Origin IGS: aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt .........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 aaaaacctccttcttaatgtgaaaattgtatcacaaaaaaagccgcttgtccagtttttattatcggcagtttttagtgaaattcatttccgtgggacatttctatggtgtattgacaaatcaaatttctgcctgttgcaagattttttgaattttgatataataacctgttaaggttatcattgatttgaagacttgtctaacatcttaaatcattatttttttatagattataaaccttaaggagtatgatt Mask Tandem Repeat Region ================================================ aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt Find is-nt database================================================ Query_seq: TDE0408:TDE0409|TDE0408:TDE0409:oxidoreductase, NAD-binding:hypothetical protein:<-->:461463..461716 254 aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0408:TDE0409|TDE0408:TDE0409:oxidoreductase, NAD-binding:hypothetical protein:<-->:461463..461716 254 aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0408:TDE0409|TDE0408:TDE0409:oxidoreductase, NAD-binding:hypothetical protein:<-->:461463..461716 254 aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 68 End: 178 ................................................................... M N D N L N R L L Y Q N S K N L A T G R N L I C Q Y T I E M S H G N E F H ............................................................................ Protein_Len: 41 Strand: - Start: 107 End: 229 .......................................................................................................... F I K C C A S I Q N T L V G Y F H G V S I F K V L F Q R Y Y F S S L R S K K H Y M ......................... Protein_Len: 51 Strand: - Start: 84 End: 236 ................................................................................... C T I I D F N L F D Q L L C F N S K D I C W L F T G R F H I E S F V A S L L F Q V L P K K Q S V I K M .................. aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt 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: 91 Start: 72 End: 101 .......................................................................TTTGATATAATAACCTGTTAAGGTTATCAT......................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 88 Start: 91 End: 120 ..........................................................................................GTTGCAAGATTTTTTGAATTTTGATATAAT...................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 201 End: 230 ........................................................................................................................................................................................................CTGGACAAGCGGCTTTTTTTGTGATACAAT........................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0408:TDE0409|TDE0408:TDE0409:oxidoreductase, NAD-binding:hypothetical protein:<-->:461463..461716 254 aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt Intra-Species Hit: Count: 1 Min: 1 Max: 254 Len: 254 Subject: NC_002967_TDE0408_TDE0409|oxidoreductase, NAD-binding:hypothetical protein|NEGATIVE:POSITIVE|[461463,461716]|254 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 254 Query Start:1 Query End:254 Subject Strand: POSITIVE Subject Start: 1 Subject End: 254 aatcatactccttaaggtttataatctatnnnnnnntaatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggcnnnnnnngtgatacaattttcacattaagaaggaggttttt aatcatactccttaaggtttataatctataaaaaaataatgatttaagatgttagacaagtcttcaaatcaatgataaccttaacaggttattatatcaaaattcaaaaaatcttgcaacaggcagaaatttgatttgtcaatacaccatagaaatgtcccacggaaatgaatttcactaaaaactgccgataataaaaactggacaagcggctttttttgtgatacaattttcacattaagaaggaggttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCAUACUCCUUAAGGUUUAUAAUCUAUAAAAAAAUAAUGAUUUAAGAUGUUAGACAAGUCUUCAAAUCAAUGAUAACCUUAACAGGUUAUUAUAUCAAAAUUCAAAAAAUCUUGCAACAGGCAGAAAUUUGAUUUGUCAAUACACCAUAGAAAUGUCCCACGGAAAUGAAUUUCACUAAAAACUGCCGAUAAUAAAAACUGGACAAGCGGCUUUUUUUGUGAUACAAUUUUCACAUUAAGAAGGAGGUUUUU .......((((((..((..(((..(((((....((((....))))....(((..((((((((.........((((((((((....))))))))))................(((.((.....))))).....))))))))...)))..))))).)))..))..((((((.....((((.(((((..((((...................))))..)))))))))....))))))........))))))...... (-52.