Origin IGS: cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat .........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 attttcccctatcttatgcttgacatatattgttaattttaacaaaaagctatatactgttatagcttaaaagaaacattatcatatcgacattagtatactctattgattagtcttgagtcaatagattataattcataaactaatggaaaagaaaaaaaatgccgacaatagattgaggctttcttaatctaaaacggaggaatctaag Mask Tandem Repeat Region ================================================ cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat Find is-nt database================================================ Query_seq: TDE1089:TDE1090|TDE1089:TDE1090:hypothetical protein:threonyl-tRNA synthetase:<-->:1121035..1121245 211 cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1089:TDE1090|TDE1089:TDE1090:hypothetical protein:threonyl-tRNA synthetase:<-->:1121035..1121245 211 cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1089:TDE1090|TDE1089:TDE1090:hypothetical protein:threonyl-tRNA synthetase:<-->:1121035..1121245 211 cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat Predict ORF larger than 30AA ================================================ cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat 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: 154 End: 183 .........................................................................................................................................................ATTGTTAATTTTAACAAAAAGCTATATACT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 49 HP_score: -4.7 Tail_Score: -2.50113 Start: 79 End: 115 Full_Region: tcatatcgacattag tatactctattgatt agtcttg agtcaatagattata attcataaactaatg ..............................................................................tatactctattgattagtcttgagtcaatagattata................................................................................................ TransTerm Strand: - Conf: 56 HP_score: -4.6 Tail_Score: -3.54029 Start: 84 End: 110 Full_Region: tcgacattagtatac tctattgatt agtcttg agtcaataga ttataattcataaac ...................................................................................tctattgattagtcttgagtcaataga..................................................................................................... TransTerm Strand: + Conf: 75 HP_score: -4.2 Tail_Score: -5.10208 Start: 146 End: 163 Full_Region: TAATGTTTCTTTTAA GCTATA ACAGTA TATAGC TTTTTGTTAAAATTA .................................................................................................................................................GCTATAACAGTATATAGC................................................ Find igs database================================================ Query_seq: TDE1089:TDE1090|TDE1089:TDE1090:hypothetical protein:threonyl-tRNA synthetase:<-->:1121035..1121245 211 cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 211 Len: 211 Subject: NC_002967_TDE1089_TDE1090|hypothetical protein:threonyl-tRNA synthetase|NEGATIVE:POSITIVE|[1121035,1121245]|211 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 211 Query Start:1 Query End:211 Subject Strand: POSITIVE Subject Start: 1 Subject End: 211 cttagattcctccgttttagattaagaaagcctcaatctattgtcggcannnnnnnncttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat cttagattcctccgttttagattaagaaagcctcaatctattgtcggcattttttttcttttccattagtttatgaattataatctattgactcaagactaatcaatagagtatactaatgtcgatatgataatgtttcttttaagctataacagtatatagctttttgttaaaattaacaatatatgtcaagcataagataggggaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAGAUUCCUCCGUUUUAGAUUAAGAAAGCCUCAAUCUAUUGUCGGCAUUUUUUUUCUUUUCCAUUAGUUUAUGAAUUAUAAUCUAUUGACUCAAGACUAAUCAAUAGAGUAUACUAAUGUCGAUAUGAUAAUGUUUCUUUUAAGCUAUAACAGUAUAUAGCUUUUUGUUAAAAUUAACAAUAUAUGUCAAGCAUAAGAUAGGGGAAAAU ......((((((..(((((((((.((.....)).))))...((((((((((......((((...((((((((.(((.(((........))).)))))))))))....))))......))))))))))(((((...........((((((((......)))))))).((((((....))))))....)))))....)))))..))))))... (-45.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCCCCUAUCUUAUGCUUGACAUAUAUUGUUAAUUUUAACAAAAAGCUAUAUACUGUUAUAGCUUAAAAGAAACAUUAUCAUAUCGACAUUAGUAUACUCUAUUGAUUAGUCUUGAGUCAAUAGAUUAUAAUUCAUAAACUAAUGGAAAAGAAAAAAAAUGCCGACAAUAGAUUGAGGCUUUCUUAAUCUAAAACGGAGGAAUCUAAG ...