Origin IGS: aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaactcctttaaaataactgccttatagtgtaacataattatgctcattattcaagttctttacactattgataattattaaaatatgttataatcttcactgttctttttacttggaggtattt Mask Tandem Repeat Region ================================================ aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt Find is-nt database================================================ Query_seq: TDE1530:TDE1531|TDE1530:TDE1531:hypothetical protein:hypothetical protein:<-->:1575963..1576090 128 aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1530:TDE1531|TDE1530:TDE1531:hypothetical protein:hypothetical protein:<-->:1575963..1576090 128 aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1530:TDE1531|TDE1530:TDE1531:hypothetical protein:hypothetical protein:<-->:1575963..1576090 128 aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt Predict ORF larger than 30AA ================================================ aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt 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: 83 Start: 70 End: 99 .....................................................................CTTGAATAATGAGCATAATTATGTTACACT............................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 90 End: 119 .........................................................................................CTTTAAAATAACTGCCTTATAGTGTAACAT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1530:TDE1531|TDE1530:TDE1531:hypothetical protein:hypothetical protein:<-->:1575963..1576090 128 aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_002967_TDE1530_TDE1531|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1575963,1576090]|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 aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt aaatacctccaagtaaaaagaacagtgaagattataacatattttaataattatcaatagtgtaaagaacttgaataatgagcataattatgttacactataaggcagttattttaaaggagtttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUACCUCCAAGUAAAAAGAACAGUGAAGAUUAUAACAUAUUUUAAUAAUUAUCAAUAGUGUAAAGAACUUGAAUAAUGAGCAUAAUUAUGUUACACUAUAAGGCAGUUAUUUUAAAGGAGUUUUUU ......((((...(((((..(((..(((.((((((...........)))))).)))(((((((((.........(((((.......))))).)))))))))......))).)))))..))))...... (-18.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAACUCCUUUAAAAUAACUGCCUUAUAGUGUAACAUAAUUAUGCUCAUUAUUCAAGUUCUUUACACUAUUGAUAAUUAUUAAAAUAUGUUAUAAUCUUCACUGUUCUUUUUACUUGGAGGUAUUU ......((((..(((((.(((..........(((((((((.........((((((..(((.......)))...))))))........))))))))).........)))..)))))...))))...... (-15.84) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 750 110 61 201 152 NC_002967:TDE1530|5end_hypothetical_protein_1575872..1576102_NEGATIVE 201 45 10 182 143 NC_002967:TDE1510|5end_hypothetical_protein_1557180..1557410_POSITIVE 195 43 6 130 96 NC_002967:TDE2145|5end_hypothetical_protein_2182925..2183155_NEGATIVE 182 96 62 87 51 NC_002967:TDE2119|5end_glycine_reductase_complex_selenoprotein_GrdB2_2152693..2152923_NEGATIVE 173 49 7 78 37 NC_002967:TDE1555|5end_hypothetical_protein_1598018..1598248_POSITIVE 170 107 61 153 115 NC_002967:TDE0926|5end_phosphonate_ABC_transporter,_permease_protein,_putative_950007..950237_NEGATIVE 168 109 61 76 15 NC_002967:TDE1238|5end_translocase_1270815..1271045_POSITIVE 168 107 64 206 163 NC_002967:TDE0706|5end_adenine-specific_DNA_modification_methyltransferase_740420..740650_POSITIVE 167 106 67 96 61 NC_002967:TDE2786|5end_DNA_polymerase_III_subunit_alpha_2842672..2842902_NEGATIVE 166 88 52 126 86 NC_002967:TDE0215|5end_hypothetical_protein_251370..251600_NEGATIVE 164 67 22 64 27 NC_002967:TDE0310|5end_hypothetical_protein_341620..341850_POSITIVE 163 110 61 71 23 NC_002967:TDE2480|5end_heat_shock_protein_90_2505288..2505518_NEGATIVE 163 31 2 128 99 NC_002967:TDE0127|5end_DNA-binding_protein_145750..145980_POSITIVE 162 120 78 136 94 NC_002967:TDE1899|5end_hypothetical_protein_1921088..1921318_NEGATIVE 162 96 54 72 37 NC_002967:TDE0981|5end_hypothetical_protein_1005496..1005726_POSITIVE 162 110 69 179 149 NC_002967:TDE0631|5end_sigma_factor_regulatory_protein,_putative_665295..665525_POSITIVE 162 105 79 43 13 NC_002967:TDE0045|5end_ABC_transporter,_ATP-binding_protein_55113..55343_NEGATIVE 158 83 50 201 164 NC_002967:TDE1596|5end_hypothetical_protein_1646680..1646910_NEGATIVE 157 36 6 128 99 NC_002967:TDE2208|5end_conserved_hypothetical_protein_TIGR00486_2246733..2246963_POSITIVE 157 109 61 165 108 NC_002967:TDE1037|5end_hypothetical_protein_1064470..1064700_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 31 1 142 114 NC_002967:TDE2012|3end_hypothetical_protein_2033800..2033950_NEGATIVE 201 45 10 56 17 NC_002967:TDE1509|3end_lipoprotein_releasing_system,_ATP-binding_protein,_putative_1557134..1557284_POSITIVE 182 96 62 75 39 NC_002967:TDE2120|3end_glycine_reductase_complex_proprotein_GrdE2_2152705..2152855_NEGATIVE 173 49 7 81 40 NC_002967:TDE1554|3end_hypothetical_protein_1598101..1598251_POSITIVE 164 67 22 60 23 NC_002967:TDE0309|3end_lipoprotein,_putative_341696..341846_POSITIVE 153 93 51 69 28 NC_002967:TDE2000|3end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_2019639..2019789_POSITIVE 151 120 85 61 26 NC_002967:TDE2672|3end_TPR_domain_protein_2711630..2711780_POSITIVE 151 118 78 114 79 NC_002967:TDE2624|3end_hypothetical_protein_2664321..2664471_NEGATIVE 151 44 1 112 74 NC_002967:TDE0752|3end_hypothetical_protein_793262..793412_POSITIVE 150 45 7 141 103 NC_002967:TDE1849|3end_hypothetical_protein_1877356..1877506_NEGATIVE 150 37 4 140 99 NC_002967:TDE1428|3end_hypothetical_protein_1472527..1472677_POSITIVE 150 98 51 86 36 NC_002967:TDE0567|3end_hypothetical_protein_598916..599066_POSITIVE 149 94 52 52 8 NC_002967:TDE2425|3end_50S_ribosomal_protein_L11_2454719..2454869_NEGATIVE 148 85 51 98 58 NC_002967:TDE2626|3end_ABC_transporter,_ATP-binding/permease_protein_2666657..2666807_NEGATIVE 148 84 60 42 13 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 147 120 90 102 74 NC_002967:TDE2058|3end_hypothetical_protein_2085354..2085504_NEGATIVE 146 31 7 36 4 NC_002967:TDE0410|3end_peptidase,_M48_family_462999..463149_POSITIVE 145 43 1 57 5 NC_002967:TDE2540|3end_lipoprotein,_putative_2565195..2565345_NEGATIVE 145 23 3 87 68 NC_002967:TDE1130|3end_methyltransferase,_putative_1163240..1163390_POSITIVE 144 110 67 78 20 NC_002967:TDE2296|3end_hypothetical_protein_2334283..2334433_NEGATIVE