Origin IGS: caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaactaaaaaaaatgataaaaatggatatatctacaatacaatatacacacaaaatgtcaataatatcaagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat .........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 attctttatattctaccctattatttaaaaatagggaagatgtataattataaaaaaatattaaaaattacttgatattattgacattttgtgtgtatattgtattgtagatatatccatttttatcattttttttagtttaatttagatatattaaagatttaagctgttttagccgataatctatcggttaaattaccgaatcggtttaggagtatttg Mask Tandem Repeat Region ================================================ caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaactaaaaaaaatgataaaaatggatatatctacaatacaatatacacacaaaatgtcaataatatcaagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat Find is-nt database================================================ Query_seq: TDE2709:TDE2710|TDE2709:TDE2710:BNR domain protein:MATE efflux family protein:<-->:2766449..2766669 221 caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaactaaaaaaaatgataaaaatggatatatctacaatacaatatacacacaaaatgtcaataatatcaagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2709:TDE2710|TDE2709:TDE2710:BNR domain protein:MATE efflux family protein:<-->:2766449..2766669 221 caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaactaaaaaaaatgataaaaatggatatatctacaatacaatatacacacaaaatgtcaataatatcaagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2709:TDE2710|TDE2709:TDE2710:BNR domain protein:MATE efflux family protein:<-->:2766449..2766669 221 caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaactaaaaaaaatgataaaaatggatatatctacaatacaatatacacacaaaatgtcaataatatcaagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaactaaaaaaaatgataaaaatggatatatctacaatacaatatacacacaaaatgtcaataatatcaagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat Predict ORF larger than 30AA ================================================ caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaactaaaaaaaatgataaaaatggatatatctacaatacaatatacacacaaaatgtcaataatatcaagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat 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: 82 Start: 183 End: 212 ......................................................................................................................................................................................CTTCCCTATTTTTAAATAATAGGGTAGAAT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaactaaaaaaaatgataaaaatggatatatctacaatacaatatacacacaaaatgtcaataatatcaagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -8.6 Tail_Score: -3.17392 Start: 32 End: 46 Full_Region: tttaagctgttttag ccgata atc tatcgg ttaaattaccgaatc ...............................ccgataatctatcgg............................................................................................................................................................................... Find igs database================================================ Query_seq: TDE2709:TDE2710|TDE2709:TDE2710:BNR domain protein:MATE efflux family protein:<-->:2766449..2766669 221 caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaactaaaaaaaatgataaaaatggatatatctacaatacaatatacacacaaaatgtcaataatatcaagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat Intra-Species Hit: Count: 1 Min: 1 Max: 221 Len: 221 Subject: NC_002967_TDE2709_TDE2710|BNR domain protein:MATE efflux family protein|NEGATIVE:POSITIVE|[2766449,2766669]|221 HSP 1 e-value: 5.0E-41 bit: 168.0 Len: 85 Query Start:1 Query End:85 Subject Strand: POSITIVE Subject Start: 1 Subject End: 85 caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaact........................................................................................................................................ caaatactcctaaaccgattcggtaatttaaccgatagattatcggctaaaacagcttaaatctttaatatatctaaattaaact........................................................................................................................................ HSP 2 e-value: 6.0E-22 bit: 105.0 Len: 74 Query Start:148 Query End:221 Subject Strand: POSITIVE Subject Start: 148 Subject End: 221 ...................................................................................................................................................caagtaatttttaatannnnnnnataattatacatcttccctatttttaaataatagggtagaatataaagaat ...................................................................................................................................................caagtaatttttaatatttttttataattatacatcttccctatttttaaataatagggtagaatataaagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUACUCCUAAACCGAUUCGGUAAUUUAACCGAUAGAUUAUCGGCUAAAACAGCUUAAAUCUUUAAUAUAUCUAAAUUAAACUAAAAAAAAUGAUAAAAAUGGAUAUAUCUACAAUACAAUAUACACACAAAAUGUCAAUAAUAUCAAGUAAUUUUUAAUAUUUUUUUAUAAUUAUACAUCUUCCCUAUUUUUAAAUAAUAGGGUAGAAUAUAAAGAAU ..............