Origin IGS: aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct .........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 aggtttaaattaagctactaaaatagcgtcacttaatttaaactgcaagtttgcttgcggcgttaactgcaagcaaactcgcttcattgtatgtacgctgccagcgtactaattggataatctccaaagtttacactttgttcaattattcaattttaatgctaagaatgtaaaataaaaaaggatgctt Mask Tandem Repeat Region ================================================ aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct Find is-nt database================================================ Query_seq: TDE0609:TDE0610|TDE0609:TDE0610:hypothetical protein:3-hydroxyacyl-CoA dehydrogenase, putative:<-<-:646257..646446 190 aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0609:TDE0610|TDE0609:TDE0610:hypothetical protein:3-hydroxyacyl-CoA dehydrogenase, putative:<-<-:646257..646446 190 aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0609:TDE0610|TDE0609:TDE0610:hypothetical protein:3-hydroxyacyl-CoA dehydrogenase, putative:<-<-:646257..646446 190 aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 21 End: 140 .................... M R L M L I S Y N F L T Y V K S I I W N T R Q C R V Y L S A L K S A T L A A L M .................................................. aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct 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: 82 Start: 9 End: 38 ........TTTTTTATTTTACATTCTTAGCATTAAAAT........................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -10.9 Tail_Score: -2.7674 Start: 82 End: 98 Full_Region: ctcgcttcattgtat gtacgct gcc agcgtac taattggataatctc .................................................................................gtacgctgccagcgtac............................................................................................ TransTerm Strand: + Conf: 78 HP_score: -8.7 Tail_Score: -3.76952 Start: 107 End: 148 Full_Region: AGCGTACATACAATG AAGCGAGTTTGCTTGCAGT TAAC GCCGCAAGCAAACTTGCAG TTTAAATTAAGTGAC ..........................................................................................................AAGCGAGTTTGCTTGCAGTTAACGCCGCAAGCAAACTTGCAG.......................................... TransTerm Strand: + Conf: 84 HP_score: -12.2 Tail_Score: -2.8585 Start: 108 End: 147 Full_Region: GCGTACATACAATGA AGCGAGTTTGCTTGCAGT TAAC GCCGCAAGCAAACTTGCA GTTTAAATTAAGTGA ...........................................................................................................AGCGAGTTTGCTTGCAGTTAACGCCGCAAGCAAACTTGCA........................................... TransTerm Strand: - Conf: 100 HP_score: -15.0 Tail_Score: -3.52316 Start: 109 End: 146 Full_Region: cacttaatttaaact gcaagtttgcttgcgg cgttaa ctgcaagcaaactcgc ttcattgtatgtacg ............................................................................................................gcaagtttgcttgcggcgttaactgcaagcaaactcgc............................................ Find igs database================================================ Query_seq: TDE0609:TDE0610|TDE0609:TDE0610:hypothetical protein:3-hydroxyacyl-CoA dehydrogenase, putative:<-<-:646257..646446 190 aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: NC_002967_TDE0609_TDE0610|hypothetical protein:3-hydroxyacyl-CoA dehydrogenase, putative|NEGATIVE:NEGATIVE|[646257,646446]|190 HSP 1 e-value: 1.0E-104 bit: 377.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct aagcatccttttttattttacattcttagcattaaaattgaataattgaacaaagtgtaaactttggagattatccaattagtacgctggcagcgtacatacaatgaagcgagtttgcttgcagttaacgccgcaagcaaacttgcagtttaaattaagtgacgctattttagtagcttaatttaaacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCAUCCUUUUUUAUUUUACAUUCUUAGCAUUAAAAUUGAAUAAUUGAACAAAGUGUAAACUUUGGAGAUUAUCCAAUUAGUACGCUGGCAGCGUACAUACAAUGAAGCGAGUUUGCUUGCAGUUAACGCCGCAAGCAAACUUGCAGUUUAAAUUAAGUGACGCUAUUUUAGUAGCUUAAUUUAAACCU .............................((((..(((((.((((((...((((((....))))))..)))))).))))).((((((.....))))))....))))..((((((((((((((.((....)).)))))))))))))).(((((((((((((...