Origin IGS: gtataaaaaataataaaaattcggaaaaaaatcaataatctaatcttaaaatatcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaagaactcctagaaaatgtatttgcctatgtaaaaaggcagtttcggcattatatatgatgattaaaaatatgacaagttggctttcttcaaattcgtctgatattttaagattagattattgatttttttccgaatttttattattttttatac Mask Tandem Repeat Region ================================================ gtataaaaaataataaaaattcggaaaaaaatcaataatctaatcttaaaatatcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc Find is-nt database================================================ Query_seq: TDE2327:TDE2328|TDE2327:TDE2328:ATP-dependent Clp protease, ATP-binding subunit ClpB:efflux pump component MtrF:<-->:2364718..2364873 156 gtataaaaaataataaaaattcggaaaaaaatcaataatctaatcttaaaatatcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2327:TDE2328|TDE2327:TDE2328:ATP-dependent Clp protease, ATP-binding subunit ClpB:efflux pump component MtrF:<-->:2364718..2364873 156 gtataaaaaataataaaaattcggaaaaaaatcaataatctaatcttaaaatatcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2327:TDE2328|TDE2327:TDE2328:ATP-dependent Clp protease, ATP-binding subunit ClpB:efflux pump component MtrF:<-->:2364718..2364873 156 gtataaaaaataataaaaattcggaaaaaaatcaataatctaatcttaaaatatcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtataaaaaataataaaaattcggaaaaaaatcaataatctaatcttaaaatatcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 51 End: 155 .................................................. M S D E F E E S Q L V I F L I I I Y N A E T A F L H R Q I H F L G V L . Protein_Len: 34 Strand: - Start: 35 End: 136 .................................. Y D L R L I D S S N S S L W S T M N K I M M Y L A S V A K K C L C M .................... gtataaaaaataataaaaattcggaaaaaaatcaataatctaatcttaaaatatcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc 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: 89 Start: 78 End: 107 .............................................................................CTTGTCATATTTTTAATCATCATATATAAT................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 7 End: 36 ......ATTGATTTTTTTCCGAATTTTTATTATTTT........................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtataaaaaataataaaaattcggaaaaaaatcaataatctaatcttaaaatatcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2327:TDE2328|TDE2327:TDE2328:ATP-dependent Clp protease, ATP-binding subunit ClpB:efflux pump component MtrF:<-->:2364718..2364873 156 gtataaaaaataataaaaattcggaaaaaaatcaataatctaatcttaaaatatcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc Intra-Species Hit: Count: 1 Min: 54 Max: 156 Len: 103 Subject: NC_002967_TDE2327_TDE2328|ATP-dependent Clp protease, ATP-binding subunit ClpB:efflux pump component MtrF|NEGATIVE:POSITIVE|[2364718,2364873]|156 HSP 1 e-value: 6.0E-52 bit: 204.0 Len: 103 Query Start:54 Query End:156 Subject Strand: POSITIVE Subject Start: 54 Subject End: 156 .....................................................tcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc .....................................................tcagacgaatttgaagaaagccaacttgtcatatttttaatcatcatatataatgccgaaactgcctttttacataggcaaatacattttctaggagttcttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAGACGAAUUUGAAGAAAGCCAACUUGUCAUAUUUUUAAUCAUCAUAUAUAAUGCCGAAACUGCCUUUUUACAUAGGCAAAUACAUUUUCUAGGAGUUCUUC ............((((((..((..................((..(((.....)))..))...(((((........))))).............))..)))))) (-15.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGAACUCCUAGAAAAUGUAUUUGCCUAUGUAAAAAGGCAGUUUCGGCAUUAUAUAUGAUGAUUAAAAAUAUGACAAGUUGGCUUUCUUCAAAUUCGUCUGA ((((((..((.....(((((..((((((........)))))).....))))).(((((...........))))).......))..))))))............ (-18.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 763 70 21 214 165 NC_002967:TDE2327|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpB_2364627..2364857_NEGATIVE 307 100 55 89 39 NC_002967:TDE1999|5end_DNA_polymerase_III_domain_protein_2017063..2017293_POSITIVE 288 47 4 172 125 NC_002967:TDE0084|5end_phosphoenolpyruvate-protein_phosphotransferase_97455..97685_NEGATIVE 262 62 21 119 77 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 224 93 56 90 48 NC_002967:TDE0607|5end_ParA_family_ATPase_644880..645110_NEGATIVE 214 99 56 77 45 NC_002967:TDE0760|5end_hypothetical_protein_799436..799666_POSITIVE 212 91 54 129 94 NC_002967:TDE0397|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_446777..447007_POSITIVE 212 100 52 231 172 NC_002967:TDE0060|5end_hypothetical_protein_67838..68068_NEGATIVE 210 67 24 87 48 NC_002967:TDE1922|5end_hypothetical_protein_1941485..1941715_NEGATIVE 210 67 22 173 130 NC_002967:TDE1350|5end_rod_shape-determining_protein_MreC_1390327..1390557_POSITIVE 208 79 35 112 74 NC_002967:TDE2662|5end_lipoprotein,_putative_2698650..2698880_NEGATIVE 207 100 51 108 67 NC_002967:TDE1541|5end_metallo-beta-lactamase_family_protein_1584898..1585128_POSITIVE 206 46 10 83 48 NC_002967:TDE1293|5end_TldD/PmbA_family_protein_1332003..1332233_NEGATIVE 206 100 52 60 10 NC_002967:TDE1079|5end_DNA-binding_protein/PTS_system,_IIA_component_1111120..1111350_POSITIVE 204 87 46 142 96 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 201 100 55 207 161 NC_002967:TDE1349|5end_rod_shape-determining_protein_MreB_1389286..1389516_POSITIVE 197 99 55 77 15 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 197 79 31 200 157 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 196 96 54 112 74 NC_002967:TDE2181|5end_PAP2_family_protein_2213035..2213265_NEGATIVE 196 99 54 131 74 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 100 55 89 39 NC_002967:TDE1998|3end_phosphohexose_mutase_family_protein_2017143..2017293_POSITIVE 262 62 21 107 65 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 261 68 21 54 3 NC_002967:TDE2214|3end_hypothetical_protein_2253465..2253615_POSITIVE 224 47 16 31 1 NC_002967:TDE0085|3end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_97596..97746_NEGATIVE 219 80 55 149 110 NC_002967:TDE1434|3end_hypothetical_protein_1478238..1478388_NEGATIVE 218 99 55 62 12 NC_002967:TDE0320|3end_CBS_domain_protein_352480..352630_NEGATIVE 212 91 54 132 97 NC_002967:TDE0396|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_446860..447010_POSITIVE 210 67 24 59 20 NC_002967:TDE1923|3end_hypothetical_protein_1941513..1941663_NEGATIVE 208 79 35 146 108 NC_002967:TDE2663|3end_isoleucyl-tRNA_synthetase_2698616..2698766_NEGATIVE 207 100 51 78 37 NC_002967:TDE1540|3end_hypothetical_protein_1584948..1585098_POSITIVE 197 99 55 84 22 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 197 82 54 83 61 NC_002967:TDE1902|3end_hypothetical_protein_1922377..1922527_NEGATIVE 196 69 53 32 14 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 196 96 54 112 74 NC_002967:TDE2182|3end_hypothetical_protein_2213035..2213185_NEGATIVE 196 99 54 67 10 NC_002967:TDE0691|3end_ABC_transporter,_ATP-binding/permease_protein_729728..729878_POSITIVE 193 78 41 99 53 NC_002967:TDE2490|3end_primosomal_protein_N'_2512703..2512853_NEGATIVE 193 99 54 71 12 NC_002967:TDE2418|3end_hypothetical_protein_2443330..2443480_NEGATIVE 189 99 54 133 92 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 189 66 28 144 98 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 188 79 40 135 87 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE