Origin IGS: aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt .........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 aaaacggctcctaatataaaaccaaccttaaaaactatacaaaagatgaggaaaaatgtcaaggtttatctttaaccgtttaaataacacggttaaaaaatacagcccggttttaaaatgataccctactttaacttatccctgctttgcggtataattgcacccgttctaaacatttatggaggttttt Mask Tandem Repeat Region ================================================ aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt Find is-nt database================================================ Query_seq: TDE0456:TDE0457|TDE0456:TDE0457:pyridoxine biosynthesis protein:hypothetical protein:<-->:513475..513664 190 aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0456:TDE0457|TDE0456:TDE0457:pyridoxine biosynthesis protein:hypothetical protein:<-->:513475..513664 190 aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0456:TDE0457|TDE0456:TDE0457:pyridoxine biosynthesis protein:hypothetical protein:<-->:513475..513664 190 aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 2 End: 91 . F G G Y I N L V P A I I G C L L S L N F Y P I M K F G P Q M ................................................................................................... aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt 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: 91 Start: 128 End: 157 ...............................................................................................................................CTTGACATTTTTCCTCATCTTTTGTATAGT................................. PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 33 End: 62 ................................CTTTAACTTATCCCTGCTTTGCGGTATAAT................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0456:TDE0457|TDE0456:TDE0457:pyridoxine biosynthesis protein:hypothetical protein:<-->:513475..513664 190 aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: NC_002967_TDE0456_TDE0457|pyridoxine biosynthesis protein:hypothetical protein|NEGATIVE:POSITIVE|[513475,513664]|190 HSP 1 e-value: 1.0E-104 bit: 377.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt aaaaacctccataaatgtttagaacgggtgcaattataccgcaaagcagggataagttaaagtagggtatcattttaaaaccgggctgtattttttaaccgtgttatttaaacggttaaagataaaccttgacatttttcctcatcttttgtatagtttttaaggttggttttatattaggagccgtttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACCUCCAUAAAUGUUUAGAACGGGUGCAAUUAUACCGCAAAGCAGGGAUAAGUUAAAGUAGGGUAUCAUUUUAAAACCGGGCUGUAUUUUUUAACCGUGUUAUUUAAACGGUUAAAGAUAAACCUUGACAUUUUUCCUCAUCUUUUGUAUAGUUUUUAAGGUUGGUUUUAUAUUAGGAGCCGUUUU .(((((((((................(((((..((((.((........)).))))...........)))))....(((((((.........(((((((((((.........)))))))))))..((((((((..........((.....))........))))))))))))))).....))))..))))) (-36.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACGGCUCCUAAUAUAAAACCAACCUUAAAAACUAUACAAAAGAUGAGGAAAAAUGUCAAGGUUUAUCUUUAACCGUUUAAAUAACACGGUUAAAAAAUACAGCCCGGUUUUAAAAUGAUACCCUACUUUAACUUAUCCCUGCUUUGCGGUAUAAUUGCACCCGUUCUAAACAUUUAUGGAGGUUUUU (((((..((((.....(((((((..(((((................)))))...........(((((((.(((((((((.........)))))))))..))).)))).)))))))................................((((((...))))))..................))))))))). (-29.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 908 70 21 161 112 NC_002967:TDE0456|5end_pyridoxine_biosynthesis_protein_513384..513614_NEGATIVE 309 96 57 189 138 NC_002967:TDE0427|5end_hypothetical_protein_483026..483256_POSITIVE 304 89 41 84 39 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 299 89 45 182 140 NC_002967:TDE0612|5end_hypothetical_protein_647471..647701_NEGATIVE 281 70 21 181 118 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 278 102 61 204 161 NC_002967:TDE2550|5end_hypothetical_protein_2576215..2576445_NEGATIVE 270 50 2 67 20 NC_002967:TDE2484|5end_hypothetical_protein_2507720..2507950_NEGATIVE 269 53 14 83 41 NC_002967:TDE1939|5end_hypothetical_protein_1954627..1954857_POSITIVE 268 89 41 105 60 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 266 50 4 136 95 NC_002967:TDE2480|5end_heat_shock_protein_90_2505288..2505518_NEGATIVE 266 47 2 151 92 NC_002967:TDE1270|5end_hypothetical_protein_1305011..1305241_NEGATIVE 266 68 25 51 13 NC_002967:TDE1052|5end_rubredoxin_1078870..1079100_NEGATIVE 262 165 128 218 177 NC_002967:TDE0472|5end_hypothetical_protein_528376..528606_POSITIVE 256 68 23 213 172 NC_002967:TDE1130|5end_methyltransferase,_putative_1162453..1162683_POSITIVE 255 58 16 81 29 NC_002967:TDE1940|5end_hypothetical_protein_1956508..1956738_NEGATIVE 255 47 5 143 101 NC_002967:TDE1078|5end_metallo-beta-lactamase_family_protein_1109739..1109969_POSITIVE 254 101 61 161 126 NC_002967:TDE2264|5end_ABC_transporter,_ATP-binding/permease_protein_2302033..2302263_NEGATIVE 254 186 141 220 187 NC_002967:TDE0807|5end_hypothetical_protein_829108..829338_NEGATIVE 253 186 144 122 80 NC_002967:TDE0956|5end_hypothetical_protein_979456..979686_POSITIVE 252 78 36 96 51 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 89 41 69 24 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 299 89 45 79 37 NC_002967:TDE0613|3end_hypothetical_protein_647574..647724_NEGATIVE 293 117 82 100 61 NC_002967:TDE2066|3end_exodeoxyribonuclease_VII,_small_subunit_2092222..2092372_POSITIVE 279 50 5 134 81 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 266 50 4 72 31 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 266 47 2 133 74 NC_002967:TDE1271|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1305029..1305179_NEGATIVE 255 58 16 84 32 NC_002967:TDE1941|3end_hypothetical_protein_1956505..1956655_NEGATIVE 254 186 141 148 115 NC_002967:TDE0808|3end_acetyltransferase,_GNAT_family_829180..829330_NEGATIVE 253 117 81 55 19 NC_002967:TDE2587|3end_endonuclease/exonuclease/phosphatase_family_protein_2623290..2623440_POSITIVE 253 186 144 116 74 NC_002967:TDE0955|3end_LemA_family_protein_979530..979680_POSITIVE 246 104 61 73 30 NC_002967:TDE1919|3end_hypothetical_protein_1938319..1938469_NEGATIVE 245 190 147 137 89 NC_002967:TDE1753|3end_UDP-glucose_4-epimerase_1805521..1805671_NEGATIVE 245 50 7 136 94 NC_002967:TDE0938|3end_hypothetical_protein_960963..961113_NEGATIVE 238 82 42 59 25 NC_002967:TDE1389|3end_hypothetical_protein_1429775..1429925_POSITIVE 238 50 5 143 93 NC_002967:TDE0920|3end_transcriptional_regulator,_AraC_family_939100..939250_NEGATIVE 235 129 81 92 33 NC_002967:TDE0940|3end_hypothetical_protein_963635..963785_POSITIVE 234 60 16 84 35 NC_002967:TDE1013|3end_hemerythrin-related_protein_1043977..1044127_NEGATIVE 233 68 24 144 95 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 233 50 2 142 82 NC_002967:TDE1074|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1106029..1106179_POSITIVE 231 69 25 83 34 NC_002967:TDE2308|3end_hypothetical_protein_2346313..2346463_POSITIVE