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACCUCCUUCUUAAUGUGAAAAUUGUAUCACAAAAAAAGCCGCUUGUCCAGUUUUUAUUAUCGGCAGUUUUUAGUGAAAUUCAUUUCCGUGGGACAUUUCUAUGGUGUAUUGACAAAUCAAAUUUCUGCCUGUUGCAAGAUUUUUUGAAUUUUGAUAUAAUAACCUGUUAAGGUUAUCAUUGAUUUGAAGACUUGUCUAACAUCUUAAAUCAUUAUUUUUUUAUAGAUUAUAAACCUUAAGGAGUAUGAUU ......((((((..(((((.((((.(((..(((((((((..((((...................))))..))))).))))...(((...((((((((...)))))))).....))).....))).))))....(((((((((..((((..((((.(((((.....((((....)))))))))..))))..)))))))))..))))........)))))....((((((...))))))....))))))....... (-47.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 754 90 41 181 132 NC_002967:TDE0408|5end_oxidoreductase,_NAD-binding_461372..461602_NEGATIVE 434 161 121 201 161 NC_002967:TDE2473|5end_30S_ribosomal_protein_S21_2496298..2496528_POSITIVE 399 161 135 172 146 NC_002967:TDE2032|5end_hypothetical_protein_2060169..2060399_NEGATIVE 297 214 176 184 151 NC_002967:TDE2038|5end_UVR_domain_protein_2068201..2068431_NEGATIVE 258 225 186 205 170 NC_002967:TDE2340|5end_FMN-binding_domain_protein_2377855..2378085_NEGATIVE 250 216 179 122 73 NC_002967:TDE2137|5end_hypothetical_protein_2166125..2166355_POSITIVE 248 226 184 175 137 NC_002967:TDE2008|5end_ABC_transporter,_ATP-binding/permease_protein_2028578..2028808_POSITIVE 245 219 185 65 34 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 240 220 172 72 30 NC_002967:TDE0306|5end_signal_peptide_peptidase_SppA_338619..338849_NEGATIVE 238 221 185 64 31 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 236 213 183 53 20 NC_002967:TDE2700|5end_citrate_carrier_protein,_CCS_family_2744396..2744626_POSITIVE 236 245 201 61 1 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 233 50 2 182 129 NC_002967:TDE2591|5end_rhodanese-like_domain_protein_2626570..2626800_POSITIVE 233 50 2 94 41 NC_002967:TDE2590|5end_hypothetical_protein_2626482..2626712_POSITIVE 233 213 171 218 167 NC_002967:TDE0350|5end_MATE_efflux_family_protein_393572..393802_POSITIVE 231 248 208 220 180 NC_002967:TDE1288|5end_CAAX_amino_terminal_protease_family_protein_1326317..1326547_POSITIVE 231 222 186 217 179 NC_002967:TDE0170|5end_nuclease_SbcCD,_D_subunit,_putative_198789..199019_POSITIVE 230 246 208 48 11 NC_002967:TDE1229|5end_hypothetical_protein_1262413..1262643_POSITIVE 229 156 112 169 113 NC_002967:TDE1660|5end_leucine_Rich_Repeat_domain_protein_1715266..1715496_NEGATIVE 228 212 173 40 1 NC_002967:TDE1947|5end_ABC_transporter,_permease_protein_1963449..1963679_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 161 121 49 9 NC_002967:TDE2472|3end_ISTde1,_transposase_2496226..2496376_POSITIVE 425 161 121 49 7 NC_002967:TDE0039|3end_ISTde1,_transposase_44489..44639_NEGATIVE 399 161 135 49 23 NC_002967:TDE2033|3end_ISTde1,_transposase_2060292..2060442_NEGATIVE 261 229 186 148 92 NC_002967:TDE2306|3end_hypothetical_protein_2344138..2344288_NEGATIVE 253 168 123 80 28 NC_002967:TDE0817|3end_histidine_kinase-related_ATPase,_putative_839959..840109_POSITIVE 250 222 187 94 60 NC_002967:TDE0696|3end_hypothetical_protein_734210..734360_POSITIVE 248 229 189 51 3 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 245 219 185 65 34 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 236 213 183 40 7 NC_002967:TDE2699|3end_antigen,_putative_2744463..2744613_POSITIVE 236 228 187 63 20 NC_002967:TDE0138|3end_alkyldihydroxyacetonephosphate_synthase,_putative_160061..160211_POSITIVE 231 248 208 108 68 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE 230 246 208 51 14 NC_002967:TDE1228|3end_pentapeptide_repeat_family_protein_1262496..1262646_POSITIVE 229 229 187 86 45 NC_002967:TDE2694|3end_hypothetical_protein_2734079..2734229_NEGATIVE 227 230 186 53 17 NC_002967:TDE2419|3end_hypothetical_protein_2444023..2444173_NEGATIVE 227 212 175 61 16 NC_002967:TDE1220|3end_hypothetical_protein_1254862..1255012_POSITIVE 225 224 182 72 25 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 224 250 201 89 41 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 224 250 201 89 42 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE 222 214 185 151 120 NC_002967:TDE1947|3end_ABC_transporter,_permease_protein_1962517..1962667_NEGATIVE 221 213 176 71 35 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE