Origin IGS: cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaattgaaactgtccagaaacttcagtttttggacagtcttcttactttaaacggcccatcttttgaaaaaccatatcggcaattccaagtaataattcttataacaaactccttactgcaactgaatttgcctctgttgtcagcttgaagcgaatg Mask Tandem Repeat Region ================================================ cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt Find is-nt database================================================ Query_seq: TDE2741:TDE2742|TDE2741:TDE2742:hypothetical protein:site-specific recombinase, phage integrase family:-><-:2796783..2796939 157 cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2741:TDE2742|TDE2741:TDE2742:hypothetical protein:site-specific recombinase, phage integrase family:-><-:2796783..2796939 157 cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2741:TDE2742|TDE2741:TDE2742:hypothetical protein:site-specific recombinase, phage integrase family:-><-:2796783..2796939 157 cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 12 End: 155 ........... A S L L P L N L Q L L S N T I L I I V Q F Q R Y P K E F S P G N L T L L S D L F Q L K Q V T E M .. cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 39 HP_score: -2.4 Tail_Score: -2.50817 Start: 26 End: 39 Full_Region: aacaaactccttact gcaa ctgaat ttgc ctctgttgtcagctt .........................gcaactgaatttgc...................................................................................................................... Find igs database================================================ Query_seq: TDE2741:TDE2742|TDE2741:TDE2742:hypothetical protein:site-specific recombinase, phage integrase family:-><-:2796783..2796939 157 cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_002967_TDE2741_TDE2742|hypothetical protein:site-specific recombinase, phage integrase family|POSITIVE:NEGATIVE|[2796783,2796939]|157 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt cattcgcttcaagctgacaacagaggcaaattcagttgcagtaaggagtttgttataagaattattacttggaattgccgatatggtttttcaaaagatgggccgtttaaagtaagaagactgtccaaaaactgaagtttctggacagtttcaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUCGCUUCAAGCUGACAACAGAGGCAAAUUCAGUUGCAGUAAGGAGUUUGUUAUAAGAAUUAUUACUUGGAAUUGCCGAUAUGGUUUUUCAAAAGAUGGGCCGUUUAAAGUAAGAAGACUGUCCAAAAACUGAAGUUUCUGGACAGUUUCAAUUU .....(((((..((((.((((.(((.....))).))))))))..)))))...............((((((.((((.(((.((.(((....)))....)).))).)))).))))))..((((((((((.((((....)))).))))))))))...... (-43.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUGAAACUGUCCAGAAACUUCAGUUUUUGGACAGUCUUCUUACUUUAAACGGCCCAUCUUUUGAAAAACCAUAUCGGCAAUUCCAAGUAAUAAUUCUUAUAACAAACUCCUUACUGCAACUGAAUUUGCCUCUGUUGUCAGCUUGAAGCGAAUG .....((((((((((((((((....))))))))))))).))).(((((..((..(((......((....)).......)))..))..)))))..................(((((.(((((((.((.......)).)))).)))....))).))... (-33.