Origin IGS: gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catcttgacttcaatccgccttgatctaattgcagttttgatttcttatttttaaattcccctatttgccaagcgtggattgaaaattcttccgttttttgatatactagtccc Mask Tandem Repeat Region ================================================ gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg Find is-nt database================================================ Query_seq: TDE1964:TDE1965|TDE1964:TDE1965:Na/Pi cotransporter family protein:sodium/hydrogen exchanger family protein:<-<-:1978871..1978984 114 gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1964:TDE1965|TDE1964:TDE1965:Na/Pi cotransporter family protein:sodium/hydrogen exchanger family protein:<-<-:1978871..1978984 114 gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1964:TDE1965|TDE1964:TDE1965:Na/Pi cotransporter family protein:sodium/hydrogen exchanger family protein:<-<-:1978871..1978984 114 gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg Predict ORF larger than 30AA ================================================ gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg 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: 88 Start: 7 End: 36 ......ATTGAAAATTCTTCCGTTTTTTGATATACT.............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1964:TDE1965|TDE1964:TDE1965:Na/Pi cotransporter family protein:sodium/hydrogen exchanger family protein:<-<-:1978871..1978984 114 gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_002967_TDE1964_TDE1965|Na/Pi cotransporter family protein:sodium/hydrogen exchanger family protein|NEGATIVE:NEGATIVE|[1978871,1978984]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg gggactagtatatcaaaaaacggaagaattttcaatccacgcttggcaaataggggaatttaaaaataagaaatcaaaactgcaattagatcaaggcggattgaagtcaagatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGACUAGUAUAUCAAAAAACGGAAGAAUUUUCAAUCCACGCUUGGCAAAUAGGGGAAUUUAAAAAUAAGAAAUCAAAACUGCAAUUAGAUCAAGGCGGAUUGAAGUCAAGAUG ..((((..............(....).....(((((((.(.((((((.(((.((.((.(((........))).))....))...))).).)))))).)))))))))))...... (-19.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCUUGACUUCAAUCCGCCUUGAUCUAAUUGCAGUUUUGAUUUCUUAUUUUUAAAUUCCCCUAUUUGCCAAGCGUGGAUUGAAAAUUCUUCCGUUUUUUGAUAUACUAGUCCC .........((((((((((((((.............(((((..........))))).............)))).)))))))))).............................. (-17.17) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 841 50 1 141 92 NC_002967:TDE1964|5end_Na/Pi_cotransporter_family_protein_1978780..1979010_NEGATIVE 318 100 52 49 1 NC_002967:TDE2012|5end_hypothetical_protein_2034351..2034581_NEGATIVE 260 49 1 130 96 NC_002967:TDE0903|5end_ATP-dependent_DNA_helicase_PcrA_920228..920458_POSITIVE 254 99 51 143 99 NC_002967:TDE1193|5end_hypothetical_protein_1219657..1219887_NEGATIVE 254 99 51 143 99 NC_002967:TDE0579|5end_hypothetical_protein_610029..610259_NEGATIVE 251 106 79 193 157 NC_002967:TDE0145|5end_thiamine_ABC_transporter,_ATP-binding_protein_166700..166930_POSITIVE 238 58 21 231 172 NC_002967:TDE2525|5end_hypothetical_protein_2553583..2553813_NEGATIVE 237 109 79 204 173 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 237 47 14 211 173 NC_002967:TDE1996|5end_hypothetical_protein_2014243..2014473_POSITIVE 237 58 21 201 164 NC_002967:TDE0292|5end_hypothetical_protein_322014..322244_NEGATIVE 236 62 27 210 172 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 235 100 52 66 26 NC_002967:TDE1389|5end_hypothetical_protein_1428238..1428468_POSITIVE 235 100 82 46 24 NC_002967:TDE0061|5end_fic_family_protein_68944..69174_NEGATIVE 227 72 31 154 114 NC_002967:TDE1828|5end_hypothetical_protein_1861752..1861982_NEGATIVE 227 72 31 154 114 NC_002967:TDE1776|5end_hypothetical_protein_1819232..1819462_NEGATIVE 226 55 12 213 176 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 226 56 18 224 184 NC_002967:TDE1671|5end_trigger_factor_1724912..1725142_POSITIVE 225 57 34 198 178 NC_002967:TDE1650|5end_ABC_transporter,_ATP-binding_protein_1698117..1698347_NEGATIVE 221 80 33 66 25 NC_002967:TDE1519|5end_hypothetical_protein_1565601..1565831_POSITIVE 220 55 21 199 170 NC_002967:TDE1681|5end_V-type_ATP_synthase_subunit_D_1733537..1733767_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 109 79 93 62 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 237 47 14 132 94 NC_002967:TDE1995|3end_magnesium_chelatase_family_protein_2014244..2014394_POSITIVE 235 100 52 60 20 NC_002967:TDE1388|3end_hypothetical_protein_1428312..1428462_POSITIVE 229 100 64 41 1 NC_002967:TDE2013|3end_hypothetical_protein_2034359..2034509_NEGATIVE 226 55 12 127 90 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 224 47 5 51 3 NC_002967:TDE0862|3end_hypothetical_protein_884126..884276_POSITIVE 217 62 38 46 13 NC_002967:TDE0923|3end_ABC_transporter,_ATP-binding/permease_protein_943920..944070_NEGATIVE 214 56 33 145 114 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 211 99 54 62 12 NC_002967:TDE2328|3end_efflux_pump_component_MtrF_2366364..2366514_POSITIVE 208 56 21 81 48 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 207 99 64 89 61 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 205 58 20 70 40 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 202 56 20 65 34 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 202 100 53 133 78 NC_002967:TDE2204|3end_Na+/H+_antiporter_family_protein_2242550..2242700_POSITIVE 202 52 25 37 14 NC_002967:TDE1429|3end_glycosyl_transferase,_group_2_family_protein_1473507..1473657_POSITIVE 200 55 16 139 93 NC_002967:TDE1887|3end_TPR_domain_protein_1908492..1908642_NEGATIVE 199 57 35 149 122 NC_002967:TDE0113|3end_Tpl_protein_133609..133759_POSITIVE 198 62 21 42 7 NC_002967:TDE2568|3end_thiamine_biosynthesis_protein_ThiI_2596385..2596535_POSITIVE 197 57 21 53 5 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 197 57 16 69 31 NC_002967:TDE1134|3end_hypothetical_protein_1165062..1165212_NEGATIVE