Origin IGS: ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatagatagcctcaaactaaatatttatttctcattttaatatattttgtcaaaattatctagtaataaaagaaaaaaaattgaaatcaacacgaatgaaaattcttaattaagatctcaaaaagatattggcaacattattaaaatatattataatataaaa Mask Tandem Repeat Region ================================================ ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata Find is-nt database================================================ Query_seq: TDE1053:TDE1054|TDE1053:TDE1054:lipoprotein, putative:methyl-accepting chemotaxis protein:<-->:1080817..1080979 163 ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1053:TDE1054|TDE1053:TDE1054:lipoprotein, putative:methyl-accepting chemotaxis protein:<-->:1080817..1080979 163 ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1053:TDE1054|TDE1053:TDE1054:lipoprotein, putative:methyl-accepting chemotaxis protein:<-->:1080817..1080979 163 ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 54 End: 143 ..................................................... N L I K M R T S K L K K E K I V L Y N Q C F I N F H S I F M .................... ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata 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: 88 Start: 7 End: 36 ......ATTGGCAACATTATTAAAATATATTATAAT............................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 101 End: 130 ....................................................................................................CTAGATAATTTTGACAAAATATATTAAAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1053:TDE1054|TDE1053:TDE1054:lipoprotein, putative:methyl-accepting chemotaxis protein:<-->:1080817..1080979 163 ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_002967_TDE1053_TDE1054|lipoprotein, putative:methyl-accepting chemotaxis protein|NEGATIVE:POSITIVE|[1080817,1080979]|163 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaannnnnnnncttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata ttttatattataatatattttaataatgttgccaatatctttttgagatcttaattaagaattttcattcgtgttgatttcaattttttttcttttattactagataattttgacaaaatatattaaaatgagaaataaatatttagtttgaggctatctata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUAUUAUAAUAUAUUUUAAUAAUGUUGCCAAUAUCUUUUUGAGAUCUUAAUUAAGAAUUUUCAUUCGUGUUGAUUUCAAUUUUUUUUCUUUUAUUACUAGAUAAUUUUGACAAAAUAUAUUAAAAUGAGAAAUAAAUAUUUAGUUUGAGGCUAUCUAUA ((((.((((.(((((((((((...........((((((.....(((((((((....))))..)))))...))))))...((((..((...(((.........))).))..)))).))))))))))).)))).))))...(((..((((.....))))..))). (-20.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAGAUAGCCUCAAACUAAAUAUUUAUUUCUCAUUUUAAUAUAUUUUGUCAAAAUUAUCUAGUAAUAAAAGAAAAAAAAUUGAAAUCAACACGAAUGAAAAUUCUUAAUUAAGAUCUCAAAAAGAUAUUGGCAACAUUAUUAAAAUAUAUUAUAAUAUAAAA .(((((((.............))))))).....(((((((((....(((((((...(((((...................(((....)))...((((....))))..................))))))))))))...)))))))))................ (-17.