Origin IGS: cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttcttaaaaaaatttaaaaaagctgtacaaattttttttgtaacagcttttgtgcattcatgttattttttatttaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaaataaaaaataacatgaatgcacaaaagctgttacaaaaaaaatttgtacagcttttttaaatttttttaagaaagctattgaaaaattttcataaatctattatgattagttaagtaatatttaacaaaatttatttatagtttttgaaggaggagaaggagaacg Mask Tandem Repeat Region ================================================ cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttcttaaaaaaatttaaaaaagctgtacaaattttttttgtaacagcttttgtgcattcatgttattttttatttaa Find is-nt database================================================ Query_seq: FN0512:FN0513|FN0512:FN0513:Flavoprotein:Flavodoxin:<-<-:1162688..1162857 170 cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttcttaaaaaaatttaaaaaagctgtacaaattttttttgtaacagcttttgtgcattcatgttattttttatttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0512:FN0513|FN0512:FN0513:Flavoprotein:Flavodoxin:<-<-:1162688..1162857 170 cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttcttaaaaaaatttaaaaaagctgtacaaattttttttgtaacagcttttgtgcattcatgttattttttatttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0512:FN0513|FN0512:FN0513:Flavoprotein:Flavodoxin:<-<-:1162688..1162857 170 cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttcttaaaaaaatttaaaaaagctgtacaaattttttttgtaacagcttttgtgcattcatgttattttttatttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttcttaaaaaaatttaaaaaagctgtacaaattttttttgtaacagcttttgtgcattcatgttattttttatttaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 70 End: 168 ..................................................................... M Y E N F S I A F L K K F K K A V Q I F F V T A F V H S C Y F L F .. cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttcttaaaaaaatttaaaaaagctgtacaaattttttttgtaacagcttttgtgcattcatgttattttttatttaa 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: 60 End: 89 ...........................................................ATTGAAAAATTTTCATAAATCTATTATGAT................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttcttaaaaaaatttaaaaaagctgtacaaattttttttgtaacagcttttgtgcattcatgttattttttatttaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 48 HP_score: -3.8 Tail_Score: -3.38584 Start: 61 End: 77 Full_Region: gctattgaaaaattt tcataa atcta ttatga ttagttaagtaatat ............................................................tcataaatctattatga............................................................................................. TransTerm Strand: + Conf: 75 HP_score: -2.5 Tail_Score: -5.93809 Start: 83 End: 124 Full_Region: AGATTTATGAAAATT TTTCAATAGCTTTCTTAAA AAAA TTTAAAAAAGCTGTACAAA TTTTTTTTGTAACAG ..................................................................................TTTCAATAGCTTTCTTAAAAAAATTTAAAAAAGCTGTACAAA.............................................. TransTerm Strand: - Conf: 73 HP_score: -8.5 Tail_Score: -3.06009 Start: 91 End: 116 Full_Region: aaaaaaatttgtaca gcttttttaaa tttt tttaagaaagc tattgaaaaattttc ..........................................................................................gcttttttaaatttttttaagaaagc...................................................... TransTerm Strand: + Conf: 54 HP_score: -5.7 Tail_Score: -2.61628 Start: 110 End: 145 Full_Region: TCTTAAAAAAATTTA AAAAAGCTGTACAAA TTTTT TTTGTAACAGCTTTTG TGCATTCATGTTATT .............................................................................................................AAAAAGCTGTACAAATTTTTTTTGTAACAGCTTTTG......................... Find igs database================================================ Query_seq: FN0512:FN0513|FN0512:FN0513:Flavoprotein:Flavodoxin:<-<-:1162688..1162857 170 cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttcttaaaaaaatttaaaaaagctgtacaaattttttttgtaacagcttttgtgcattcatgttattttttatttaa Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_003454_FN0512_FN0513|Flavoprotein:Flavodoxin|NEGATIVE:NEGATIVE |[1162688,1162857]|170 HSP 1 e-value: 7.0E-49 bit: 194.0 Len: 98 Query Start:1 Query End:98 Subject Strand: POSITIVE Subject Start: 1 Subject End: 98 cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttctt........................................................................ cgttctccttctcctccttcaaaaactataaataaattttgttaaatattacttaactaatcataatagatttatgaaaatttttcaatagctttctt........................................................................ HSP 2 e-value: 4.0E-13 bit: 75.8 Len: 38 Query Start:133 Query End:170 Subject Strand: POSITIVE Subject Start: 133 Subject End: 170 ....................................................................................................................................gtaacagcttttgtgcattcatgttattttttatttaa ....................................................................................................................................gtaacagcttttgtgcattcatgttattttttatttaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUCUCCUUCUCCUCCUUCAAAAACUAUAAAUAAAUUUUGUUAAAUAUUACUUAACUAAUCAUAAUAGAUUUAUGAAAAUUUUUCAAUAGCUUUCUUAAAAAAAUUUAAAAAAGCUGUACAAAUUUUUUUUGUAACAGCUUUUGUGCAUUCAUGUUAUUUUUUAUUUAA ............................((((((((....(((((.......)))))...((((((.....)))))).........((((((.....((((....)))).((((((((((((((.....))))).)))))))))..........)))))).)))))))). (-23.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAUAAAAAAUAACAUGAAUGCACAAAAGCUGUUACAAAAAAAAUUUGUACAGCUUUUUUAAAUUUUUUUAAGAAAGCUAUUGAAAAAUUUUCAUAAAUCUAUUAUGAUUAGUUAAGUAAUAUUUAACAAAAUUUAUUUAUAGUUUUUGAAGGAGGAGAAGGAGAACG ..........................(((((((((.(((((.....)))))))))))))).....(((((((..(((((((((.((.((((((((((((.....))))))...(((((((...))))))).)))))).)).)))))))))....)))))))......... (-30.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 705 50 1 141 92 NC_003454:FN0512|5end_Flavoprotein_1162597..1162827_NEGATIVE 272 144 115 154 123 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 221 27 1 113 89 NC_003454:FN0699|5end_Protein_translocase_subunit_secD_1357051..1357281_POSITIVE 220 31 3 224 194 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 219 169 126 175 129 NC_003454:FN1667|5end_dTDP-glucose_4,6-dehydratase_164472..164702_NEGATIVE 209 44 4 62 16 NC_003454:FN0959|5end_Precorrin-2_C20-methyltransferase_1615058..1615288_NEGATIVE 207 148 109 166 123 NC_003454:FN0078|5end_Ethanolamine_utilization_protein_eutA_716205..716435_POSITIVE 205 46 1 135 89 NC_003454:FN0906|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1565131..1565361_NEGATIVE 205 163 123 55 17 NC_003454:FN1718|5end_translocase_215299..215529_POSITIVE 204 146 102 185 134 NC_003454:FN1257|5end_C4-dicarboxylate_transporter_small_subunit_1913664..1913894_NEGATIVE 204 154 114 91 51 NC_003454:FN1665|5end_Virulence-associated_protein_I_162515..162745_POSITIVE 200 42 3 131 84 NC_003454:FN0466|5end_Lysyl-tRNA_synthetase_1111301..1111531_POSITIVE 196 47 1 208 160 NC_003454:FN1095|5end_hypothetical_protein_1740232..1740462_POSITIVE 196 152 115 100 60 NC_003454:FN0214|5end_Crossover_junction_endodeoxyribonuclease_ruvC_839240..839470_NEGATIVE 194 155 124 92 63 NC_003454:FN1088|5end_NADH_oxidase_1731708..1731938_POSITIVE 194 23 1 109 89 NC_003454:FN0549|5end_O-sialoglycoprotein_endopeptidase_1201326..1201556_POSITIVE 194 141 101 227 188 NC_003454:FN0165|5end_hypothetical_protein_793491..793721_POSITIVE 194 29 6 43 23 NC_003454:FN1734|5end_V-type_ATP_synthase_subunit_B_234258..234488_NEGATIVE 191 136 91 72 27 NC_003454:FN2065|5end_Transcriptional_repressor_575850..576080_POSITIVE 190 44 4 122 84 NC_003454:FN0595|5end_UDP-N-acetylglucosamine_acyltransferase_1249228..1249458_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 144 115 77 46 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 268 144 101 69 15 NC_003454:FN1807|3end_hypothetical_protein_288685..288835_NEGATIVE 251 143 102 79 37 NC_003454:FN1006|3end_Acetyltransferase_1660998..1661148_NEGATIVE 248 144 102 82 39 NC_003454:FN0276|3end_Sodium-dependent_phosphate_transporter_901746..901896_NEGATIVE 246 158 111 103 56 NC_003454:FN0039|3end_DNA_primase_(bacterial_type)_and_small_primase-like_proteins_678661..678811_NEGATIVE 239 144 111 85 51 NC_003454:FN1276|3end_hypothetical_protein_1935280..1935430_POSITIVE 236 170 130 105 69 NC_003454:FN0316|3end_hypothetical_protein_953234..953384_NEGATIVE 234 143 101 81 31 NC_003454:FN1005|3end_hypothetical_protein_1660975..1661125_POSITIVE 234 146 108 82 41 NC_003454:FN1800|3end_Peptidyl-prolyl_cis-trans_isomerase_282534..282684_POSITIVE 232 144 105 87 42 NC_003454:FN1277|3end_Aminoacyl-histidine_dipeptidase_1935294..1935444_NEGATIVE 221 27 1 89 65 NC_003454:FN0698|3end_DNA_integration/recombination/invertion_protein_1357107..1357257_POSITIVE 207 157 115 97 55 NC_003454:FN1080|3end_Export_ABC_transporter_1727308..1727458_POSITIVE 207 148 109 53 10 NC_003454:FN0077|3end_Ethanolamine_two-component_sensor_kinase_716172..716322_POSITIVE 204 146 102 57 6 NC_003454:FN1258|3end_C4-dicarboxylate-binding_protein_1913792..1913942_NEGATIVE 200 42 3 108 61 NC_003454:FN0465|3end_hypothetical_protein_1111358..1111508_POSITIVE 196 152 115 100 60 NC_003454:FN0215|3end_MGTC/SAPB_Family_membrane_protein_839240..839390_NEGATIVE 194 23 1 112 92 NC_003454:FN0548|3end_Regulatory_protein_recX_1201409..1201559_POSITIVE 194 29 6 50 30 NC_003454:FN1735|3end_V-type_ATP_synthase_subunit_A_234251..234401_NEGATIVE 191 139 96 82 38 NC_003454:FN0853|3end_Glycogen_synthase_1510922..1511072_NEGATIVE 191 144 109 84 48 NC_003454:FN0212|3end_hypothetical_protein_837583..837733_NEGATIVE