Origin IGS: attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata .........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 tataatcaatatttcccacgttttactgtgtatttaggtgaatgcaaactaacattccttattaaccttatttataaagataaatcgaagagtgttcttactgtttttggaattgataatttgaatcttcttaaggaaaaaatagataatggctatttcctttatgataaactgtataccgattattataatagaattccaaagttgacatcattaatagatcaaaaattatggggaactaaataattatacctaatatccacttcaagctttagcatgaaatttactagagtgaatattaacagaacgattttccacaaaaaggagaaaat Mask Tandem Repeat Region ================================================ attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata Find is-nt database================================================ Query_seq: TDE1815:TDE1816|TDE1815:TDE1816:hypothetical protein:hypothetical protein:<-<-:1850235..1850566 332 attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1815:TDE1816|TDE1815:TDE1816:hypothetical protein:hypothetical protein:<-<-:1850235..1850566 332 attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1815:TDE1816|TDE1815:TDE1816:hypothetical protein:hypothetical protein:<-<-:1850235..1850566 332 attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 1 End: 108 M F S F L W K I V L L I F T L V N F M L K L E V D I R Y N Y L V P H N F ................................................................................................................................................................................................................................ Protein_Len: 33 Strand: + Start: 101 End: 199 .................................................................................................... M I F D L L M M S T L E F Y Y N N R Y T V Y H K G N S H Y L F F P ..................................................................................................................................... Protein_Len: 47 Strand: + Start: 141 End: 281 ............................................................................................................................................ M I I I G I Q F I I K E I A I I Y F F L K K I Q I I N S K N S K N T L R F I F I N K V N K E C ................................................... Protein_Len: 60 Strand: - Start: 90 End: 305 ......................................................................................... L K P I R N Y Y D T Y L K D Y L F Y G N D I K E K L L N L N D I G F V T L V S K S K D K Y I L N I L F T L K C E G L Y M ........................... attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata 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: 141 End: 170 ............................................................................................................................................TATGATAAACTGTATACCGATTATTATAAT.................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 144 End: 173 ...............................................................................................................................................CTTTATGATAAACTGTATACCGATTATTAT............................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1815:TDE1816|TDE1815:TDE1816:hypothetical protein:hypothetical protein:<-<-:1850235..1850566 332 attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata Intra-Species Hit: Count: 1 Min: 1 Max: 332 Len: 332 Subject: NC_002967_TDE1815_TDE1816|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1850235,1850566]|332 HSP 1 e-value: 0.0 bit: 658.0 Len: 332 Query Start:1 Query End:332 Subject Strand: POSITIVE Subject Start: 1 Subject End: 332 attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata attttctcctttttgtggaaaatcgttctgttaatattcactctagtaaatttcatgctaaagcttgaagtggatattaggtataattatttagttccccataatttttgatctattaatgatgtcaactttggaattctattataataatcggtatacagtttatcataaaggaaatagccattatctattttttccttaagaagattcaaattatcaattccaaaaacagtaagaacactcttcgatttatctttataaataaggttaataaggaatgttagtttgcattcacctaaatacacagtaaaacgtgggaaatattgattata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCUCCUUUUUGUGGAAAAUCGUUCUGUUAAUAUUCACUCUAGUAAAUUUCAUGCUAAAGCUUGAAGUGGAUAUUAGGUAUAAUUAUUUAGUUCCCCAUAAUUUUUGAUCUAUUAAUGAUGUCAACUUUGGAAUUCUAUUAUAAUAAUCGGUAUACAGUUUAUCAUAAAGGAAAUAGCCAUUAUCUAUUUUUUCCUUAAGAAGAUUCAAAUUAUCAAUUCCAAAAACAGUAAGAACACUCUUCGAUUUAUCUUUAUAAAUAAGGUUAAUAAGGAAUGUUAGUUUGCAUUCACCUAAAUACACAGUAAAACGUGGGAAAUAUUGAUUAUA ((((((..(.....)..)))))).......((((((((((((..........(((.((....)).))))))))))))))).((((((((.....((((((.......((((((((((.((((.(((...(((((((((..............((((.......))))...(((((((................)))))))..................)))))))))