Origin IGS: ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaagaaaaaaaaatattttttttatatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaattttttgctttttaagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct .........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 agccggcatggaattatagcctttttatatgcgaaattttctaaaacctaaagcactgatagttctataaatagtattatcataataaattattatagttttcttatttgctgcgaagatttatcttaaaaagcaaaaaatttaaagtatattcaattaaaatctctaaaatatcaatttttagctgtaataaagttgttcaattgacgtaaattgtcataaatataaaaaaaatatttttttttcttgacataatgaattataggttttatactattaataggatgttctattaataggatataatagaaaagtaaaatttgttaaaaaggagataaaa Mask Tandem Repeat Region ================================================ ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaagaaaaaaaaatattttttttatatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaattttttgctttttaagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct Find is-nt database================================================ Query_seq: TDE0080:TDE0081|TDE0080:TDE0081:betaine aldehyde dehydrogenase:hypothetical protein:<-<-:92303..92642 340 ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaagaaaaaaaaatattttttttatatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaattttttgctttttaagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0080:TDE0081|TDE0080:TDE0081:betaine aldehyde dehydrogenase:hypothetical protein:<-<-:92303..92642 340 ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaagaaaaaaaaatattttttttatatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaattttttgctttttaagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0080:TDE0081|TDE0080:TDE0081:betaine aldehyde dehydrogenase:hypothetical protein:<-<-:92303..92642 340 ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaagaaaaaaaaatattttttttatatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaattttttgctttttaagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaagaaaaaaaaatattttttttatatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaattttttgctttttaagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 21 End: 164 .................... M L L F Y Y I L L I E H P I N S I K P I I H Y V K K K K Y F F Y I Y D N L R Q L N N F I T A K N ................................................................................................................................................................................ Protein_Len: 31 Strand: + Start: 221 End: 313 ............................................................................................................................................................................................................................ M F A A N K K T I I I Y Y D N T I Y R T I S A L G F R K F R I ........................... Protein_Len: 34 Strand: - Start: 132 End: 233 ................................................................................................................................... T L Q V V K N C S F I S I K S I K I S Y V K F K K S K L I F R R L M ........................................................................................................... ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaagaaaaaaaaatattttttttatatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaattttttgctttttaagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct 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: 66 End: 95 .................................................................CTTGACATAATGAATTATAGGTTTTATACT..................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaagaaaaaaaaatattttttttatatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaattttttgctttttaagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -3.7 Tail_Score: -2.62735 Start: 45 End: 64 Full_Region: TTCTATTATATCCTA TTAATAG AACATC CTATTAA TAGTATAAAACCTAT ............................................TTAATAGAACATCCTATTAA.................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TDE0080:TDE0081|TDE0080:TDE0081:betaine aldehyde dehydrogenase:hypothetical protein:<-<-:92303..92642 340 ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaagaaaaaaaaatattttttttatatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaattttttgctttttaagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct Intra-Species Hit: Count: 1 Min: 1 Max: 340 Len: 340 Subject: NC_002967_TDE0080_TDE0081|betaine aldehyde dehydrogenase:hypothetical protein|NEGATIVE:NEGATIVE|[92303,92642]|340 HSP 1 e-value: 7.0E-66 bit: 252.0 Len: 127 Query Start:214 Query End:340 Subject Strand: POSITIVE Subject Start: 214 Subject End: 340 .....................................................................................................................................................................................................................aagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct .....................................................................................................................................................................................................................aagataaatcttcgcagcaaataagaaaactataataatttattatgataatactatttatagaactatcagtgctttaggttttagaaaatttcgcatataaaaaggctataattccatgccggct HSP 2 e-value: 9.0E-47 bit: 188.0 Len: 95 Query Start:1 Query End:95 Subject Strand: POSITIVE Subject Start: 1 Subject End: 95 ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaag..................................................................................................................................................................................................................................................... ttttatctcctttttaacaaattttacttttctattatatcctattaatagaacatcctattaatagtataaaacctataattcattatgtcaag..................................................................................................................................................................................................................................................... HSP 3 e-value: 2.0E-41 bit: 170.0 Len: 86 Query Start:115 Query End:200 Subject Strand: POSITIVE Subject Start: 115 Subject End: 200 ..................................................................................................................atatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaa............................................................................................................................................ ..................................................................................................................atatttatgacaatttacgtcaattgaacaactttattacagctaaaaattgatattttagagattttaattgaatatactttaaa............................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUCUCCUUUUUAACAAAUUUUACUUUUCUAUUAUAUCCUAUUAAUAGAACAUCCUAUUAAUAGUAUAAAACCUAUAAUUCAUUAUGUCAAGAAAAAAAAAUAUUUUUUUUAUAUUUAUGACAAUUUACGUCAAUUGAACAACUUUAUUACAGCUAAAAAUUGAUAUUUUAGAGAUUUUAAUUGAAUAUACUUUAAAUUUUUUGCUUUUUAAGAUAAAUCUUCGCAGCAAAUAAGAAAACUAUAAUAAUUUAUUAUGAUAAUACUAUUUAUAGAACUAUCAGUGCUUUAGGUUUUAGAAAAUUUCGCAUAUAAAAAGGCUAUAAUUCCAUGCCGGCU ..((((..((((((((.........................((((((((((......))))))))))..(((((((((...(((....(((((.(((.((((((....))))))...))).))))).......(((((((((...(((((......(........)......)))))..)))))))))...............((((((....((((....))))...))))))...)))..((((((.....(((((...)))))....))))))..............)))))))))..............))))))))..))))............. (-50.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCGGCAUGGAAUUAUAGCCUUUUUAUAUGCGAAAUUUUCUAAAACCUAAAGCACUGAUAGUUCUAUAAAUAGUAUUAUCAUAAUAAAUUAUUAUAGUUUUCUUAUUUGCUGCGAAGAUUUAUCUUAAAAAGCAAAAAAUUUAAAGUAUAUUCAAUUAAAAUCUCUAAAAUAUCAAUUUUUAGCUGUAAUAAAGUUGUUCAAUUGACGUAAAUUGUCAUAAAUAUAAAAAAAAUAUUUUUUUUUCUUGACAUAAUGAAUUAUAGGUUUUAUACUAUUAAUAGGAUGUUCUAUUAAUAGGAUAUAAUAGAAAAGUAAAAUUUGUUAAAAAGGAGAUAAAA ..((.....))..((((..((((((((...(((((.((((((((((((((......(((((((.(((....))).))))))).......(((((((((........((((((...((((....))))....))))))............................((((((.......)))))))))))))))....(((((..(((((.....)))))....((..(((((((....)))))))..))......)))))..))))))))...(((((((((((....)))))))))))........))))))......)))))))))))))..)))).. (-61.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 679 90 41 181 132 NC_002967:TDE0080|5end_betaine_aldehyde_dehydrogenase_92212..92442_NEGATIVE 246 339 298 64 10 NC_002967:TDE1315|5end_hypothetical_protein_1353017..1353247_POSITIVE 238 99 56 51 8 NC_002967:TDE0905|5end_hypothetical_protein_922432..922662_POSITIVE 233 73 33 113 79 NC_002967:TDE1366|5end_CDP-alcohol_phosphatidyltransferase_family_protein_1408358..1408588_POSITIVE 223 230 199 109 78 NC_002967:TDE2645|5end_hypothetical_protein_2684972..2685202_POSITIVE 222 325 291 128 91 NC_002967:TDE2717|5end_phosphatidate_cytidylyltransferase,_putative_2774547..2774777_NEGATIVE 222 50 5 132 96 NC_002967:TDE1122|5end_anti-anti-sigma_factor_1153711..1153941_NEGATIVE 221 323 282 139 97 NC_002967:TDE1730|5end_glycosyl_hydrolase,_family_2_1785545..1785775_NEGATIVE 218 335 295 219 168 NC_002967:TDE0166|5end_hypothetical_protein_195871..196101_NEGATIVE 217 339 298 40 3 NC_002967:TDE1862|5end_hypothetical_protein_1886928..1887158_POSITIVE 216 340 304 121 75 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 215 340 304 231 200 NC_002967:TDE1485|5end_hypothetical_protein_1529697..1529927_POSITIVE 214 340 293 211 155 NC_002967:TDE2609|5end_MiaB-like_tRNA_modifying_enzyme_YliG,_TIGR01125_2650421..2650651_POSITIVE 214 340 318 171 142 NC_002967:TDE0176|5end_hypothetical_protein_209798..210028_NEGATIVE 212 239 195 140 95 NC_002967:TDE1516|5end_ABC_transporter,_ATP-binding_protein,_putative_1563127..1563357_POSITIVE 207 98 66 225 196 NC_002967:TDE1757|5end_hypothetical_protein_1807732..1807962_POSITIVE 204 340 293 64 33 NC_002967:TDE1638|5end_dephospho-CoA_kinase,_putative_1688882..1689112_POSITIVE 203 335 293 89 44 NC_002967:TDE2441|5end_hypothetical_protein_2472496..2472726_NEGATIVE 201 340 301 133 92 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 201 340 295 56 5 NC_002967:TDE1246|5end_lipoprotein,_putative_1279039..1279269_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 339 298 83 29 NC_002967:TDE1314|3end_penicillin-binding_protein_1353116..1353266_POSITIVE 241 338 303 72 25 NC_002967:TDE0949|3end_enolase_973391..973541_POSITIVE 234 340 320 86 63 NC_002967:TDE2066|3end_exodeoxyribonuclease_VII,_small_subunit_2092222..2092372_POSITIVE 233 337 304 109 72 NC_002967:TDE1679|3end_ATP_synthase_subunit_K_1730627..1730777_NEGATIVE 233 73 33 88 54 NC_002967:TDE1365|3end_transcriptional_regulator,_TetR_family_1408413..1408563_POSITIVE 223 230 199 116 85 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 222 325 291 123 86 NC_002967:TDE2718|3end_magnesium_transporter_2774552..2774702_NEGATIVE 222 50 5 106 70 NC_002967:TDE1123|3end_sigma_factor_regulatory_protein,_putative_1153737..1153887_NEGATIVE 220 338 293 59 9 NC_002967:TDE0995|3end_hypothetical_protein_1022442..1022592_NEGATIVE 216 340 319 68 48 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 213 210 163 42 1 NC_002967:TDE0219|3end_hypothetical_protein_253356..253506_NEGATIVE 212 239 195 112 67 NC_002967:TDE1515|3end_permease_domain_protein_1563179..1563329_POSITIVE 204 337 291 60 6 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 204 340 293 64 33 NC_002967:TDE1637|3end_DNA_polymerase_I_1688962..1689112_POSITIVE 203 335 293 114 69 NC_002967:TDE2442|3end_surface_protein,_putative_2472471..2472621_NEGATIVE 203 300 263 70 41 NC_002967:TDE1942|3end_hypothetical_protein_1959438..1959588_POSITIVE 202 322 282 151 110 NC_002967:TDE1731|3end_hypothetical_protein_1785532..1785682_NEGATIVE 201 338 300 151 115 NC_002967:TDE2187|3end_ParB-like_nuclease_domain_protein_2221147..2221297_NEGATIVE 201 340 301 65 24 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 199 338 291 107 59 NC_002967:TDE1233|3end_hypothetical_protein_1267609..1267759_POSITIVE