Origin IGS: taaaattacctccttaaaatatactgctttaattgtataattttagctaattattgtcaagtatttttaaagttatgtaaattttttacttatattttatatattgacagacaaatatttagtttatataatgaatttaagttcaataataaattaaaaattaaggagaagtaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tattacttctccttaatttttaatttattattgaacttaaattcattatataaactaaatatttgtctgtcaatatataaaatataagtaaaaaatttacataactttaaaaatacttgacaataattagctaaaattatacaattaaagcagtatattttaaggaggtaatttta Mask Tandem Repeat Region ================================================ taaaattacctccttaaaatatactgctttaattgtataattttagctaattattgtcaagtatttttaaagttatgtaaattttttacttatattttatatattgacagacaaatatttagtttatataatgaatttaagttcaataataaattaaaaattaaggagaagtaata Find is-nt database================================================ Query_seq: FN0472:FN0473|FN0472:FN0473:flavodoxin:Regulatory protein betI:<-->:1118256..1118431 176 taaaattacctccttaaaatatactgctttaattgtataattttagctaattattgtcaagtatttttaaagttatgtaaattttttacttatattttatatattgacagacaaatatttagtttatataatgaatttaagttcaataataaattaaaaattaaggagaagtaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0472:FN0473|FN0472:FN0473:flavodoxin:Regulatory protein betI:<-->:1118256..1118431 176 taaaattacctccttaaaatatactgctttaattgtataattttagctaattattgtcaagtatttttaaagttatgtaaattttttacttatattttatatattgacagacaaatatttagtttatataatgaatttaagttcaataataaattaaaaattaaggagaagtaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0472:FN0473|FN0472:FN0473:flavodoxin:Regulatory protein betI:<-->:1118256..1118431 176 taaaattacctccttaaaatatactgctttaattgtataattttagctaattattgtcaagtatttttaaagttatgtaaattttttacttatattttatatattgacagacaaatatttagtttatataatgaatttaagttcaataataaattaaaaattaaggagaagtaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaattacctccttaaaatatactgctttaattgtataattttagctaattattgtcaagtatttttaaagttatgtaaattttttacttatattttatatattgacagacaaatatttagtttatataatgaatttaagttcaataataaattaaaaattaaggagaagtaata Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 19 End: 171 .................. M Y C F N C I I L A N Y C Q V F L K L C K F F T Y I L Y I D R Q I F S L Y N E F K F N N K L K I K E K * ..... taaaattacctccttaaaatatactgctttaattgtataattttagctaattattgtcaagtatttttaaagttatgtaaattttttacttatattttatatattgacagacaaatatttagtttatataatgaatttaagttcaataataaattaaaaattaaggagaagtaata 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: 89 Start: 103 End: 132 ......................................................................................................ATTGACAGACAAATATTTAGTTTATATAAT............................................ PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 32 End: 61 ...............................CTTGACAATAATTAGCTAAAATTATACAAT................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaattacctccttaaaatatactgctttaattgtataattttagctaattattgtcaagtatttttaaagttatgtaaattttttacttatattttatatattgacagacaaatatttagtttatataatgaatttaagttcaataataaattaaaaattaaggagaagtaata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0472:FN0473|FN0472:FN0473:flavodoxin:Regulatory protein betI:<-->:1118256..1118431 176 taaaattacctccttaaaatatactgctttaattgtataattttagctaattattgtcaagtatttttaaagttatgtaaattttttacttatattttatatattgacagacaaatatttagtttatataatgaatttaagttcaataataaattaaaaattaaggagaagtaata Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_003454_FN0472_FN0473|flavodoxin:Regulatory protein betI|NEGATIVE:POSITIVE|[1118256,1118431]|176 HSP 1 e-value: 1.0E-19 bit: 97.6 Len: 49 Query Start:128 Query End:176 Subject Strand: POSITIVE Subject Start: 128 Subject End: 176 ...............................................................................................................................ataatgaatttaagttcaataataaattaaaaattaaggagaagtaata ...............................................................................................................................ataatgaatttaagttcaataataaattaaaaattaaggagaagtaata HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 39 Query Start:1 Query End:39 Subject Strand: POSITIVE Subject Start: 1 Subject End: 39 taaaattacctccttaaaatatactgctttaattgtata......................................................................................................................................... taaaattacctccttaaaatatactgctttaattgtata......................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUUACCUCCUUAAAAUAUACUGCUUUAAUUGUAUAAUUUUAGCUAAUUAUUGUCAAGUAUUUUUAAAGUUAUGUAAAUUUUUUACUUAUAUUUUAUAUAUUGACAGACAAAUAUUUAGUUUAUAUAAUGAAUUUAAGUUCAAUAAUAAAUUAAAAAUUAAGGAGAAGUAAUA ....