Origin IGS: tttcttatctcccataaaaatattgttaatttataaaaatataaatcagcaattatcataattataacaaaaaccaaattcgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattttactatgacatggtaaaatctagttgcacaagtatattgtagtaataaatatttgtaaaaatatttattactacaaattagcgtttatagcagcattaaggaggagttgtatatgagttaatattacatgctaatttatggcaaagaagttaatatttaactatttgcgttgtagatggaaataacaaatatcgaatttggtttttgttataattatgataattgctgatttatatttttataaattaacaatatttttatgggagataagaaa Mask Tandem Repeat Region ================================================ tttcttatctcccataaaaatattgttaatttataaaaatataaatcagcaattatcataattataacaaaaaccaaattcgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc Find is-nt database================================================ Query_seq: TDE2443:TDE2444|TDE2443:TDE2444:hypothetical protein:hypothetical protein:<-<-:2473550..2473828 279 tttcttatctcccataaaaatattgttaatttataaaaatataaatcagcaattatcataattataacaaaaaccaaattcgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2443:TDE2444|TDE2443:TDE2444:hypothetical protein:hypothetical protein:<-<-:2473550..2473828 279 tttcttatctcccataaaaatattgttaatttataaaaatataaatcagcaattatcataattataacaaaaaccaaattcgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2443:TDE2444|TDE2443:TDE2444:hypothetical protein:hypothetical protein:<-<-:2473550..2473828 279 tttcttatctcccataaaaatattgttaatttataaaaatataaatcagcaattatcataattataacaaaaaccaaattcgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcttatctcccataaaaatattgttaatttataaaaatataaatcagcaattatcataattataacaaaaaccaaattcgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 162 End: 251 ................................................................................................................................................................. I C S R R L A A I F A L K Y Y Y I N K C I N I V V I Y K H M ............................ tttcttatctcccataaaaatattgttaatttataaaaatataaatcagcaattatcataattataacaaaaaccaaattcgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc 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: 83 Start: 215 End: 244 ......................................................................................................................................................................................................................TTTTACAAATATTTATTACTACAATATACT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttcttatctcccataaaaatattgttaatttataaaaatataaatcagcaattatcataattataacaaaaaccaaattcgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -2.9 Tail_Score: -3.98913 Start: 75 End: 89 Full_Region: AATTATAACAAAAAC CAAAT TCGAT ATTTG TTATTTCCATCTACA ..........................................................................CAAATTCGATATTTG.............................................................................................................................................................................................. TransTerm Strand: - Conf: 48 HP_score: -2.9 Tail_Score: -3.73023 Start: 75 End: 89 Full_Region: tgtagatggaaataa caaat atcga atttg gtttttgttataatt ..........................................................................caaatatcgaatttg.............................................................................................................................................................................................. TransTerm Strand: + Conf: 71 HP_score: -8.3 Tail_Score: -3.3164 Start: 194 End: 243 Full_Region: ATGCTGCTATAAACG CTAATTTGTAGTAATAAATATTT TTAC AAATATTTATTACTACAATATAC TTGTGCAACTAGATT .................................................................................................................................................................................................CTAATTTGTAGTAATAAATATTTTTACAAATATTTATTACTACAATATAC.................................... TransTerm Strand: + Conf: 100 HP_score: -17.0 Tail_Score: -2.96452 Start: 199 End: 238 Full_Region: GCTATAAACGCTAAT TTGTAGTAATAAATATTT TTAC AAATATTTATTACTACAA TATACTTGTGCAACT ......................................................................................................................................................................................................TTGTAGTAATAAATATTTTTACAAATATTTATTACTACAA......................................... Find igs database================================================ Query_seq: TDE2443:TDE2444|TDE2443:TDE2444:hypothetical protein:hypothetical protein:<-<-:2473550..2473828 279 tttcttatctcccataaaaatattgttaatttataaaaatataaatcagcaattatcataattataacaaaaaccaaattcgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc Intra-Species Hit: Count: 1 Min: 81 Max: 279 Len: 199 Subject: NC_002967_TDE2443_TDE2444|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2473550,2473828]|279 HSP 1 e-value: 1.0E-109 bit: 394.0 Len: 199 Query Start:81 Query End:279 Subject Strand: POSITIVE Subject Start: 81 Subject End: 279 ................................................................................cgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc ................................................................................cgatatttgttatttccatctacaacgcaaatagttaaatattaacttctttgccataaattagcatgtaatattaactcatatacaactcctccttaatgctgctataaacgctaatttgtagtaataaatatttttacaaatatttattactacaatatacttgtgcaactagattttaccatgtcatagtaaaatc HSP 2 e-value: 3.0E-9 bit: 63.9 Len: 40 Query Start:199 Query End:238 Subject Strand: NEGATIVE Subject Start: 199 Subject End: 238 ......................................................................................................................................................................................................ttgtagtaataaatatttttacaaatatttattactacaa......................................... ......................................................................................................................................................................................................ttgtagtaataaatatttgtaaaaatatttattactacaa......................