Origin IGS: agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actctaggctcctgtaatccttaaatttattttttaaatctttcacatagtctatgtcttatacgatattatgtcaatcggcggtcaaaggcttttgactaagattaaaaaagatagtataataaact Mask Tandem Repeat Region ================================================ agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt Find is-nt database================================================ Query_seq: TDE0646:TDE0647|TDE0646:TDE0647:hypothetical protein:chemotaxis protein methyltransferase:<-->:681956..682083 128 agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0646:TDE0647|TDE0646:TDE0647:hypothetical protein:chemotaxis protein methyltransferase:<-->:681956..682083 128 agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0646:TDE0647|TDE0646:TDE0647:hypothetical protein:chemotaxis protein methyltransferase:<-->:681956..682083 128 agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 2 End: 91 . N I I S D K K I K T L L R Q G G I S M I D Y L V Y V I H F M ..................................... agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt 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: 87 Start: 6 End: 35 .....TTTGACTAAGATTAAAAAAGATAGTATAAT............................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 51 End: 80 ..................................................ATTGACATAATATCGTATAAGACATAGACT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0646:TDE0647|TDE0646:TDE0647:hypothetical protein:chemotaxis protein methyltransferase:<-->:681956..682083 128 agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_002967_TDE0646_TDE0647|hypothetical protein:chemotaxis protein methyltransferase|NEGATIVE:POSITIVE|[681956,682083]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt agtttattatactatcttttttaatcttagtcaaaagcctttgaccgccgattgacataatatcgtataagacatagactatgtgaaagatttaaaaaataaatttaaggattacaggagcctagagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUAUUAUACUAUCUUUUUUAAUCUUAGUCAAAAGCCUUUGACCGCCGAUUGACAUAAUAUCGUAUAAGACAUAGACUAUGUGAAAGAUUUAAAAAAUAAAUUUAAGGAUUACAGGAGCCUAGAGU .(((..((((((.((.((..((((((...((((((....))))))....))))))...)).)).))))))))).(((.((.(((((....((((((.......))))))..)))))..)).))).... (-17.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUAGGCUCCUGUAAUCCUUAAAUUUAUUUUUUAAAUCUUUCACAUAGUCUAUGUCUUAUACGAUAUUAUGUCAAUCGGCGGUCAAAGGCUUUUGACUAAGAUUAAAAAAGAUAGUAUAAUAAACU ....(((....)))............(((((((((.(((((((((...(((((.((.((....((((.........))))..)).)).)))))..)))..))))))..)))))))))........... (-18.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 864 80 31 171 122 NC_002967:TDE0646|5end_hypothetical_protein_681865..682095_NEGATIVE 263 67 30 198 164 NC_002967:TDE1527|5end_hypothetical_protein_1570804..1571034_POSITIVE 249 80 31 226 165 NC_002967:TDE1735|5end_hypothetical_protein_1789802..1790032_POSITIVE 245 77 37 228 191 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 245 51 30 222 200 NC_002967:TDE0208|5end_glycerate_kinase_242982..243212_POSITIVE 241 51 11 182 142 NC_002967:TDE1311|5end_ABC_transporter,_ATP-binding/permease_protein_1347371..1347601_POSITIVE 240 73 31 135 99 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 238 68 38 130 98 NC_002967:TDE2636|5end_hypothetical_protein_2676070..2676300_POSITIVE 235 70 21 220 160 NC_002967:TDE2553|5end_lysyl-tRNA_synthetase_2580633..2580863_NEGATIVE 234 60 16 169 115 NC_002967:TDE2623|5end_hypothetical_protein_2664324..2664554_NEGATIVE 234 80 37 212 164 NC_002967:TDE2573|5end_glucose-6-phosphate_isomerase_2598802..2599032_POSITIVE 234 48 17 159 128 NC_002967:TDE2474|5end_acetyltransferase,_GNAT_family_2497096..2497326_NEGATIVE 231 78 37 54 5 NC_002967:TDE0189|5end_hypothetical_protein_226460..226690_NEGATIVE 226 53 11 68 35 NC_002967:TDE0530|5end_hypothetical_protein_574363..574593_POSITIVE 225 76 35 216 173 NC_002967:TDE1733|5end_methionine_aminopeptidase,_type_I_1787853..1788083_POSITIVE 225 73 31 148 91 NC_002967:TDE0281|5end_hypothetical_protein_310490..310720_NEGATIVE 223 50 7 123 88 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 220 78 31 137 96 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 218 51 31 188 167 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 217 53 29 203 177 NC_002967:TDE2112|5end_hypothetical_protein_2138669..2138899_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 88 44 70 34 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 246 57 13 149 100 NC_002967:TDE1017|3end_exodeoxyribonuclease_VII,_large_subunit_1049211..1049361_POSITIVE 244 71 39 49 9 NC_002967:TDE1620|3end_hypothetical_protein_1666959..1667109_NEGATIVE 241 51 11 71 31 NC_002967:TDE1310|3end_modulator_of_DNA_gyrase_family_protein_1347340..1347490_POSITIVE 238 60 24 99 60 NC_002967:TDE2715|3end_hypothetical_protein_2772936..2773086_POSITIVE 234 48 17 125 94 NC_002967:TDE2475|3end_MATE_efflux_family_protein_2497130..2497280_NEGATIVE 223 50 7 121 86 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 220 78 31 132 91 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 220 72 36 47 9 NC_002967:TDE1174|3end_hypothetical_protein_1202651..1202801_NEGATIVE 214 54 17 137 103 NC_002967:TDE1064|3end_hypothetical_protein_1093031..1093181_NEGATIVE 213 59 27 70 31 NC_002967:TDE2268|3end_hypothetical_protein_2304822..2304972_NEGATIVE 212 57 12 55 16 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 212 116 72 151 106 NC_002967:TDE1853|3end_hypothetical_protein_1881966..1882116_NEGATIVE 212 109 63 67 11 NC_002967:TDE1698|3end_serine/threonine_protein_phosphatase_family_protein_1756336..1756486_NEGATIVE 211 80 35 117 68 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 210 80 35 142 101 NC_002967:TDE0759|3end_hypothetical_protein_799128..799278_NEGATIVE 209 74 31 62 7 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 208 90 45 115 64 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE 206 51 30 126 106 NC_002967:TDE1947|3end_ABC_transporter,_permease_protein_1962517..1962667_NEGATIVE 205 48 2 126 85 NC_002967:TDE0670|3end_ATP-dependent_protease_La_710393..710543_POSITIVE