Origin IGS: tttaattcctccttatatgttatgttttatatattttaccataataatagtttatttttaagaaggcacttttttgaattttagttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa .........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 tttttctcctcatttaaaaacaatatactattgtttattataacatagtcaacagattttttctataataatgaaattataaatatttaaagtaggtttctatttggtaactaaaattcaaaaaagtgccttcttaaaaataaactattattatggtaaaatatataaaacataacatataaggaggaattaaa Mask Tandem Repeat Region ================================================ tttaattcctccttatatgttatgttttatatattttaccataataatagtttatttttaagaaggcacttttttgaattttagttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa Find is-nt database================================================ Query_seq: FN0390:FN0391|FN0390:FN0391:hypothetical protein:Hydrolase (HAD superfamily):<-->:1028559..1028752 194 tttaattcctccttatatgttatgttttatatattttaccataataatagtttatttttaagaaggcacttttttgaattttagttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0390:FN0391|FN0390:FN0391:hypothetical protein:Hydrolase (HAD superfamily):<-->:1028559..1028752 194 tttaattcctccttatatgttatgttttatatattttaccataataatagtttatttttaagaaggcacttttttgaattttagttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0390:FN0391|FN0390:FN0391:hypothetical protein:Hydrolase (HAD superfamily):<-->:1028559..1028752 194 tttaattcctccttatatgttatgttttatatattttaccataataatagtttatttttaagaaggcacttttttgaattttagttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaattcctccttatatgttatgttttatatattttaccataataatagtttatttttaagaaggcacttttttgaattttagttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 23 End: 112 ...................... T K Y I K G Y Y Y N I K L F A S K Q I K T V L Y F G V K F M .................................................................................. tttaattcctccttatatgttatgttttatatattttaccataataatagtttatttttaagaaggcacttttttgaattttagttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa 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: 87 Start: 129 End: 158 ................................................................................................................................ATAGAAAAAATCTGTTGACTATGTTATAAT.................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 154 End: 183 .........................................................................................................................................................ATTTAAAAACAATATACTATTGTTTATTAT........... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 33 End: 62 ................................CTTAAAAATAAACTATTATTATGGTAAAAT.................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttaattcctccttatatgttatgttttatatattttaccataataatagtttatttttaagaaggcacttttttgaattttagttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0390:FN0391|FN0390:FN0391:hypothetical protein:Hydrolase (HAD superfamily):<-->:1028559..1028752 194 tttaattcctccttatatgttatgttttatatattttaccataataatagtttatttttaagaaggcacttttttgaattttagttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa Intra-Species Hit: Count: 1 Min: 84 Max: 194 Len: 111 Subject: NC_003454_FN0390_FN0391|hypothetical protein:Hydrolase (HAD superfamily)|NEGATIVE:POSITIVE|[1028559,1028752]|194 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 111 Query Start:84 Query End:194 Subject Strand: POSITIVE Subject Start: 84 Subject End: 194 ...................................................................................gttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa ...................................................................................gttaccaaatagaaacctactttaaatatttataatttcattattatagaaaaaatctgttgactatgttataataaacaatagtatattgtttttaaatgaggagaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUACCAAAUAGAAACCUACUUUAAAUAUUUAUAAUUUCAUUAUUAUAGAAAAAAUCUGUUGACUAUGUUAUAAUAAACAAUAGUAUAUUGUUUUUAAAUGAGGAGAAAAA ...............(((..((((((..((((((((......))))))))......((((((..(((......)))..)))))).........))))))..)))....... (-13.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCUCCUCAUUUAAAAACAAUAUACUAUUGUUUAUUAUAACAUAGUCAACAGAUUUUUUCUAUAAUAAUGAAAUUAUAAAUAUUUAAAGUAGGUUUCUAUUUGGUAAC .......(((..((((((.((((((...))))))((((((((....((((....)))).....))))))))..............))))))..)))............... (-10.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 624 50 1 224 175 NC_003454:FN0390|5end_hypothetical_protein_1028468..1028698_NEGATIVE 198 60 11 52 7 NC_003454:FN0030|5end_5-nitroimidazole_antibiotic_resistance_protein_667120..667350_POSITIVE 198 108 67 223 183 NC_003454:FN1717|5end_NAD-dependent_DNA_ligase_213150..213380_POSITIVE 190 50 2 143 96 NC_003454:FN0931|5end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1584550..1584780_NEGATIVE 177 106 67 220 181 NC_003454:FN0687|5end_hypothetical_protein_1342563..1342793_POSITIVE 174 50 2 192 147 NC_003454:FN1374|5end_Transcriptional_regulator_2022301..2022531_NEGATIVE 174 88 51 129 96 NC_003454:FN1879|5end_SSU_ribosomal_protein_S20P_367155..367385_POSITIVE 169 45 8 61 26 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 163 68 54 210 196 NC_003454:FN0310|5end_Iron(III)-transport_ATP-binding_protein_sfuC_945796..946026_POSITIVE 161 88 43 226 177 NC_003454:FN0923|5end_Cardiolipin_synthetase_1578977..1579207_NEGATIVE 159 95 55 211 177 NC_003454:FN0010|5end_nicotinate-nucleotide_pyrophosphorylase_650178..650408_POSITIVE 155 43 3 219 174 NC_003454:FN1039|5end_Branched-chain_amino_acid_transport_protein_azlC_1690997..1691227_POSITIVE 155 42 13 101 69 NC_003454:FN0732|5end_hypothetical_protein_1388270..1388500_POSITIVE 154 47 4 211 174 NC_003454:FN0312|5end_Anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_949316..949546_POSITIVE 152 88 46 122 76 NC_003454:FN0484|5end_Lipase_1129470..1129700_POSITIVE 152 70 21 155 103 NC_003454:FN2078|5end_Transcriptional_regulator,_DeoR_family_590266..590496_NEGATIVE 152 106 79 63 34 NC_003454:FN1595|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_B_105827..106057_NEGATIVE 150 67 36 61 28 NC_003454:FN0941|5end_Gamma-glutamyltranspeptidase_1595266..1595496_NEGATIVE 150 97 62 90 53 NC_003454:FN0379|5end_hypothetical_protein_1010511..1010741_POSITIVE 149 96 56 71 30 NC_003454:FN1765|5end_pyruvate_kinase_259450..259680_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 198 108 67 118 78 NC_003454:FN1716|3end_hypothetical_protein_213125..213275_POSITIVE 170 87 48 68 31 NC_003454:FN2082|3end_Formate--tetrahydrofolate_ligase_593257..593407_NEGATIVE 163 93 57 124 79 NC_003454:FN0046|3end_3-dehydroquinate_dehydratase_684265..684415_POSITIVE 155 42 13 84 52 NC_003454:FN0731|3end_hypothetical_protein_1388333..1388483_POSITIVE 152 70 21 79 27 NC_003454:FN2079|3end_ABC_transporter_ATP-binding_protein_590342..590492_NEGATIVE 152 106 79 37 8 NC_003454:FN1596|3end_Nitrogen_fixation_iron-sulphur_protein_RNFC_105853..106003_NEGATIVE 147 107 73 87 54 NC_003454:FN1465|3end_Permease_2148941..2149091_POSITIVE 146 35 10 110 84 NC_003454:FN1476|3end_N-acetylmannosamine-6-phosphate_2-epimerase_2159426..2159576_POSITIVE 146 60 17 76 28 NC_003454:FN0718|3end_hypothetical_protein_1376004..1376154_POSITIVE 144 62 28 44 11 NC_003454:FN0461|3end_Probable_sigma(54)_modulation_protein_1107147..1107297_POSITIVE 140 86 49 69 36 NC_003454:FN2097|3end_hypothetical_protein_606449..606599_NEGATIVE 138 109 89 69 48 NC_003454:FN1860|3end_NA+/H+_antiporter_NHAC_349900..350050_NEGATIVE 137 90 55 124 86 NC_003454:FN1763|3end_Hypothetical_cytosolic_protein_256008..256158_NEGATIVE 136 65 29 140 110 NC_003454:FN0733|3end_peptidase_T_1390882..1391032_POSITIVE 134 103 67 148 106 NC_003454:FN1997|3end_Transcriptional_regulator_500158..500308_POSITIVE 133 99 52 141 93 NC_003454:FN0292|3end_Hemolysin_activator_protein_precursor_925011..925161_NEGATIVE 132 40 3 63 29 NC_003454:FN1926|3end_Nitrogen_regulatory_IIA_protein_424352..424502_NEGATIVE 130 67 28 60 17 NC_003454:FN1289|3end_hypothetical_protein_1944732..1944882_NEGATIVE 130 75 31 135 97 NC_003454:FN0672|3end_ATPase_1329042..1329192_POSITIVE 130 86 56 142 110 NC_003454:FN2071|3end_hypothetical_protein_582124..582274_NEGATIVE