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 50 1 111 56 NC_002967:TDE1824|5end_hypothetical_protein_1857011..1857241_POSITIVE 314 48 1 180 134 NC_002967:TDE0672|5end_hypothetical_protein_711110..711340_POSITIVE 310 48 3 49 2 NC_002967:TDE2217|5end_galactose/glucose-binding_lipoprotein_2257975..2258205_NEGATIVE 298 50 1 175 123 NC_002967:TDE0268|5end_hypothetical_protein_300049..300279_NEGATIVE 293 41 3 179 136 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 280 120 75 55 3 NC_002967:TDE1245|5end_hypothetical_protein_1278894..1279124_NEGATIVE 278 140 95 118 69 NC_002967:TDE1512|5end_hypothetical_protein_1559203..1559433_POSITIVE 277 59 12 81 32 NC_002967:TDE0364|5end_ABC_transporter,_ATP-binding_protein_411605..411835_NEGATIVE 273 114 76 78 32 NC_002967:TDE0358|5end_cinnamoyl_ester_hydrolase_401638..401868_NEGATIVE 266 106 68 189 154 NC_002967:TDE2429|5end_hypothetical_protein_2458037..2458267_NEGATIVE 257 48 7 58 6 NC_002967:TDE2527|5end_hypothetical_protein_2556219..2556449_NEGATIVE 256 45 12 214 186 NC_002967:TDE2329|5end_hypothetical_protein_2366493..2366723_NEGATIVE 256 79 33 190 144 NC_002967:TDE1400|5end_NAD(+)_synthetase_1440402..1440632_POSITIVE 254 46 1 206 153 NC_002967:TDE1978|5end_hypothetical_protein_1991758..1991988_NEGATIVE 252 108 79 33 3 NC_002967:TDE1942|5end_hypothetical_protein_1959257..1959487_POSITIVE 246 127 86 174 133 NC_002967:TDE1643|5end_PASTA_domain_protein_1694551..1694781_NEGATIVE 245 50 3 65 23 NC_002967:TDE1987|5end_hypothetical_protein_2002312..2002542_POSITIVE 241 78 32 221 185 NC_002967:TDE2703|5end_hypothetical_protein_2748390..2748620_NEGATIVE 241 137 98 213 172 NC_002967:TDE1354|5end_hypothetical_protein_1394886..1395116_POSITIVE 240 48 7 67 25 NC_002967:TDE2098|5end_hypothetical_protein_2125085..2125315_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 108 67 134 83 NC_002967:TDE1942|3end_hypothetical_protein_1959438..1959588_POSITIVE 314 48 1 68 22 NC_002967:TDE0671|3end_PIN_domain_protein_711078..711228_POSITIVE 311 49 6 141 95 NC_002967:TDE0823|3end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_845252..845402_POSITIVE 302 50 1 96 40 NC_002967:TDE1827|3end_hydrolase,_carbon-nitrogen_family_1859943..1860093_NEGATIVE 275 50 1 92 37 NC_002967:TDE0098|3end_hypothetical_protein_114842..114992_NEGATIVE 258 50 3 78 28 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 257 48 7 57 5 NC_002967:TDE2528|3end_hypothetical_protein_2556220..2556370_NEGATIVE 246 127 86 147 106 NC_002967:TDE1644|3end_methionyl-tRNA_formyltransferase_1694578..1694728_NEGATIVE 244 68 21 70 7 NC_002967:TDE0488|3end_lipoprotein,_putative_545145..545295_POSITIVE 236 46 15 110 75 NC_002967:TDE2496|3end_methyl-accepting_chemotaxis_protein_2521170..2521320_NEGATIVE 236 80 35 43 3 NC_002967:TDE0649|3end_hypothetical_protein_684034..684184_NEGATIVE 236 47 3 60 6 NC_002967:TDE0621|3end_MATE_efflux_family_protein_654776..654926_POSITIVE 235 48 6 70 11 NC_002967:TDE1751|3end_ribosomal_protein_L21_1803831..1803981_NEGATIVE 234 47 3 151 107 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 233 128 83 69 22 NC_002967:TDE1943|3end_30S_ribosomal_protein_S4_1959436..1959586_NEGATIVE 233 49 3 70 28 NC_002967:TDE1402|3end_hypothetical_protein_1444515..1444665_POSITIVE 233 116 86 60 32 NC_002967:TDE1372|3end_hypothetical_protein_1415233..1415383_NEGATIVE 232 42 3 65 27 NC_002967:TDE1224|3end_zinc_ABC_transporter,_permease_protein_1257840..1257990_NEGATIVE 230 150 108 62 22 NC_002967:TDE0407|3end_glutamate_synthase_(NADPH),_homotetrameric_459011..459161_NEGATIVE 229 149 104 68 28 NC_002967:TDE1673|3end_ATP-dependent_protease_ATP-binding_subunit_1728205..1728355_POSITIVE