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 707 80 31 171 122 NC_002967:TDE1053|5end_lipoprotein,_putative_1080726..1080956_NEGATIVE 245 96 51 103 57 NC_002967:TDE0276|5end_HD_domain_protein_308029..308259_NEGATIVE 221 99 62 117 78 NC_002967:TDE2026|5end_hypothetical_protein_2052502..2052732_NEGATIVE 217 105 71 47 14 NC_002967:TDE0582|5end_hypothetical_protein_620383..620613_POSITIVE 211 69 24 76 37 NC_002967:TDE1675|5end_ribosomal_protein_L9_1729242..1729472_NEGATIVE 208 49 18 231 202 NC_002967:TDE2578|5end_hypothetical_protein_2603154..2603384_NEGATIVE 205 80 36 219 165 NC_002967:TDE1102|5end_hypothetical_protein_1136175..1136405_NEGATIVE 205 77 31 78 15 NC_002967:TDE0477|5end_hypothetical_protein_534277..534507_NEGATIVE 203 80 34 227 183 NC_002967:TDE1449|5end_GTPase_YjeQ_1494352..1494582_POSITIVE 201 108 62 155 104 NC_002967:TDE0581|5end_transglutaminase-like_domain_protein_616620..616850_POSITIVE 198 97 61 118 84 NC_002967:TDE1819|5end_hypothetical_protein_1854151..1854381_NEGATIVE 193 60 25 121 81 NC_002967:TDE2352|5end_flagellar_hook-associated_protein_2387235..2387465_POSITIVE 190 77 31 144 86 NC_002967:TDE1617|5end_hypothetical_protein_1664859..1665089_NEGATIVE 190 77 31 116 76 NC_002967:TDE0832|5end_hypothetical_protein_852549..852779_POSITIVE 190 99 68 56 24 NC_002967:TDE0348|5end_transcriptional_regulator,_TetR_family_390457..390687_POSITIVE 189 103 62 90 40 NC_002967:TDE1626|5end_glycine_cleavage_system_H_protein_1675279..1675509_NEGATIVE 187 76 31 164 119 NC_002967:TDE2096|5end_hypothetical_protein_2123200..2123430_POSITIVE 186 81 48 120 81 NC_002967:TDE0182|5end_ABC_transporter,_ATP-binding_protein_216783..217013_NEGATIVE 183 117 78 125 86 NC_002967:TDE0398|5end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein_447773..448003_POSITIVE 182 67 26 47 8 NC_002967:TDE2170|5end_hypothetical_protein_2201749..2201979_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 208 49 18 97 68 NC_002967:TDE2579|3end_ATP-dependent_DNA_helicase_RecG_2603288..2603438_NEGATIVE 204 160 136 107 84 NC_002967:TDE2716|3end_HAD-superfamily_hydrolase,_subfamily_IA_2773931..2774081_POSITIVE 193 60 25 110 70 NC_002967:TDE2351|3end_hypothetical_protein_2387304..2387454_POSITIVE 186 81 48 120 81 NC_002967:TDE0183|3end_ABC_transporter,_permease_protein_216783..216933_NEGATIVE 183 117 78 106 67 NC_002967:TDE0397|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_447834..447984_POSITIVE 182 88 44 151 107 NC_002967:TDE0580|3end_hypothetical_protein_616716..616866_POSITIVE 180 90 49 121 83 NC_002967:TDE2457|3end_hypothetical_protein_2484698..2484848_NEGATIVE 177 50 19 92 63 NC_002967:TDE1345|3end_DNA_primase_1385306..1385456_POSITIVE 177 79 35 92 54 NC_002967:TDE0014|3end_hypothetical_protein_19487..19637_POSITIVE 172 49 25 124 98 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 171 99 58 79 36 NC_002967:TDE2439|3end_hypothetical_protein_2469270..2469420_NEGATIVE 171 81 55 34 4 NC_002967:TDE1738|3end_M23/M37_peptidase_domain_protein_1791527..1791677_POSITIVE 170 75 31 145 110 NC_002967:TDE0006|3end_Snf2_family_protein_6110..6260_NEGATIVE 169 90 44 100 52 NC_002967:TDE1233|3end_hypothetical_protein_1267609..1267759_POSITIVE 168 61 26 149 116 NC_002967:TDE2091|3end_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_2119626..2119776_POSITIVE 168 80 35 47 10 NC_002967:TDE0554|3end_hypothetical_protein_590339..590489_NEGATIVE 167 100 59 59 25 NC_002967:TDE0008|3end_copper-translocating_P-type_ATPase_13646..13796_POSITIVE 165 156 133 124 98 NC_002967:TDE2212|3end_galactokinase_2251482..2251632_NEGATIVE 165 70 33 140 102 NC_002967:TDE2055|3end_hemin-binding_protein_B_2082558..2082708_NEGATIVE 164 75 31 113 70 NC_002967:TDE0015|3end_lipoprotein,_putative_20544..20694_POSITIVE