((((((((((......)))))......)))))...............((((((...................(((((((((.(((((((.(((((((..(((...................)))..)).))))).....))))))).)))))))))...........(((.(((((((.......))))))).)))...)))))).. (-34.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUUUAUAUUCUACCCUAUUAUUUAAAAAUAGGGAAGAUGUAUAAUUAUAAAAAAAUAUUAAAAAUUACUUGAUAUUAUUGACAUUUUGUGUGUAUAUUGUAUUGUAGAUAUAUCCAUUUUUAUCAUUUUUUUUAGUUUAAUUUAGAUAUAUUAAAGAUUUAAGCUGUUUUAGCCGAUAAUCUAUCGGUUAAAUUACCGAAUCGGUUUAGGAGUAUUUG ..((((((...(((.(((((((.......))))))).))).(((((....((((.....((((((((.....(((((..(.((......(((((.((((......)))).)))))..)).)..)))))...))))))))....))))..))))))))))).....(((.((..(((((((......(((((......)))))))))))).)).)))..... (-41.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 830 50 1 141 92 NC_002967:TDE2709|5end_BNR_domain_protein_2766358..2766588_NEGATIVE 281 68 22 143 94 NC_002967:TDE0211|5end_ABC_transporter,_permease_protein,_cysTW_family_247286..247516_NEGATIVE 255 57 15 43 4 NC_002967:TDE2510|5end_ABC_transporter,_ATP-binding/permease_protein_2534182..2534412_POSITIVE 246 48 6 75 24 NC_002967:TDE0327|5end_CRISPR-associated_SAG0894_family_protein_360881..361111_POSITIVE 242 41 13 42 20 NC_002967:TDE2754|5end_ornithine_cyclodeaminase_2811780..2812010_NEGATIVE 240 50 7 49 13 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 240 50 7 159 99 NC_002967:TDE0182|5end_ABC_transporter,_ATP-binding_protein_216783..217013_NEGATIVE 238 50 7 151 100 NC_002967:TDE1409|5end_flagellar_filament_outer_layer_protein_FlaA,_putative_1451561..1451791_POSITIVE 233 67 31 231 202 NC_002967:TDE1887|5end_TPR_domain_protein_1909133..1909363_NEGATIVE 233 219 182 143 98 NC_002967:TDE1631|5end_citrate_lyase,_alpha_subunit_1681556..1681786_NEGATIVE 232 34 7 65 35 NC_002967:TDE0300|5end_leucyl_aminopeptidase_330843..331073_POSITIVE 230 56 27 40 11 NC_002967:TDE0866|5end_hypothetical_protein_887614..887844_POSITIVE 230 41 8 183 138 NC_002967:TDE0516|5end_hypothetical_protein_564122..564352_NEGATIVE 229 59 15 50 2 NC_002967:TDE1093|5end_hypothetical_protein_1127374..1127604_POSITIVE 228 44 4 52 1 NC_002967:TDE0263|5end_spermidine_N1-acetyltransferase,_putative_296942..297172_NEGATIVE 226 56 12 188 128 NC_002967:TDE1314|5end_penicillin-binding_protein_1351174..1351404_POSITIVE 224 56 13 229 176 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 224 50 7 64 8 NC_002967:TDE0420|5end_hypothetical_protein_472218..472448_POSITIVE 220 49 1 185 145 NC_002967:TDE2038|5end_UVR_domain_protein_2068201..2068431_NEGATIVE 220 75 31 68 17 NC_002967:TDE0783|5end_ribosomal_protein_L18_813520..813750_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 50 7 129 78 NC_002967:TDE1408|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1451619..1451769_POSITIVE 233 219 182 130 85 NC_002967:TDE1632|3end_citrate_lyase,_beta_subunit_1681569..1681719_NEGATIVE 230 49 7 69 23 NC_002967:TDE1534|3end_hypothetical_protein_1578667..1578817_NEGATIVE 229 58 15 35 2 NC_002967:TDE2066|3end_exodeoxyribonuclease_VII,_small_subunit_2092222..2092372_POSITIVE 228 36 8 150 113 NC_002967:TDE0517|3end_hypothetical_protein_564147..564297_NEGATIVE 220 75 31 57 6 NC_002967:TDE0782|3end_50S_ribosomal_protein_L6_813589..813739_POSITIVE 218 63 21 150 99 NC_002967:TDE0448|3end_deoxyribose-phosphate_aldolase_506526..506676_POSITIVE 217 52 15 151 123 NC_002967:TDE1384|3end_cadmium-translocating_P-type_ATPase_1424776..1424926_POSITIVE 215 48 20 37 5 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 215 56 28 31 3 NC_002967:TDE0780|3end_ribosomal_protein_S14_812629..812779_POSITIVE 212 48 7 145 104 NC_002967:TDE1672|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_ClpP_1726965..1727115_POSITIVE 212 50 15 52 4 NC_002967:TDE0419|3end_hypothetical_protein_472286..472436_POSITIVE 208 56 21 147 116 NC_002967:TDE2708|3end_hypothetical_protein_2755136..2755286_NEGATIVE 207 58 15 59 11 NC_002967:TDE0946|3end_hypothetical_protein_968735..968885_POSITIVE 204 48 16 38 6 NC_002967:TDE0769|3end_ribosomal_protein_L23_807998..808148_POSITIVE 203 48 8 62 21 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 203 46 2 60 14 NC_002967:TDE2400|3end_50S_ribosomal_protein_L34_2426172..2426322_NEGATIVE 203 58 15 134 96 NC_002967:TDE2301|3end_FlhB_domain_protein_2341852..2342002_POSITIVE 203 66 21 135 87 NC_002967:TDE0877|3end_hypothetical_protein_899619..899769_POSITIVE 200 58 15 87 39 NC_002967:TDE2724|3end_hypothetical_protein_2782282..2782432_POSITIVE