Origin IGS: agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatcataaaatgataaaaatgtaaagattacggcaaaaaaatgtcaataaaaaaaataaaaacaaaataaaaaaaatatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta .........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 taaattcctcctgttgtttttatgtgttaaaaacactacttattattaaaacatactattgaggatttgtcaaatattttttttattttgtttttattttttttattgacatttttttgccgtaatctttacatttttatcattttatgatacacttctcttcggtaatttatcttaccgacaaaaatacttggaggacact Mask Tandem Repeat Region ================================================ agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatcataaaatgataaaaatgtaaagattacggcaaaaaaatgtcaataaaaaaaataaaaacaaaataaaaaaaatatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta Find is-nt database================================================ Query_seq: TDE1071:TDE1072|TDE1071:TDE1072:peptide ABC transporter, peptide-binding protein OppA:lipoprotein, putative:<-->:1100679..1100880 202 agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatcataaaatgataaaaatgtaaagattacggcaaaaaaatgtcaataaaaaaaataaaaacaaaataaaaaaaatatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1071:TDE1072|TDE1071:TDE1072:peptide ABC transporter, peptide-binding protein OppA:lipoprotein, putative:<-->:1100679..1100880 202 agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatcataaaatgataaaaatgtaaagattacggcaaaaaaatgtcaataaaaaaaataaaaacaaaataaaaaaaatatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1071:TDE1072|TDE1071:TDE1072:peptide ABC transporter, peptide-binding protein OppA:lipoprotein, putative:<-->:1100679..1100880 202 agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatcataaaatgataaaaatgtaaagattacggcaaaaaaatgtcaataaaaaaaataaaaacaaaataaaaaaaatatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatcataaaatgataaaaatgtaaagattacggcaaaaaaatgtcaataaaaaaaataaaaacaaaataaaaaaaatatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 56 End: 145 ....................................................... L I I F I Y L N R C F F T L L F F L F L I F F I N S L D E M ......................................................... agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatcataaaatgataaaaatgtaaagattacggcaaaaaaatgtcaataaaaaaaataaaaacaaaataaaaaaaatatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta 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: 89 Start: 129 End: 158 ................................................................................................................................TTTGACAAATCCTCAATAGTATGTTTTAAT............................................ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 47 End: 76 ..............................................CTTTACATTTTTATCATTTTATGATACACT.............................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 69 End: 98 ....................................................................ATTGACATTTTTTTGCCGTAATCTTTACAT........................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatcataaaatgataaaaatgtaaagattacggcaaaaaaatgtcaataaaaaaaataaaaacaaaataaaaaaaatatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1071:TDE1072|TDE1071:TDE1072:peptide ABC transporter, peptide-binding protein OppA:lipoprotein, putative:<-->:1100679..1100880 202 agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatcataaaatgataaaaatgtaaagattacggcaaaaaaatgtcaataaaaaaaataaaaacaaaataaaaaaaatatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: NC_002967_TDE1071_TDE1072|peptide ABC transporter, peptide-binding protein OppA:lipoprotein, putative|NEGATIVE:POSITIVE|[1100679,1100880]|202 HSP 1 e-value: 1.0E-35 bit: 151.0 Len: 76 Query Start:127 Query End:202 Subject Strand: POSITIVE Subject Start: 127 Subject End: 202 ..............................................................................................................................tatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta ..............................................................................................................................tatttgacaaatcctcaatagtatgttttaataataagtagtgtttttaacacataaaaacaacaggaggaattta HSP 2 e-value: 4.0E-23 bit: 109.0 Len: 55 Query Start:1 Query End:55 Subject Strand: POSITIVE Subject Start: 1 Subject End: 55 agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatca................................................................................................................................................... agtgtcctccaagtatttttgtcggtaagataaattaccgaagagaagtgtatca................