Origin IGS: aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccgtttttcggcgataaaattccttttgcttttacaaaatgcatgagatattataacataaaatcttgacaaggtcttgctggcagtagacttaaaaataaaaaatatttataatctatcgaaagaatttcgattcttcttttaagaacggaattttattaggagggttgtt Mask Tandem Repeat Region ================================================ aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga Find is-nt database================================================ Query_seq: TDE2529:TDE2530|TDE2529:TDE2530:hypothetical protein:radical SAM domain protein:<-->:2557329..2557501 173 aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2529:TDE2530|TDE2529:TDE2530:hypothetical protein:radical SAM domain protein:<-->:2557329..2557501 173 aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2529:TDE2530|TDE2529:TDE2530:hypothetical protein:radical SAM domain protein:<-->:2557329..2557501 173 aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 65 End: 172 ................................................................ M F F I F K S T A S K T L S R F Y V I I S H A F C K S K R N F I A E K R . aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga 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: 83 Start: 58 End: 87 .........................................................GTAGACTTAAAAATAAAAAATATTTATAAT...................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 114 End: 143 .................................................................................................................TTTTACAAAATGCATGAGATATTATAACAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -7.2 Tail_Score: -4.20868 Start: 40 End: 54 Full_Region: aatatttataatcta tcgaaa gaa tttcga ttcttcttttaagaa .......................................tcgaaagaatttcga....................................................................................................................... Find igs database================================================ Query_seq: TDE2529:TDE2530|TDE2529:TDE2530:hypothetical protein:radical SAM domain protein:<-->:2557329..2557501 173 aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: NC_002967_TDE2529_TDE2530|hypothetical protein:radical SAM domain protein|NEGATIVE:POSITIVE|[2557329,2557501]|173 HSP 1 e-value: 4.0E-72 bit: 272.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatannnnnnnnnnnnaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga aacaaccctcctaataaaattccgttcttaaaagaagaatcgaaattctttcgatagattataaatattttttatttttaagtctactgccagcaagaccttgtcaagattttatgttataatatctcatgcattttgtaaaagcaaaaggaattttatcgccgaaaaacgga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAACCCUCCUAAUAAAAUUCCGUUCUUAAAAGAAGAAUCGAAAUUCUUUCGAUAGAUUAUAAAUAUUUUUUAUUUUUAAGUCUACUGCCAGCAAGACCUUGUCAAGAUUUUAUGUUAUAAUAUCUCAUGCAUUUUGUAAAAGCAAAAGGAAUUUUAUCGCCGAAAAACGGA .............((((((((((..........(((((((....)))))))...((((((..(((((.....)))))...)))))).(((..((((((...(((..((((.((((...)))).))))...)))))))))....)))...))))))))))..(((.....))). (-27.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGUUUUUCGGCGAUAAAAUUCCUUUUGCUUUUACAAAAUGCAUGAGAUAUUAUAACAUAAAAUCUUGACAAGGUCUUGCUGGCAGUAGACUUAAAAAUAAAAAAUAUUUAUAAUCUAUCGAAAGAAUUUCGAUUCUUCUUUUAAGAACGGAAUUUUAUUAGGAGGGUUGUU .......(((..(((((......(((.(((...........))).)))..(((((((...............((((((.((.....))))))))...............))))))).)))))...)))...((((((((((..(((((......)))))..)))))))))).. (-28.