Origin IGS: tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccagatataaaagaaaagcaatagcaaatagataaaaaaatattgctttaattataaaatcaaaaacggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa .........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 ttataagaaagcctttcaaaacttcagttttgtaaaggctttccatgatagctttgcgatgtttttcataagtcattgataagtaaagacttatgaaaaactcgtcaggtaattataaaaatcaaacaagatttttataattaccgacggcaaggcttattttagctttgccgtttttgattttataattaaagcaatatttttttatctatttgctattgcttttcttttatatctggtgtacaatatggttaactgggaggcgtgttttgaaagaacaaaaaagcagttttaaa Mask Tandem Repeat Region ================================================ tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccagatataaaagaaaagcaatagcaaatagataaaaaaatattgctttaattataaaatcaaaaacggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa Find is-nt database================================================ Query_seq: TDE1628:TDE1629|TDE1628:TDE1629:hypothetical protein:dihydrolipoamide dehydrogenase:<-<-:1676947..1677242 296 tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccagatataaaagaaaagcaatagcaaatagataaaaaaatattgctttaattataaaatcaaaaacggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1628:TDE1629|TDE1628:TDE1629:hypothetical protein:dihydrolipoamide dehydrogenase:<-<-:1676947..1677242 296 tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccagatataaaagaaaagcaatagcaaatagataaaaaaatattgctttaattataaaatcaaaaacggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1628:TDE1629|TDE1628:TDE1629:hypothetical protein:dihydrolipoamide dehydrogenase:<-<-:1676947..1677242 296 tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccagatataaaagaaaagcaatagcaaatagataaaaaaatattgctttaattataaaatcaaaaacggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccagatataaaagaaaagcaatagcaaatagataaaaaaatattgctttaattataaaatcaaaaacggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 203 End: 295 .......................................................................................................................................................................................................... M S L Y L S M T Y E K H R K A I M E S L Y K T E V L K G F L I . Protein_Len: 55 Strand: - Start: 5 End: 166 .... * F Q K K T R E F C A E W N V M N Y V L Y L L F A I A F L Y F F I A K I I F D F V A F S F Y A K G D T I I F M .................................................................................................................................. Protein_Len: 30 Strand: - Start: 1 End: 90 K F S S K Q E K L V R R G T L W I T C W I Y F F L L L L Y M .............................................................................................................................................................................................................. tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccagatataaaagaaaagcaatagcaaatagataaaaaaatattgctttaattataaaatcaaaaacggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa 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: 108 End: 137 ...........................................................................................................TTTTAGCTTTGCCGTTTTTGATTTTATAAT............................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 156 End: 185 ...........................................................................................................................................................ATTATAAAAATCTTGTTTGATTTTTATAAT............................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 50 End: 79 .................................................ATTGCTTTTCTTTTATATCTGGTGTACAAT......................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 156 End: 185 ...........................................................................................................................................................ATTATAAAAATCAAACAAGATTTTTATAAT............................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccagatataaaagaaaagcaatagcaaatagataaaaaaatattgctttaattataaaatcaaaaacggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.2 Tail_Score: -5.1417 Start: 124 End: 149 Full_Region: ttttataattaccga cggcaaggct tatttt agctttgccg tttttgattttataa ...........................................................................................................................cggcaaggcttattttagctttgccg................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.9 Tail_Score: -3.44902 Start: 147 End: 195 Full_Region: CTAAAATAAGCCTTG CCGTCGGTAATTATAAAAATC TTGTTT GATTTTTATAATTACCTGACGA GTTTTTCATAAGTCT ..................................................................................................................................................CCGTCGGTAATTATAAAAATCTTGTTTGATTTTTATAATTACCTGACGA..................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.7 Tail_Score: -4.76644 Start: 147 End: 196 Full_Region: CTAAAATAAGCCTTG CCGTCGGTAATTATAAAAATC TTGTTT GATTTTTATAATTACCTGACGAG TTTTTCATAAGTCTT ..................................................................................................................................................CCGTCGGTAATTATAAAAATCTTGTTTGATTTTTATAATTACCTGACGAG.................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -16.4 Tail_Score: -2.66218 Start: 148 End: 194 Full_Region: TAAAATAAGCCTTGC CGTCGGTAATTATAAAAATC TTGTTT GATTTTTATAATTACCTGACG AGTTTTTCATAAGTC ...................................................................................................................................................CGTCGGTAATTATAAAAATCTTGTTTGATTTTTATAATTACCTGACG...................................................................................................... TransTerm Strand: - Conf: 48 HP_score: -4.6 Tail_Score: -2.70932 Start: 160 End: 181 Full_Region: ctcgtcaggtaatta taaaaatc aaacaa gattttta taattaccgacggca ...............................................................................................................................................................taaaaatcaaacaagattttta................................................................................................................... TransTerm Strand: - Conf: 71 HP_score: -8.8 Tail_Score: -2.83271 Start: 188 End: 245 Full_Region: ggctttccatgatag ctttgcgatgtttttcataagtcattg ataag taaagacttatgaaaaactcgtcagg taattataaaaatca ...........................................................................................................................................................................................ctttgcgatgtttttcataagtcattgataagtaaagacttatgaaaaactcgtcagg................................................... Find igs database================================================ Query_seq: TDE1628:TDE1629|TDE1628:TDE1629:hypothetical protein:dihydrolipoamide dehydrogenase:<-<-:1676947..1677242 296 tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccagatataaaagaaaagcaatagcaaatagataaaaaaatattgctttaattataaaatcaaaaacggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa Intra-Species Hit: Count: 1 Min: 1 Max: 296 Len: 296 Subject: NC_002967_TDE1628_TDE1629|hypothetical protein:dihydrolipoamide dehydrogenase|NEGATIVE:NEGATIVE|[1676947,1677242]|296 HSP 1 e-value: 2.0E-93 bit: 343.0 Len: 173 Query Start:124 Query End:296 Subject Strand: POSITIVE Subject Start: 124 Subject End: 296 ...........................................................................................................................cggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa ...........................................................................................................................cggcaaagctaaaataagccttgccgtcggtaattataaaaatcttgtttgatttttataattacctgacgagtttttcataagtctttacttatcaatgacttatgaaaaacatcgcaaagctatcatggaaagcctttacaaaactgaagttttgaaaggctttcttataa HSP 2 e-value: 1.0E-26 bit: 121.0 Len: 61 Query Start:1 Query End:61 Subject Strand: POSITIVE Subject Start: 1 Subject End: 61 tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccag........................................................................................................................................................................................................................................... tttaaaactgcttttttgttctttcaaaacacgcctcccagttaaccatattgtacaccag........................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAAACUGCUUUUUUGUUCUUUCAAAACACGCCUCCCAGUUAACCAUAUUGUACACCAGAUAUAAAAGAAAAGCAAUAGCAAAUAGAUAAAAAAAUAUUGCUUUAAUUAUAAAAUCAAAAACGGCAAAGCUAAAAUAAGCCUUGCCGUCGGUAAUUAUAAAAAUCUUGUUUGAUUUUUAUAAUUACCUGACGAGUUUUUCAUAAGUCUUUACUUAUCAAUGACUUAUGAAAAACAUCGCAAAGCUAUCAUGGAAAGCCUUUACAAAACUGAAGUUUUGAAAGGCUUUCUUAUAA .........(((((((((......)))))...(((............(((((........)))))......(((((((((.................)))))))))..................))).)))).......(((.((((((((((((((((((((((((......)))))))))))))))).)))).((((((((((((((.............))))))))))))))...)))).))).....(((((((((((.((((((....)))))))))))))))))..... (-85.25) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAAGAAAGCCUUUCAAAACUUCAGUUUUGUAAAGGCUUUCCAUGAUAGCUUUGCGAUGUUUUUCAUAAGUCAUUGAUAAGUAAAGACUUAUGAAAAACUCGUCAGGUAAUUAUAAAAAUCAAACAAGAUUUUUAUAAUUACCGACGGCAAGGCUUAUUUUAGCUUUGCCGUUUUUGAUUUUAUAAUUAAAGCAAUAUUUUUUUAUCUAUUUGCUAUUGCUUUUCUUUUAUAUCUGGUGUACAAUAUGGUUAACUGGGAGGCGUGUUUUGAAAGAACAAAAAAGCAGUUUUAAA ......((((((((((((((((....)))))).)))))))))).......(((((((((.((((((((((((((.(((.....))).))))))))))))))))))..((((((((((((((((......)))))))))))))))).(((((((((((......)))))))))))................))))).................(((((...((((..(..((((((.((.....))))))))......)..)))).(((((.....)))))....)))))....... (-95.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 841 70 21 161 112 NC_002967:TDE1628|5end_hypothetical_protein_1676856..1677086_NEGATIVE 559 240 193 224 177 NC_002967:TDE1507|5end_L-serine_dehydratase,_iron-sulfur-dependent,_beta_subunit_1555724..1555954_NEGATIVE 401 240 193 230 183 NC_002967:TDE1852|5end_ABC_transporter,_ATP-binding_protein_1881866..1882096_NEGATIVE 357 240 193 159 120 NC_002967:TDE2514|5end_serine/threonine_protein_phosphatase_family_protein_2540532..2540762_NEGATIVE 354 249 202 202 154 NC_002967:TDE1551|5end_lipoyltransferase_and_lipoate-protein_ligase_family_protein_1595533..1595763_NEGATIVE 352 190 148 200 156 NC_002967:TDE2505|5end_hypothetical_protein_2530125..2530355_POSITIVE 300 159 123 210 171 NC_002967:TDE2130|5end_hypothetical_protein_2162059..2162289_NEGATIVE 293 279 231 53 5 NC_002967:TDE1853|5end_hypothetical_protein_1882082..1882312_NEGATIVE 284 158 123 66 21 NC_002967:TDE0374|5end_glycosyl_transferase,_group_1_family_protein_429200..429430_NEGATIVE 280 49 8 193 141 NC_002967:TDE1168|5end_hypothetical_protein_1199482..1199712_NEGATIVE 280 289 244 85 41 NC_002967:TDE0902|5end_hypothetical_protein_920132..920362_NEGATIVE 271 189 141 110 54 NC_002967:TDE1535|5end_hypothetical_protein_1579940..1580170_NEGATIVE 267 157 123 71 48 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 266 42 7 107 69 NC_002967:TDE2417|5end_nitroimidazole_resistance_protein,_putative_2443288..2443518_NEGATIVE 263 260 213 126 74 NC_002967:TDE1285|5end_flagellar_motor_switch_protein_FliG_,_putative_1320924..1321154_POSITIVE 262 156 129 33 2 NC_002967:TDE2215|5end_galactoside_ABC_transporter,_permease_protein,_putative_2255135..2255365_NEGATIVE 262 290 251 201 164 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 254 169 123 68 17 NC_002967:TDE1763|5end_hypothetical_protein_1811205..1811435_NEGATIVE 253 290 255 35 1 NC_002967:TDE2464|5end_hypothetical_protein_2489143..2489373_POSITIVE 251 190 142 99 43 NC_002967:TDE0435|5end_ATP-dependent_DNA_helicase,_RecQ_family_491261..491491_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 600 240 191 130 77 NC_002967:TDE2464|3end_hypothetical_protein_2489369..2489519_POSITIVE 401 240 193 130 83 NC_002967:TDE1853|3end_hypothetical_protein_1881966..1882116_NEGATIVE 352 190 148 92 48 NC_002967:TDE2504|3end_O-sialoglycoprotein_endopeptidase_2530097..2530247_POSITIVE 284 158 123 69 24 NC_002967:TDE0375|3end_ABC_transporter,_ATP-binding_protein_429197..429347_NEGATIVE 277 240 196 47 4 NC_002967:TDE2465|3end_hypothetical_protein_2489391..2489541_NEGATIVE 275 290 248 68 24 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 271 189 141 106 50 NC_002967:TDE1536|3end_TPR_domain_protein_1579944..1580094_NEGATIVE 269 286 245 89 40 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 266 42 7 65 27 NC_002967:TDE2418|3end_hypothetical_protein_2443330..2443480_NEGATIVE 266 149 113 71 40 NC_002967:TDE0949|3end_enolase_973391..973541_POSITIVE 265 285 245 79 42 NC_002967:TDE1993|3end_aspartate_ammonia-lyase,_putative_2010917..2011067_NEGATIVE 262 290 251 77 40 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 253 47 7 83 46 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 252 153 127 53 25 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 244 290 253 84 50 NC_002967:TDE0356|3end_hypothetical_protein_399732..399882_NEGATIVE 243 186 141 83 19 NC_002967:TDE0394|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_445023..445173_POSITIVE 242 155 118 90 52 NC_002967:TDE2319|3end_hypothetical_protein_2355835..2355985_NEGATIVE 242 290 252 81 48 NC_002967:TDE1195|3end_prolyl_endopeptidase_1227634..1227784_NEGATIVE 241 261 225 46 6 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 241 158 125 75 40 NC_002967:TDE0320|3end_CBS_domain_protein_352480..352630_NEGATIVE