Origin IGS: ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaccgataaactcttaaaataaagacgaaaaaagtttttaatcataattatcacgcaaaacacaaaaccgctgtaaaaattcgcgactgccgatgtcagcaaaactttgataataattattcataccatcctcttagtttaa Mask Tandem Repeat Region ================================================ ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt Find is-nt database================================================ Query_seq: TDE1999:TDE2000|TDE1999:TDE2000:DNA polymerase III domain protein:ABC transporter, ATP-binding/permease protein, HlyB family:->->:2017857..2017998 142 ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1999:TDE2000|TDE1999:TDE2000:DNA polymerase III domain protein:ABC transporter, ATP-binding/permease protein, HlyB family:->->:2017857..2017998 142 ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1999:TDE2000|TDE1999:TDE2000:DNA polymerase III domain protein:ABC transporter, ATP-binding/permease protein, HlyB family:->->:2017857..2017998 142 ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 23 End: 142 ...................... M I I I K V L L T S A V A N F Y S G F V F C V I I M I K N F F R L Y F K S L S V Protein_Len: 41 Strand: - Start: 2 End: 124 . L S L P H Y S Y N N D F N Q Q C R C D R I K V A T K H K A H Y N H N F V K K T K M .................. ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt 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================================================ ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1999:TDE2000|TDE1999:TDE2000:DNA polymerase III domain protein:ABC transporter, ATP-binding/permease protein, HlyB family:->->:2017857..2017998 142 ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_002967_TDE1999_TDE2000|DNA polymerase III domain protein:ABC transporter, ATP-binding/permease protein, HlyB family|POSITIVE:POSITIVE|[2017857,2017998]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt ttaaactaagaggatggtatgaataattattatcaaagttttgctgacatcggcagtcgcgaatttttacagcggttttgtgttttgcgtgataattatgattaaaaacttttttcgtctttattttaagagtttatcggtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAACUAAGAGGAUGGUAUGAAUAAUUAUUAUCAAAGUUUUGCUGACAUCGGCAGUCGCGAAUUUUUACAGCGGUUUUGUGUUUUGCGUGAUAAUUAUGAUUAAAAACUUUUUUCGUCUUUAUUUUAAGAGUUUAUCGGUU .((((((...(((((((.(((((((((((((((((.....((((((....)))))).((((((....(((((.....))))).)))))))))))...))))))).........)))))..)))))))...))))))...... (-27.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCGAUAAACUCUUAAAAUAAAGACGAAAAAAGUUUUUAAUCAUAAUUAUCACGCAAAACACAAAACCGCUGUAAAAAUUCGCGACUGCCGAUGUCAGCAAAACUUUGAUAAUAAUUAUUCAUACCAUCCUCUUAGUUUAA ......((((((.......(((((((.......)))))))......(((((((.(.....)........((((.....(((.((....)).)))..)))).......))))))).....................)))))). (-16.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 91 52 215 163 NC_002967:TDE1808|5end_hypothetical_protein_1845049..1845279_NEGATIVE 293 80 31 68 29 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 292 88 42 87 25 NC_002967:TDE1583|5end_hypothetical_protein_1631808..1632038_POSITIVE 288 77 43 132 96 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 285 89 41 206 152 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 284 90 49 72 26 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 283 82 43 63 17 NC_002967:TDE2517|5end_DNA_repair_protein_RadA_2543842..2544072_NEGATIVE 282 95 51 75 27 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 280 75 44 106 69 NC_002967:TDE1824|5end_hypothetical_protein_1857011..1857241_POSITIVE 278 80 31 73 10 NC_002967:TDE2589|5end_putative_aminopeptidase_1_2626406..2626636_NEGATIVE 278 85 45 79 38 NC_002967:TDE0351|5end_L-lactate_dehydrogenase_395998..396228_NEGATIVE 275 90 44 114 54 NC_002967:TDE2493|5end_hypothetical_protein_2518364..2518594_NEGATIVE 275 89 44 159 95 NC_002967:TDE0123|5end_hypothetical_protein_142223..142453_NEGATIVE 269 90 44 198 148 NC_002967:TDE1211|5end_ATP-dependent_protease_ATP-binding_subunit_1243865..1244095_POSITIVE 266 92 53 192 152 NC_002967:TDE1034|5end_magnesium_and_cobalt_transporter,_putative_1062454..1062684_POSITIVE 266 88 43 52 3 NC_002967:TDE0605|5end_hypothetical_protein_643215..643445_NEGATIVE 262 80 31 80 13 NC_002967:TDE2627|5end_transcriptional_regulator,_TetR_family_2669140..2669370_NEGATIVE 262 89 43 80 39 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 262 90 41 91 34 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 262 87 42 75 25 NC_002967:TDE0977|5end_hypothetical_protein_1000415..1000645_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 91 51 49 7 NC_002967:TDE1809|3end_hypothetical_protein_1845215..1845365_NEGATIVE 293 80 31 62 23 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 282 95 51 64 16 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 275 89 41 59 12 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 275 88 42 55 3 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 275 89 44 138 74 NC_002967:TDE0124|3end_rhomboid_family_protein_142244..142394_NEGATIVE 269 75 32 65 19 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 263 87 41 150 104 NC_002967:TDE0345|3end_methyl-accepting_chemotaxis_protein_DmcB_385744..385894_NEGATIVE 262 90 44 104 53 NC_002967:TDE2706|3end_hypothetical_protein_2751916..2752066_NEGATIVE 262 89 42 51 12 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 262 87 42 78 28 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 262 79 33 62 20 NC_002967:TDE0068|3end_succinyl-diaminopimelate_desuccinylase_76612..76762_POSITIVE 257 98 52 119 80 NC_002967:TDE0904|3end_hypothetical_protein_922278..922428_NEGATIVE 255 60 11 132 81 NC_002967:TDE2739|3end_hypothetical_protein_2795169..2795319_POSITIVE 255 59 34 149 126 NC_002967:TDE0804|3end_hypothetical_protein_826872..827022_NEGATIVE 254 63 38 146 107 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 254 87 53 150 113 NC_002967:TDE1033|3end_polyA_polymerase_family_protein_1062495..1062645_POSITIVE 251 88 41 67 9 NC_002967:TDE0773|3end_30S_ribosomal_protein_S3_810242..810392_POSITIVE 251 95 51 69 2 NC_002967:TDE0544|3end_hypothetical_protein_584866..585016_POSITIVE 249 88 41 105 55 NC_002967:TDE0463|3end_purine_nucleoside_phosphorylase_517964..518114_POSITIVE