Origin IGS: ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttctacctcatataaaaattattttcaaagaagaaagctttttctccttccataattattgtatgaatagtttgcactagatagtaaaatttgaaaaaataaagtagttgaatgaccaaataattacatatattcaa Mask Tandem Repeat Region ================================================ ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa Find is-nt database================================================ Query_seq: TDE1975:TDE1976|TDE1975:TDE1976:hypothetical protein:hypothetical protein:->->:1989117..1989254 138 ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1975:TDE1976|TDE1975:TDE1976:hypothetical protein:hypothetical protein:->->:1989117..1989254 138 ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1975:TDE1976|TDE1975:TDE1976:hypothetical protein:hypothetical protein:->->:1989117..1989254 138 ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 1 End: 132 M N I C N Y L V I Q L L Y F F K F Y Y L V Q T I H T I I M E G E K A F F F E N N F Y M R ...... ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa 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: 109 End: 138 ............................................................................................................TTTGAAAATAATTTTTATATGAGGTAGAAA Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1975:TDE1976|TDE1975:TDE1976:hypothetical protein:hypothetical protein:->->:1989117..1989254 138 ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_002967_TDE1975_TDE1976|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1989117,1989254]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa ttgaatatatgtaattatttggtcattcaactactttattttttcaaattttactatctagtgcaaactattcatacaataattatggaaggagaaaaagctttcttctttgaaaataatttttatatgaggtagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAAUAUAUGUAAUUAUUUGGUCAUUCAACUACUUUAUUUUUUCAAAUUUUACUAUCUAGUGCAAACUAUUCAUACAAUAAUUAUGGAAGGAGAAAAAGCUUUCUUCUUUGAAAAUAAUUUUUAUAUGAGGUAGAAA (((((.....((((.((.((((....)))).))..))))...))))).(((((((...((((....)))).(((((.((.((((((.((((((((((....))))))))))....)))))).)).)))))))))))). (-23.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUACCUCAUAUAAAAAUUAUUUUCAAAGAAGAAAGCUUUUUCUCCUUCCAUAAUUAUUGUAUGAAUAGUUUGCACUAGAUAGUAAAAUUUGAAAAAAUAAAGUAGUUGAAUGACCAAAUAAUUACAUAUAUUCAA ((((....((((((((.((((((......((((((.....))))))......)))))).))))))))....(((((........)))))....)))).......(((((((..........))))))).......... (-17.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 479 100 54 47 1 NC_002967:TDE2099|5end_hypothetical_protein_2125027..2125257_POSITIVE 364 90 41 172 123 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 294 126 81 223 179 NC_002967:TDE0861|5end_tyrosyl-tRNA_synthetase_883098..883328_NEGATIVE 289 110 64 134 89 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 280 90 41 208 159 NC_002967:TDE0670|5end_ATP-dependent_protease_La_707938..708168_POSITIVE 259 24 1 231 208 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 220 90 46 230 186 NC_002967:TDE2718|5end_magnesium_transporter_2775910..2776140_NEGATIVE 209 115 71 195 143 NC_002967:TDE1441|5end_dTDP-glucose_4,6-dehydratase_1486247..1486477_POSITIVE 205 110 64 138 94 NC_002967:TDE2098|5end_hypothetical_protein_2125085..2125315_NEGATIVE 201 110 64 136 94 NC_002967:TDE2136|5end_hypothetical_protein_2165659..2165889_NEGATIVE 195 130 82 121 69 NC_002967:TDE2035|5end_glucose-1-phosphate_adenylyltransferase_2062801..2063031_POSITIVE 194 59 19 185 143 NC_002967:TDE2434|5end_polysaccharide_deacetylase_family_protein_2465657..2465887_NEGATIVE 186 103 61 175 132 NC_002967:TDE0796|5end_histidinol_phosphate_phosphatase_HisJ_family_protein_820057..820287_POSITIVE 183 105 65 68 28 NC_002967:TDE2012|5end_hypothetical_protein_2034351..2034581_NEGATIVE 181 93 61 121 86 NC_002967:TDE1431|5end_glycosyl_transferase,_group_1_family_protein_1474394..1474624_POSITIVE 180 111 71 140 99 NC_002967:TDE2707|5end_hypothetical_protein_2753947..2754177_POSITIVE 180 68 25 226 189 NC_002967:TDE2706|5end_hypothetical_protein_2753793..2754023_NEGATIVE 179 114 72 65 21 NC_002967:TDE2302|5end_HD_domain_protein_2341790..2342020_POSITIVE 179 117 82 40 2 NC_002967:TDE0014|5end_hypothetical_protein_18790..19020_POSITIVE 175 60 18 135 83 NC_002967:TDE1197|5end_conserved_hypothetical_protein_TIGR00242_1229952..1230182_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 82 49 151 118 NC_002967:TDE2099|3end_hypothetical_protein_2125229..2125379_POSITIVE 216 110 63 128 79 NC_002967:TDE0649|3end_hypothetical_protein_684034..684184_NEGATIVE 195 130 82 63 11 NC_002967:TDE2034|3end_glycosyl_transferase,_group_1_family_protein_2062823..2062973_POSITIVE 185 95 63 89 53 NC_002967:TDE2358|3end_hypothetical_protein_2393129..2393279_NEGATIVE 183 105 65 60 20 NC_002967:TDE2013|3end_hypothetical_protein_2034359..2034509_NEGATIVE 181 113 86 62 38 NC_002967:TDE0926|3end_phosphonate_ABC_transporter,_permease_protein,_putative_949192..949342_NEGATIVE 179 114 72 47 3 NC_002967:TDE2301|3end_FlhB_domain_protein_2341852..2342002_POSITIVE 179 105 61 92 46 NC_002967:TDE0323|3end_hypothetical_protein_355750..355900_NEGATIVE 176 104 78 92 62 NC_002967:TDE1578|3end_phosphoesterase,_putative_1626109..1626259_POSITIVE 173 102 63 42 1 NC_002967:TDE0761|3end_protease_complex-associated_polypeptide_801968..802118_POSITIVE 172 106 61 99 48 NC_002967:TDE2235|3end_methylaspartate_ammonia-lyase_2273350..2273500_NEGATIVE 172 114 78 89 48 NC_002967:TDE0044|3end_ABC_transporter,_ATP-binding_protein_51660..51810_NEGATIVE 170 53 20 109 76 NC_002967:TDE2251|3end_uracil_permease_2290782..2290932_POSITIVE 170 102 84 61 39 NC_002967:TDE1113|3end_hypothetical_protein_1147729..1147879_NEGATIVE 169 113 77 76 33 NC_002967:TDE0151|3end_integral_membrane_protein,_YeeE/YedE_family_171845..171995_NEGATIVE 167 65 21 138 100 NC_002967:TDE1230|3end_hypothetical_protein_1263505..1263655_POSITIVE 166 49 1 121 67 NC_002967:TDE2362|3end_hypothetical_protein_2396963..2397113_NEGATIVE 166 102 63 45 4 NC_002967:TDE1172|3end_hypothetical_protein_1201280..1201430_POSITIVE 164 106 85 55 35 NC_002967:TDE0813|3end_ABC_transporter,_ATP-binding_protein/permease_835707..835857_POSITIVE 162 74 33 146 99 NC_002967:TDE0669|3end_hypothetical_protein_706949..707099_NEGATIVE