Origin IGS: taatataactgattgtaaattttaaaatttttacaatcagtttttttatttaatattagaggatttagtgaaataaaataaaattttttaaaaacaaaaatttttttaaactattttataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctcattttattttttaaaaaatttaaaacttttataaatgtttaaaagtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg .........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 catgaaaaaggactgttacaaatactgcaatagtccttttcttatataattacttagtatttcatcaattcttctttatgtactaatattctgtctattttttttaaatgaaataccaaaaaatcacaatacattgtgttagacttttaaacatttataaaagttttaaattttttaaaaaataaaatgagcagttataattatcgtattttcgatattatactgctcattgttaggggggtattttatcaattttatctgtatacttatttgacagtgaaagttataaaatagtttaaaaaaatttttgtttttaaaaaattttattttatttcactaaatcctctaatattaaataaaaaaactgattgtaaaaattttaaaatttacaatcagttatatta Mask Tandem Repeat Region ================================================ taatataactgattgtaaattttaaaatttttacaatcagtttttttatttaatattagaggatttagtgaaataaaataaaattttttaaaaacaaaaatttttttaaactattttataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctcattttattttttaaaaaatttaaaacttttataaatgtttaaaagtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg Find is-nt database================================================ Query_seq: FN0315:FN0316|FN0315:FN0316:Transcriptional regulator, AraC family:hypothetical protein:-><-:952920..953323 404 taatataactgattgtaaattttaaaatttttacaatcagtttttttatttaatattagaggatttagtgaaataaaataaaattttttaaaaacaaaaatttttttaaactattttataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctcattttattttttaaaaaatttaaaacttttataaatgtttaaaagtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0315:FN0316|FN0315:FN0316:Transcriptional regulator, AraC family:hypothetical protein:-><-:952920..953323 404 taatataactgattgtaaattttaaaatttttacaatcagtttttttatttaatattagaggatttagtgaaataaaataaaattttttaaaaacaaaaatttttttaaactattttataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctcattttattttttaaaaaatttaaaacttttataaatgtttaaaagtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0315:FN0316|FN0315:FN0316:Transcriptional regulator, AraC family:hypothetical protein:-><-:952920..953323 404 taatataactgattgtaaattttaaaatttttacaatcagtttttttatttaatattagaggatttagtgaaataaaataaaattttttaaaaacaaaaatttttttaaactattttataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctcattttattttttaaaaaatttaaaacttttataaatgtttaaaagtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatataactgattgtaaattttaaaatttttacaatcagtttttttatttaatattagaggatttagtgaaataaaataaaattttttaaaaacaaaaatttttttaaactattttataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctcattttattttttaaaaaatttaaaacttttataaatgtttaaaagtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 78 End: 227 ............................................................................. M K F F K N K N F F K L F Y N F H C Q I S I Q I K L I K Y P P N N E Q Y N I E N T I I I T A H F I F ................................................................................................................................................................................. Protein_Len: 45 Strand: - Start: 114 End: 248 ................................................................................................................. K I V K V T L Y T Y L Y F Q Y F V G R V I L L I I D F I R Y N Y S S M K N K L F N L V K M ............................................................................................................................................................ Protein_Len: 33 Strand: - Start: 3 End: 101 .. Y L Q N Y I K F N K C D T K K N L I L P N L S I F Y F K K F V F M ............................................................................................................................................................................................................................................................................................................... taatataactgattgtaaattttaaaatttttacaatcagtttttttatttaatattagaggatttagtgaaataaaataaaattttttaaaaacaaaaatttttttaaactattttataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctcattttattttttaaaaaatttaaaacttttataaatgtttaaaagtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg 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: 81 Start: 204 End: 233 ...........................................................................................................................................................................................................TTTTTAAAAAATAAAATGAGCAGTTATAAT........................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatataactgattgtaaattttaaaatttttacaatcagtttttttatttaatattagaggatttagtgaaataaaataaaattttttaaaaacaaaaatttttttaaactattttataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctcattttattttttaaaaaatttaaaacttttataaatgtttaaaagtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -7.7 Tail_Score: -5.42198 Start: 176 End: 217 Full_Region: ATACCCCCCTAACAA TGAGCAGTATAATATCG AAAATA CGATAATTATAACTGCTCA TTTTATTTTTTAAAA ...............................................................................................................................................................................TGAGCAGTATAATATCGAAAATACGATAATTATAACTGCTCA........................................................................................................................................................................................... TransTerm Strand: - Conf: 72 HP_score: -7.7 Tail_Score: -3.62224 Start: 176 End: 217 Full_Region: ttttaaaaaataaaa tgagcagttataattatcg tatttt cgatattatactgctca ttgttaggggggtat ...............................................................................................................................................................................tgagcagttataattatcgtattttcgatattatactgctca........................................................................................................................................................................................... Find igs database================================================ Query_seq: FN0315:FN0316|FN0315:FN0316:Transcriptional regulator, AraC family:hypothetical protein:-><-:952920..953323 404 taatataactgattgtaaattttaaaatttttacaatcagtttttttatttaatattagaggatttagtgaaataaaataaaattttttaaaaacaaaaatttttttaaactattttataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctcattttattttttaaaaaatttaaaacttttataaatgtttaaaagtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg Intra-Species Hit: Count: 1 Min: 1 Max: 404 Len: 404 Subject: NC_003454_FN0315_FN0316|Transcriptional regulator, AraC family:hypothetical protein|POSITIVE:NEGATIVE|[952920,953323]|404 HSP 1 e-value: 1.0E-61 bit: 238.0 Len: 144 Query Start:261 Query End:404 Subject Strand: POSITIVE Subject Start: 261 Subject End: 404 ....................................................................................................................................................................................................................................................................gtctaacacaatgtattgtgattttttggtatttcatttnnnnnnnntagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg ....................................................................................................................................................................................................................................................................gtctaacacaatgtattgtgattttttggtatttcatttaaaaaaaatagacagaatattagtacataaagaagaattgatgaaatactaagtaattatataagaaaaggactattgcagtatttgtaacagtcctttttcatg HSP 2 e-value: 1.0E-49 bit: 198.0 Len: 100 Query Start:118 Query End:217 Subject Strand: POSITIVE Subject Start: 118 Subject End: 217 .....................................................................................................................ataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctca........................................................................................................................................................................................... .....................................................................................................................ataactttcactgtcaaataagtatacagataaaattgataaaatacccccctaacaatgagcagtataatatcgaaaatacgataattataactgctca........................................................................................................................................................................................... HSP 3 e-value: 7.0E-14 bit: 79.8 Len: 40 Query Start:1 Query End:40 Subject Strand: POSITIVE Subject Start: 1 Subject End: 40 taatataactgattgtaaattttaaaatttttacaatcag............................................................................................................................................................................................................................................................................................................................................................................ taatataactgattgtaaattttaaaatttttacaatcag............................................................................................................................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUAACUGAUUGUAAAUUUUAAAAUUUUUACAAUCAGUUUUUUUAUUUAAUAUUAGAGGAUUUAGUGAAAUAAAAUAAAAUUUUUUAAAAACAAAAAUUUUUUUAAACUAUUUUAUAACUUUCACUGUCAAAUAAGUAUACAGAUAAAAUUGAUAAAAUACCCCCCUAACAAUGAGCAGUAUAAUAUCGAAAAUACGAUAAUUAUAACUGCUCAUUUUAUUUUUUAAAAAAUUUAAAACUUUUAUAAAUGUUUAAAAGUCUAACACAAUGUAUUGUGAUUUUUUGGUAUUUCAUUUAAAAAAAAUAGACAGAAUAUUAGUACAUAAAGAAGAAUUGAUGAAAUACUAAGUAAUUAUAUAAGAAAAGGACUAUUGCAGUAUUUGUAACAGUCCUUUUUCAUG ......(((((((((((((..........)))))))))))))((((((...((((.(((.((....(((((((....(((((((..((((((((........))))))))..)))))))...)))))))(((((.....(((....)))...)))))........)).)))..(((((((((((((((((((......)))).))))).)))))))))).))))