((((...)))).))))))))))))).. (-62.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUUUAAAUUAAGCUACUAAAAUAGCGUCACUUAAUUUAAACUGCAAGUUUGCUUGCGGCGUUAACUGCAAGCAAACUCGCUUCAUUGUAUGUACGCUGCCAGCGUACUAAUUGGAUAAUCUCCAAAGUUUACACUUUGUUCAAUUAUUCAAUUUUAAUGCUAAGAAUGUAAAAUAAAAAAGGAUGCUU .(((((((((((((..((.........))..)))))))))))))(((.((((((((((((......))))))))))))..(((((...((((((((((.....)))))).(((((((((((...((((((....))))))....)))))))))))...))))...))).))..............))).. (-55.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 973 130 81 221 172 NC_002967:TDE0609|5end_hypothetical_protein_646166..646396_NEGATIVE 441 149 101 105 67 NC_002967:TDE2521|5end_hypothetical_protein_2548074..2548304_NEGATIVE 379 140 93 66 14 NC_002967:TDE2543|5end_hypothetical_protein_2570950..2571180_NEGATIVE 379 140 93 190 138 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 312 132 92 82 38 NC_002967:TDE1408|5end_flagellar_filament_outer_layer_protein_FlaA,_putative_1450829..1451059_POSITIVE 310 138 92 229 183 NC_002967:TDE2418|5end_hypothetical_protein_2443833..2444063_NEGATIVE 310 120 75 213 160 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 305 146 106 76 37 NC_002967:TDE0472|5end_hypothetical_protein_528376..528606_POSITIVE 300 148 102 219 164 NC_002967:TDE0259|5end_transcriptional_regulator,_MarR_family_293257..293487_POSITIVE 294 125 81 126 83 NC_002967:TDE0229|5end_ATPase_family_protein_262746..262976_NEGATIVE 287 142 107 41 11 NC_002967:TDE2605|5end_phosphoglycerate_mutase_family_protein_2645818..2646048_POSITIVE 282 148 101 152 114 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 282 148 101 51 13 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 282 134 93 226 177 NC_002967:TDE0048|5end_hypothetical_protein_57822..58052_NEGATIVE 281 148 108 190 138 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 279 119 71 59 15 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 278 123 81 205 154 NC_002967:TDE2396|5end_putative_inner_membrane_protein_translocase_component_YidC_2425398..2425628_NEGATIVE 278 166 122 190 141 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 277 135 94 73 37 NC_002967:TDE0130|5end_sodium/dicarboxylate_symporter_family_protein_150545..150775_POSITIVE 274 130 81 200 144 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 140 93 81 29 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 307 150 108 45 2 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 300 139 105 85 55 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 294 125 81 73 30 NC_002967:TDE0230|3end_DNA_replication_and_repair_protein_RecF_262799..262949_NEGATIVE 290 139 92 62 10 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 280 148 105 67 15 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 278 148 101 38 1 NC_002967:TDE2419|3end_hypothetical_protein_2444023..2444173_NEGATIVE 278 98 52 142 101 NC_002967:TDE0941|3end_NLP/P60_family_protein_963623..963773_NEGATIVE 273 140 92 77 11 NC_002967:TDE2075|3end_GGDEF_domain/EAL_domain_protein_2101504..2101654_NEGATIVE 272 122 86 128 96 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 271 150 110 44 3 NC_002967:TDE2393|3end_hypothetical_protein_2422588..2422738_POSITIVE 271 150 103 137 93 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 271 150 110 105 64 NC_002967:TDE1902|3end_hypothetical_protein_1922377..1922527_NEGATIVE 270 121 85 108 65 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 270 149 104 144 102 NC_002967:TDE0031|3end_hypothetical_protein_38835..38985_NEGATIVE 269 129 85 69 24 NC_002967:TDE0496|3end_DNA-binding_protein,_putative_550971..551121_NEGATIVE 263 156 113 89 54 NC_002967:TDE2290|3end_transcriptional_regulator,_putative_2328183..2328333_POSITIVE 263 151 116 128 94 NC_002967:TDE0302|3end_hypothetical_protein_333581..333731_POSITIVE 262 138 98 148 114 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 260 141 103 65 26 NC_002967:TDE2571|3end_hypothetical_protein_2597922..2598072_NEGATIVE