Origin IGS: atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaacccttatttttattttttataaattcaataaatttttaatctttaatttattagaatatatgttaaaataatcattaagaaaggaggaatttttatggtaaaaatagaagttgcaaaagctatttgttttaaccaacttataaattcaaaagaaacagaagttgtaagtatgagaattttaaatcaatctaatagttatatttctttattttcattagctaaaaatgaagaaattacagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct .........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 agcttcatctcctattttttctccaatttcaataagttttaaagtatctgatgattttatagaataattattatgagctaaaacttctaaaaaatcaccatttgaaatatgttttttattattttcaatagatacttctccactaccattaaaacaataataatatctatttcctaacatagcttcagctgtaatttcttcatttttagctaatgaaaataaagaaatataactattagattgatttaaaattctcatacttacaacttctgtttcttttgaatttataagttggttaaaacaaatagcttttgcaacttctatttttaccataaaaattcctcctttcttaatgattattttaacatatattctaataaattaaagattaaaaatttattgaatttataaaaaataaaaataagggttgacttatttttaaattgaatttagaataaatatataacattgaaataagagaggagaaaaat Mask Tandem Repeat Region ================================================ atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaacccttatttttattttttataaattcaataaatttttaatctttaatttattagaatatatgttaaaataatcattaagaaaggaggaatttttatggtaaaaatagaagttgcaaaagctatttgttttaaccaacttataaattcaaaagaaacagaagttgtaagtatgagaattttaaatcaatctaatagttatatttctttattttcattagctaaaaatgaagaaattacagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct Find is-nt database================================================ Query_seq: FN1304:FN1305|FN1304:FN1305:Single-strand DNA binding protein:Hypothetical cytosolic protein:<-->:1960854..1961344 491 atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaacccttatttttattttttataaattcaataaatttttaatctttaatttattagaatatatgttaaaataatcattaagaaaggaggaatttttatggtaaaaatagaagttgcaaaagctatttgttttaaccaacttataaattcaaaagaaacagaagttgtaagtatgagaattttaaatcaatctaatagttatatttctttattttcattagctaaaaatgaagaaattacagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1304:FN1305|FN1304:FN1305:Single-strand DNA binding protein:Hypothetical cytosolic protein:<-->:1960854..1961344 491 atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaacccttatttttattttttataaattcaataaatttttaatctttaatttattagaatatatgttaaaataatcattaagaaaggaggaatttttatggtaaaaatagaagttgcaaaagctatttgttttaaccaacttataaattcaaaagaaacagaagttgtaagtatgagaattttaaatcaatctaatagttatatttctttattttcattagctaaaaatgaagaaattacagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1304:FN1305|FN1304:FN1305:Single-strand DNA binding protein:Hypothetical cytosolic protein:<-->:1960854..1961344 491 atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaacccttatttttattttttataaattcaataaatttttaatctttaatttattagaatatatgttaaaataatcattaagaaaggaggaatttttatggtaaaaatagaagttgcaaaagctatttgttttaaccaacttataaattcaaaagaaacagaagttgtaagtatgagaattttaaatcaatctaatagttatatttctttattttcattagctaaaaatgaagaaattacagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 171 Max: 299 Len: 129 Subject: UniRef90_Q7P2E7 Cluster: Hypothetical Cytosolic Protein; n=1; Fusobacterium nucleatum subsp. vincentii ATCC 49256|Rep: Hypothetical Cytosolic Protein - Fusobacterium nucleatum subsp. vincentii ATCC 49256 HSP 1 e-value: 1.0E-13 bit: 77.8 Len: 129 Query Start:171 Query End:299 Subject Strand: null Subject Start: 14 Subject End: 56 .......................................................................................................................................................................... E V A K A I C F N Q L I N S K E T E V V S M R I L N Q S N S Y I S L F S L A K N E E I ................................................................................................................................................................................................ .......................................................................................................................................................................... E V A K A I D F N Q L I N S K E A E V V S M R I L N Q S N S Y I S L F S L A K N E E I ................................................................................................................................................................................................ atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaacccttatttttattttttataaattcaataaatttttaatctttaatttattagaatatatgttaaaataatcattaagaaaggaggaatttttatggtaaaaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 43 End: 132 .......................................... M Q F K N K S T L I F I F Y K F N K F L I F N L L E Y M L K ....................