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 824 130 81 221 172 NC_002967:TDE2529|5end_hypothetical_protein_2557238..2557468_NEGATIVE 243 111 79 38 7 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 239 108 64 141 99 NC_002967:TDE1549|5end_recombination_protein_RecR_1592140..1592370_POSITIVE 239 128 83 103 39 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 229 90 45 107 59 NC_002967:TDE1310|5end_modulator_of_DNA_gyrase_family_protein_1345962..1346192_POSITIVE 225 90 41 170 108 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 223 127 83 162 118 NC_002967:TDE0889|5end_hypothetical_protein_905090..905320_POSITIVE 223 54 22 104 58 NC_002967:TDE0172|5end_undecaprenyl_pyrophosphate_phosphatase_203136..203366_POSITIVE 218 170 121 151 99 NC_002967:TDE2426|5end_transcription_antitermination_protein_NusG_2455799..2456029_NEGATIVE 217 140 93 117 61 NC_002967:TDE2559|5end_ABC_transporter,_ATP-binding/permease_protein_2587204..2587434_NEGATIVE 214 112 86 38 6 NC_002967:TDE1985|5end_hypothetical_protein_2000329..2000559_NEGATIVE 213 164 121 175 124 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 212 167 123 186 146 NC_002967:TDE2576|5end_RNA_pseudouridylate_synthase_family_protein_2601672..2601902_POSITIVE 211 50 5 223 186 NC_002967:TDE1910|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1928837..1929067_NEGATIVE 209 125 88 151 114 NC_002967:TDE0340|5end_fructose-bisphosphate_aldolase_378639..378869_POSITIVE 208 109 85 59 41 NC_002967:TDE0604|5end_hypothetical_protein_642631..642861_NEGATIVE 205 117 91 57 22 NC_002967:TDE1743|5end_chromate_transport_protein_1798503..1798733_NEGATIVE 204 33 6 228 196 NC_002967:TDE0961|5end_DnaJ_domain_protein_983519..983749_POSITIVE 202 110 67 180 141 NC_002967:TDE0615|5end_cobalamin_biosynthesis_protein_CbiG_648733..648963_POSITIVE 202 101 85 192 176 NC_002967:TDE0566|5end_hypothetical_protein_597185..597415_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 108 64 123 81 NC_002967:TDE1548|3end_conserved_hypothetical_protein_TIGR00103_1592202..1592352_POSITIVE 239 128 83 89 25 NC_002967:TDE1144|3end_hypothetical_protein_1181848..1181998_NEGATIVE 229 90 45 107 59 NC_002967:TDE1309|3end_modulator_of_DNA_gyrase_family_protein_1346042..1346192_POSITIVE 226 165 126 70 37 NC_002967:TDE2647|3end_lipoyltransferase_and_lipoate-protein_ligase_family_protein_2686002..2686152_NEGATIVE 218 170 121 147 95 NC_002967:TDE2427|3end_preprotein_translocase,_SecE_subunit_2455803..2455953_NEGATIVE 214 112 86 84 52 NC_002967:TDE1986|3end_adenylate_cyclase,_putative_2000283..2000433_NEGATIVE 213 164 130 115 85 NC_002967:TDE2422|3end_ribosomal_protein_L7/L12_2452911..2453061_NEGATIVE 213 127 85 148 104 NC_002967:TDE1939|3end_hypothetical_protein_1955435..1955585_POSITIVE 213 164 121 73 22 NC_002967:TDE0692|3end_hypothetical_protein_729920..730070_POSITIVE 212 105 66 149 118 NC_002967:TDE2750|3end_GTP-binding_protein_HflX,_truncation_2807288..2807438_POSITIVE 212 167 123 146 106 NC_002967:TDE2575|3end_hypothetical_protein_2601712..2601862_POSITIVE 211 50 5 117 80 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE 208 109 85 59 41 NC_002967:TDE0605|3end_hypothetical_protein_642631..642781_NEGATIVE 206 170 125 83 29 NC_002967:TDE2488|3end_modification_methylase,_HemK_family_2510395..2510545_NEGATIVE 205 117 91 57 22 NC_002967:TDE1744|3end_chromate_transport_protein_1798503..1798653_NEGATIVE 204 108 89 129 109 NC_002967:TDE2180|3end_tRNA_modification_GTPase_2210590..2210740_NEGATIVE 204 110 66 73 17 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 202 139 93 122 80 NC_002967:TDE1620|3end_hypothetical_protein_1666959..1667109_NEGATIVE 201 165 124 143 115 NC_002967:TDE0638|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_672488..672638_NEGATIVE 198 126 87 141 109 NC_002967:TDE2556|3end_hypothetical_protein_2582316..2582466_NEGATIVE