Origin IGS: ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccgatggcgtataccaactgataataacatagatgcaatgcgattacttgaaaaacctgatattttaatgtatcataccggcaagtttaatgttcggtagatgcaccactgctgtgctctggaggaaaa Mask Tandem Repeat Region ================================================ ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg Find is-nt database================================================ Query_seq: TDE0034:TDE0035|TDE0034:TDE0035:hypothetical protein:acetyltransferase, GNAT family:<-<-:41541..41669 129 ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0034:TDE0035|TDE0034:TDE0035:hypothetical protein:acetyltransferase, GNAT family:<-<-:41541..41669 129 ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0034:TDE0035|TDE0034:TDE0035:hypothetical protein:acetyltransferase, GNAT family:<-<-:41541..41669 129 ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg Predict ORF larger than 30AA ================================================ ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg 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: 88 Start: 54 End: 83 .....................................................CTTGAAAAACCTGATATTTTAATGTATCAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0034:TDE0035|TDE0034:TDE0035:hypothetical protein:acetyltransferase, GNAT family:<-<-:41541..41669 129 ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_002967_TDE0034_TDE0035|hypothetical protein:acetyltransferase, GNAT family|NEGATIVE:NEGATIVE|[41541,41669]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg ttttcctccagagcacagcagtggtgcatctaccgaacattaaacttgccggtatgatacattaaaatatcaggtttttcaagtaatcgcattgcatctatgttattatcagttggtatacgccatcgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCUCCAGAGCACAGCAGUGGUGCAUCUACCGAACAUUAAACUUGCCGGUAUGAUACAUUAAAAUAUCAGGUUUUUCAAGUAAUCGCAUUGCAUCUAUGUUAUUAUCAGUUGGUAUACGCCAUCGG .......((..((((.((..(..((((...(((((..((.......)).)))))(((((........)))))................))))..)..)).)))).........((((....))))..)) (-21.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGAUGGCGUAUACCAACUGAUAAUAACAUAGAUGCAAUGCGAUUACUUGAAAAACCUGAUAUUUUAAUGUAUCAUACCGGCAAGUUUAAUGUUCGGUAGAUGCACCACUGCUGUGCUCUGGAGGAAAA ((..(((......))).............((((.(((..(((.....((((((.........)))))).(((((.((((((((.......)).))))))))))).....)))..)))))))..)).... (-24.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 965 50 1 141 92 NC_002967:TDE0034|5end_hypothetical_protein_41450..41680_NEGATIVE 327 59 11 191 141 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 316 87 44 190 147 NC_002967:TDE0281|5end_hypothetical_protein_310490..310720_NEGATIVE 302 52 13 170 122 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 283 52 13 171 122 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 278 41 1 131 94 NC_002967:TDE2636|5end_hypothetical_protein_2676070..2676300_POSITIVE 274 51 20 103 71 NC_002967:TDE1512|5end_hypothetical_protein_1559203..1559433_POSITIVE 272 51 13 50 3 NC_002967:TDE1627|5end_glycine_cleavage_system_T_protein_1676411..1676641_NEGATIVE 270 50 3 157 95 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 270 55 20 124 81 NC_002967:TDE1751|5end_ribosomal_protein_L21_1804142..1804372_NEGATIVE 265 38 9 194 168 NC_002967:TDE1425|5end_hypothetical_protein_1467548..1467778_POSITIVE 261 49 6 169 133 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 258 50 14 199 153 NC_002967:TDE0870|5end_phosphatase/nucleotidase_892698..892928_POSITIVE 254 49 1 138 94 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 249 37 3 70 29 NC_002967:TDE2752|5end_hypothetical_protein_2809118..2809348_POSITIVE 249 53 11 231 202 NC_002967:TDE2634|5end_hypothetical_protein_2674625..2674855_POSITIVE 249 62 22 193 145 NC_002967:TDE2109|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2135287..2135517_NEGATIVE 247 118 79 188 147 NC_002967:TDE0969|5end_hypothetical_protein_993260..993490_POSITIVE 247 36 2 40 3 NC_002967:TDE0794|5end_hypothetical_protein_819586..819816_NEGATIVE 247 52 11 79 31 NC_002967:TDE0405|5end_major_outer_sheath_protein_455470..455700_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 51 13 57 10 NC_002967:TDE0470|3end_cell_division_protein_FtsH_526557..526707_POSITIVE 270 50 3 84 22 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 266 55 14 45 2 NC_002967:TDE0904|3end_hypothetical_protein_922278..922428_NEGATIVE 258 50 14 83 37 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 249 37 3 66 25 NC_002967:TDE2751|3end_hypothetical_protein_2809194..2809344_POSITIVE 247 59 13 77 19 NC_002967:TDE2647|3end_lipoyltransferase_and_lipoate-protein_ligase_family_protein_2686002..2686152_NEGATIVE 247 36 2 38 1 NC_002967:TDE0795|3end_hypothetical_protein_819588..819738_NEGATIVE 245 35 2 149 104 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 245 54 15 115 76 NC_002967:TDE0248|3end_hypothetical_protein_282516..282666_POSITIVE 241 50 5 102 64 NC_002967:TDE0612|3end_hypothetical_protein_647367..647517_NEGATIVE 237 57 13 63 7 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 237 49 1 57 9 NC_002967:TDE1772|3end_hypothetical_protein_1815443..1815593_NEGATIVE 234 47 6 59 17 NC_002967:TDE0409|3end_hypothetical_protein_462133..462283_POSITIVE 229 50 1 134 86 NC_002967:TDE1668|3end_amino_acid_permease_family_protein_1722674..1722824_POSITIVE 229 49 3 52 5 NC_002967:TDE0369|3end_type_I_restriction-modification_system,_M_subunit_418356..418506_NEGATIVE 227 118 71 78 41 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 227 51 18 148 120 NC_002967:TDE0923|3end_ABC_transporter,_ATP-binding/permease_protein_943920..944070_NEGATIVE 226 52 18 43 5 NC_002967:TDE2118|3end_DNA_topoisomerase_IV_subunit_A_2149154..2149304_NEGATIVE 226 52 13 107 59 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 225 59 13 53 15 NC_002967:TDE1719|3end_transcriptional_regulator,_MarR_family_1774546..1774696_POSITIVE