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 114 End: 491 ................................................................................................................. M R I Y V K I I I K K G G I F M V K I E V A K A I C F N Q L I N S K E T E V V S M R I L N Q S N S Y I S L F S L A K N E Protein_Len: 44 Strand: - Start: 110 End: 241 ............................................................................................................. N I L I Y T L I I M L F P P I K I T F I S T A F A I Q K L W S I F E F S V S T T L I L M .......................................................................................................................................................................................................................................................... Protein_Len: 42 Strand: - Start: 84 End: 209 ................................................................................... L N L L N K I K L K N S Y I N F Y D N L F S S N K H Y F Y F N C F S N T K V L K Y M .......................................................................................................................................................................................................................................................................................... atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaacccttatttttattttttataaattcaataaatttttaatctttaatttattagaatatatgttaaaataatcattaagaaaggaggaatttttatggtaaaaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct 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: 88 Start: 36 End: 65 ...................................GTTGACTTATTTTTAAATTGAATTTAGAAT.......................................................................................................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaacccttatttttattttttataaattcaataaatttttaatctttaatttattagaatatatgttaaaataatcattaagaaaggaggaatttttatggtaaaaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -6.4 Tail_Score: -5.31456 Start: 51 End: 76 Full_Region: ATTCTAAATTCAATT TAAAAATAAG TCAACC CTTATTTTTA TTTTTTATAAATTCA ..................................................TAAAAATAAGTCAACCCTTATTTTTA............................................................................................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN1304:FN1305|FN1304:FN1305:Single-strand DNA binding protein:Hypothetical cytosolic protein:<-->:1960854..1961344 491 atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaacccttatttttattttttataaattcaataaatttttaatctttaatttattagaatatatgttaaaataatcattaagaaaggaggaatttttatggtaaaaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct Intra-Species Hit: Count: 1 Min: 1 Max: 491 Len: 491 Subject: NC_003454_FN1304_FN1305|Single-strand DNA binding protein:Hypothetical cytosolic protein|NEGATIVE:POSITIVE|[1960854,1961344]|491 HSP 1 e-value: 1.0E-104 bit: 381.0 Len: 192 Query Start:300 Query End:491 Subject Strand: POSITIVE Subject Start: 300 Subject End: 491 ...........................................................................................................................................................................................................................................................................................................acagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct ...........................................................................................................................................................................................................................................................................................................acagctgaagctatgttaggaaatagatattattattgttttaatggtagtggagaagtatctattgaaaataataaaaaacatatttcaaatggtgattttttagaagttttagctcataataattattctataaaatcatcagatactttaaaacttattgaaattggagaaaaaataggagatgaagct HSP 2 e-value: 6.0E-30 bit: 133.0 Len: 67 Query Start:1 Query End:67 Subject Strand: POSITIVE Subject Start: 1 Subject End: 67 atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaaccc........................................................................................................................................................................................................................................................................................................................................................................................................................................ atttttctcctctcttatttcaatgttatatatttattctaaattcaatttaaaaataagtcaaccc........................................................................................................................................................................................................................................................................................................................................................................................................................................ HSP 3 e-value: 1.0E-6 bit: 56.0 Len: 28 Query Start:143 Query End:170 Subject Strand: POSITIVE Subject Start: 143 Subject End: 170 ..............................................................................................................................................gaaaggaggaatttttatggtaaaaata................................................................................................................................................................................................................................................................................................................................. ..............................................................................................................................................gaaaggaggaatttttatggtaaaaata................................................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUCUCCUCUCUUAUUUCAAUGUUAUAUAUUUAUUCUAAAUUCAAUUUAAAAAUAAGUCAACCCUUAUUUUUAUUUUUUAUAAAUUCAAUAAAUUUUUAAUCUUUAAUUUAUUAGAAUAUAUGUUAAAAUAAUCAUUAAGAAAGGAGGAAUUUUUAUGGUAAAAAUAGAAGUUGCAAAAGCUAUUUGUUUUAACCAACUUAUAAAUUCAAAAGAAACAGAAGUUGUAAGUAUGAGAAUUUUAAAUCAAUCUAAUAGUUAUAUUUCUUUAUUUUCAUUAGCUAAAAAUGAAGAAAUUACAGCUGAAGCUAUGUUAGGAAAUAGAUAUUAUUAUUGUUUUAAUGGUAGUGGAGAAGUAUCUAUUGAAAAUAAUAAAAAACAUAUUUCAAAUGGUGAUUUUUUAGAAGUUUUAGCUCAUAAUAAUUAUUCUAUAAAAUCAUCAGAUACUUUAAAACUUAUUGAAAUUGGAGAAAAAAUAGGAGAUGAAGCU .(((.((((((((((.(((((((((....((((.((((((((........((((((((((......))))))))))....(((.(((((.....))))).)))...........)))))))).)))).......((((((((((.....((((((((((.(((.((((((((((((.....)))).)))))))).))).((((((((.(((..........))).)))))))).)))))))))).........(((((((..((((((((..((((((((.......))))))))......(((....))).....))))))))...)))))))...)))))))))).((...((((((((..((((((...............))))))..(((((((((.(((((...(((........)))...))))).))))))))).))))))))...)).))))))))).))))).......))))).)))... (-102.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUCAUCUCCUAUUUUUUCUCCAAUUUCAAUAAGUUUUAAAGUAUCUGAUGAUUUUAUAGAAUAAUUAUUAUGAGCUAAAACUUCUAAAAAAUCACCAUUUGAAAUAUGUUUUUUAUUAUUUUCAAUAGAUACUUCUCCACUACCAUUAAAACAAUAAUAAUAUCUAUUUCCUAACAUAGCUUCAGCUGUAAUUUCUUCAUUUUUAGCUAAUGAAAAUAAAGAAAUAUAACUAUUAGAUUGAUUUAAAAUUCUCAUACUUACAACUUCUGUUUCUUUUGAAUUUAUAAGUUGGUUAAAACAAAUAGCUUUUGCAACUUCUAUUUUUACCAUAAAAAUUCCUCCUUUCUUAAUGAUUAUUUUAACAUAUAUUCUAAUAAAUUAAAGAUUAAAAAUUUAUUGAAUUUAUAAAAAAUAAAAAUAAGGGUUGACUUAUUUUUAAAUUGAAUUUAGAAUAAAUAUAUAACAUUGAAAUAAGAGAGGAGAAAAAU .......(((((.......((((..((((((((..(((((((((((((((.(((((((.(((((...(((........)))...))))).)))))))....((((((.(((.....)))...))))))))))))))............)))))))........(((.(((((.........((...((((((.(((((((.(((((((.....))))))).)))))))..........(((..(((((((((((........(((.....))).......)))))).)))))..))).......))))))...))...(((((..((((...(((((((...((..((((((....(((((((...(((.((((.((((((((..........)))))))))))).)))..)))))))...))))))..))...)))))))...))))..))))).))))).)))..))))))))..)))))))))..... (-83.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 631 50 1 141 92 NC_003454:FN1304|5end_Single-strand_DNA_binding_protein_1960763..1960993_NEGATIVE 237 350 301 161 98 NC_003454:FN0582|5end_Lipoprotein_releasing_system_ATP-binding_protein_lolD_1238246..1238476_POSITIVE 237 179 134 224 175 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 226 340 300 86 48 NC_003454:FN1806|5end_Integral_membrane_protein_287724..287954_POSITIVE 222 320 277 206 166 NC_003454:FN0115|5end_hypothetical_protein_748511..748741_NEGATIVE 218 177 146 227 195 NC_003454:FN1129|5end_Chromosome_partition_protein_smc_1774204..1774434_POSITIVE 217 356 311 160 112 NC_003454:FN1882|5end_hypothetical_protein_368560..368790_POSITIVE 216 294 252 57 8 NC_003454:FN0535|5end_hypothetical_protein_1189351..1189581_POSITIVE 216 38 4 124 91 NC_003454:FN1827|5end_Replicative_DNA_helicase_317239..317469_NEGATIVE 214 432 392 216 179 NC_003454:FN1898|5end_Sugar_transport_ATP-binding_protein_386569..386799_NEGATIVE 214 41 1 137 90 NC_003454:FN1725|5end_Potassium_uptake_protein_KtrB_224671..224901_NEGATIVE 211 50 1 146 97 NC_003454:FN0270|5end_GTP-binding_protein_era_896770..897000_POSITIVE 206 45 5 139 91 NC_003454:FN1698|5end_dTDP-4-dehydrorhamnose_reductase_194593..194823_NEGATIVE 205 434 391 214 174 NC_003454:FN1030|5end_Hypothetical_membrane-spanning_protein_1684721..1684951_NEGATIVE 205 268 221 102 48 NC_003454:FN0923|5end_Cardiolipin_synthetase_1578977..1579207_NEGATIVE 205 285 247 215 175 NC_003454:FN1787|5end_Tetratricopeptide_repeat_family_protein_267762..267992_POSITIVE 204 190 146 228 187 NC_003454:FN1275|5end_Acriflavin_resistance_protein_B_1931725..1931955_POSITIVE 204 284 251 185 152 NC_003454:FN0698|5end_DNA_integration/recombination/invertion_protein_1356611..1356841_POSITIVE 204 438 393 126 83 NC_003454:FN0050|5end_Fumarate_reductase_flavoprotein_subunit_687043..687273_POSITIVE 202 447 407 172 133 NC_003454:FN1371|5end_Ribonuclease_HII_2020002..2020232_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 305 261 149 99 NC_003454:FN1345|3end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase_1998130..1998280_NEGATIVE 216 38 4 112 79 NC_003454:FN1828|3end_LSU_ribosomal_protein_L9P_317251..317401_NEGATIVE 214 432 392 71 34 NC_003454:FN1899|3end_Hypothetical_lipoprotein_386714..386864_NEGATIVE 214 41 1 122 75 NC_003454:FN1726|3end_Na+_driven_multidrug_efflux_pump_224686..224836_NEGATIVE 211 50 1 142 93 NC_003454:FN0269|3end_Transposase_896846..896996_POSITIVE 209 184 142 76 31 NC_003454:FN0094|3end_hypothetical_protein_729516..729666_NEGATIVE 206 45 5 129 81 NC_003454:FN1699|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_194603..194753_NEGATIVE 200 20 2 96 78 NC_003454:FN2059|3end_Outer_membrane_protein_572877..573027_NEGATIVE 200 20 2 96 78 NC_003454:FN2048|3end_Outer_membrane_protein_558801..558951_NEGATIVE 199 47 6 127 80 NC_003454:FN0421|3end_carbamoyl-phosphate_synthase_small_subunit_1063092..1063242_POSITIVE 196 294 256 72 27 NC_003454:FN1385|3end_hypothetical_protein_2038394..2038544_NEGATIVE 194 43 3 114 75 NC_003454:FN1030|3end_Hypothetical_membrane-spanning_protein_1683630..1683780_NEGATIVE 194 488 461 54 27 NC_003454:FN0683|3end_hypothetical_protein_1338514..1338664_NEGATIVE 193 213 172 58 4 NC_003454:FN0286|3end_hypothetical_protein_914183..914333_NEGATIVE 193 189 141 52 1 NC_003454:FN1546|3end_translation_elongation_factor_EF-G_59529..59679_NEGATIVE 192 268 226 130 91 NC_003454:FN1051|3end_hypothetical_protein_1700580..1700730_POSITIVE 192 413 372 84 42 NC_003454:FN0852|3end_Hydrolase_1510903..1511053_POSITIVE 191 446 407 151 113 NC_003454:FN1372|3end_Ribosomal_large_subunit_pseudouridine_synthase_D_2020022..2020172_NEGATIVE 191 350 302 108 51 NC_003454:FN0757|3end_Hypothetical_cytosolic_protein_1415656..1415806_NEGATIVE 190 32 7 108 77 NC_003454:FN0643|3end_hypothetical_protein_1299434..1299584_NEGATIVE