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAUAUUUGUUAUUUCCAUCUACAACGCAAAUAGUUAAAUAUUAACUUCUUUGCCAUAAAUUAGCAUGUAAUAUUAACUCAUAUACAACUCCUCCUUAAUGCUGCUAUAAACGCUAAUUUGUAGUAAUAAAUAUUUUUACAAAUAUUUAUUACUACAAUAUACUUGUGCAACUAGAUUUUACCAUGUCAUAGUAAAAUC ..((((..((((.((.((((((....(((((.(((((.....)))))..))))).......))).))).))...))))..))))...............(((.((.......))....((((((((((((((((((....)))))))))))))))))).........)))....((((((((.........)))))))) (-34.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUACUAUGACAUGGUAAAAUCUAGUUGCACAAGUAUAUUGUAGUAAUAAAUAUUUGUAAAAAUAUUUAUUACUACAAAUUAGCGUUUAUAGCAGCAUUAAGGAGGAGUUGUAUAUGAGUUAAUAUUACAUGCUAAUUUAUGGCAAAGAAGUUAAUAUUUAACUAUUUGCGUUGUAGAUGGAAAUAACAAAUAUCG (((((((((((...)))))))))))..((((..........((((((((((((((((((....)))))))))))))))))).....((((((((((........(((..((((((((((......))).)))).)))..)))...(((((..(((((.....))))).)))))))))))))))....))))........ (-50.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 719 60 11 231 182 NC_002967:TDE2443|5end_hypothetical_protein_2473459..2473689_NEGATIVE 256 123 81 126 88 NC_002967:TDE0999|5end_formate/nitrite_transporter_1025870..1026100_POSITIVE 243 103 66 116 76 NC_002967:TDE0497|5end_hypothetical_protein_551880..552110_NEGATIVE 242 121 84 127 86 NC_002967:TDE0361|5end_transporter,_putative_405989..406219_POSITIVE 241 115 78 230 187 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 237 60 18 108 65 NC_002967:TDE0305|5end_GTP-binding_protein_YchF_336751..336981_NEGATIVE 229 114 79 124 88 NC_002967:TDE2064|5end_ferrous_iron_transport_protein_A_2091492..2091722_NEGATIVE 229 96 65 104 76 NC_002967:TDE1113|5end_hypothetical_protein_1148250..1148480_NEGATIVE 223 114 86 30 1 NC_002967:TDE1050|5end_hypothetical_protein_1077387..1077617_POSITIVE 219 117 77 49 5 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 215 106 78 115 87 NC_002967:TDE1076|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1106936..1107166_POSITIVE 213 125 90 138 98 NC_002967:TDE0492|5end_sensor_histidine_kinase/response_regulator_547468..547698_POSITIVE 212 114 73 117 78 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 211 104 62 110 72 NC_002967:TDE0563|5end_hypothetical_protein_595732..595962_POSITIVE 210 108 71 42 7 NC_002967:TDE1555|5end_hypothetical_protein_1598018..1598248_POSITIVE 208 124 89 65 31 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 207 109 63 117 68 NC_002967:TDE0204|5end_glutamyl-tRNA_synthetase_236968..237198_POSITIVE 206 126 92 134 101 NC_002967:TDE2511|5end_ABC_transporter,_ATP-binding/permease_protein_2535917..2536147_POSITIVE 206 101 73 109 78 NC_002967:TDE1624|5end_glycine_dehydrogenase_subunit_2_1673519..1673749_NEGATIVE 206 122 89 172 143 NC_002967:TDE1556|5end_hypothetical_protein_1598787..1599017_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 103 66 70 30 NC_002967:TDE0498|3end_hypothetical_protein_551926..552076_NEGATIVE 237 60 18 69 26 NC_002967:TDE0306|3end_signal_peptide_peptidase_SppA_336790..336940_NEGATIVE 229 114 79 100 64 NC_002967:TDE2065|3end_FeoA_family_protein_2091516..2091666_NEGATIVE 229 96 65 120 92 NC_002967:TDE1114|3end_transcriptional_regulator,_TetR_family_1148234..1148384_NEGATIVE 219 190 146 79 31 NC_002967:TDE0912|3end_hypothetical_protein_931528..931678_POSITIVE 215 106 78 118 90 NC_002967:TDE1075|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1107019..1107169_POSITIVE 213 125 90 138 98 NC_002967:TDE0491|3end_hypothetical_protein_547548..547698_POSITIVE 210 108 71 45 10 NC_002967:TDE1554|3end_hypothetical_protein_1598101..1598251_POSITIVE 207 109 63 127 78 NC_002967:TDE0203|3end_hypothetical_protein_237058..237208_POSITIVE 206 126 92 132 99 NC_002967:TDE2510|3end_ABC_transporter,_ATP-binding/permease_protein_2535995..2536145_POSITIVE 206 101 73 109 78 NC_002967:TDE1625|3end_glycine_cleavage_system_P_protein,_subunit_1_1673519..1673669_NEGATIVE 206 55 13 103 66 NC_002967:TDE1447|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_1493588..1493738_POSITIVE 205 115 86 73 47 NC_002967:TDE2365|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2398930..2399080_NEGATIVE 205 58 14 80 46 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 202 62 25 73 37 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 200 140 91 60 16 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE 197 127 91 146 107 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 197 106 61 115 69 NC_002967:TDE1959|3end_hypothetical_protein_1973805..1973955_NEGATIVE 196 92 52 118 68 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 196 95 51 109 51 NC_002967:TDE2431|3end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_2459170..2459320_NEGATIVE