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGUCCUCCAAGUAUUUUUGUCGGUAAGAUAAAUUACCGAAGAGAAGUGUAUCAUAAAAUGAUAAAAAUGUAAAGAUUACGGCAAAAAAAUGUCAAUAAAAAAAAUAAAAACAAAAUAAAAAAAAUAUUUGACAAAUCCUCAAUAGUAUGUUUUAAUAAUAAGUAGUGUUUUUAACACAUAAAAACAACAGGAGGAAUUUA ....((((((.....(((((.(((((((......))))))).)))))...((((((...))))))...((((.........((((......))))...........((((((((...((.......((((.((((.((........)).))))..)))).....)).))))))))..))))..........))))))..... (-34.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUCCUCCUGUUGUUUUUAUGUGUUAAAAACACUACUUAUUAUUAAAACAUACUAUUGAGGAUUUGUCAAAUAUUUUUUUUAUUUUGUUUUUAUUUUUUUUAUUGACAUUUUUUUGCCGUAAUCUUUACAUUUUUAUCAUUUUAUGAUACACUUCUCUUCGGUAAUUUAUCUUACCGACAAAAAUACUUGGAGGACACU .....((((((...(((((((..((((.....))))........................(((((..(((((................((((..((.......))..))))..........(((.....)))...............)))))...))))).(((((((......))))))).)))))))...)))))).... (-32.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 50 1 141 92 NC_002967:TDE1071|5end_peptide_ABC_transporter,_peptide-binding_protein_OppA_1100588..1100818_NEGATIVE 268 47 6 151 101 NC_002967:TDE0756|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_796859..797089_NEGATIVE 252 72 38 145 116 NC_002967:TDE0354|5end_general_stress_protein_14_398367..398597_POSITIVE 248 50 2 107 59 NC_002967:TDE1782|5end_hypothetical_protein_1823417..1823647_NEGATIVE 243 47 9 217 169 NC_002967:TDE1448|5end_glutamate_racemase,_putative_1493535..1493765_POSITIVE 240 50 2 52 3 NC_002967:TDE2089|5end_signal_recognition_particle_protein_2117563..2117793_NEGATIVE 231 44 13 191 159 NC_002967:TDE1960|5end_hypothetical_protein_1974298..1974528_POSITIVE 225 41 1 226 188 NC_002967:TDE1498|5end_hypothetical_protein_1543669..1543899_POSITIVE 218 27 1 68 36 NC_002967:TDE0627|5end_co-chaperone_protein_GrpE_659845..660075_POSITIVE 216 50 1 107 57 NC_002967:TDE0587|5end_hypothetical_protein_625749..625979_POSITIVE 214 50 1 230 159 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 212 46 8 51 11 NC_002967:TDE1011|5end_hypothetical_protein_1038101..1038331_POSITIVE 210 90 42 212 157 NC_002967:TDE1741|5end_penicillin-binding_protein_1792792..1793022_POSITIVE 209 50 1 169 121 NC_002967:TDE2330|5end_hypothetical_protein_2366454..2366684_POSITIVE 206 51 16 168 119 NC_002967:TDE1321|5end_conserved_hypothetical_protein_TIGR00257_1359335..1359565_POSITIVE 204 29 1 56 29 NC_002967:TDE2332|5end_hypothetical_protein_2367774..2368004_NEGATIVE 204 39 1 229 191 NC_002967:TDE2032|5end_hypothetical_protein_2060169..2060399_NEGATIVE 204 41 5 141 99 NC_002967:TDE0554|5end_hypothetical_protein_590968..591198_NEGATIVE 204 43 8 68 30 NC_002967:TDE0524|5end_hypothetical_protein_570017..570247_POSITIVE 202 40 1 214 160 NC_002967:TDE2129|5end_hypothetical_protein_2161463..2161693_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 47 6 151 101 NC_002967:TDE0757|3end_iron_compound_ABC_transporter,_permease_protein,_putative_796859..797009_NEGATIVE 259 49 3 66 16 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 248 50 2 86 38 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE 248 50 2 75 27 NC_002967:TDE1771|3end_hypothetical_protein_1814579..1814729_NEGATIVE 240 50 2 52 3 NC_002967:TDE2090|3end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2117563..2117713_NEGATIVE 226 50 1 86 36 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 219 47 1 74 24 NC_002967:TDE1252|3end_lipoprotein,_putative_1287094..1287244_POSITIVE 212 46 8 41 1 NC_002967:TDE1010|3end_excinuclease_ABC,_A_subunit_1038171..1038321_POSITIVE 210 50 1 111 49 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 210 28 6 122 102 NC_002967:TDE1497|3end_hypothetical_protein_1543704..1543854_POSITIVE 204 39 1 106 68 NC_002967:TDE2472|3end_ISTde1,_transposase_2496226..2496376_POSITIVE 204 39 1 106 68 NC_002967:TDE2033|3end_ISTde1,_transposase_2060292..2060442_NEGATIVE 204 41 5 126 84 NC_002967:TDE0555|3end_hypothetical_protein_590983..591133_NEGATIVE 204 39 1 106 68 NC_002967:TDE0039|3end_ISTde1,_transposase_44489..44639_NEGATIVE 199 49 6 90 46 NC_002967:TDE1294|3end_phosphocarrier_protein_HPr_1332055..1332205_NEGATIVE 199 59 13 81 43 NC_002967:TDE1173|3end_site-specific_recombinase,_phage_integrase_family_1201257..1201407_NEGATIVE 197 40 3 70 29 NC_002967:TDE0438|3end_queuine_tRNA-ribosyltransferase_493672..493822_NEGATIVE 196 88 66 103 79 NC_002967:TDE0172|3end_undecaprenyl_pyrophosphate_phosphatase_204025..204175_POSITIVE 194 50 2 133 79 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 191 55 14 134 92 NC_002967:TDE2287|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2324309..2324459_NEGATIVE