......((((....)))).)))......)))).))).)))))))....((((((......))))))....................).)))))....)))))))) (-55.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAUCAAUAUUUCCCACGUUUUACUGUGUAUUUAGGUGAAUGCAAACUAACAUUCCUUAUUAACCUUAUUUAUAAAGAUAAAUCGAAGAGUGUUCUUACUGUUUUUGGAAUUGAUAAUUUGAAUCUUCUUAAGGAAAAAAUAGAUAAUGGCUAUUUCCUUUAUGAUAAACUGUAUACCGAUUAUUAUAAUAGAAUUCCAAAGUUGACAUCAUUAAUAGAUCAAAAAUUAUGGGGAACUAAAUAAUUAUACCUAAUAUCCACUUCAAGCUUUAGCAUGAAAUUUACUAGAGUGAAUAUUAACAGAACGAUUUUCCACAAAAAGGAGAAAAU ((((((...((.(((((.(((.......((.(((((.((((.((..((((....(((((((......((((((....))))))...(((((..(((((..........)))))............))))).)))))))...........(((....(((..(((((((((.(.(....).).)))))))))..)))..))).))))..))))))...)))))))......)))))))).))....))))))..((((((.(((((((.((....)).)))..........)))).)))))).........((((((.......))))))... (-52.56) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 788 100 51 191 142 NC_002967:TDE1815|5end_hypothetical_protein_1850144..1850374_NEGATIVE 253 198 155 81 35 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 238 319 275 115 78 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 237 74 37 137 95 NC_002967:TDE1021|5end_lipoprotein,_putative_1053564..1053794_NEGATIVE 231 101 62 102 62 NC_002967:TDE1987|5end_hypothetical_protein_2002312..2002542_POSITIVE 230 99 52 231 180 NC_002967:TDE2506|5end_radical_SAM_domain_protein_2530581..2530811_POSITIVE 230 70 21 130 82 NC_002967:TDE1385|5end_hypothetical_protein_1424900..1425130_NEGATIVE 229 319 274 39 8 NC_002967:TDE2665|5end_inositol-5-monophosphate_dehydrogenase_2702017..2702247_POSITIVE 229 286 242 93 48 NC_002967:TDE0729|5end_hypothetical_protein_769124..769354_NEGATIVE 225 139 91 130 76 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 221 196 151 188 147 NC_002967:TDE0455|5end_kinase,_GHMP_family_511192..511422_POSITIVE 220 29 1 126 97 NC_002967:TDE2502|5end_sensor_histidine_kinase/response_regulator_2525734..2525964_POSITIVE 218 240 191 51 5 NC_002967:TDE0180|5end_hypothetical_protein_213018..213248_NEGATIVE 218 240 191 188 142 NC_002967:TDE0179|5end_hypothetical_protein_212881..213111_NEGATIVE 216 87 41 188 138 NC_002967:TDE1765|5end_hypothetical_protein_1811878..1812108_NEGATIVE 213 298 252 206 156 NC_002967:TDE1480|5end_hypothetical_protein_1525581..1525811_NEGATIVE 212 165 124 175 141 NC_002967:TDE0708|5end_nitroreductase_family_protein_743900..744130_POSITIVE 211 73 52 223 198 NC_002967:TDE2716|5end_HAD-superfamily_hydrolase,_subfamily_IA_2773195..2773425_POSITIVE 211 106 62 108 68 NC_002967:TDE2563|5end_hypothetical_protein_2589794..2590024_POSITIVE 210 79 45 216 186 NC_002967:TDE0011|5end_alkyl_hydroperoxide_reductase/peroxiredoxin_15408..15638_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 229 319 274 55 24 NC_002967:TDE2664|3end_hypothetical_protein_2702113..2702263_POSITIVE 228 298 251 73 20 NC_002967:TDE2755|3end_hypothetical_protein_2811941..2812091_POSITIVE 225 139 91 117 63 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 224 80 41 87 45 NC_002967:TDE0117|3end_lipoprotein,_putative_136607..136757_POSITIVE 220 29 1 139 110 NC_002967:TDE2501|3end_response_regulator_2525827..2525977_POSITIVE 218 240 191 82 36 NC_002967:TDE0181|3end_methyl-accepting_chemotaxis_protein_212987..213137_NEGATIVE 212 165 124 135 101 NC_002967:TDE0707|3end_hypothetical_protein_743940..744090_POSITIVE 211 127 93 60 22 NC_002967:TDE2129|3end_hypothetical_protein_2161635..2161785_POSITIVE 207 289 244 51 5 NC_002967:TDE0757|3end_iron_compound_ABC_transporter,_permease_protein,_putative_796859..797009_NEGATIVE 206 45 6 106 65 NC_002967:TDE2177|3end_hypothetical_protein_2206300..2206450_NEGATIVE 204 44 22 111 90 NC_002967:TDE2681|3end_hypothetical_protein_2721069..2721219_NEGATIVE 204 77 31 50 7 NC_002967:TDE2347|3end_30S_ribosomal_protein_S2_2383503..2383653_NEGATIVE 201 101 63 101 62 NC_002967:TDE0280|3end_PIN_domain_protein_309895..310045_NEGATIVE 200 199 165 98 67 NC_002967:TDE2595|3end_hypothetical_protein_2630034..2630184_NEGATIVE 200 84 41 98 44 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 197 219 174 85 42 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE 196 276 235 100 56 NC_002967:TDE1151|3end_hypothetical_protein_1188268..1188418_NEGATIVE 194 209 171 132 93 NC_002967:TDE2350|3end_lipoprotein,_putative_2386053..2386203_NEGATIVE 194 99 62 119 71 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 192 108 62 120 75 NC_002967:TDE0263|3end_spermidine_N1-acetyltransferase,_putative_296400..296550_NEGATIVE