...)))))).......(((((((........)))))))..............(((((((.((((((((((((((........................................)))))))))))))).)))))))...((((((((((.((((((...)))))).)))))))))).... (-86.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUGAAAAAGGACUGUUACAAAUACUGCAAUAGUCCUUUUCUUAUAUAAUUACUUAGUAUUUCAUCAAUUCUUCUUUAUGUACUAAUAUUCUGUCUAUUUUUUUUAAAUGAAAUACCAAAAAAUCACAAUACAUUGUGUUAGACUUUUAAACAUUUAUAAAAGUUUUAAAUUUUUUAAAAAAUAAAAUGAGCAGUUAUAAUUAUCGUAUUUUCGAUAUUAUACUGCUCAUUGUUAGGGGGGUAUUUUAUCAAUUUUAUCUGUAUACUUAUUUGACAGUGAAAGUUAUAAAAUAGUUUAAAAAAAUUUUUGUUUUUAAAAAAUUUUAUUUUAUUUCACUAAAUCCUCUAAUAUUAAAUAAAAAAACUGAUUGUAAAAAUUUUAAAAUUUACAAUCAGUUAUAUUA .((((((((((((((((.((.....)).)))))))))))).))))........(((((((...................))))))).........((((((((..((((...............(((((....)))))..(((((((((........)))))))))...))))...))))))))..(((((((((.(((((.((((......))))))))))))))))))((((((((((........((((..................)))).(((((((...(((((((..((((((((........))))))))..)))))))....)))))))...))))))))))...........(((((((((((((..........)))))))))))))...... (-86.78) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 220 173 74 13 NC_003454:FN0980|5end_hypothetical_protein_1632478..1632708_POSITIVE 259 395 363 146 111 NC_003454:FN0340|5end_Hypothetical_membrane-spanning_Protein_973948..974178_NEGATIVE 249 399 351 155 106 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 222 170 123 101 62 NC_003454:FN0867|5end_Long-chain-fatty-acid--CoA_ligase_1527048..1527278_NEGATIVE 218 397 372 190 164 NC_003454:FN0074|5end_Ethanolamine_utilization_protein_eutS_713328..713558_POSITIVE 217 397 360 213 175 NC_003454:FN2010|5end_Transcriptional_regulator,_MarR_family_510302..510532_NEGATIVE 216 400 359 74 19 NC_003454:FN2068|5end_dGTP_triphosphohydrolase_578986..579216_NEGATIVE 209 215 172 221 186 NC_003454:FN1353|5end_ABC_transporter_permease_protein_2005386..2005616_NEGATIVE 205 397 363 148 119 NC_003454:FN1136|5end_Phosphonates_transport_ATP-binding_protein_phnC_1783057..1783287_POSITIVE 205 400 368 158 121 NC_003454:FN0786|5end_Transposase_1442465..1442695_POSITIVE 203 396 351 141 92 NC_003454:FN1660|5end_ATP-dependent_DNA_helicase_recG_157908..158138_NEGATIVE 201 187 160 116 92 NC_003454:FN1319|5end_DNA_primase_1974197..1974427_NEGATIVE 201 184 160 62 35 NC_003454:FN1744|5end_Transporter_242920..243150_NEGATIVE 200 250 203 53 10 NC_003454:FN0511|5end_D-lactate_dehydrogenase_1160285..1160515_POSITIVE 198 176 132 110 61 NC_003454:FN1052|5end_hypothetical_protein_1700520..1700750_POSITIVE 196 148 107 58 2 NC_003454:FN0928|5end_O-sialoglycoprotein_endopeptidase_1583026..1583256_NEGATIVE 195 158 115 133 87 NC_003454:FN0479|5end_RNA_polymerase_sigma-E_factor_1127003..1127233_POSITIVE 194 396 375 170 148 NC_003454:FN1554|5end_Fusobacterium_outer_membrane_protein_family_73467..73697_NEGATIVE 193 207 161 102 66 NC_003454:FN0247|5end_Hypothetical_cytosolic_protein_870707..870937_POSITIVE 190 396 365 169 141 NC_003454:FN2104|5end_hypothetical_protein_614237..614467_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 50 7 92 49 NC_003454:FN0315|3end_Transcriptional_regulator,_AraC_family_952859..953009_POSITIVE 276 220 176 60 6 NC_003454:FN0979|3end_hypothetical_protein_1632544..1632694_POSITIVE 272 399 352 106 55 NC_003454:FN1044|3end_hypothetical_protein_1694453..1694603_NEGATIVE 259 395 363 41 6 NC_003454:FN0341|3end_transport_protein_974053..974203_NEGATIVE 249 399 351 78 29 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 241 396 351 78 28 NC_003454:FN0514|3end_hypothetical_protein_1163912..1164062_POSITIVE 237 396 365 76 43 NC_003454:FN1043|3end_hypothetical_protein_1694450..1694600_POSITIVE 226 399 362 87 49 NC_003454:FN1277|3end_Aminoacyl-histidine_dipeptidase_1935294..1935444_NEGATIVE 223 399 369 79 47 NC_003454:FN0026|3end_Hypothetical_exported_24-amino_acid_repeat_protein_664832..664982_POSITIVE 222 94 52 83 45 NC_003454:FN1017|3end_hypothetical_protein_1672164..1672314_POSITIVE 217 397 360 82 44 NC_003454:FN2011|3end_Valyl-tRNA_synthetase_510433..510583_NEGATIVE 214 400 365 87 52 NC_003454:FN0657|3end_Acetyltransferase_1314867..1315017_POSITIVE 212 399 367 104 74 NC_003454:FN1168|3end_Macrolide-efflux_protein_1826651..1826801_NEGATIVE 205 397 363 70 41 NC_003454:FN1135|3end_Phosphonates-binding_protein_1783059..1783209_POSITIVE 203 45 7 67 34 NC_003454:FN0662|3end_Formiminoglutamase_1319188..1319338_POSITIVE 203 396 351 86 37 NC_003454:FN1661|3end_Hypothetical_cytosolic_protein_157963..158113_NEGATIVE 202 393 360 44 8 NC_003454:FN1944|3end_Sodium-dependent_tryptophan_transporter_448026..448176_POSITIVE 201 187 160 52 28 NC_003454:FN1320|3end_Peptidyl-prolyl_cis-trans_isomerase_1974261..1974411_NEGATIVE 201 184 160 29 2 NC_003454:FN1745|3end_Cystathionine_gamma-synthase_242953..243103_NEGATIVE 200 400 359 85 44 NC_003454:FN0212|3end_hypothetical_protein_837583..837733_NEGATIVE