Origin IGS: aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatttaccattttttaaaataatccgtataaatataatgaggagttaactcgaggtttatccccgacacagaagccgggaataaaccgaattataaattagcgcattaccaattt Mask Tandem Repeat Region ================================================ aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata Find is-nt database================================================ Query_seq: TDE0978:TDE0979|TDE0978:TDE0979:hypothetical protein:penicillin binding protein:-><-:1002485..1002599 115 aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0978:TDE0979|TDE0978:TDE0979:hypothetical protein:penicillin binding protein:-><-:1002485..1002599 115 aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0978:TDE0979|TDE0978:TDE0979:hypothetical protein:penicillin binding protein:-><-:1002485..1002599 115 aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata Predict ORF larger than 30AA ================================================ aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata 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: 81 Start: 84 End: 113 ...................................................................................TTTACCATTTTTTAAAATAATCCGTATAAA.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -3.9 Tail_Score: -3.11955 Start: 26 End: 67 Full_Region: TGCGCTAATTTATAA TTCGGTTTATTCCCGGC TTCTGT GTCGGGGATAAACCTCGAG TTAACTCCTCATTAT .........................TTCGGTTTATTCCCGGCTTCTGTGTCGGGGATAAACCTCGAG................................................ TransTerm Strand: - Conf: 41 HP_score: -2.6 Tail_Score: -2.64912 Start: 27 End: 64 Full_Region: atgaggagttaactc gaggtttatccccgac acagaa gccgggaataaaccga attataaattagcgc ..........................gaggtttatccccgacacagaagccgggaataaaccga................................................... Find igs database================================================ Query_seq: TDE0978:TDE0979|TDE0978:TDE0979:hypothetical protein:penicillin binding protein:-><-:1002485..1002599 115 aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE0978_TDE0979|hypothetical protein:penicillin binding protein|POSITIVE:NEGATIVE|[1002485,1002599]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata aaattggtaatgcgctaatttataattcggtttattcccggcttctgtgtcggggataaacctcgagttaactcctcattatatttatacggattattttaaaaaatggtaaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUGGUAAUGCGCUAAUUUAUAAUUCGGUUUAUUCCCGGCUUCUGUGUCGGGGAUAAACCUCGAGUUAACUCCUCAUUAUAUUUAUACGGAUUAUUUUAAAAAAUGGUAAAUA .....((((((.((......((((((..((((((((((((((......))))))))))))))..(((....)))...))))))......)).))))))................. (-32.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUACCAUUUUUUAAAAUAAUCCGUAUAAAUAUAAUGAGGAGUUAACUCGAGGUUUAUCCCCGACACAGAAGCCGGGAAUAAACCGAAUUAUAAAUUAGCGCAUUACCAAUUU ...................((((.(((.....((((((...(((....)))..(((((((.((((.(......).)))).)))))))..)))))).....))).))))....... (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 66 28 231 192 NC_002967:TDE0104|5end_3-dehydroquinate_synthase_124714..124944_NEGATIVE 341 57 11 125 62 NC_002967:TDE2138|5end_ankyrin_repeat_protein_2171631..2171861_POSITIVE 336 70 25 90 30 NC_002967:TDE2564|5end_PemK_family_protein_2589975..2590205_POSITIVE 336 110 62 144 100 NC_002967:TDE1891|5end_hypothetical_protein_1911206..1911436_POSITIVE 325 76 35 183 146 NC_002967:TDE1975|5end_hypothetical_protein_1988869..1989099_POSITIVE 321 76 35 44 1 NC_002967:TDE1967|5end_hypothetical_protein_1981557..1981787_POSITIVE 321 79 35 91 45 NC_002967:TDE1914|5end_Holliday_junction_DNA_helicase_RuvB_1931920..1932150_NEGATIVE 315 67 26 72 33 NC_002967:TDE2544|5end_hypothetical_protein_2571036..2571266_NEGATIVE 315 67 26 158 119 NC_002967:TDE2543|5end_hypothetical_protein_2570950..2571180_NEGATIVE 308 57 11 185 145 NC_002967:TDE1985|5end_hypothetical_protein_2000329..2000559_NEGATIVE 303 68 27 174 126 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 292 60 20 208 174 NC_002967:TDE2085|5end_uridylate_kinase_2114182..2114412_POSITIVE 288 80 36 135 98 NC_002967:TDE2247|5end_PemK_family_protein_2286362..2286592_POSITIVE 283 68 28 80 28 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 282 53 22 141 105 NC_002967:TDE1312|5end_hypothetical_protein_1349088..1349318_POSITIVE 281 77 31 63 12 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 279 63 30 37 2 NC_002967:TDE2277|5end_transcriptional_regulator,_Sir2_family_2312680..2312910_POSITIVE 278 70 34 36 1 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 276 69 30 123 80 NC_002967:TDE2149|5end_transglycosylase,_SLT_family_2187293..2187523_NEGATIVE 276 70 46 36 11 NC_002967:TDE1599|5end_ABC_transporter,_ATP-binding/permease_protein_1650644..1650874_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 480 70 23 68 21 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 341 57 11 123 60 NC_002967:TDE2137|3end_hypothetical_protein_2171709..2171859_POSITIVE 336 70 25 103 43 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 336 110 62 87 43 NC_002967:TDE1890|3end_hypothetical_protein_1911229..1911379_POSITIVE 321 79 35 83 37 NC_002967:TDE1915|3end_alcohol_dehydrogenase,_iron-containing_1931928..1932078_NEGATIVE 304 53 13 54 13 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 300 53 11 71 25 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 297 67 22 141 80 NC_002967:TDE0013|3end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_17758..17908_NEGATIVE 296 68 27 109 50 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 296 68 27 62 3 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 295 55 26 140 99 NC_002967:TDE0040|3end_AMP-binding_protein_45776..45926_NEGATIVE 294 67 27 120 81 NC_002967:TDE0250|3end_sodium-dependent_transporter,_putative_283310..283460_NEGATIVE 288 80 36 147 110 NC_002967:TDE2246|3end_hypothetical_protein_2286454..2286604_POSITIVE 285 80 34 71 14 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 281 77 31 52 1 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 280 55 12 125 83 NC_002967:TDE0640|3end_methyl-accepting_chemotaxis_protein_674531..674681_NEGATIVE 276 70 46 35 10 NC_002967:TDE1600|3end_ABC_transporter,_ATP-binding/permease_protein_1650645..1650795_NEGATIVE 272 55 33 127 105 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 270 54 30 147 119 NC_002967:TDE2150|3end_hypothetical_protein_2187254..2187404_NEGATIVE 270 55 38 51 33 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE