Origin IGS: aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccgccatggacggcggtggtttcaaacttcgagagtttgcgcttgccgcaaactctaagattaaaaatgtgcatggacgcacatttttaatccaccccctttttcttttcccaaaagaatgatataatcgcttgttgttttaataaataattttttaaggatgggaacaattt Mask Tandem Repeat Region ================================================ aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg Find is-nt database================================================ Query_seq: TDE1889:TDE1890|TDE1889:TDE1890:branched-chain amino acid transport system II carrier protein:hypothetical protein:<-->:1910979..1911151 173 aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1889:TDE1890|TDE1889:TDE1890:branched-chain amino acid transport system II carrier protein:hypothetical protein:<-->:1910979..1911151 173 aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1889:TDE1890|TDE1889:TDE1890:branched-chain amino acid transport system II carrier protein:hypothetical protein:<-->:1910979..1911151 173 aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 3 End: 110 .. M V P I L K K L F I K T T S D Y I I L L G K E K G G G L K M C V H A H F ............................................................... Protein_Len: 30 Strand: + Start: 83 End: 172 .................................................................................. M K N V R P C T F L I L E F A A S A N S R S L K P P P S M A . Protein_Len: 38 Strand: - Start: 55 End: 168 ...................................................... E K P F L F L P H I L F T R G H V N K I K S N A A L A F E R L K F G G G D M ..... aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg 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================================================ aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 84 HP_score: -11.7 Tail_Score: -3.12668 Start: 84 End: 113 Full_Region: GAAAAAGGGGGTGGA TTAAAAATGTGCG TCCA TGCACATTTTTAA TCTTAGAGTTTGCGG ...................................................................................TTAAAAATGTGCGTCCATGCACATTTTTAA............................................................ TransTerm Strand: + Conf: 77 HP_score: -5.4 Tail_Score: -4.87626 Start: 91 End: 106 Full_Region: GGGGTGGATTAAAAA TGTGCG TCCA TGCACA TTTTTAATCTTAGAG ..........................................................................................TGTGCGTCCATGCACA................................................................... TransTerm Strand: - Conf: 72 HP_score: -4.7 Tail_Score: -4.72272 Start: 91 End: 106 Full_Region: ctctaagattaaaaa tgtgc atggac gcaca tttttaatccacccc ..........................................................................................tgtgcatggacgcaca................................................................... TransTerm Strand: + Conf: 51 HP_score: -5.6 Tail_Score: -2.71712 Start: 114 End: 146 Full_Region: CATGCACATTTTTAA TCTTAGAGTTTGCG GCAAG CGCAAACTCTCGAA GTTTGAAACCACCGC .................................................................................................................TCTTAGAGTTTGCGGCAAGCGCAAACTCTCGAA........................... TransTerm Strand: + Conf: 57 HP_score: -5.1 Tail_Score: -3.53012 Start: 115 End: 147 Full_Region: ATGCACATTTTTAAT CTTAGAGTTTGCG GCAAG CGCAAACTCTCGAAG TTTGAAACCACCGCC ..................................................................................................................CTTAGAGTTTGCGGCAAGCGCAAACTCTCGAAG.......................... Find igs database================================================ Query_seq: TDE1889:TDE1890|TDE1889:TDE1890:branched-chain amino acid transport system II carrier protein:hypothetical protein:<-->:1910979..1911151 173 aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: NC_002967_TDE1889_TDE1890|branched-chain amino acid transport system II carrier protein:hypothetical protein|NEGATIVE:POSITIVE|[1910979,1911151]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg aaattgttcccatccttaaaaaattatttattaaaacaacaagcgattatatcattcttttgggaaaagaaaaagggggtggattaaaaatgtgcgtccatgcacatttttaatcttagagtttgcggcaagcgcaaactctcgaagtttgaaaccaccgccgtccatggcgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUGUUCCCAUCCUUAAAAAAUUAUUUAUUAAAACAACAAGCGAUUAUAUCAUUCUUUUGGGAAAAGAAAAAGGGGGUGGAUUAAAAAUGUGCGUCCAUGCACAUUUUUAAUCUUAGAGUUUGCGGCAAGCGCAAACUCUCGAAGUUUGAAACCACCGCCGUCCAUGGCGG .......................................