Origin IGS: ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacgtgcatgccggataaaattcgaagcctagcagccgagggatgcctctgaccaaatatttttaaatagctacagctctttgataaggtatacatcgtgtcttggattgagacctgtcaatctaaaagaggaggaccatag Mask Tandem Repeat Region ================================================ ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt Find is-nt database================================================ Query_seq: TDE0178:TDE0179|TDE0178:TDE0179:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:212719..212860 142 ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0178:TDE0179|TDE0178:TDE0179:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:212719..212860 142 ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0178:TDE0179|TDE0178:TDE0179:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:212719..212860 142 ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 35 End: 142 .................................. M Q D T M Y T L S K S C S Y L K I F G Q R H P S A A R L R I L S G M H V ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt 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================================================ ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0178:TDE0179|TDE0178:TDE0179:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:212719..212860 142 ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_002967_TDE0178_TDE0179|methyl-accepting chemotaxis protein:hypothetical protein|NEGATIVE:NEGATIVE|[212719,212860]|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 ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt ctatggtcctcctcttttagattgacaggtctcaatccaagacacgatgtataccttatcaaagagctgtagctatttaaaaatatttggtcagaggcatccctcggctgctaggcttcgaattttatccggcatgcacgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUGGUCCUCCUCUUUUAGAUUGACAGGUCUCAAUCCAAGACACGAUGUAUACCUUAUCAAAGAGCUGUAGCUAUUUAAAAAUAUUUGGUCAGAGGCAUCCCUCGGCUGCUAGGCUUCGAAUUUUAUCCGGCAUGCACGUU ....((....))..((((.((((((......)))))).)))).(((.(((((.((..((.(((((((((((((...(((((....)))))...((((....)))).)))))..)))))....))).))..)).)))))))). (-26.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGUGCAUGCCGGAUAAAAUUCGAAGCCUAGCAGCCGAGGGAUGCCUCUGACCAAAUAUUUUUAAAUAGCUACAGCUCUUUGAUAAGGUAUACAUCGUGUCUUGGAUUGAGACCUGUCAAUCUAAAAGAGGAGGACCAUAG ..((.((.(((..(..............)..))))))).((..(.(((((......(((((((((((.(((....))).)))))..))))))..........(((((((((......))))))))).))))).)..)).... (-31.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1071 140 91 231 182 NC_002967:TDE0178|5end_methyl-accepting_chemotaxis_protein_212628..212858_NEGATIVE 575 50 2 142 93 NC_002967:TDE0181|5end_methyl-accepting_chemotaxis_protein_215077..215307_NEGATIVE 351 137 91 151 107 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 333 140 92 225 159 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 332 140 92 191 144 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 326 130 87 165 119 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 317 139 93 216 161 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 310 130 88 180 134 NC_002967:TDE1863|5end_Holliday_junction_DNA_helicase_RuvA_1888579..1888809_NEGATIVE 310 140 100 142 95 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 310 140 104 120 71 NC_002967:TDE0118|5end_hypothetical_protein_137047..137277_NEGATIVE 309 136 94 223 184 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 307 137 93 175 126 NC_002967:TDE1042|5end_deoxyuridine_5'triphosphate_nucleotidohydrolase_1070492..1070722_POSITIVE 307 138 96 80 44 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 305 140 96 163 108 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 304 138 92 176 121 NC_002967:TDE1300|5end_hypothetical_protein_1337419..1337649_NEGATIVE 303 133 95 66 24 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 302 140 93 207 160 NC_002967:TDE1907|5end_holo-(acyl-carrier-protein)_synthase_1925097..1925327_NEGATIVE 301 134 93 196 147 NC_002967:TDE0436|5end_Recombination_protein_O_492133..492363_NEGATIVE 299 134 96 183 149 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 299 136 97 222 185 NC_002967:TDE2008|5end_ABC_transporter,_ATP-binding/permease_protein_2028578..2028808_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 575 50 2 85 36 NC_002967:TDE0182|3end_ABC_transporter,_ATP-binding_protein_215134..215284_NEGATIVE 414 120 74 107 61 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 379 137 94 58 14 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 342 137 93 109 57 NC_002967:TDE2293|3end_hypothetical_protein_2329325..2329475_NEGATIVE 332 140 92 59 12 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 327 121 84 108 71 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 326 130 87 91 45 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 310 140 100 145 98 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 310 140 104 109 60 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 307 137 93 103 54 NC_002967:TDE1041|3end_polyribonucleotide_nucleotidyltransferase_1070500..1070650_POSITIVE 304 137 100 51 15 NC_002967:TDE0452|3end_hypothetical_protein_509949..510099_NEGATIVE 303 133 95 82 40 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 300 140 94 147 97 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 298 140 92 82 36 NC_002967:TDE2004|3end_hypothetical_protein_2023845..2023995_POSITIVE 297 120 77 115 60 NC_002967:TDE0915|3end_hypothetical_protein_933147..933297_NEGATIVE 296 135 95 102 59 NC_002967:TDE1487|3end_conserved_hypothetical_protein_TIGR01033_1531528..1531678_POSITIVE 295 140 94 151 104 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 289 134 94 76 32 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 287 138 99 47 10 NC_002967:TDE2263|3end_acetyl_hydrolase,_putative_2299277..2299427_NEGATIVE 286 118 71 132 89 NC_002967:TDE2049|3end_bacterial_extracellular_solute-binding_proteins,_family_5_2079537..2079687_POSITIVE