Origin IGS: actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataatcaagtgaaattactaaaaatagttcgttactgagtagattttttatctaaaatctacattcataattcacttatttttaggtaatgttaattatattacaaaatggaggaatggaatgtttaaaaaattattattagttctaggcatacttacatcagttagt Mask Tandem Repeat Region ================================================ actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata Find is-nt database================================================ Query_seq: FN1347:FN1348|FN1347:FN1348:Hypothetical cytosolic protein:ABC transporter ATP-binding protein:<-<-:2000391..2000559 169 actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1347:FN1348|FN1347:FN1348:Hypothetical cytosolic protein:ABC transporter ATP-binding protein:<-<-:2000391..2000559 169 actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1347:FN1348|FN1347:FN1348:Hypothetical cytosolic protein:ABC transporter ATP-binding protein:<-<-:2000391..2000559 169 actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 1 End: 126 S V S T L I G L V L L L K K F M G N R W K T I Y N V N G L F L H I I F T S K L Y F M ........................................... actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -3.4 Tail_Score: -3.28984 Start: 106 End: 131 Full_Region: aatagttcgttactg agtagatttt ttatct aaaatctaca ttcataattcactta .........................................................................................................agtagattttttatctaaaatctaca...................................... TransTerm Strand: - Conf: 59 HP_score: -6.9 Tail_Score: -2.56908 Start: 107 End: 130 Full_Region: atagttcgttactga gtagatttt ttatct aaaatctac attcataattcactt ..........................................................................................................gtagattttttatctaaaatctac....................................... Find igs database================================================ Query_seq: FN1347:FN1348|FN1347:FN1348:Hypothetical cytosolic protein:ABC transporter ATP-binding protein:<-<-:2000391..2000559 169 actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: NC_003454_FN1347_FN1348|Hypothetical cytosolic protein:ABC transporter ATP-binding protein|NEGATIVE:NEGATIVE|[2000391,2000559]|169 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata actaactgatgtaagtatgcctagaactaataataattttttaaacattccattcctccattttgtaatataattaacattacctaaaaataagtgaattatgaatgtagattttagataaaaaatctactcagtaacgaactatttttagtaatttcacttgattata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAACUGAUGUAAGUAUGCCUAGAACUAAUAAUAAUUUUUUAAACAUUCCAUUCCUCCAUUUUGUAAUAUAAUUAACAUUACCUAAAAAUAAGUGAAUUAUGAAUGUAGAUUUUAGAUAAAAAAUCUACUCAGUAACGAACUAUUUUUAGUAAUUUCACUUGAUUAUA (((.((....)).)))....................................................(((((((((.(((((.((((((((.((...((((....(((((((((......)))))))))...))))...))))))))))))))).....))))))))) (-22.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAUCAAGUGAAAUUACUAAAAAUAGUUCGUUACUGAGUAGAUUUUUUAUCUAAAAUCUACAUUCAUAAUUCACUUAUUUUUAGGUAAUGUUAAUUAUAUUACAAAAUGGAGGAAUGGAAUGUUUAAAAAAUUAUUAUUAGUUCUAGGCAUACUUACAUCAGUUAGU .........(((.....(((((.(((((((..(((....(((((((((......))))))))).(((...((((..(((((((...(((((((.....))))))))))))))..)))).)))....)))..))))))).)))))......)))................ (-29.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 736 60 11 151 102 NC_003454:FN1347|5end_Hypothetical_cytosolic_protein_2000300..2000530_NEGATIVE 590 137 91 231 185 NC_003454:FN1350|5end_Integral_membrane_protein_2002796..2003026_NEGATIVE 518 150 101 213 164 NC_003454:FN0423|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1066328..1066558_POSITIVE 433 140 91 195 142 NC_003454:FN0921|5end_hypothetical_protein_1576482..1576712_NEGATIVE 398 137 91 196 146 NC_003454:FN2080|5end_ABC_transporter_integral_membrane_protein_591957..592187_NEGATIVE 264 75 33 114 76 NC_003454:FN1860|5end_NA+/H+_antiporter_NHAC_351477..351707_NEGATIVE 259 69 21 128 73 NC_003454:FN1835|5end_hypothetical_protein_323680..323910_NEGATIVE 248 126 85 173 133 NC_003454:FN1810|5end_Manganese_transport_system_membrane_protein_mntB_291953..292183_NEGATIVE 246 66 21 138 91 NC_003454:FN0026|5end_Hypothetical_exported_24-amino_acid_repeat_protein_664285..664515_POSITIVE 245 149 114 179 145 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 242 80 36 173 132 NC_003454:FN1871|5end_hypothetical_protein_362551..362781_NEGATIVE 235 49 1 68 5 NC_003454:FN1332|5end_Bacterial_Peptide_Chain_Release_Factor_1_(RF-1)_1987163..1987393_NEGATIVE 235 67 26 114 72 NC_003454:FN1910|5end_hypothetical_protein_403208..403438_NEGATIVE 233 140 91 177 133 NC_003454:FN0670|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1325702..1325932_POSITIVE 232 59 14 102 50 NC_003454:FN0947|5end_hypothetical_protein_1600457..1600687_POSITIVE 228 126 84 195 154 NC_003454:FN2036|5end_DNA-directed_RNA_polymerase_beta_chain_546371..546601_NEGATIVE 224 58 17 104 55 NC_003454:FN2120|5end_Hypothetical_exported_24-amino_acid_repeat_protein_628930..629160_NEGATIVE 219 62 21 103 66 NC_003454:FN0981|5end_phosphoribosylamine--glycine_ligase_1634120..1634350_NEGATIVE 219 59 20 104 69 NC_003454:FN1597|5end_peptidyl-tRNA_hydrolase_107810..108040_NEGATIVE 217 148 123 99 74 NC_003454:FN0171|5end_Hypothetical_cytosolic_protein_796548..796778_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 590 137 91 77 31 NC_003454:FN1351|3end_15_kDa_lipoprotein_precursor_2002950..2003100_NEGATIVE 518 150 101 88 39 NC_003454:FN0422|3end_carbamoyl-phosphate_synthase_large_subunit_1066283..1066433_POSITIVE 433 140 91 89 36 NC_003454:FN0922|3end_Homoserine_kinase_1576588..1576738_NEGATIVE 398 137 91 78 28 NC_003454:FN2081|3end_ABC_transporter_substrate-binding_protein_592075..592225_NEGATIVE 262 149 116 54 21 NC_003454:FN1428|3end_Branched-chain_amino_acid_transport_ATP-binding_protein_livF_2096860..2097010_NEGATIVE 246 66 21 99 52 NC_003454:FN0025|3end_Hypothetical_exported_24-amino_acid_repeat_protein_664326..664476_POSITIVE 245 149 114 60 26 NC_003454:FN1069|3end_DNA_topoisomerase_I_1717082..1717232_POSITIVE 240 127 86 111 70 NC_003454:FN0797|3end_hypothetical_protein_1455668..1455818_NEGATIVE 235 49 1 67 4 NC_003454:FN1333|3end_hypothetical_protein_1987164..1987314_NEGATIVE 235 67 26 73 31 NC_003454:FN1911|3end_Outer_membrane_protein_403249..403399_NEGATIVE 233 140 91 89 45 NC_003454:FN0669|3end_High-affinity_zinc_uptake_system_ATP-binding_protein_znuC_1325694..1325844_POSITIVE 219 62 21 86 49 NC_003454:FN0982|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1634137..1634287_NEGATIVE 217 148 123 84 59 NC_003454:FN0170|3end_GTP-binding_protein_796613..796763_POSITIVE 214 150 123 93 66 NC_003454:FN0391|3end_Hydrolase_(HAD_superfamily)_1029496..1029646_POSITIVE 214 150 123 79 52 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 211 159 129 109 74 NC_003454:FN0907|3end_Ribosomal_RNA_small_subunit_methyltransferase_C_1565324..1565474_NEGATIVE 209 64 22 97 59 NC_003454:FN0024|3end_Hypothetical_exported_24-amino_acid_repeat_protein_663817..663967_POSITIVE 204 97 53 112 64 NC_003454:FN1355|3end_Integral_membrane_protein_2006679..2006829_NEGATIVE 204 60 16 110 77 NC_003454:FN0548|3end_Regulatory_protein_recX_1201409..1201559_POSITIVE 200 68 35 96 61 NC_003454:FN0286|3end_hypothetical_protein_914183..914333_NEGATIVE