(((((........(((((((((...........)))))))))(((((((((((((((....)))))))))))))))..((((((((((.....))))))))))....)))))......((((((....)))))) (-49.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGCCAUGGACGGCGGUGGUUUCAAACUUCGAGAGUUUGCGCUUGCCGCAAACUCUAAGAUUAAAAAUGUGCAUGGACGCACAUUUUUAAUCCACCCCCUUUUUCUUUUCCCAAAAGAAUGAUAUAAUCGCUUGUUGUUUUAAUAAAUAAUUUUUUAAGGAUGGGAACAAUUU (((((......))))).(((...........((((((((((.....))))))))))..((((((((((((((......)))))))))))))).)))...........((((((..((((..(((........)))..))))..((((......))))....))))))...... (-53.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 926 140 91 231 182 NC_002967:TDE1889|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_1910888..1911118_NEGATIVE 565 158 115 229 187 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 560 170 122 218 172 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 505 120 73 115 66 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 486 170 121 151 98 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 377 169 121 179 129 NC_002967:TDE2624|5end_hypothetical_protein_2664905..2665135_NEGATIVE 370 129 82 220 173 NC_002967:TDE2339|5end_leucyl-tRNA_synthetase_2374845..2375075_POSITIVE 354 170 125 153 115 NC_002967:TDE1876|5end_glycosyl_transferase,_WecB/TagA/CpsF_family_1897679..1897909_NEGATIVE 353 170 150 21 1 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 350 140 91 200 152 NC_002967:TDE0495|5end_hypothetical_protein_550841..551071_NEGATIVE 344 140 91 218 166 NC_002967:TDE2549|5end_methyl-accepting_chemotaxis_protein_2573285..2573515_POSITIVE 311 152 123 189 148 NC_002967:TDE0906|5end_ABC_transporter,_ATP-binding_protein_923164..923394_POSITIVE 307 154 114 213 178 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 301 125 82 180 136 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 299 166 121 190 141 NC_002967:TDE0545|5end_hypothetical_protein_584774..585004_POSITIVE 298 150 107 173 106 NC_002967:TDE0772|5end_50S_ribosomal_protein_L22_809084..809314_POSITIVE 297 170 121 186 128 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 297 170 121 64 16 NC_002967:TDE0473|5end_heavy_metal_translocating_P-type_ATPase_528621..528851_POSITIVE 296 170 123 224 175 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 294 137 94 211 162 NC_002967:TDE1790|5end_hypothetical_protein_1828007..1828237_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 587 170 121 149 96 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 531 169 124 45 1 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 477 170 137 34 1 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 434 160 115 58 9 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 431 170 125 45 1 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE 373 170 122 54 6 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 363 169 125 72 14 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 350 140 91 70 22 NC_002967:TDE0496|3end_DNA-binding_protein,_putative_550971..551121_NEGATIVE 330 130 84 143 91 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 329 150 113 142 101 NC_002967:TDE2625|3end_ABC_transporter,_ATP-binding/permease_protein_2664925..2665075_NEGATIVE 314 166 122 145 101 NC_002967:TDE2165|3end_hydrogenase_accessory_protein_HypB_2197053..2197203_NEGATIVE 310 154 115 60 19 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 285 167 124 55 1 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 285 169 125 58 11 NC_002967:TDE2345|3end_ribosome_recycling_factor_2381946..2382096_NEGATIVE 284 170 124 59 10 NC_002967:TDE0564|3end_hypothetical_protein_597015..597165_POSITIVE 283 139 93 148 103 NC_002967:TDE0905|3end_hypothetical_protein_923228..923378_POSITIVE 282 170 122 58 12 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 281 170 130 74 41 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE 276 137 94 71 25 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 274 137 95 57 12 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE