Origin IGS: aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt .........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 aaagcattgttattttctatataattttatatataagagctattgaccatctttatttttttttgtaaattgttccccgtttgttatctttaatcgcagtgtgcttctatcttttaacaagattttattctgtaagtatataaaactttagcttacagaataaaatatttaacctacactcaaattaagcacatttcaattattgaatcttttataatatttaggaggataaattt Mask Tandem Repeat Region ================================================ aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt Find is-nt database================================================ Query_seq: TDE0640:TDE0641|TDE0640:TDE0641:methyl-accepting chemotaxis protein:UDP-N-acetylglucosamine 1-carboxyvinyltransferase:<-<-:676856..677091 236 aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0640:TDE0641|TDE0640:TDE0641:methyl-accepting chemotaxis protein:UDP-N-acetylglucosamine 1-carboxyvinyltransferase:<-<-:676856..677091 236 aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0640:TDE0641|TDE0640:TDE0641:methyl-accepting chemotaxis protein:UDP-N-acetylglucosamine 1-carboxyvinyltransferase:<-<-:676856..677091 236 aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 96 End: 194 ............................................................................................... M Y L Q N K I L L K D R S T L R L K I T N G E Q F T K K N K D G Q .......................................... aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt 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: 84 Start: 166 End: 195 .....................................................................................................................................................................ATTGACCATCTTTATTTTTTTTTGTAAATT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -3.4 Tail_Score: -3.62597 Start: 70 End: 116 Full_Region: TGAGTGTAGGTTAAA TATTTTATTCTGTAAGCTAAA GTTTTA TATACTTACAGAATAAAATC TTGTTAAAAGATAGA .....................................................................TATTTTATTCTGTAAGCTAAAGTTTTATATACTTACAGAATAAAATC........................................................................................................................ TransTerm Strand: + Conf: 61 HP_score: -6.0 Tail_Score: -3.39288 Start: 72 End: 114 Full_Region: AGTGTAGGTTAAATA TTTTATTCTGTAAGCTAAA GTTTTA TATACTTACAGAATAAAA TCTTGTTAAAAGATA .......................................................................TTTTATTCTGTAAGCTAAAGTTTTATATACTTACAGAATAAAA.......................................................................................................................... Find igs database================================================ Query_seq: TDE0640:TDE0641|TDE0640:TDE0641:methyl-accepting chemotaxis protein:UDP-N-acetylglucosamine 1-carboxyvinyltransferase:<-<-:676856..677091 236 aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt Intra-Species Hit: Count: 1 Min: 1 Max: 236 Len: 236 Subject: NC_002967_TDE0640_TDE0641|methyl-accepting chemotaxis protein:UDP-N-acetylglucosamine 1-carboxyvinyltransferase|NEGATIVE:NEGATIVE|[676856, 677091]|236 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 236 Query Start:1 Query End:236 Subject Strand: POSITIVE Subject Start: 1 Subject End: 236 aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacnnnnnnnnntaaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt aaatttatcctcctaaatattataaaagattcaataattgaaatgtgcttaatttgagtgtaggttaaatattttattctgtaagctaaagttttatatacttacagaataaaatcttgttaaaagatagaagcacactgcgattaaagataacaaacggggaacaatttacaaaaaaaaataaagatggtcaatagctcttatatataaaattatatagaaaataacaatgcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUAUCCUCCUAAAUAUUAUAAAAGAUUCAAUAAUUGAAAUGUGCUUAAUUUGAGUGUAGGUUAAAUAUUUUAUUCUGUAAGCUAAAGUUUUAUAUACUUACAGAAUAAAAUCUUGUUAAAAGAUAGAAGCACACUGCGAUUAAAGAUAACAAACGGGGAACAAUUUACAAAAAAAAAUAAAGAUGGUCAAUAGCUCUUAUAUAUAAAAUUAUAUAGAAAAUAACAAUGCUUU .......(((((......................((((((...(((((((......................(((((((((((((...............)))))))))))))(((((.....)))))..)))))))...))))))..(....)....)))))...................................(((.(((((......))))))))............... (-35.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCAUUGUUAUUUUCUAUAUAAUUUUAUAUAUAAGAGCUAUUGACCAUCUUUAUUUUUUUUUGUAAAUUGUUCCCCGUUUGUUAUCUUUAAUCGCAGUGUGCUUCUAUCUUUUAACAAGAUUUUAUUCUGUAAGUAUAUAAAACUUUAGCUUACAGAAUAAAAUAUUUAACCUACACUCAAAUUAAGCACAUUUCAAUUAUUGAAUCUUUUAUAAUAUUUAGGAGGAUAAAUUU ((((.((.((((..(((((((((......))))).))))....)))).))))))...............((((((.((...(((((((..((((.(.(((((((((..(((((.....)))))((((((((((((((.............))))))))))))))......................))))))))).).))))..))........)))))....)).)))))).... (-41.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 708 140 91 231 182 NC_002967:TDE0640|5end_methyl-accepting_chemotaxis_protein_676765..676995_NEGATIVE 239 167 124 66 33 NC_002967:TDE0681|5end_protein_export_protein_SecD_720619..720849_NEGATIVE 235 160 122 56 11 NC_002967:TDE1053|5end_lipoprotein,_putative_1080726..1080956_NEGATIVE 228 164 126 35 2 NC_002967:TDE0284|5end_hypothetical_protein_313428..313658_NEGATIVE 218 177 132 56 8 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 218 66 27 136 94 NC_002967:TDE2369|5end_hypothetical_protein_2402292..2402522_POSITIVE 208 75 38 88 43 NC_002967:TDE1816|5end_hypothetical_protein_1851673..1851903_NEGATIVE 206 142 101 138 100 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 202 160 133 64 39 NC_002967:TDE1404|5end_lipoprotein,_putative_1447827..1448057_NEGATIVE 200 162 130 210 166 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 199 157 115 181 143 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 199 144 110 79 48 NC_002967:TDE0123|5end_hypothetical_protein_142223..142453_NEGATIVE 197 87 44 169 125 NC_002967:TDE0789|5end_30S_ribosomal_protein_S13_816562..816792_POSITIVE 194 226 181 206 157 NC_002967:TDE2672|5end_TPR_domain_protein_2710210..2710440_POSITIVE 192 127 85 172 119 NC_002967:TDE1055|5end_MATE_efflux_family_protein_1084331..1084561_NEGATIVE 188 166 127 43 1 NC_002967:TDE1540|5end_hypothetical_protein_1584422..1584652_POSITIVE 188 107 80 111 82 NC_002967:TDE1396|5end_hypothetical_protein_1435661..1435891_POSITIVE 188 125 90 53 15 NC_002967:TDE0206|5end_surface_antigen,_putative_241527..241757_NEGATIVE 188 179 137 71 23 NC_002967:TDE0139|5end_hypothetical_protein_162583..162813_NEGATIVE 187 199 154 83 37 NC_002967:TDE1519|5end_hypothetical_protein_1565601..1565831_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 166 137 125 95 NC_002967:TDE0464|3end_NifU_domain_protein_517948..518098_NEGATIVE 236 163 125 80 45 NC_002967:TDE0004|3end_hypothetical_protein_4997..5147_POSITIVE 218 177 132 56 8 NC_002967:TDE2500|3end_DJ-1_family_protein_2523952..2524102_NEGATIVE 209 162 123 64 31 NC_002967:TDE0238|3end_thioredoxin,_selenocysteine-containing_271783..271933_POSITIVE 206 142 101 64 26 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 202 160 123 68 42 NC_002967:TDE1551|3end_lipoyltransferase_and_lipoate-protein_ligase_family_protein_1594538..1594688_NEGATIVE 202 160 133 29 4 NC_002967:TDE1405|3end_phosphoribosylformylglycinamidine_synthetase_I_1447862..1448012_NEGATIVE 201 163 125 46 4 NC_002967:TDE2075|3end_GGDEF_domain/EAL_domain_protein_2101504..2101654_NEGATIVE 199 144 110 58 27 NC_002967:TDE0124|3end_rhomboid_family_protein_142244..142394_NEGATIVE 195 66 33 35 3 NC_002967:TDE2368|3end_YbaK/prolyl-tRNA_synthetase_domain_protein_2402271..2402421_POSITIVE 192 141 117 25 1 NC_002967:TDE2647|3end_lipoyltransferase_and_lipoate-protein_ligase_family_protein_2686002..2686152_NEGATIVE 189 160 124 38 1 NC_002967:TDE1496|3end_chromosome_partition_protein_SmC,_putative_1543307..1543457_POSITIVE 188 107 80 48 19 NC_002967:TDE1395|3end_glycosyl_hydrolase,_family_57_1435678..1435828_POSITIVE 188 166 130 136 102 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 186 189 147 44 11 NC_002967:TDE2449|3end_hypothetical_protein_2477460..2477610_NEGATIVE 184 164 125 53 20 NC_002967:TDE2144|3end_hypothetical_protein_2180451..2180601_NEGATIVE 183 86 44 149 108 NC_002967:TDE0788|3end_ribosomal_protein_L36_816625..816775_POSITIVE 181 197 158 59 6 NC_002967:TDE1412|3end_sodium/hydrogen_exchanger_family_protein_1455266..1455416_POSITIVE 181 198 152 41 5 NC_002967:TDE1109|3end_decarboxylase,_pyridoxal-dependent_family_1144329..1144479_POSITIVE 181 87 41 130 79 NC_002967:TDE0669|3end_hypothetical_protein_706949..707099_NEGATIVE