((((((..((((....((((((.....))))))..........((((((((......))))))))..))))............(((.((((..((((.((((((((((.......)))))))))).)))).(((((......)))))..........)))).)))...(((((((((.....)))))))))....)).))))...... (-45.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 857 50 1 141 92 NC_002967:TDE1089|5end_hypothetical_protein_1120944..1121174_NEGATIVE 309 44 2 141 91 NC_002967:TDE2336|5end_sodium/dicarboxylate_symporter_family_protein_2373196..2373426_NEGATIVE 264 65 29 90 54 NC_002967:TDE0152|5end_amino_acid_permease_family_protein_174477..174707_NEGATIVE 263 50 6 137 99 NC_002967:TDE0181|5end_methyl-accepting_chemotaxis_protein_215077..215307_NEGATIVE 260 67 29 92 50 NC_002967:TDE0627|5end_co-chaperone_protein_GrpE_659845..660075_POSITIVE 259 50 4 175 135 NC_002967:TDE2407|5end_amidophosphoribosyltransferase_2435107..2435337_NEGATIVE 259 206 162 208 150 NC_002967:TDE1029|5end_Hsp20/alpha_crystallin_family_protein_1058574..1058804_POSITIVE 259 206 162 78 20 NC_002967:TDE1028|5end_hypothetical_protein_1058444..1058674_POSITIVE 257 49 7 131 95 NC_002967:TDE0334|5end_hypothetical_protein_374048..374278_NEGATIVE 256 49 4 204 149 NC_002967:TDE0566|5end_hypothetical_protein_597185..597415_POSITIVE 247 48 9 198 161 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 246 34 7 30 5 NC_002967:TDE2192|5end_threonine_synthase_2227761..2227991_POSITIVE 245 68 29 93 52 NC_002967:TDE2342|5end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2380383..2380613_NEGATIVE 245 48 1 67 18 NC_002967:TDE1727|5end_hypothetical_protein_1781190..1781420_NEGATIVE 241 66 21 91 35 NC_002967:TDE0768|5end_50S_ribosomal_protein_L4_806996..807226_POSITIVE 241 128 85 46 4 NC_002967:TDE0650|5end_hypothetical_protein_684697..684927_POSITIVE 237 47 3 138 91 NC_002967:TDE0437|5end_PBS_lyase_HEAT-like_repeat_domain_protein_493605..493835_NEGATIVE 237 200 161 188 140 NC_002967:TDE0210|5end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_245551..245781_POSITIVE 231 76 31 134 93 NC_002967:TDE2048|5end_hypothetical_protein_2076411..2076641_POSITIVE 231 58 11 149 99 NC_002967:TDE1949|5end_ABC_transporter,_ATP-binding_protein_1966067..1966297_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 65 29 79 43 NC_002967:TDE0153|3end_coenzyme_A_disulfide_reductase,_putative_174488..174638_NEGATIVE 263 50 6 80 42 NC_002967:TDE0182|3end_ABC_transporter,_ATP-binding_protein_215134..215284_NEGATIVE 259 50 4 65 25 NC_002967:TDE2408|3end_hypothetical_protein_2435217..2435367_NEGATIVE 257 49 7 59 23 NC_002967:TDE0335|3end_ribonucleotide-diphosphate_reductase_beta_subunit_374120..374270_NEGATIVE 254 64 24 124 73 NC_002967:TDE0994|3end_hypothetical_protein_1022447..1022597_POSITIVE 247 48 9 73 36 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 245 68 29 93 52 NC_002967:TDE2343|3end_phosphatidate_cytidylyltransferase_2380383..2380533_NEGATIVE 245 50 12 107 73 NC_002967:TDE2293|3end_hypothetical_protein_2329325..2329475_NEGATIVE 241 66 21 76 20 NC_002967:TDE0767|3end_ribosomal_protein_L3_807061..807211_POSITIVE 239 66 30 65 24 NC_002967:TDE1728|3end_hypothetical_protein_1781216..1781366_NEGATIVE 238 63 21 117 78 NC_002967:TDE2118|3end_DNA_topoisomerase_IV_subunit_A_2149154..2149304_NEGATIVE 237 48 11 34 2 NC_002967:TDE1132|3end_chorismate_synthase_1164580..1164730_POSITIVE 237 47 3 71 24 NC_002967:TDE0438|3end_queuine_tRNA-ribosyltransferase_493672..493822_NEGATIVE 237 200 161 118 70 NC_002967:TDE0209|3end_arsenical_pump_membrane_protein,_putative_245561..245711_POSITIVE 233 49 2 118 71 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 230 49 5 61 21 NC_002967:TDE2778|3end_PspC_domain_protein_2829371..2829521_NEGATIVE 229 65 32 143 107 NC_002967:TDE2476|3end_carbamate_kinase_2498521..2498671_NEGATIVE 226 49 19 127 88 NC_002967:TDE2336|3end_sodium/dicarboxylate_symporter_family_protein_2371925..2372075_NEGATIVE 223 66 30 148 98 NC_002967:TDE2313|3end_hypothetical_protein_2349506..2349656_NEGATIVE 221 64 26 82 49 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE