Origin IGS: tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa .........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 ttttctatatttaaaaagtaaatctccgtatatctaatgaaattggtttatgcttctataaattacaaatttgattaccgtgtcaaagtcaagggcttcttaccccttgattttttatataaaatgacttaaacttaatctaatgcagttattgcaggattcaacaatgtaccggaggacaaa Mask Tandem Repeat Region ================================================ tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa Find is-nt database================================================ Query_seq: TDE1921:TDE1922|TDE1921:TDE1922:hypothetical protein:hypothetical protein:<-<-:1940820..1941002 183 tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1921:TDE1922|TDE1921:TDE1922:hypothetical protein:hypothetical protein:<-<-:1940820..1941002 183 tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1921:TDE1922|TDE1921:TDE1922:hypothetical protein:hypothetical protein:<-<-:1940820..1941002 183 tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 55 End: 162 ...................................................... T M K Y L F D L P L F G K V K V R Y D F K Y N I S A Y V L K M L Y V S M ..................... tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa 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: 81 Start: 49 End: 78 ................................................CTTGATTTTTTATATAAAATGACTTAAACT......................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.3 Tail_Score: -5.37043 Start: 74 End: 95 Full_Region: attaccgtgtcaaag tcaagggct tctt accccttga ttttttatataaaat .........................................................................tcaagggcttcttaccccttga........................................................................................ Find igs database================================================ Query_seq: TDE1921:TDE1922|TDE1921:TDE1922:hypothetical protein:hypothetical protein:<-<-:1940820..1941002 183 tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: NC_002967_TDE1921_TDE1922|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1940820,1941002]|183 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa tttgtcctccggtacattgttgaatcctgcaataactgcattagattaagtttaagtcattttatataaaaaatcaaggggtaagaagcccttgactttgacacggtaatcaaatttgtaatttatagaagcataaaccaatttcattagatatacggagatttactttttaaatatagaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUCCUCCGGUACAUUGUUGAAUCCUGCAAUAACUGCAUUAGAUUAAGUUUAAGUCAUUUUAUAUAAAAAAUCAAGGGGUAAGAAGCCCUUGACUUUGACACGGUAAUCAAAUUUGUAAUUUAUAGAAGCAUAAACCAAUUUCAUUAGAUAUACGGAGAUUUACUUUUUAAAUAUAGAAAA ......(((((.((.(((..((((...((((.....)))).........(((((.((..(((((((.......(((((((.(....).))))))).(((((........))))).........))))))))).)))))....))))...))).)))))))......((((((....)))))). (-31.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUAUAUUUAAAAAGUAAAUCUCCGUAUAUCUAAUGAAAUUGGUUUAUGCUUCUAUAAAUUACAAAUUUGAUUACCGUGUCAAAGUCAAGGGCUUCUUACCCCUUGAUUUUUUAUAUAAAAUGACUUAAACUUAAUCUAAUGCAGUUAUUGCAGGAUUCAACAAUGUACCGGAGGACAAA ......................(((((((((((.((((.(((((.(((((((....)))))))....))))).))))....((((((((((((((........))))))))))...........))))........(((((..(((((...)))))))))).....))))).))))))..... (-34.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 852 50 1 141 92 NC_002967:TDE1921|5end_hypothetical_protein_1940729..1940959_NEGATIVE 361 39 4 52 7 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 353 33 1 169 130 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 306 39 1 228 192 NC_002967:TDE0255|5end_ABC_transporter,_ATP-binding_protein_290742..290972_NEGATIVE 279 45 1 44 8 NC_002967:TDE0189|5end_hypothetical_protein_226460..226690_NEGATIVE 270 41 1 144 96 NC_002967:TDE1721|5end_radical_SAM_domain_protein_1775140..1775370_POSITIVE 266 39 3 133 91 NC_002967:TDE1678|5end_ribosomal_protein_S6_1730483..1730713_NEGATIVE 265 130 81 69 7 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 264 47 2 147 95 NC_002967:TDE0437|5end_PBS_lyase_HEAT-like_repeat_domain_protein_493605..493835_NEGATIVE 255 112 77 171 135 NC_002967:TDE0084|5end_phosphoenolpyruvate-protein_phosphotransferase_97455..97685_NEGATIVE 250 48 3 134 94 NC_002967:TDE2749|5end_hypothetical_protein_2805626..2805856_POSITIVE 241 41 10 201 166 NC_002967:TDE2488|5end_modification_methylase,_HemK_family_2511384..2511614_NEGATIVE 240 39 9 106 72 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 234 47 4 167 107 NC_002967:TDE1475|5end_flagellar_filament_core_protein_1522191..1522421_NEGATIVE 233 140 92 90 40 NC_002967:TDE0226|5end_hypothetical_protein_256693..256923_NEGATIVE 232 31 5 121 98 NC_002967:TDE2760|5end_flagellar_biosynthesis_protein_2815881..2816111_NEGATIVE 232 47 6 96 45 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 232 108 69 158 117 NC_002967:TDE1373|5end_HD_domain_protein_1417841..1418071_NEGATIVE 230 118 74 63 18 NC_002967:TDE1382|5end_transcriptional_regulator,_ArsR_family_1422000..1422230_POSITIVE 229 120 74 47 6 NC_002967:TDE2118|5end_DNA_topoisomerase_IV_subunit_A_2151265..2151495_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 47 2 80 28 NC_002967:TDE0438|3end_queuine_tRNA-ribosyltransferase_493672..493822_NEGATIVE 263 38 1 150 108 NC_002967:TDE1720|3end_radical_SAM_domain_protein_1775232..1775382_POSITIVE 260 117 78 59 28 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE 259 40 4 147 104 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 250 48 3 74 34 NC_002967:TDE2748|3end_acetyltransferase,_GNAT_family_2805646..2805796_POSITIVE 243 33 4 130 102 NC_002967:TDE2089|3end_signal_recognition_particle_protein_2116232..2116382_NEGATIVE 239 38 2 118 80 NC_002967:TDE0735|3end_hypothetical_protein_774746..774896_NEGATIVE 232 31 5 124 101 NC_002967:TDE2761|3end_hypothetical_protein_2815878..2816028_NEGATIVE 232 108 69 105 64 NC_002967:TDE1374|3end_hypothetical_protein_1417894..1418044_NEGATIVE 226 106 86 116 93 NC_002967:TDE0618|3end_hypothetical_protein_650242..650392_NEGATIVE 223 45 5 115 77 NC_002967:TDE1838|3end_hypothetical_protein_1869968..1870118_NEGATIVE 223 104 77 43 17 NC_002967:TDE1477|3end_flagellar_filament_core_protein_1522473..1522623_NEGATIVE 223 106 67 80 45 NC_002967:TDE0236|3end_PIN_domain_protein_269647..269797_POSITIVE 222 29 1 124 97 NC_002967:TDE0703|3end_transcriptional_regulator,_AbrB_family_737966..738116_NEGATIVE 222 120 83 85 49 NC_002967:TDE0567|3end_hypothetical_protein_598916..599066_POSITIVE 221 39 8 74 36 NC_002967:TDE2704|3end_hypothetical_protein_2748383..2748533_NEGATIVE 221 31 8 42 22 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 217 37 9 91 60 NC_002967:TDE2078|3end_TPR_domain_protein_2106788..2106938_NEGATIVE 217 108 76 46 15 NC_002967:TDE0360|3end_ABC_transporter,_ATP-binding/permease_protein_404102..404252_NEGATIVE 216 106 64 69 30 NC_002967:TDE1360|3end_xanthine/uracil_permease_family_protein_1400681..1400831_POSITIVE