Origin IGS: aattggcgatattatataaaaaaaaattgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 attttcccttcctataatttataaaatttaaaatatcatatggagtatagactcatcaaaaaaaaatgtcaacataatattacataaacaatgttattttttgcaatttaatttatggtaacctcttaaaaacttcagtttttagaggttttccttaaatccaacttgcgatgtttttcataagtccttgatatataaagacttatgaaaaactcgacgggtatatataaaaaccaacaaggtttttataaatgaccgcatattgacctcagcaatttttttttatataatatcgccaatt Mask Tandem Repeat Region ================================================ aattggcgatattatataaaaaaaaattgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat Find is-nt database================================================ Query_seq: TDE1507:TDE1508|TDE1507:TDE1508:L-serine dehydratase, iron-sulfur-dependent, beta subunit:hypothetical protein:<-->:1555815..1556115 301 aattggcgatattatataaaaaaaaattgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1507:TDE1508|TDE1507:TDE1508:L-serine dehydratase, iron-sulfur-dependent, beta subunit:hypothetical protein:<-->:1555815..1556115 301 aattggcgatattatataaaaaaaaattgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1507:TDE1508|TDE1507:TDE1508:L-serine dehydratase, iron-sulfur-dependent, beta subunit:hypothetical protein:<-->:1555815..1556115 301 aattggcgatattatataaaaaaaaattgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattggcgatattatataaaaaaaaattgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 26 End: 121 ......................... M A E V N M R S F I K T L L V F I Y T R R V F H K S L Y I K D L .................................................................................................................................................................................... aattggcgatattatataaaaaaaaattgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat 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: 89 Start: 11 End: 40 ..........ATTGACCTCAGCAATTTTTTTTTATATAAT..................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 89 Start: 229 End: 258 ....................................................................................................................................................................................................................................GTTGACATTTTTTTTTGATGAGTCTATACT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattggcgatattatataaaaaaaaattgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 41 HP_score: -2.2 Tail_Score: -3.05844 Start: 42 End: 86 Full_Region: acttatgaaaaactc gacgggtatatataaaaacc aacaa ggtttttataaatgaccgca tattgacctcagcaa .........................................gacgggtatatataaaaaccaacaaggtttttataaatgaccgca....................................................................................................................................................................................................................... TransTerm Strand: + Conf: 61 HP_score: -7.0 Tail_Score: -2.88544 Start: 54 End: 74 Full_Region: ATATGCGGTCATTTA TAAAAACC TTGTT GGTTTTTA TATATACCCGTCGAG .....................................................TAAAAACCTTGTTGGTTTTTA................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 65 HP_score: -7.7 Tail_Score: -2.98823 Start: 81 End: 137 Full_Region: tttccttaaatccaa cttgcgatgtttttcataagtccttg atata taaagacttatgaaaaactcgacggg tatatataaaaacca ................................................................................cttgcgatgtttttcataagtccttgatatataaagacttatgaaaaactcgacggg.................................................................................................................................................................... TransTerm Strand: + Conf: 63 HP_score: -6.9 Tail_Score: -3.27525 Start: 83 End: 137 Full_Region: GTTTTTATATATACC CGTCGAGTTTTTCATAAGTCTTT ATATATC AAGGACTTATGAAAAACATCGCAAG TTGGATTTAAGGAAA ..................................................................................CGTCGAGTTTTTCATAAGTCTTTATATATCAAGGACTTATGAAAAACATCGCAAG.................................................................................................................................................................... TransTerm Strand: - Conf: 78 HP_score: -7.5 Tail_Score: -4.43477 Start: 154 End: 180 Full_Region: tttaatttatggtaa cctcttaaaaac ttca gtttttagagg ttttccttaaatcca .........................................................................................................................................................cctcttaaaaacttcagtttttagagg......................................................................................................................... Find igs database================================================ Query_seq: TDE1507:TDE1508|TDE1507:TDE1508:L-serine dehydratase, iron-sulfur-dependent, beta subunit:hypothetical protein:<-->:1555815..1556115 301 aattggcgatattatataaaaaaaaattgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat Intra-Species Hit: Count: 1 Min: 27 Max: 301 Len: 275 Subject: NC_002967_TDE1507_TDE1508|L-serine dehydratase, iron-sulfur-dependent, beta subunit:hypothetical protein|NEGATIVE:POSITIVE|[1555815,1556115]|301 HSP 1 e-value: 1.0E-138 bit: 492.0 Len: 275 Query Start:27 Query End:301 Subject Strand: POSITIVE Subject Start: 27 Subject End: 301 ..........................ttgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacannnnnnnnngatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat ..........................ttgctgaggtcaatatgcggtcatttataaaaaccttgttggtttttatatatacccgtcgagtttttcataagtctttatatatcaaggacttatgaaaaacatcgcaagttggatttaaggaaaacctctaaaaactgaagtttttaagaggttaccataaattaaattgcaaaaaataacattgtttatgtaatattatgttgacatttttttttgatgagtctatactccatatgatattttaaattttataaattataggaagggaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUGAGGUCAAUAUGCGGUCAUUUAUAAAAACCUUGUUGGUUUUUAUAUAUACCCGUCGAGUUUUUCAUAAGUCUUUAUAUAUCAAGGACUUAUGAAAAACAUCGCAAGUUGGAUUUAAGGAAAACCUCUAAAAACUGAAGUUUUUAAGAGGUUACCAUAAAUUAAAUUGCAAAAAAUAACAUUGUUUAUGUAAUAUUAUGUUGACAUUUUUUUUUGAUGAGUCUAUACUCCAUAUGAUAUUUUAAAUUUUAUAAAUUAUAGGAAGGGAAAAU ........((((((((((((..((.((((((((((.....)))))))))).))..))))...(((((((((((((((((.......)))))))))))))))))...((((....((((((.((..(((((((((((((....)))))).))))))).)).))))))...))))........((((.....))))......)))))))).((((((((((..((((....))))..(((((...........))))).....)))))))))).... (-72.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCCCUUCCUAUAAUUUAUAAAAUUUAAAAUAUCAUAUGGAGUAUAGACUCAUCAAAAAAAAAUGUCAACAUAAUAUUACAUAAACAAUGUUAUUUUUUGCAAUUUAAUUUAUGGUAACCUCUUAAAAACUUCAGUUUUUAGAGGUUUUCCUUAAAUCCAACUUGCGAUGUUUUUCAUAAGUCCUUGAUAUAUAAAGACUUAUGAAAAACUCGACGGGUAUAUAUAAAAACCAACAAGGUUUUUAUAAAUGACCGCAUAUUGACCUCAGCAA ...........(((((.((((((..((.......))..)))))).))))).................(((((.((((((((........))))))))....(((......(((((.((.(((((((.((((((....)))))))))))))..)).)))))...((((((((.((((((((((((((.((........))))))))))))))))))).)))))...((((((((((.....)))))))))).......)))..)))))........ (-64.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 782 50 1 167 118 NC_002967:TDE1507|5end_L-serine_dehydratase,_iron-sulfur-dependent,_beta_subunit_1555724..1555954_NEGATIVE 430 108 61 231 184 NC_002967:TDE1852|5end_ABC_transporter,_ATP-binding_protein_1881866..1882096_NEGATIVE 399 148 101 54 8 NC_002967:TDE1853|5end_hypothetical_protein_1882082..1882312_NEGATIVE 361 159 122 201 167 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 323 107 63 159 124 NC_002967:TDE2514|5end_serine/threonine_protein_phosphatase_family_protein_2540532..2540762_NEGATIVE 309 160 122 109 75 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 285 161 122 211 176 NC_002967:TDE0332|5end_transcriptional_regulator,_TetR_family_370940..371170_POSITIVE 279 68 27 67 26 NC_002967:TDE2376|5end_hypothetical_protein_2407527..2407757_NEGATIVE 272 166 126 166 127 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 272 105 69 190 154 NC_002967:TDE1551|5end_lipoyltransferase_and_lipoate-protein_ligase_family_protein_1595533..1595763_NEGATIVE 269 86 42 83 38 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 268 164 130 126 94 NC_002967:TDE1994|5end_hypothetical_protein_2012449..2012679_NEGATIVE 261 159 116 150 112 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 257 59 17 43 3 NC_002967:TDE0952|5end_ABC_transporter,_ATP-binding_protein_975322..975552_POSITIVE 254 110 65 143 96 NC_002967:TDE2132|5end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2163541..2163771_NEGATIVE 254 93 57 172 139 NC_002967:TDE0161|5end_hypothetical_protein_187829..188059_NEGATIVE 252 60 17 180 141 NC_002967:TDE0123|5end_hypothetical_protein_142223..142453_NEGATIVE 250 159 121 147 110 NC_002967:TDE0346|5end_protease_PrtB_387897..388127_NEGATIVE 245 70 21 173 123 NC_002967:TDE1098|5end_hypothetical_protein_1133678..1133908_NEGATIVE 239 158 116 46 5 NC_002967:TDE2377|5end_hypothetical_protein_2407667..2407897_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 596 107 61 130 84 NC_002967:TDE2464|3end_hypothetical_protein_2489369..2489519_POSITIVE 516 159 112 65 20 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 456 110 61 133 84 NC_002967:TDE1853|3end_hypothetical_protein_1881966..1882116_NEGATIVE 439 156 114 81 41 NC_002967:TDE1993|3end_aspartate_ammonia-lyase,_putative_2010917..2011067_NEGATIVE 409 116 74 49 1 NC_002967:TDE1629|3end_dihydrolipoamide_dehydrogenase_1677153..1677303_NEGATIVE 378 107 63 47 4 NC_002967:TDE2465|3end_hypothetical_protein_2489391..2489541_NEGATIVE 361 159 122 77 43 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 358 159 119 84 47 NC_002967:TDE0356|3end_hypothetical_protein_399732..399882_NEGATIVE 340 159 121 84 47 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 324 149 105 77 29 NC_002967:TDE0861|3end_tyrosyl-tRNA_synthetase_881878..882028_NEGATIVE 313 161 121 64 27 NC_002967:TDE2270|3end_methyl-accepting_chemotaxis_protein_2306280..2306430_NEGATIVE 312 159 120 82 45 NC_002967:TDE1263|3end_hypothetical_protein_1298136..1298286_POSITIVE 309 160 122 71 37 NC_002967:TDE0628|3end_molecular_chaperone_DnaK_662629..662779_POSITIVE 304 159 124 90 54 NC_002967:TDE1992|3end_OmpA_family_protein_2010902..2011052_POSITIVE 296 159 113 87 43 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 284 159 112 85 38 NC_002967:TDE2029|3end_hydrolase,_TatD_family_2057148..2057298_NEGATIVE 279 68 27 64 23 NC_002967:TDE2377|3end_hypothetical_protein_2407530..2407680_NEGATIVE 272 166 126 80 41 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 263 156 111 60 19 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 251 164 128 44 5 NC_002967:TDE2257|3end_5'-nucleotidase_family_protein_2293503..2293653_NEGATIVE