Origin IGS: ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattatagattataacataaaagtcaaaataaaacaccatattttgactgtataacctctgtattttttttagaatatatgttaatatatgattaagttttgtggataacttttttattgctgtataaccagtaataaagtgtttataattttactgacttataaatattttaattccatatccaatatagaattaagtaacttatcaacaaattcacatggcttactactataactactaattattataaaagatataaggagaaaaaa Mask Tandem Repeat Region ================================================ ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt Find is-nt database================================================ Query_seq: TDE0231:TDE0232|TDE0231:TDE0232:DNA polymerase III, beta subunit:appr-1-p processing enzyme domain protein:<-->:265084..265353 270 ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0231:TDE0232|TDE0231:TDE0232:DNA polymerase III, beta subunit:appr-1-p processing enzyme domain protein:<-->:265084..265353 270 ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0231:TDE0232|TDE0231:TDE0232:DNA polymerase III, beta subunit:appr-1-p processing enzyme domain protein:<-->:265084..265353 270 ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 13 End: 108 ............ M S F I I I S S Y S S K P C E F V D K L L N S I L D M E L K Y L .................................................................................................................................................................. Protein_Len: 45 Strand: + Start: 135 End: 269 ...................................................................................................................................... M T G Y T A I K K L S T K L N H I L T Y I L K K I Q R L Y S Q N M V F Y F D F Y V I I Y N . Protein_Len: 36 Strand: - Start: 39 End: 146 ...................................... L L L G H S N T S L N S L E I N S I S N F Y K Y T L L I I F V K N S T M ............................................................................................................................ ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt 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: 81 Start: 233 End: 262 ........................................................................................................................................................................................................................................GGTGTTTTATTTTGACTTTTATGTTATAAT........ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 68 HP_score: -4.9 Tail_Score: -4.75289 Start: 223 End: 248 Full_Region: TACAGAGGTTATACA GTCAAAATA TGGTGTTT TATTTTGAC TTTTATGTTATAATC ..............................................................................................................................................................................................................................GTCAAAATATGGTGTTTTATTTTGAC...................... Find igs database================================================ Query_seq: TDE0231:TDE0232|TDE0231:TDE0232:DNA polymerase III, beta subunit:appr-1-p processing enzyme domain protein:<-->:265084..265353 270 ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt Intra-Species Hit: Count: 1 Min: 1 Max: 270 Len: 270 Subject: NC_002967_TDE0231_TDE0232|DNA polymerase III, beta subunit:appr-1-p processing enzyme domain protein|NEGATIVE:POSITIVE|[265084,265353]|270 HSP 1 e-value: 1.0E-137 bit: 488.0 Len: 270 Query Start:1 Query End:270 Subject Strand: POSITIVE Subject Start: 1 Subject End: 270 ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctnnnnnnnntacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt ttttttctccttatatcttttataataattagtagttatagtagtaagccatgtgaatttgttgataagttacttaattctatattggatatggaattaaaatatttataagtcagtaaaattataaacactttattactggttatacagcaataaaaaagttatccacaaaacttaatcatatattaacatatattctaaaaaaaatacagaggttatacagtcaaaatatggtgttttattttgacttttatgttataatctataatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUCUCCUUAUAUCUUUUAUAAUAAUUAGUAGUUAUAGUAGUAAGCCAUGUGAAUUUGUUGAUAAGUUACUUAAUUCUAUAUUGGAUAUGGAAUUAAAAUAUUUAUAAGUCAGUAAAAUUAUAAACACUUUAUUACUGGUUAUACAGCAAUAAAAAAGUUAUCCACAAAACUUAAUCAUAUAUUAACAUAUAUUCUAAAAAAAAUACAGAGGUUAUACAGUCAAAAUAUGGUGUUUUAUUUUGACUUUUAUGUUAUAAUCUAUAAUU ..........(((((....((((((((................(((((((.((((..(((((.(((((.((..((((((((((((...))))))))))))....(((((((..........)))))))...((((((.(((......))).)))))).)).))))).)))))........((((((....))))))...........))))..)))).))).(((((((((........))))))))).....))))))))..))))).. (-45.