Origin IGS: tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcgatcaggtttaaaagttcttaaaatgccgaagaagggaggctctttctgaaagatgaaaggtctccctttgttgtttttttgattagatttaggagaatttgagaaa Mask Tandem Repeat Region ================================================ tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga Find is-nt database================================================ Query_seq: TDE2407:TDE2408|TDE2407:TDE2408:amidophosphoribosyltransferase:hypothetical protein:<-<-:2435198..2435306 109 tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2407:TDE2408|TDE2407:TDE2408:amidophosphoribosyltransferase:hypothetical protein:<-<-:2435198..2435306 109 tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2407:TDE2408|TDE2407:TDE2408:amidophosphoribosyltransferase:hypothetical protein:<-<-:2435198..2435306 109 tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga Predict ORF larger than 30AA ================================================ tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 88 HP_score: -5.3 Tail_Score: -5.64006 Start: 34 End: 80 Full_Region: aagttcttaaaatgc cgaagaagggaggctctttc tgaaagat gaaaggtctccctttgttg tttttttgattagat .................................cgaagaagggaggctctttctgaaagatgaaaggtctccctttgttg............................. TransTerm Strand: - Conf: 82 HP_score: -6.4 Tail_Score: -4.89605 Start: 41 End: 73 Full_Region: taaaatgccgaagaa gggaggctctttc tgaaagat gaaaggtctccc tttgttgtttttttg ........................................gggaggctctttctgaaagatgaaaggtctccc.................................... Find igs database================================================ Query_seq: TDE2407:TDE2408|TDE2407:TDE2408:amidophosphoribosyltransferase:hypothetical protein:<-<-:2435198..2435306 109 tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_002967_TDE2407_TDE2408|amidophosphoribosyltransferase:hypothetic al protein|NEGATIVE:NEGATIVE|[2435198,2435306]|109 HSP 1 e-value: 4.0E-43 bit: 174.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 tttctcaaattctcctaaatctaatcnnnnnnncaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga tttctcaaattctcctaaatctaatcaaaaaaacaacaaagggagacctttcatctttcagaaagagcctcccttcttcggcattttaagaacttttaaacctgatcga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCAAAUUCUCCUAAAUCUAAUCAAAAAAACAACAAAGGGAGACCUUUCAUCUUUCAGAAAGAGCCUCCCUUCUUCGGCAUUUUAAGAACUUUUAAACCUGAUCGA ......................................(((((((.((((((........))))).).)))))))..((((((.((((((....))))))..)).)))) (-17.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGAUCAGGUUUAAAAGUUCUUAAAAUGCCGAAGAAGGGAGGCUCUUUCUGAAAGAUGAAAGGUCUCCCUUUGUUGUUUUUUUGAUUAGAUUUAGGAGAAUUUGAGAAA .................((((((((....(((.((((((((((.(((((........))))))))))))))).))).((((((((......)))))))).)))))))). (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 933 90 41 181 132 NC_002967:TDE2407|5end_amidophosphoribosyltransferase_2435107..2435337_NEGATIVE 325 87 41 72 5 NC_002967:TDE1726|5end_polyA_polymerase_family_protein_1779546..1779776_POSITIVE 293 73 33 102 66 NC_002967:TDE1018|5end_hypothetical_protein_1049227..1049457_POSITIVE 291 79 32 172 129 NC_002967:TDE1576|5end_tRNA-i(6)A37_modification_enzyme_MiaB_1622778..1623008_POSITIVE 284 87 46 144 90 NC_002967:TDE1089|5end_hypothetical_protein_1120944..1121174_NEGATIVE 283 82 52 203 182 NC_002967:TDE0961|5end_DnaJ_domain_protein_983519..983749_POSITIVE 283 82 41 107 63 NC_002967:TDE0128|5end_HAMP_domain/GGDEF_domain/EAL_domain_protein_146240..146470_POSITIVE 278 80 36 50 6 NC_002967:TDE2447|5end_shikimate_kinase_2476928..2477158_NEGATIVE 277 86 45 149 111 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 275 79 32 68 12 NC_002967:TDE0484|5end_methyl-accepting_chemotaxis_protein_541816..542046_NEGATIVE 269 90 47 188 143 NC_002967:TDE0343|5end_hydrolase,_alpha/beta_fold_family_385365..385595_NEGATIVE 260 83 47 135 97 NC_002967:TDE1948|5end_ABC_transporter,_permease_protein_1964551..1964781_NEGATIVE 257 82 41 70 15 NC_002967:TDE0768|5end_50S_ribosomal_protein_L4_806996..807226_POSITIVE 256 92 59 61 22 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 253 80 38 145 115 NC_002967:TDE1910|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1928837..1929067_NEGATIVE 252 82 41 196 157 NC_002967:TDE2118|5end_DNA_topoisomerase_IV_subunit_A_2151265..2151495_NEGATIVE 249 84 64 25 4 NC_002967:TDE2676|5end_threonine_synthase_2714285..2714515_POSITIVE 247 79 40 149 115 NC_002967:TDE1543|5end_conserved_hypothetical_protein_TIGR00247_1586068..1586298_POSITIVE 247 95 67 137 100 NC_002967:TDE1092|5end_hypothetical_protein_1127165..1127395_NEGATIVE 245 80 40 191 143 NC_002967:TDE0658|5end_ABC_transporter,_permease_protein_693554..693784_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 81 42 140 104 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 270 83 43 124 84 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 260 83 47 142 104 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 256 92 59 48 9 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 255 81 42 62 17 NC_002967:TDE1247|3end_hypothetical_protein_1282425..1282575_POSITIVE 253 80 38 39 9 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE 252 82 41 63 24 NC_002967:TDE2119|3end_glycine_reductase_complex_selenoprotein_GrdB2_2151398..2151548_NEGATIVE 247 79 40 129 95 NC_002967:TDE1542|3end_hypothetical_protein_1586128..1586278_POSITIVE 243 69 21 104 66 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 243 81 46 138 101 NC_002967:TDE1280|3end_hypothetical_protein_1315750..1315900_NEGATIVE 241 80 33 57 3 NC_002967:TDE2614|3end_ApbE_family_protein_2656018..2656168_NEGATIVE 241 81 47 67 23 NC_002967:TDE2272|3end_hypothetical_protein_2308980..2309130_NEGATIVE 241 88 60 38 2 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 240 90 41 78 39 NC_002967:TDE1650|3end_ABC_transporter,_ATP-binding_protein_1697377..1697527_NEGATIVE 240 83 43 145 106 NC_002967:TDE0716|3end_CAAX_amino_terminal_protease_family_protein_751744..751894_POSITIVE 239 68 34 66 38 NC_002967:TDE2313|3end_hypothetical_protein_2349506..2349656_NEGATIVE 236 78 36 62 3 NC_002967:TDE2326|3end_cobyric_acid_synthase_CobQ,_putative_2362027..2362177_POSITIVE 236 82 41 48 1 NC_002967:TDE1499|3end_adenylosuccinate_lyase,_putative_1546788..1546938_POSITIVE 236 88 41 128 70 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE 234 82 48 135 98 NC_002967:TDE0470|3end_cell_division_protein_FtsH_526557..526707_POSITIVE