(((((((((((((........(((..((((....))))..)))......(((((((.(((...((((((...((((.....))))....)))))).)))))))))).......((((((((((.((.(((((....))))).))))))))))))..))))))))..))))). (-33.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUACUUCUCCUUAAUUUUUAAUUUAUUAUUGAACUUAAAUUCAUUAUAUAAACUAAAUAUUUGUCUGUCAAUAUAUAAAAUAUAAGUAAAAAAUUUACAUAACUUUAAAAAUACUUGACAAUAAUUAGCUAAAAUUAUACAAUUAAAGCAGUAUAUUUUAAGGAGGUAAUUUUA .(((((..((((((((..((((.(((((...((((......))))....))))).))))...((((.(((((((((((...))))).((((.....))))................))))))))))...(((..((((....))))..)))........))))))))))))).... (-21.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 656 60 11 151 102 NC_003454:FN0472|5end_flavodoxin_1118165..1118395_NEGATIVE 224 68 25 194 149 NC_003454:FN1739|5end_V-type_sodium_ATP_synthase_subunit_E_237902..238132_NEGATIVE 221 49 8 140 104 NC_003454:FN1089|5end_hypothetical_protein_1733042..1733272_POSITIVE 211 86 44 180 132 NC_003454:FN0761|5end_Bvg_accessory_factor_1418869..1419099_POSITIVE 206 60 18 226 177 NC_003454:FN0641|5end_Methyltransferase_1298978..1299208_NEGATIVE 202 44 9 145 99 NC_003454:FN0829|5end_hypothetical_protein_1489873..1490103_NEGATIVE 191 109 66 90 50 NC_003454:FN0577|5end_hypothetical_protein_1227237..1227467_POSITIVE 191 97 54 225 178 NC_003454:FN2064|5end_hypothetical_protein_575716..575946_NEGATIVE 181 60 17 91 49 NC_003454:FN1453|5end_hypothetical_protein_2134648..2134878_NEGATIVE 179 37 5 126 90 NC_003454:FN0272|5end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_898704..898934_POSITIVE 178 68 24 151 105 NC_003454:FN1307|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_1963377..1963607_POSITIVE 178 91 60 185 152 NC_003454:FN0208|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase_beta-subunit_834968..835198_POSITIVE 176 39 9 142 102 NC_003454:FN0788|5end_hypothetical_protein_1444359..1444589_NEGATIVE 176 100 60 112 69 NC_003454:FN1924|5end_Arsenical_pump_membrane_protein_422993..423223_NEGATIVE 175 88 45 196 153 NC_003454:FN1747|5end_Cysteine_permease_245647..245877_POSITIVE 174 63 23 219 171 NC_003454:FN0883|5end_hypothetical_protein_1544357..1544587_POSITIVE 174 73 39 164 127 NC_003454:FN0557|5end_hypothetical_protein_1210334..1210564_NEGATIVE 172 49 5 160 113 NC_003454:FN1333|5end_hypothetical_protein_1987580..1987810_NEGATIVE 171 59 14 135 88 NC_003454:FN1330|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1984958..1985188_NEGATIVE 170 48 4 139 92 NC_003454:FN1380|5end_Citrate_lyase_beta_chain_2027248..2027478_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 49 8 113 77 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE 203 90 44 105 58 NC_003454:FN1762|3end_Protein_yaaA_255258..255408_NEGATIVE 191 109 66 75 35 NC_003454:FN0576|3end_D-amino_acid_dehydrogenase_large_subunit_1227302..1227452_POSITIVE 179 37 5 63 27 NC_003454:FN0271|3end_Enoyl-CoA_hydratase_898721..898871_POSITIVE 178 68 24 148 102 NC_003454:FN1306|3end_Methyltransferase_1963454..1963604_POSITIVE 176 39 9 65 25 NC_003454:FN0789|3end_Transporter_1444436..1444586_NEGATIVE 176 100 60 44 1 NC_003454:FN1925|3end_Arsenical_pump_membrane_protein_423061..423211_NEGATIVE 175 88 45 149 106 NC_003454:FN1746|3end_Cystathionine_beta-lyase_245680..245830_POSITIVE 172 49 5 137 90 NC_003454:FN1334|3end_N-acetylmuramoyl-L-alanine_amidase_1987603..1987753_NEGATIVE 170 48 4 136 89 NC_003454:FN1379|3end_Citrate_lyase_beta_chain_2027325..2027475_POSITIVE 170 68 33 103 70 NC_003454:FN0919|3end_DNA-dependent_DNA_polymerase_III_alpha_chain_1574299..1574449_NEGATIVE 169 98 57 47 5 NC_003454:FN0642|3end_hypothetical_protein_1298991..1299141_NEGATIVE 169 139 102 70 33 NC_003454:FN0380|3end_hypothetical_protein_1012361..1012511_POSITIVE 166 48 9 124 78 NC_003454:FN0594|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1249290..1249440_POSITIVE 162 48 5 97 64 NC_003454:FN1536|3end_(S)-2-hydroxy-acid_oxidase_chain_D_48291..48441_NEGATIVE 161 45 9 75 33 NC_003454:FN1271|3end_Protease_IV_1926745..1926895_NEGATIVE 161 44 9 117 79 NC_003454:FN0985|3end_Phosphoribosylglycinamide_formyltransferase_1637315..1637465_NEGATIVE 160 69 24 116 76 NC_003454:FN1117|3end_LSU_ribosomal_protein_L21P_1760636..1760786_POSITIVE 160 46 9 71 29 NC_003454:FN0149|3end_Malonyl-CoA-[acyl-carrier-protein]_transacylase_778465..778615_POSITIVE 160 79 44 104 63 NC_003454:FN1802|3end_hypothetical_protein_284186..284336_POSITIVE