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUAGAUUAUAACAUAAAAGUCAAAAUAAAACACCAUAUUUUGACUGUAUAACCUCUGUAUUUUUUUUAGAAUAUAUGUUAAUAUAUGAUUAAGUUUUGUGGAUAACUUUUUUAUUGCUGUAUAACCAGUAAUAAAGUGUUUAUAAUUUUACUGACUUAUAAAUAUUUUAAUUCCAUAUCCAAUAUAGAAUUAAGUAACUUAUCAACAAAUUCACAUGGCUUACUACUAUAACUACUAAUUAUUAUAAAAGAUAUAAGGAGAAAAAA .....................((((((((((........)))))))))).......((((.(((.(((((((.((((...((...((((....(((((..(((((((......((((((((((......))))))))))((((((((((.((....)).))))))))))((((((((.((((...)))).))))))))..............)))))))..)))))....))))...))....)))).))))))).))).))))...... (-50.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 742 90 41 181 132 NC_002967:TDE0231|5end_DNA_polymerase_III,_beta_subunit_264993..265223_NEGATIVE 225 99 53 123 78 NC_002967:TDE1028|5end_hypothetical_protein_1058444..1058674_POSITIVE 224 72 32 164 124 NC_002967:TDE2540|5end_lipoprotein,_putative_2567981..2568211_NEGATIVE 220 250 206 228 177 NC_002967:TDE0457|5end_hypothetical_protein_513525..513755_POSITIVE 208 252 218 175 145 NC_002967:TDE2686|5end_flagellar_biosynthetic_protein_FlhF_2727125..2727355_NEGATIVE 198 173 135 179 141 NC_002967:TDE0405|5end_major_outer_sheath_protein_455470..455700_POSITIVE 196 71 32 188 152 NC_002967:TDE1717|5end_hypothetical_protein_1771431..1771661_POSITIVE 195 258 214 95 59 NC_002967:TDE2009|5end_hypothetical_protein_2030382..2030612_POSITIVE 194 46 1 132 95 NC_002967:TDE1102|5end_hypothetical_protein_1136175..1136405_NEGATIVE 192 167 135 167 131 NC_002967:TDE2211|5end_hypothetical_protein_2251316..2251546_NEGATIVE 189 245 205 105 59 NC_002967:TDE0866|5end_hypothetical_protein_887614..887844_POSITIVE 188 249 209 198 151 NC_002967:TDE1754|5end_desulfoferrodoxin/neelaredoxin_1807023..1807253_NEGATIVE 188 90 47 56 20 NC_002967:TDE0766|5end_30S_ribosomal_protein_S10_805984..806214_POSITIVE 186 174 136 43 1 NC_002967:TDE1660|5end_leucine_Rich_Repeat_domain_protein_1715266..1715496_NEGATIVE 186 64 27 69 31 NC_002967:TDE0554|5end_hypothetical_protein_590968..591198_NEGATIVE 185 229 181 66 21 NC_002967:TDE2022|5end_YD_repeat_protein_2049222..2049452_NEGATIVE 184 249 211 155 113 NC_002967:TDE2607|5end_hypothetical_protein_2648586..2648816_POSITIVE 183 255 212 215 172 NC_002967:TDE0915|5end_hypothetical_protein_933320..933550_NEGATIVE 181 50 6 141 99 NC_002967:TDE2361|5end_high-affinity_branched_chain_amino_acid_ABC_transporter,_amino_acid-binding_protein_2396966..2397196_NEGATIVE 181 27 6 118 98 NC_002967:TDE0186|5end_hypothetical_protein_223698..223928_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 76 43 97 63 NC_002967:TDE0588|3end_histidine_ammonia-lyase_628053..628203_POSITIVE 229 80 32 99 48 NC_002967:TDE0160|3end_hypothetical_protein_187145..187295_NEGATIVE 208 252 218 104 74 NC_002967:TDE2687|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_2727196..2727346_NEGATIVE 198 240 194 121 70 NC_002967:TDE1562|3end_hypothetical_protein_1615645..1615795_POSITIVE 195 258 214 48 12 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 186 98 52 70 20 NC_002967:TDE1763|3end_hypothetical_protein_1810876..1811026_NEGATIVE 186 64 27 54 16 NC_002967:TDE0555|3end_hypothetical_protein_590983..591133_NEGATIVE 181 50 6 144 102 NC_002967:TDE2362|3end_hypothetical_protein_2396963..2397113_NEGATIVE 180 270 230 82 36 NC_002967:TDE1900|3end_hypothetical_protein_1921458..1921608_POSITIVE 180 258 211 151 112 NC_002967:TDE1755|3end_hypothetical_protein_1807187..1807337_POSITIVE 179 89 46 109 60 NC_002967:TDE1910|3end_1-deoxy-D-xylulose-5-phosphate_synthase_1926876..1927026_NEGATIVE 177 21 1 44 24 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 173 80 32 101 57 NC_002967:TDE1422|3end_glycosyl_transferase,_group_2_family_protein_1466850..1467000_POSITIVE 172 240 211 63 35 NC_002967:TDE2497|3end_hypothetical_protein_2521982..2522132_NEGATIVE 171 77 37 70 31 NC_002967:TDE2773|3end_hypothetical_protein_2825823..2825973_NEGATIVE 170 240 194 121 70 NC_002967:TDE1568|3end_hypothetical_protein_1619827..1619977_POSITIVE 169 88 49 140 108 NC_002967:TDE1457|3end_hypothetical_protein_1504739..1504889_NEGATIVE 168 247 214 80 43 NC_002967:TDE1112|3end_adenylate_kinase_1147627..1147777_POSITIVE 167 89 47 134 98 NC_002967:TDE2133|3end_cobalt_transport_protein,_putative_2163529..2163679_NEGATIVE 167 257 211 97 46 NC_002967:TDE2043|3end_signal_recognition_particle-docking_protein_FtsY_2072180..2072330_NEGATIVE