Origin IGS: tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgctattttttttca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaaaaaaaatagcatctttttcctataagattatgggcagggaatatccaaaaattgatttccgcgccccacttgggtacttgcattataagcctcaatgtagtataataagtatgattttacatacttattatactattctgggaggtataaa Mask Tandem Repeat Region ================================================ tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgctattttttttca Find is-nt database================================================ Query_seq: TDE0344:TDE0345|TDE0344:TDE0345:transcriptional regulator, AbrB family:methyl-accepting chemotaxis protein DmcB:<-<-:385679..385833 155 tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgctattttttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0344:TDE0345|TDE0344:TDE0345:transcriptional regulator, AbrB family:methyl-accepting chemotaxis protein DmcB:<-<-:385679..385833 155 tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgctattttttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0344:TDE0345|TDE0344:TDE0345:transcriptional regulator, AbrB family:methyl-accepting chemotaxis protein DmcB:<-<-:385679..385833 155 tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgctattttttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgctattttttttca Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 57 End: 155 ........................................................ M R L I M Q V P K W G A E I N F W I F P A H N L I G K R C Y F F S Protein_Len: 48 Strand: - Start: 3 End: 146 .. I G G L I T Y Y T H L I M S I I S C Q P K Y H L Y G L P A R F D I K P Y E R G M I K Y S F S A M ......... tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgctattttttttca 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: 86 Start: 46 End: 75 .............................................CTTGCATTATAAGCCTCAATGTAGTATAAT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgctattttttttca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -14.6 Tail_Score: -3.30771 Start: 17 End: 54 Full_Region: ttataagcctcaatg tagtataataagtatg atttta catacttattatacta ttctgggaggtataa ................tagtataataagtatgattttacatacttattatacta..................................................................................................... TransTerm Strand: - Conf: 62 HP_score: -6.0 Tail_Score: -3.54771 Start: 25 End: 46 Full_Region: ctcaatgtagtataa taagtatg atttta catactta ttatactattctggg ........................taagtatgattttacatactta............................................................................................................. Find igs database================================================ Query_seq: TDE0344:TDE0345|TDE0344:TDE0345:transcriptional regulator, AbrB family:methyl-accepting chemotaxis protein DmcB:<-<-:385679..385833 155 tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgctattttttttca Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002967_TDE0344_TDE0345|transcriptional regulator, AbrB family:methyl-accepting chemotaxis protein DmcB|NEGATIVE:NEGATIVE|[385679,385833]|155 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgcta.......... tttatacctcccagaatagtataataagtatgtaaaatcatacttattatactacattgaggcttataatgcaagtacccaagtggggcgcggaaatcaatttttggatattccctgcccataatcttataggaaaaagatgcta.......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUACCUCCCAGAAUAGUAUAAUAAGUAUGUAAAAUCAUACUUAUUAUACUACAUUGAGGCUUAUAAUGCAAGUACCCAAGUGGGGCGCGGAAAUCAAUUUUUGGAUAUUCCCUGCCCAUAAUCUUAUAGGAAAAAGAUGCUA .(((((((((......((((((((((((((((......))))))))))))))))....))))..))))).((.............(((((.(((((((........))).)))).)))))...(((((........))))))).. (-41.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAUCUUUUUCCUAUAAGAUUAUGGGCAGGGAAUAUCCAAAAAUUGAUUUCCGCGCCCCACUUGGGUACUUGCAUUAUAAGCCUCAAUGUAGUAUAAUAAGUAUGAUUUUACAUACUUAUUAUACUAUUCUGGGAGGUAUAAA ..(((.......((((.........((((.((((((............))))))..))))....))))....))).......(((((...(((((((((((((((((......))))))))))))))))).....)))))..... (-44.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1000 120 71 211 162 NC_002967:TDE0344|5end_transcriptional_regulator,_AbrB_family_385588..385818_NEGATIVE 341 94 58 172 133 NC_002967:TDE1730|5end_glycosyl_hydrolase,_family_2_1785545..1785775_NEGATIVE 321 120 73 59 16 NC_002967:TDE0607|5end_ParA_family_ATPase_644880..645110_NEGATIVE 316 89 46 159 116 NC_002967:TDE1637|5end_DNA_polymerase_I_1686072..1686302_POSITIVE 274 94 55 43 3 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 272 110 61 230 171 NC_002967:TDE1091|5end_hypothetical_protein_1123775..1124005_NEGATIVE 266 119 79 60 19 NC_002967:TDE1881|5end_methyltransferase,_putative_1903000..1903230_POSITIVE 266 110 69 223 165 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 263 119 74 172 115 NC_002967:TDE0844|5end_pyruvate_phosphate_dikinase,_putative_864886..865116_POSITIVE 262 127 89 60 7 NC_002967:TDE0949|5end_enolase_972010..972240_POSITIVE 262 101 61 79 37 NC_002967:TDE0473|5end_heavy_metal_translocating_P-type_ATPase_528621..528851_POSITIVE 259 107 61 227 182 NC_002967:TDE1909|5end_conserved_hypothetical_protein_TIGR00159_1926872..1927102_NEGATIVE 258 89 43 181 134 NC_002967:TDE1075|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1105962..1106192_POSITIVE 256 118 73 73 39 NC_002967:TDE1375|5end_pantetheine-phosphate_adenylyltransferase_1418081..1418311_POSITIVE 255 95 56 123 68 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 255 115 71 63 28 NC_002967:TDE0360|5end_ABC_transporter,_ATP-binding/permease_protein_405844..406074_NEGATIVE 254 105 61 42 9 NC_002967:TDE2144|5end_hypothetical_protein_2181746..2181976_NEGATIVE 254 127 82 190 148 NC_002967:TDE1695|5end_CoA-substrate-specific_enzyme_activase_domain_protein_1754000..1754230_NEGATIVE 254 100 53 207 164 NC_002967:TDE1026|5end_acyl_carrier_protein_1057302..1057532_POSITIVE 252 118 72 227 193 NC_002967:TDE1772|5end_hypothetical_protein_1815817..1816047_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 133 97 51 7 NC_002967:TDE2460|3end_aminotransferase,_class_V_2487229..2487379_POSITIVE 262 101 61 52 10 NC_002967:TDE0472|3end_hypothetical_protein_528674..528824_POSITIVE 261 95 55 49 2 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 259 118 77 124 77 NC_002967:TDE0440|3end_DNA-binding_protein_496306..496456_POSITIVE 256 120 74 63 26 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 250 93 61 65 27 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 248 120 71 87 21 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 248 93 63 128 98 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE 242 128 83 147 87 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 242 119 83 38 2 NC_002967:TDE1880|3end_hypothetical_protein_1903058..1903208_POSITIVE 242 106 61 44 13 NC_002967:TDE0772|3end_50S_ribosomal_protein_L22_809520..809670_POSITIVE 237 120 81 44 14 NC_002967:TDE1540|3end_hypothetical_protein_1584948..1585098_POSITIVE 236 118 77 149 104 NC_002967:TDE1254|3end_Smr_domain_protein_1289003..1289153_POSITIVE 235 90 41 111 65 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 235 89 41 140 88 NC_002967:TDE0295|3end_DNA_gyrase,_A_subunit_324220..324370_NEGATIVE 234 119 82 53 14 NC_002967:TDE0925|3end_peptidase_T_949132..949282_POSITIVE 231 109 71 71 42 NC_002967:TDE2061|3end_hypothetical_protein_2086779..2086929_NEGATIVE 231 121 81 135 94 NC_002967:TDE1302|3end_hemerythrin_family_protein_1339213..1339363_NEGATIVE 231 130 81 86 36 NC_002967:TDE1040|3end_ribosomal_protein_S15_1068288..1068438_POSITIVE 229 119 78 57 9 NC_002967:TDE2304|3end_hypothetical_protein_2343735..2343885_POSITIVE