================ Query_seq: FN1950:FN1951|FN1950:FN1951:Serine protease:ATPase associated with chromosome architecture/replication:<-<-:457946..458489 544 tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaacttannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncttcatttttagatttatcttcttaaatagccttttaatctaatattttttaattaatacttaatataaaataaaaagagaattttttaagtttctattcttaaaaaattctctacagtttattt Intra-Species Hit: Count: 1 Min: 1 Max: 262 Len: 262 Subject: NC_003454_FN1950_FN1951|Serine protease:ATPase associated with chromosome architecture/replication|NEGATIVE:NEGATIVE|[457946, 458489]|544 HSP 1 e-value: 1.0E-146 bit: 519.0 Len: 262 Query Start:1 Query End:262 Subject Strand: POSITIVE Subject Start: 1 Subject End: 262 tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaactta.......................................................................................................................................................................................................................................................................................... tcttgccctaagttcttcaagcgattctctttttacattattagtaggattagttggtttacttggtgttggtacacttggattaactgtactttcaggattagtcggatttattttatcttctattcctggttttttaggtgtaggtgatacattatttcctggatttattggtgcatttgaacttcctcctccacctccacttccactgccttcacaacttacaagtaaaacagctgacaaagctattaatattaactta.......................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUGCCCUAAGUUCUUCAAGCGAUUCUCUUUUUACAUUAUUAGUAGGAUUAGUUGGUUUACUUGGUGUUGGUACACUUGGAUUAACUGUACUUUCAGGAUUAGUCGGAUUUAUUUUAUCUUCUAUUCCUGGUUUUUUAGGUGUAGGUGAUACAUUAUUUCCUGGAUUUAUUGGUGCAUUUGAACUUCCUCCUCCACCUCCACUUCCACUGCCUUCACAACUUACAAGUAAAACAGCUGACAAAGCUAUUAAUAUUAACUUA ........((((((..((....))..............(((((((((..(((((((.((((((((..(((((((((((((.((...(((.....((((((.(((..((((.......)))).))).)))))).....))))).)))))).))).........((((......((((.....(......).....))))......)))).........))))...)))))))).))))))).....)))))))))..)))))) (-55.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUUAAUAUUAAUAGCUUUGUCAGCUGUUUUACUUGUAAGUUGUGAAGGCAGUGGAAGUGGAGGUGGAGGAGGAAGUUCAAAUGCACCAAUAAAUCCAGGAAAUAAUGUAUCACCUACACCUAAAAAACCAGGAAUAGAAGAUAAAAUAAAUCCGACUAAUCCUGAAAGUACAGUUAAUCCAAGUGUACCAACACCAAGUAAACCAACUAAUCCUACUAAUAAUGUAAAAAGAGAAUCGCUUGAAGAACUUAGGGCAAGA ............(((((((.....)))))))...((((((((((.(..((((..((((..((..((((.(.(((....)))...).))))..))..))))(((.....(((....................(((((.(((..(((.......)))...))).)))))...(((((.((.....)).)))))..)))...(((......)))..)))........................))))..).)))))...))))). (-47.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 875 110 61 201 152 NC_003454:FN1950|5end_Serine_protease_457855..458085_NEGATIVE 554 227 188 231 192 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 349 248 204 99 52 NC_003454:FN1886|5end_hypothetical_protein_371399..371629_POSITIVE 343 240 191 166 118 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 339 203 161 91 42 NC_003454:FN1560|5end_hypothetical_protein_82982..83212_NEGATIVE 330 228 191 63 24 NC_003454:FN1825|5end_hypothetical_protein_313994..314224_POSITIVE 283 215 172 212 168 NC_003454:FN0469|5end_Copper_homeostasis_protein_cutC_1113926..1114156_POSITIVE 280 219 186 41 4 NC_003454:FN2098|5end_MRP-family_nucleotide-binding_protein_608146..608376_NEGATIVE 263 125 82 218 171 NC_003454:FN1302|5end_hypothetical_protein_1959369..1959599_POSITIVE 256 215 171 148 84 NC_003454:FN0120|5end_hypothetical_protein_752891..753121_NEGATIVE 254 187 144 205 165 NC_003454:FN0890|5end_Thiamin_pyrophosphokinase_1552087..1552317_NEGATIVE 253 217 177 197 158 NC_003454:FN1381|5end_hypothetical_protein_2032434..2032664_NEGATIVE 253 217 171 101 32 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 251 199 156 190 162 NC_003454:FN0526|5end_Florfenicol_resistance_protein_1182977..1183207_NEGATIVE 250 163 121 92 35 NC_003454:FN1625|5end_LSU_ribosomal_protein_L15P_132864..133094_NEGATIVE 248 220 171 50 7 NC_003454:FN0116|5end_Chaperone_protein_dnaK_748253..748483_POSITIVE 245 212 182 126 78 NC_003454:FN0659|5end_ABC_transporter_permease_protein_1316391..1316621_NEGATIVE 244 199 158 213 169 NC_003454:FN0090|5end_Ethanolamine_utilization_protein_eutQ_726315..726545_POSITIVE 244 130 87 224 184 NC_003454:FN0088|5end_hypothetical_protein_724887..725117_POSITIVE 244 228 187 146 97 NC_003454:FN1580|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90919..91149_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 240 191 146 98 NC_003454:FN1127|3end_Hypothetical_membrane-spanning_protein_1770307..1770457_NEGATIVE 263 125 82 137 90 NC_003454:FN1301|3end_ABC_transporter_ATP-binding_protein_1959368..1959518_POSITIVE 262 203 164 41 1 NC_003454:FN1561|3end_Hypothetical_cytosolic_protein_83032..83182_NEGATIVE 256 215 171 131 67 NC_003454:FN0121|3end_hypothetical_protein_752908..753058_NEGATIVE 250 163 121 92 35 NC_003454:FN1626|3end_LSU_ribosomal_protein_L30P_132864..133014_NEGATIVE 245 212 182 136 88 NC_003454:FN0660|3end_ABC_transporter_ATP-binding_protein_1316381..1316531_NEGATIVE 239 246 210 141 106 NC_003454:FN0581|3end_Lipoprotein_releasing_system_transmembrane_protein_lolE_1238357..1238507_POSITIVE 236 205 174 142 110 NC_003454:FN1581|3end_DNA_mismatch_repair_protein_mutS_90895..91045_NEGATIVE 231 190 145 48 6 NC_003454:FN0710|3end_hypothetical_protein_1369632..1369782_POSITIVE 230 215 189 133 105 NC_003454:FN0016|3end_hypothetical_protein_654366..654516_POSITIVE 230 45 5 120 82 NC_003454:FN1789|3end_Na+_driven_multidrug_efflux_pump_271579..271729_POSITIVE 229 216 176 52 5 NC_003454:FN1091|3end_Sigma_factor_sigB_regulation_protein_rsbU_1737338..1737488_POSITIVE 229 192 151 88 27 NC_003454:FN0333|3end_Glycerol_uptake_operon_antiterminator_regulatory_protein_967247..967397_NEGATIVE 229 168 128 103 63 NC_003454:FN0140|3end_Transposase_772179..772329_NEGATIVE 228 208 184 48 26 NC_003454:FN1472|3end_N-acetylneuraminate-binding_protein_2155088..2155238_POSITIVE 226 210 162 83 24 NC_003454:FN0415|3end_hypothetical_protein_1053996..1054146_POSITIVE 224 208 161 65 19 NC_003454:FN0754|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1413183..1413333_NEGATIVE 224 48 5 56 12 NC_003454:FN1964|3end_O-linked_GLCNAC_transferase_461646..461796_NEGATIVE 221 240 198 102 53 NC_003454:FN0132|3end_Hemolysin_769183..769333_POSITIVE 217 222 186 115 76 NC_003454:FN1645|3end_LSU_ribosomal_protein_L3P_140666..140816_NEGATIVE