Origin IGS: aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggttttaaatttttcgattaagacgggatcggttatcggtttatctatcataggcggattataccagagtttgggcttttgtacaaggattgacaccttctctttttttgtataaaatatcctgcttttgtctatatttaaatgtttttaaggaagaaatt Mask Tandem Repeat Region ================================================ aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc Find is-nt database================================================ Query_seq: TDE2553:TDE2554|TDE2553:TDE2554:lysyl-tRNA synthetase:chaperonin, 33 kDa family:<-->:2580724..2580884 161 aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2553:TDE2554|TDE2553:TDE2554:lysyl-tRNA synthetase:chaperonin, 33 kDa family:<-->:2580724..2580884 161 aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2553:TDE2554|TDE2553:TDE2554:lysyl-tRNA synthetase:chaperonin, 33 kDa family:<-->:2580724..2580884 161 aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 2 End: 100 . M S S L K T F K Y R Q K Q D I L Y K K R E G V N P C T K A Q T L V ............................................................. Protein_Len: 45 Strand: + Start: 27 End: 161 .......................... M D K S R I F Y T K K E K V S I L V Q K P K L W Y N P P M I D K P I T D P V L I E K F K T Protein_Len: 32 Strand: - Start: 50 End: 145 ................................................. V F F S F T D I R T C F G L S Q Y L G G I I S L G I V S G T K M ................ aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc 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: 92 Start: 44 End: 73 ...........................................ATTGACACCTTCTCTTTTTTTGTATAAAAT........................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 75 End: 104 ..........................................................................CTTGTACAAAAGCCCAAACTCTGGTATAAT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2553:TDE2554|TDE2553:TDE2554:lysyl-tRNA synthetase:chaperonin, 33 kDa family:<-->:2580724..2580884 161 aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: NC_002967_TDE2553_TDE2554|lysyl-tRNA synthetase:chaperonin, 33 kDa family|NEGATIVE:POSITIVE|[2580724,2580884]|161 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacnnnnnnngagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc aatttcttccttaaaaacatttaaatatagacaaaagcaggatattttatacaaaaaaagagaaggtgtcaatccttgtacaaaagcccaaactctggtataatccgcctatgatagataaaccgataaccgatcccgtcttaatcgaaaaatttaaaacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCUUCCUUAAAAACAUUUAAAUAUAGACAAAAGCAGGAUAUUUUAUACAAAAAAAGAGAAGGUGUCAAUCCUUGUACAAAAGCCCAAACUCUGGUAUAAUCCGCCUAUGAUAGAUAAACCGAUAACCGAUCCCGUCUUAAUCGAAAAAUUUAAAACC ...................(((((((..........((.((((....(((((......((((..(((..................)))....)))).)))))))))))...((((((((....((.....)).....))))..))))....)))))))... (-15.77) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUUUAAAUUUUUCGAUUAAGACGGGAUCGGUUAUCGGUUUAUCUAUCAUAGGCGGAUUAUACCAGAGUUUGGGCUUUUGUACAAGGAUUGACACCUUCUCUUUUUUUGUAUAAAAUAUCCUGCUUUUGUCUAUAUUUAAAUGUUUUUAAGGAAGAAAUU .........((((((.....((((((....(((.(((.((((((.....)))))).)))...))).((((..(((.(((((((((((((..((.......))..)))))))))))))..))).))))))))))....(((((....))))).))))))... (-33.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 929 140 91 231 182 NC_002967:TDE2553|5end_lysyl-tRNA_synthetase_2580633..2580863_NEGATIVE 300 138 94 177 137 NC_002967:TDE0283|5end_transporter,_putative_312825..313055_NEGATIVE 285 147 102 59 10 NC_002967:TDE1632|5end_citrate_lyase,_beta_subunit_1682438..1682668_NEGATIVE 280 138 93 45 2 NC_002967:TDE2290|5end_transcriptional_regulator,_putative_2327477..2327707_POSITIVE 274 136 99 69 29 NC_002967:TDE1045|5end_hypothetical_protein_1073240..1073470_POSITIVE 272 148 106 64 25 NC_002967:TDE1682|5end_V-type_ATP_synthase_subunit_B_1734843..1735073_NEGATIVE 265 135 93 50 6 NC_002967:TDE2270|5end_methyl-accepting_chemotaxis_protein_2308379..2308609_NEGATIVE 262 125 82 81 36 NC_002967:TDE1188|5end_NAD(P)_transhydrogenase,_beta_subunit_1216622..1216852_NEGATIVE 262 142 104 220 177 NC_002967:TDE0026|5end_TraB_family_protein_33016..33246_NEGATIVE 261 126 85 168 128 NC_002967:TDE2185|5end_lipoprotein,_putative_2218052..2218282_POSITIVE 259 137 96 186 134 NC_002967:TDE0396|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_445812..446042_POSITIVE 258 110 86 164 136 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 257 117 73 184 137 NC_002967:TDE1550|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_1592747..1592977_POSITIVE 257 110 64 215 173 NC_002967:TDE1011|5end_hypothetical_protein_1038101..1038331_POSITIVE 256 126 84 39 5 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 254 109 62 62 12 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 253 140 107 58 21 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 252 118 76 214 175 NC_002967:TDE2194|5end_8-amino-7-oxononanoate_synthase,_putative_2231032..2231262_NEGATIVE 250 108 61 229 191 NC_002967:TDE0625|5end_ABC_transporter,_ATP-binding_protein_657253..657483_POSITIVE 247 149 104 112 65 NC_002967:TDE1145|5end_hypothetical_protein_1184811..1185041_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 147 102 69 20 NC_002967:TDE1633|3end_citrate_lyase_acyl_carrier_protein_1682428..1682578_NEGATIVE 272 148 106 62 23 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 259 96 59 79 33 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 257 110 66 68 26 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 247 149 104 99 52 NC_002967:TDE1146|3end_hypothetical_protein_1184824..1184974_NEGATIVE 242 126 86 48 1 NC_002967:TDE2403|3end_metallo-beta-lactamase_family_protein_2428641..2428791_NEGATIVE 242 140 94 54 16 NC_002967:TDE2050|3end_hypothetical_protein_2079707..2079857_NEGATIVE 240 99 62 59 23 NC_002967:TDE2004|3end_hypothetical_protein_2023845..2023995_POSITIVE 240 119 86 82 51 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 240 147 105 145 99 NC_002967:TDE0396|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_446860..447010_POSITIVE 238 110 61 87 44 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 237 138 92 79 24 NC_002967:TDE1095|3end_alanine_racemase_1131045..1131195_POSITIVE 235 141 104 71 19 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 234 149 105 120 73 NC_002967:TDE0104|3end_3-dehydroquinate_synthase_123683..123833_NEGATIVE 233 140 93 92 31 NC_002967:TDE1744|3end_chromate_transport_protein_1798503..1798653_NEGATIVE 232 109 62 54 6 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 227 118 85 148 118 NC_002967:TDE2184|3end_hypothetical_protein_2218122..2218272_POSITIVE 227 113 72 109 54 NC_002967:TDE0361|3end_transporter,_putative_407442..407592_POSITIVE 226 109 61 151 101 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 224 139 104 139 105 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE