Origin IGS: aattttctataataaaaaaagacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccttattgttttgataaaatatttataagcctataattatatttatgtgcacctctaaaaaccttgttggatttgcttagcatccttcggaatagaggtgcattatcagtaaagctgataacgagttttcataagtctttatgtctttttttattatagaaaatt Mask Tandem Repeat Region ================================================ aattttctataataaaaaaagacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg Find is-nt database================================================ Query_seq: TDE2000:TDE2001|TDE2000:TDE2001:ABC transporter, ATP-binding/permease protein, HlyB family:oligoendopeptidase F, putative:-><-:2019700..2019864 165 aattttctataataaaaaaagacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2000:TDE2001|TDE2000:TDE2001:ABC transporter, ATP-binding/permease protein, HlyB family:oligoendopeptidase F, putative:-><-:2019700..2019864 165 aattttctataataaaaaaagacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2000:TDE2001|TDE2000:TDE2001:ABC transporter, ATP-binding/permease protein, HlyB family:oligoendopeptidase F, putative:-><-:2019700..2019864 165 aattttctataataaaaaaagacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttctataataaaaaaagacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 47 End: 160 .............................................. M S F T D N A P L F R R M L S K S N K V F R G A H K Y N Y R L I N I L S K Q * ..... Protein_Len: 31 Strand: - Start: 10 End: 102 ......... L L F L C L S K H F S T I L K V S L A G R N R L I S L L D L M ............................................................... aattttctataataaaaaaagacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg 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: 81 Start: 129 End: 158 ................................................................................................................................GTTTTGATAAAATATTTATAAGCCTATAAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattttctataataaaaaaagacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2000:TDE2001|TDE2000:TDE2001:ABC transporter, ATP-binding/permease protein, HlyB family:oligoendopeptidase F, putative:-><-:2019700..2019864 165 aattttctataataaaaaaagacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg Intra-Species Hit: Count: 1 Min: 21 Max: 165 Len: 145 Subject: NC_002967_TDE2000_TDE2001|ABC transporter, ATP-binding/permease protein, HlyB family:oligoendopeptidase F, putative|POSITIVE:NEGATIVE|[2019700,2019864]|165 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 145 Query Start:21 Query End:165 Subject Strand: POSITIVE Subject Start: 21 Subject End: 165 ....................gacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg ....................gacataaagacttatgaaaactcgttatcagctttactgataatgcacctctattccgaaggatgctaagcaaatccaacaaggtttttagaggtgcacataaatataattataggcttataaatattttatcaaaacaataagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAUAAAGACUUAUGAAAACUCGUUAUCAGCUUUACUGAUAAUGCACCUCUAUUCCGAAGGAUGCUAAGCAAAUCCAACAAGGUUUUUAGAGGUGCACAUAAAUAUAAUUAUAGGCUUAUAAAUAUUUUAUCAAAACAAUAAGG ......(((.(((((((......((((((((.....))))))))(((((((((..((...((((.........)))).....))....)))))))))............)))))))))).......................... (-34.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUAUUGUUUUGAUAAAAUAUUUAUAAGCCUAUAAUUAUAUUUAUGUGCACCUCUAAAAACCUUGUUGGAUUUGCUUAGCAUCCUUCGGAAUAGAGGUGCAUUAUCAGUAAAGCUGAUAACGAGUUUUCAUAAGUCUUUAUGUC .((((((((((.....)))))...)))))..(((((....(((((((.(((((((((....((.....(((..(((...))))))...))..))))))))).(((((((.....)))))))........)))))))..))))).. (-30.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 120 72 210 159 NC_002967:TDE0106|5end_hypothetical_protein_126546..126776_NEGATIVE 289 72 48 53 25 NC_002967:TDE2719|5end_hypothetical_protein_2776045..2776275_POSITIVE 288 66 21 130 87 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 288 99 54 99 59 NC_002967:TDE0352|5end_ribose_5-phosphate_isomerase_B_396207..396437_POSITIVE 286 59 14 126 74 NC_002967:TDE0689|5end_5-methylthioribose_kinase_725690..725920_POSITIVE 282 57 17 217 181 NC_002967:TDE1589|5end_purine-binding_chemotaxis_protein_1637004..1637234_POSITIVE 278 66 21 151 107 NC_002967:TDE2254|5end_hypothetical_protein_2291642..2291872_NEGATIVE 273 100 58 160 115 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 266 59 21 182 132 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 257 77 35 70 25 NC_002967:TDE0445|5end_amino_acid_permease_499744..499974_POSITIVE 255 66 27 144 106 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 255 52 16 102 72 NC_002967:TDE1519|5end_hypothetical_protein_1565601..1565831_POSITIVE 255 66 21 79 21 NC_002967:TDE0802|5end_hypothetical_protein_825107..825337_NEGATIVE 250 102 72 92 62 NC_002967:TDE2462|5end_hypothetical_protein_2488424..2488654_NEGATIVE 248 89 45 41 2 NC_002967:TDE0859|5end_hypothetical_protein_880100..880330_POSITIVE 245 100 52 61 8 NC_002967:TDE1644|5end_methionyl-tRNA_formyltransferase_1695546..1695776_NEGATIVE 244 87 45 38 1 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 240 58 12 155 112 NC_002967:TDE0345|5end_methyl-accepting_chemotaxis_protein_DmcB_386976..387206_NEGATIVE 238 68 22 63 19 NC_002967:TDE1712|5end_flagellar_filament_outer_layer_protein_1767915..1768145_NEGATIVE 238 98 56 74 16 NC_002967:TDE0866|5end_hypothetical_protein_887614..887844_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 757 97 51 68 22 NC_002967:TDE1090|3end_threonyl-tRNA_synthetase_1122943..1123093_POSITIVE 356 100 57 95 46 NC_002967:TDE2465|3end_hypothetical_protein_2489391..2489541_NEGATIVE 301 120 72 115 64 NC_002967:TDE0107|3end_alpha-amylase_family_protein_126641..126791_NEGATIVE 288 66 21 128 85 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 286 59 14 113 61 NC_002967:TDE0688|3end_hypothetical_protein_725757..725907_POSITIVE 283 78 32 147 89 NC_002967:TDE0031|3end_hypothetical_protein_38835..38985_NEGATIVE 282 57 17 99 63 NC_002967:TDE1588|3end_tryptophanyl-tRNA_synthetase_1636966..1637116_POSITIVE 273 100 58 55 10 NC_002967:TDE2235|3end_methylaspartate_ammonia-lyase_2273350..2273500_NEGATIVE 262 66 23 128 89 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 261 77 43 51 13 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 251 77 38 39 7 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 245 100 52 64 11 NC_002967:TDE1645|3end_polypeptide_deformylase_1695543..1695693_NEGATIVE 240 58 12 58 15 NC_002967:TDE0346|3end_protease_PrtB_387073..387223_NEGATIVE 232 66 27 51 16 NC_002967:TDE2664|3end_hypothetical_protein_2702113..2702263_POSITIVE 231 57 14 90 45 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 227 96 61 80 48 NC_002967:TDE2200|3end_methionine_gamma-lyase_2237250..2237400_NEGATIVE 227 76 35 144 89 NC_002967:TDE2137|3end_hypothetical_protein_2171709..2171859_POSITIVE 226 66 21 88 27 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 223 68 21 143 99 NC_002967:TDE0912|3end_hypothetical_protein_931528..931678_POSITIVE 221 46 8 98 53 NC_002967:TDE1904|3end_hypothetical_protein_1923197..1923347_NEGATIVE