Origin IGS: ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt .........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 aaggtaaacattatacacaaaaaatgaggttttgtgaataagtatcacatacttagaatttctaaaaatttatactaagtaccgtgtaactattaaaacttttaagtatttatcttgatacttcatacatattttacaactcacacattcaaaattattttatttgagggagaaacctat Mask Tandem Repeat Region ================================================ ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt Find is-nt database================================================ Query_seq: TDE1009:TDE1010|TDE1009:TDE1010:methyl-accepting chemotaxis protein:excinuclease ABC, A subunit:<-->:1035187..1035366 180 ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1009:TDE1010|TDE1009:TDE1010:methyl-accepting chemotaxis protein:excinuclease ABC, A subunit:<-->:1035187..1035366 180 ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1009:TDE1010|TDE1009:TDE1010:methyl-accepting chemotaxis protein:excinuclease ABC, A subunit:<-->:1035187..1035366 180 ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt Predict ORF larger than 30AA ================================================ ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt 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: 142 End: 171 .............................................................................................................................................ATTCACAAAACCTCATTTTTTGTGTATAAT......... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 20 End: 49 ...................TTTTACAACTCACACATTCAAAATTATTTT................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1009:TDE1010|TDE1009:TDE1010:methyl-accepting chemotaxis protein:excinuclease ABC, A subunit:<-->:1035187..1035366 180 ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_002967_TDE1009_TDE1010|methyl-accepting chemotaxis protein:excinuclease ABC, A subunit|NEGATIVE:POSITIVE|[1035187,1035366]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt ataggtttctccctcaaataaaataattttgaatgtgtgagttgtaaaatatgtatgaagtatcaagataaatacttaaaagttttaatagttacacggtacttagtataaatttttagaaattctaagtatgtgatacttattcacaaaacctcattttttgtgtataatgtttacctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGGUUUCUCCCUCAAAUAAAAUAAUUUUGAAUGUGUGAGUUGUAAAAUAUGUAUGAAGUAUCAAGAUAAAUACUUAAAAGUUUUAAUAGUUACACGGUACUUAGUAUAAAUUUUUAGAAAUUCUAAGUAUGUGAUACUUAUUCACAAAACCUCAUUUUUUGUGUAUAAUGUUUACCUU ..((((...........((((((......(((...(((((((...............((((((((......(((((((.((.((((((...(((.((........)).)))....)))))).)).))))))).))))))))))))))).....)))..))))))...........)))). (-27.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGUAAACAUUAUACACAAAAAAUGAGGUUUUGUGAAUAAGUAUCACAUACUUAGAAUUUCUAAAAAUUUAUACUAAGUACCGUGUAACUAUUAAAACUUUUAAGUAUUUAUCUUGAUACUUCAUACAUAUUUUACAACUCACACAUUCAAAAUUAUUUUAUUUGAGGGAGAAACCUAU .((((..........(((((((.......)))))))...((((((((.((((((((((.((.(((....((((((........))))))...))).)).))))))))))......))))))))................(((.....((((((.........)))))).)))..)))).. (-28.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 714 140 91 231 182 NC_002967:TDE1009|5end_methyl-accepting_chemotaxis_protein_1035096..1035326_NEGATIVE 228 60 11 207 164 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 212 179 132 100 44 NC_002967:TDE0674|5end_hypothetical_protein_713161..713391_POSITIVE 209 178 134 128 80 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 207 118 71 176 128 NC_002967:TDE0437|5end_PBS_lyase_HEAT-like_repeat_domain_protein_493605..493835_NEGATIVE 199 168 124 63 2 NC_002967:TDE0547|5end_hypothetical_protein_586882..587112_NEGATIVE 196 43 1 119 90 NC_002967:TDE0659|5end_hypothetical_protein_696202..696432_NEGATIVE 195 48 1 137 90 NC_002967:TDE2332|5end_hypothetical_protein_2367774..2368004_NEGATIVE 194 104 62 66 15 NC_002967:TDE0055|5end_flagellar_biosynthesis_protein_63565..63795_POSITIVE 189 179 148 51 10 NC_002967:TDE0831|5end_hypothetical_protein_852295..852525_NEGATIVE 188 46 9 143 99 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 187 180 151 72 46 NC_002967:TDE0578|5end_hypothetical_protein_609493..609723_POSITIVE 183 109 71 144 106 NC_002967:TDE1485|5end_hypothetical_protein_1529697..1529927_POSITIVE 183 50 1 75 29 NC_002967:TDE0658|5end_ABC_transporter,_permease_protein_693554..693784_POSITIVE 179 49 7 137 98 NC_002967:TDE2379|5end_hypothetical_protein_2408669..2408899_POSITIVE 178 66 27 231 193 NC_002967:TDE1491|5end_chemotaxis_protein_CheA_1534809..1535039_POSITIVE 177 95 55 78 33 NC_002967:TDE0445|5end_amino_acid_permease_499744..499974_POSITIVE 176 180 139 103 59 NC_002967:TDE0244|5end_ABC_transporter,_ATP-binding/permease_protein_279213..279443_NEGATIVE 176 40 1 127 90 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 175 155 112 63 9 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 180 137 132 89 NC_002967:TDE0369|3end_type_I_restriction-modification_system,_M_subunit_418356..418506_NEGATIVE 207 118 71 109 61 NC_002967:TDE0438|3end_queuine_tRNA-ribosyltransferase_493672..493822_NEGATIVE 201 41 2 61 24 NC_002967:TDE2753|3end_LysM_domain/M23/M37_peptidase_domain_protein_2809558..2809708_NEGATIVE 201 130 83 75 29 NC_002967:TDE2446|3end_malate_dehydrogenase_2474774..2474924_NEGATIVE 199 168 124 63 2 NC_002967:TDE0548|3end_hypothetical_protein_586882..587032_NEGATIVE 196 43 1 42 13 NC_002967:TDE0660|3end_transcriptional_regulator,_putative_696279..696429_NEGATIVE 194 104 62 57 6 NC_002967:TDE0054|3end_flagellar_biosynthesis_protein_63636..63786_POSITIVE 188 46 9 57 13 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 183 109 71 111 73 NC_002967:TDE1484|3end_hypothetical_protein_1529744..1529894_POSITIVE 183 50 1 47 1 NC_002967:TDE0657|3end_ABC_transporter,_ATP-binding_protein_693606..693756_POSITIVE 179 49 7 125 86 NC_002967:TDE2378|3end_ABC_transporter,_ATP-binding_protein,_putative_2408737..2408887_POSITIVE 176 180 139 91 47 NC_002967:TDE0245|3end_ABC_transporter,_ATP-binding/permease_protein_279225..279375_NEGATIVE 176 40 1 104 67 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 175 155 112 61 7 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 175 117 80 100 64 NC_002967:TDE0477|3end_hypothetical_protein_532970..533120_NEGATIVE 174 46 6 121 83 NC_002967:TDE1520|3end_fumarate_hydratase_1567276..1567426_POSITIVE 172 162 122 123 88 NC_002967:TDE0624|3end_precorrin-6X_reductase,_putative_657340..657490_POSITIVE 169 101 64 68 24 NC_002967:TDE1932|3end_hypothetical_protein_1949131..1949281_NEGATIVE 163 49 1 139 99 NC_002967:TDE2526|3end_hypothetical_protein_2553586..2553736_NEGATIVE 162 47 1 55 16 NC_002967:TDE1752|3end_ISTde2,_transposase_1804322..1804472_NEGATIVE