Origin IGS: ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attttactccaagaaaattgatgaatctatcaaaattgacggaaaatattctatagaaaagaggagaaaaatgcaagtgccgatgaaaaatgtacttccatgtacatttttcatcttagagttttagacttgcgtctaaaactctcaaggctggaaacaccggcatccgtgccgg Mask Tandem Repeat Region ================================================ ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat Find is-nt database================================================ Query_seq: TDE2338:TDE2339|TDE2338:TDE2339:hypothetical protein:leucyl-tRNA synthetase:<-->:2374810..2374984 175 ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2338:TDE2339|TDE2338:TDE2339:hypothetical protein:leucyl-tRNA synthetase:<-->:2374810..2374984 175 ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2338:TDE2339|TDE2338:TDE2339:hypothetical protein:leucyl-tRNA synthetase:<-->:2374810..2374984 175 ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 62 End: 169 ............................................................. M K N V H G S T F F I G T C I F L L F S I E Y F P S I L I D S S I F L E ...... Protein_Len: 30 Strand: + Start: 85 End: 174 .................................................................................... M F H R H L H F S P L F Y R I F S V N F D R F I N F L G V K . Protein_Len: 36 Strand: - Start: 52 End: 159 ................................................... F E L I F F T C P L V N K M P V Q M K R R K E I S Y K G D I K I S E D M ................ Protein_Len: 43 Strand: - Start: 2 End: 130 . P V S A P T E L R S L K L R L D L V R L H F I Y M S T C K E D A S A N K E E K R Y F M ............................................. ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat 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: 84 Start: 99 End: 128 ..................................................................................................CTTGCATTTTTCTCCTCTTTTCTATAGAAT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -11.0 Tail_Score: -3.15366 Start: 63 End: 92 Full_Region: aaatgcaagtgccga tgaaaaatgtac ttccat gtacatttttca tcttagagttttaga ..............................................................tgaaaaatgtacttccatgtacatttttca................................................................................... Find igs database================================================ Query_seq: TDE2338:TDE2339|TDE2338:TDE2339:hypothetical protein:leucyl-tRNA synthetase:<-->:2374810..2374984 175 ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: NC_002967_TDE2338_TDE2339|hypothetical protein:leucyl-tRNA synthetase|NEGATIVE:POSITIVE|[2374810,2374984]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat ccggcacggatgccggtgtttccagccttgagagttttagacgcaagtctaaaactctaagatgaaaaatgtacatggaagtacatttttcatcggcacttgcatttttctcctcttttctatagaatattttccgtcaattttgatagattcatcaattttcttggagtaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGGCACGGAUGCCGGUGUUUCCAGCCUUGAGAGUUUUAGACGCAAGUCUAAAACUCUAAGAUGAAAAAUGUACAUGGAAGUACAUUUUUCAUCGGCACUUGCAUUUUUCUCCUCUUUUCUAUAGAAUAUUUUCCGUCAAUUUUGAUAGAUUCAUCAAUUUUCUUGGAGUAAAAU ((((((....))))))........(((...((((((((((((....))))))))))))..((((((((((((((......)))))))))))))))))......(((((.((((....(((....))).....((..(((....)))..))...............)))).))))) (-60.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUACUCCAAGAAAAUUGAUGAAUCUAUCAAAAUUGACGGAAAAUAUUCUAUAGAAAAGAGGAGAAAAAUGCAAGUGCCGAUGAAAAAUGUACUUCCAUGUACAUUUUUCAUCUUAGAGUUUUAGACUUGCGUCUAAAACUCUCAAGGCUGGAAACACCGGCAUCCGUGCCGG (((((.((((.......((((((....)))))).......((((....))))..........)))).)))))......(((((((((((((((((......))))))))))))))..((((((((((((....))))))))))))...))).(....).((((((....)))))) (-59.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1055 50 1 141 92 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 795 50 1 118 67 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 719 79 31 223 175 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 520 46 2 199 154 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 503 46 2 231 184 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 434 95 51 47 3 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 428 79 31 77 33 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 406 49 1 206 157 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 388 46 1 67 21 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 362 57 14 220 168 NC_002967:TDE2143|5end_penicillin-binding_protein_2178107..2178337_POSITIVE 338 58 23 220 187 NC_002967:TDE2549|5end_methyl-accepting_chemotaxis_protein_2573285..2573515_POSITIVE 338 49 1 153 107 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 331 79 31 160 113 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 330 94 61 170 136 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 325 103 61 176 131 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 322 50 1 114 45 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 313 48 1 93 34 NC_002967:TDE2544|5end_hypothetical_protein_2571036..2571266_NEGATIVE 313 48 1 179 120 NC_002967:TDE2543|5end_hypothetical_protein_2570950..2571180_NEGATIVE 312 49 1 179 126 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 311 50 2 174 123 NC_002967:TDE2312|5end_hypothetical_protein_2348451..2348681_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 746 79 31 72 24 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 719 79 31 71 23 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 393 50 1 92 40 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 388 46 1 85 39 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 384 96 54 90 48 NC_002967:TDE0834|3end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854291..854441_NEGATIVE 381 89 42 151 105 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 362 37 2 148 111 NC_002967:TDE0038|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_43036..43186_NEGATIVE 338 58 23 39 6 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 330 45 1 80 38 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 319 49 3 47 12 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE 318 100 54 92 46 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 312 49 1 70 17 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 311 50 2 80 29 NC_002967:TDE2311|3end_hypothetical_protein_2348437..2348587_POSITIVE 311 49 1 54 5 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 307 44 1 58 2 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 304 49 1 106 39 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 298 38 4 43 3 NC_002967:TDE0606|3end_ParB_family_protein_643239..643389_NEGATIVE 292 50 3 146 104 NC_002967:TDE1591|3end_inorganic_polyphosphate/ATP-NAD_kinase,_putative_1639516..1639666_POSITIVE 292 50 1 76 33 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 290 47 1 88 30 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE