Origin IGS: tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggctttatatttgaatttttaaagatttatattttttttgacttttttgctaatatttcaatattttgattttttatcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct .........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 agcctcctagtagaaattcattattacatatttagacattttcgtcaactagcgataaaaaatcaaaatattgaaatattagcaaaaaagtcaaaaaaaatataaatctttaaaaattcaaatataaagccttgcgttatttacaatatgggtgtagactatttataagacataatctaaaaaatatgttttaggaggaaaaa Mask Tandem Repeat Region ================================================ tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggctttatatttgaatttttaaagatttatattttttttgacttttttgctaatatttcaatattttgattttttatcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct Find is-nt database================================================ Query_seq: TDE0850:TDE0851|TDE0850:TDE0851:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:874636..874838 203 tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggctttatatttgaatttttaaagatttatattttttttgacttttttgctaatatttcaatattttgattttttatcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0850:TDE0851|TDE0850:TDE0851:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:874636..874838 203 tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggctttatatttgaatttttaaagatttatattttttttgacttttttgctaatatttcaatattttgattttttatcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0850:TDE0851|TDE0850:TDE0851:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:874636..874838 203 tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggctttatatttgaatttttaaagatttatattttttttgacttttttgctaatatttcaatattttgattttttatcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggctttatatttgaatttttaaagatttatattttttttgacttttttgctaatatttcaatattttgattttttatcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct Predict ORF larger than 30AA ================================================ tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggctttatatttgaatttttaaagatttatattttttttgacttttttgctaatatttcaatattttgattttttatcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct 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: 155 End: 184 ..........................................................................................................................................................GTTGACGAAAATGTCTAAATATGTAATAAT................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 143 End: 172 ..............................................................................................................................................TTAGACATTTTCGTCAACTAGCGATAAAAA............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggctttatatttgaatttttaaagatttatattttttttgacttttttgctaatatttcaatattttgattttttatcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0850:TDE0851|TDE0850:TDE0851:methyl-accepting chemotaxis protein:hypothetical protein:<-<-:874636..874838 203 tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggctttatatttgaatttttaaagatttatattttttttgacttttttgctaatatttcaatattttgattttttatcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: NC_002967_TDE0850_TDE0851|methyl-accepting chemotaxis protein:hypothetical protein|NEGATIVE:NEGATIVE|[874636,874838]|203 HSP 1 e-value: 4.0E-35 bit: 149.0 Len: 75 Query Start:1 Query End:75 Subject Strand: POSITIVE Subject Start: 1 Subject End: 75 tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggc................................................................................................................................ tttttcctcctaaaacatattttttagattatgtcttataaatagtctacacccatattgtaaataacgcaaggc................................................................................................................................ HSP 2 e-value: 9.0E-24 bit: 111.0 Len: 56 Query Start:148 Query End:203 Subject Strand: POSITIVE Subject Start: 148 Subject End: 203 ...................................................................................................................................................atcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct ...................................................................................................................................................atcgctagttgacgaaaatgtctaaatatgtaataatgaatttctactaggaggct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCCUCCUAAAACAUAUUUUUUAGAUUAUGUCUUAUAAAUAGUCUACACCCAUAUUGUAAAUAACGCAAGGCUUUAUAUUUGAAUUUUUAAAGAUUUAUAUUUUUUUUGACUUUUUUGCUAAUAUUUCAAUAUUUUGAUUUUUUAUCGCUAGUUGACGAAAAUGUCUAAAUAUGUAAUAAUGAAUUUCUACUAGGAGGCU .....(((((((..((((((((..((((((((.........))))))))....((...((((((...(....)..))))))..))...............((((((((.(..(((.....(((((.(..((((....))))..).)))..)).)))..).))))))))..))))))))......(.....)...))))))).. (-33.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCUCCUAGUAGAAAUUCAUUAUUACAUAUUUAGACAUUUUCGUCAACUAGCGAUAAAAAAUCAAAAUAUUGAAAUAUUAGCAAAAAAGUCAAAAAAAAUAUAAAUCUUUAAAAAUUCAAAUAUAAAGCCUUGCGUUAUUUACAAUAUGGGUGUAGACUAUUUAUAAGACAUAAUCUAAAAAAUAUGUUUUAGGAGGAAAAA ..(((((((..............((((((.....(((......))).....................(((((((((((...((((..............................................))))..))))).))))))..))))))..........(((((((..........))))))))))))))..... (-27.85) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 776 80 31 171 122 NC_002967:TDE0850|5end_methyl-accepting_chemotaxis_protein_874545..874775_NEGATIVE 247 158 115 139 97 NC_002967:TDE0567|5end_hypothetical_protein_597853..598083_POSITIVE 246 159 115 140 81 NC_002967:TDE0596|5end_hypothetical_protein_636010..636240_NEGATIVE 220 72 37 93 64 NC_002967:TDE0585|5end_hypothetical_protein_625024..625254_NEGATIVE 210 185 146 159 114 NC_002967:TDE1465|5end_signal_peptidase_I,_putative_1513564..1513794_POSITIVE 206 139 94 98 52 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 206 74 46 155 115 NC_002967:TDE1209|5end_site-specific_recombinase,_phage_integrase_family_1242345..1242575_POSITIVE 203 78 34 138 86 NC_002967:TDE0112|5end_hypothetical_protein_132044..132274_POSITIVE 201 143 107 133 94 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 201 158 111 154 94 NC_002967:TDE0704|5end_SPFH_domain/Band_7_family_protein_739346..739576_NEGATIVE 201 158 113 48 1 NC_002967:TDE0448|5end_deoxyribose-phosphate_aldolase_505796..506026_POSITIVE 199 100 52 141 103 NC_002967:TDE1077|5end_hypothetical_protein_1108395..1108625_POSITIVE 198 76 32 187 144 NC_002967:TDE1580|5end_hypothetical_protein_1629726..1629956_NEGATIVE 197 48 3 108 58 NC_002967:TDE1916|5end_glycerol_kinase_1934767..1934997_NEGATIVE 196 72 32 58 27 NC_002967:TDE0452|5end_hypothetical_protein_510143..510373_NEGATIVE 193 123 81 148 96 NC_002967:TDE1579|5end_fibronectin/fibrinogen-binding_protein,_internal_deletion_1627489..1627719_NEGATIVE 192 85 46 78 42 NC_002967:TDE1213|5end_flagellar_basal_body_rod_protein_1245817..1246047_POSITIVE 191 75 34 121 81 NC_002967:TDE2277|5end_transcriptional_regulator,_Sir2_family_2312680..2312910_POSITIVE 191 135 97 120 86 NC_002967:TDE0820|5end_transcriptional_regulator,_TetR_family_844373..844603_NEGATIVE 190 149 104 141 94 NC_002967:TDE1368|5end_hypothetical_protein_1409795..1410025_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 78 34 57 9 NC_002967:TDE0949|3end_enolase_973391..973541_POSITIVE 247 158 115 142 100 NC_002967:TDE0566|3end_hypothetical_protein_597936..598086_POSITIVE 246 159 115 131 72 NC_002967:TDE0597|3end_hypothetical_protein_636019..636169_NEGATIVE 231 82 52 151 125 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 229 147 107 148 103 NC_002967:TDE2783|3end_methyl-accepting_chemotaxis_protein_2836607..2836757_POSITIVE 225 76 47 37 5 NC_002967:TDE2539|3end_hypothetical_protein_2564274..2564424_NEGATIVE 210 137 91 135 78 NC_002967:TDE0640|3end_methyl-accepting_chemotaxis_protein_674531..674681_NEGATIVE 203 78 34 128 76 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 202 75 31 56 4 NC_002967:TDE2308|3end_hypothetical_protein_2346313..2346463_POSITIVE 197 48 3 111 61 NC_002967:TDE1917|3end_cytidylyltransferase_domain_protein_1934764..1934914_NEGATIVE 196 72 32 58 27 NC_002967:TDE0453|3end_hypothetical_protein_510143..510293_NEGATIVE 195 47 6 47 14 NC_002967:TDE0670|3end_ATP-dependent_protease_La_710393..710543_POSITIVE 193 123 81 148 96 NC_002967:TDE1580|3end_hypothetical_protein_1627489..1627639_NEGATIVE 192 85 46 54 18 NC_002967:TDE1212|3end_flagellar_basal-body_rod_protein_FlgB_1245873..1246023_POSITIVE 190 169 140 112 85 NC_002967:TDE1402|3end_hypothetical_protein_1444515..1444665_POSITIVE 190 149 104 132 85 NC_002967:TDE1369|3end_excinuclease_ABC_subunit_B_1409804..1409954_NEGATIVE 185 170 133 55 23 NC_002967:TDE1179|3end_iron_compound_ABC_transporter,_permease_protein_1207929..1208079_NEGATIVE 182 87 42 62 11 NC_002967:TDE1690|3end_hypothetical_protein_1746583..1746733_NEGATIVE 182 77 49 24 4 NC_002967:TDE0907|3end_hypothetical_protein_925320..925470_POSITIVE 181 47 2 106 59 NC_002967:TDE2216|3end_galactoside_ABC_transporter,_ATP-binding_protein_2255160..2255310_NEGATIVE