Origin IGS: cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt .........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 aaattataaccaaactatatctatagacaaattatttgattttgagtatcataaaaaaaatcttgacaaaaaacagagtccatttaatttatttcaatacagattgaaataccttattcagccgcaaagcgtagtgctccgacgcttaaaacggagtaaaataaaatttcataaggagattatg Mask Tandem Repeat Region ================================================ cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt Find is-nt database================================================ Query_seq: TDE0748:TDE0749|TDE0748:TDE0749:iron compound ABC transporter, periplasmic iron compound-binding protein, putative:cobalamin biosynthesis protein CobN, putative:<-<-:784379..784562 184 cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0748:TDE0749|TDE0748:TDE0749:iron compound ABC transporter, periplasmic iron compound-binding protein, putative:cobalamin biosynthesis protein CobN, putative:<-<-:784379..784562 184 cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0748:TDE0749|TDE0748:TDE0749:iron compound ABC transporter, periplasmic iron compound-binding protein, putative:cobalamin biosynthesis protein CobN, putative:<-<-:784379..784562 184 cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: - Start: 1 End: 168 M I E K H F K I K S R K L R R L V V S Q P Q I L Y K L R Y Q F L N F P S Q K K D L N K K H Y E F D F L K D I S M ................ cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt 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: 133 End: 162 ....................................................................................................................................ATAGACAAATTATTTGATTTTGAGTATCAT...................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 153 End: 182 ........................................................................................................................................................ATTTGTCTATAGATATAGTTTGGTTATAAT.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0748:TDE0749|TDE0748:TDE0749:iron compound ABC transporter, periplasmic iron compound-binding protein, putative:cobalamin biosynthesis protein CobN, putative:<-<-:784379..784562 184 cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: NC_002967_TDE0748_TDE0749|iron compound ABC transporter, periplasmic iron compound-binding protein, putative:cobalamin biosynthesis protein CobN, putative|NEGATIVE:NEGATIVE|[784379,784562]|184 HSP 1 e-value: 7.0E-86 bit: 317.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagannnnnnnnatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt cataatctccttatgaaattttattttactccgttttaagcgtcggagcactacgctttgcggctgaataaggtatttcaatctgtattgaaataaattaaatggactctgttttttgtcaagattttttttatgatactcaaaatcaaataatttgtctatagatatagtttggttataattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAAUCUCCUUAUGAAAUUUUAUUUUACUCCGUUUUAAGCGUCGGAGCACUACGCUUUGCGGCUGAAUAAGGUAUUUCAAUCUGUAUUGAAAUAAAUUAAAUGGACUCUGUUUUUUGUCAAGAUUUUUUUUAUGAUACUCAAAAUCAAAUAAUUUGUCUAUAGAUAUAGUUUGGUUAUAAUUU .((((((......(((((((((((((....((((...((((((.(.....).)))))).))))..)))))))..))))))..(((((((.(.((((((((....(((..........)))..((((((.............))))))...)))))))).)...)))))))...))))))..... (-34.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUAUAACCAAACUAUAUCUAUAGACAAAUUAUUUGAUUUUGAGUAUCAUAAAAAAAAUCUUGACAAAAAACAGAGUCCAUUUAAUUUAUUUCAAUACAGAUUGAAAUACCUUAUUCAGCCGCAAAGCGUAGUGCUCCGACGCUUAAAACGGAGUAAAAUAAAAUUUCAUAAGGAGAUUAUG ..............((((....))))........((((...(((((((................(((..........))).........(((((((((....)))))))))...)))))))...))))......(((((((..........)))))))......((((((.....))))))... (-25.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 966 80 31 171 122 NC_002967:TDE0748|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_784288..784518_NEGATIVE 326 66 39 107 79 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 326 66 39 107 79 NC_002967:TDE1981|5end_hypothetical_protein_1992016..1992246_POSITIVE 306 67 29 64 25 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 303 79 33 82 30 NC_002967:TDE0875|5end_ribosomal_large_subunit_pseudouridine_synthase_B_897489..897719_POSITIVE 300 67 29 178 135 NC_002967:TDE1978|5end_hypothetical_protein_1991758..1991988_NEGATIVE 298 88 41 199 155 NC_002967:TDE0644|5end_ABC_transporter,_ATP-binding_protein_680576..680806_NEGATIVE 294 74 31 42 4 NC_002967:TDE1327|5end_hypothetical_protein_1362949..1363179_NEGATIVE 294 75 32 211 169 NC_002967:TDE0325|5end_hypothetical_protein_358051..358281_POSITIVE 292 66 21 47 1 NC_002967:TDE1048|5end_30S_ribosomal_protein_S7_1074482..1074712_POSITIVE 289 65 21 148 88 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 287 90 42 153 123 NC_002967:TDE1127|5end_TPR_domain_protein_1158278..1158508_POSITIVE 285 65 30 172 139 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 284 90 41 175 115 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 283 90 45 161 117 NC_002967:TDE2725|5end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2783208..2783438_NEGATIVE 282 78 31 75 27 NC_002967:TDE0782|5end_50S_ribosomal_protein_L6_812970..813200_POSITIVE 281 68 30 200 155 NC_002967:TDE2768|5end_flagellar_hook_protein_2822510..2822740_NEGATIVE 277 63 31 221 190 NC_002967:TDE0294|5end_TrkA_domain_protein_324210..324440_NEGATIVE 276 75 31 153 105 NC_002967:TDE0268|5end_hypothetical_protein_300049..300279_NEGATIVE 275 46 1 220 178 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 66 39 45 17 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 326 66 39 55 27 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 304 65 21 57 1 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 299 74 31 89 33 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 299 66 23 139 88 NC_002967:TDE0938|3end_hypothetical_protein_960963..961113_NEGATIVE 291 65 28 63 14 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 290 79 33 146 88 NC_002967:TDE0823|3end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_845252..845402_POSITIVE 290 66 29 145 113 NC_002967:TDE0761|3end_protease_complex-associated_polypeptide_801968..802118_POSITIVE 284 90 41 82 22 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 282 86 41 53 1 NC_002967:TDE0874|3end_transcriptional_regulator,_putative_897534..897684_POSITIVE 282 78 31 64 16 NC_002967:TDE0781|3end_30S_ribosomal_protein_S8_813039..813189_POSITIVE 277 66 29 77 18 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 276 65 31 48 5 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 276 65 31 44 1 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 275 87 41 63 19 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 275 46 1 101 59 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 274 64 29 65 23 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 274 73 39 49 18 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 273 66 33 132 88 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 272 66 23 148 101 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE