Origin IGS: atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactccattatatcacaaatataaaaaaaaacaaggaaacaaataaattttcaaatttttttctatgtaacttgacttaaaagtcattgttttagtattataattatgtagtgaggttagatat Mask Tandem Repeat Region ================================================ atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt Find is-nt database================================================ Query_seq: TDE2300:TDE2301|TDE2300:TDE2301:trypsin domain/PDZ domain protein:FlhB domain protein:<-->:2341525..2341648 124 atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2300:TDE2301|TDE2300:TDE2301:trypsin domain/PDZ domain protein:FlhB domain protein:<-->:2341525..2341648 124 atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2300:TDE2301|TDE2300:TDE2301:trypsin domain/PDZ domain protein:FlhB domain protein:<-->:2341525..2341648 124 atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt Predict ORF larger than 30AA ================================================ atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2300:TDE2301|TDE2300:TDE2301:trypsin domain/PDZ domain protein:FlhB domain protein:<-->:2341525..2341648 124 atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_002967_TDE2300_TDE2301|trypsin domain/PDZ domain protein:FlhB domain protein|NEGATIVE:POSITIVE|[2341525,2341648]|124 HSP 1 e-value: 6.0E-36 bit: 151.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagnnnnnnntttgaaaatttatttgtttccttgnnnnnnnnnatatttgtgatataatggagtt atatctaacctcactacataattataatactaaaacaatgacttttaagtcaagttacatagaaaaaaatttgaaaatttatttgtttccttgtttttttttatatttgtgatataatggagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUCUAACCUCACUACAUAAUUAUAAUACUAAAACAAUGACUUUUAAGUCAAGUUACAUAGAAAAAAAUUUGAAAAUUUAUUUGUUUCCUUGUUUUUUUUUAUAUUUGUGAUAUAAUGGAGUU ............(((.(...((((((.(((........(((((....)))))......((((((((((((..(.((((......)))).)..))))))))))))....))).)))))).)))). (-18.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUCCAUUAUAUCACAAAUAUAAAAAAAAACAAGGAAACAAAUAAAUUUUCAAAUUUUUUUCUAUGUAACUUGACUUAAAAGUCAUUGUUUUAGUAUUAUAAUUAUGUAGUGAGGUUAGAUAU (((..((((((((....(((((.((((...(((.(((((.((((..........)))).))))).)))....(((((....)))))...)))).)))))......))))))))..)))...... (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 681 50 1 141 92 NC_002967:TDE2300|5end_trypsin_domain/PDZ_domain_protein_2341434..2341664_NEGATIVE 215 120 80 54 19 NC_002967:TDE1365|5end_transcriptional_regulator,_TetR_family_1407755..1407985_POSITIVE 204 120 87 199 167 NC_002967:TDE0979|5end_penicillin_binding_protein_1003946..1004176_NEGATIVE 200 106 72 66 29 NC_002967:TDE0558|5end_hypothetical_protein_592804..593034_POSITIVE 185 114 78 97 57 NC_002967:TDE2718|5end_magnesium_transporter_2775910..2776140_NEGATIVE 181 120 78 134 87 NC_002967:TDE1752|5end_ISTde2,_transposase_1805398..1805628_NEGATIVE 181 120 78 134 87 NC_002967:TDE1022|5end_ISTde2,_transposase_1054988..1055218_NEGATIVE 181 120 78 134 87 NC_002967:TDE0140|5end_ISTde2,_transposase_162731..162961_POSITIVE 172 116 82 201 163 NC_002967:TDE1329|5end_ATPase,_AAA_family_1363503..1363733_POSITIVE 170 46 3 134 93 NC_002967:TDE2563|5end_hypothetical_protein_2589794..2590024_POSITIVE 166 110 77 119 90 NC_002967:TDE1493|5end_chemotaxis_protein_CheX_1538590..1538820_POSITIVE 164 120 79 209 168 NC_002967:TDE2695|5end_transcript_cleavage_factor/unknown_domain_fusion_protein_2739079..2739309_NEGATIVE 164 120 78 199 152 NC_002967:TDE1686|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1741763..1741993_NEGATIVE 162 120 80 217 176 NC_002967:TDE1963|5end_selenocysteine-specific_translation_elongation_factor_1975289..1975519_POSITIVE 161 101 69 114 81 NC_002967:TDE0836|5end_Na(+)-translocating_NADH-quinone_reductase,_C_subunit_856096..856326_NEGATIVE 161 46 2 183 134 NC_002967:TDE0377|5end_hypothetical_protein_431977..432207_NEGATIVE 161 120 82 105 64 NC_002967:TDE0148|5end_histidine_kinase-related_ATPase,_putative_168971..169201_POSITIVE 154 109 76 146 106 NC_002967:TDE2009|5end_hypothetical_protein_2030382..2030612_POSITIVE 154 104 78 211 185 NC_002967:TDE1798|5end_hypothetical_protein_1836676..1836906_NEGATIVE 153 113 82 137 100 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 179 120 74 149 93 NC_002967:TDE0128|3end_HAMP_domain/GGDEF_domain/EAL_domain_protein_148725..148875_POSITIVE 170 46 3 48 7 NC_002967:TDE2562|3end_cation_ABC_transporter,_permease_protein,_putative_2589788..2589938_POSITIVE 166 110 77 94 65 NC_002967:TDE1492|3end_chemotaxis_protein_CheW_1538645..1538795_POSITIVE 161 101 69 117 84 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE 154 109 76 99 59 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 153 113 82 132 95 NC_002967:TDE1948|3end_ABC_transporter,_permease_protein_1963454..1963604_NEGATIVE 150 99 51 109 60 NC_002967:TDE1952|3end_hypothetical_protein_1968396..1968546_NEGATIVE 150 68 21 87 32 NC_002967:TDE0297|3end_hypothetical_protein_327796..327946_NEGATIVE 150 120 72 80 34 NC_002967:TDE0082|3end_transcriptional_regulator,_MerR_family_93934..94084_NEGATIVE 149 105 63 67 25 NC_002967:TDE2216|3end_galactoside_ABC_transporter,_ATP-binding_protein_2255160..2255310_NEGATIVE 149 29 2 54 24 NC_002967:TDE2023|3end_TPR_domain_protein_2049505..2049655_NEGATIVE 148 111 77 100 64 NC_002967:TDE0258|3end_methlytransferase,_UbiE/COQ5_family_292132..292282_NEGATIVE 146 111 73 121 79 NC_002967:TDE2371|3end_iron-sulfur_cluster-binding_protein_2404496..2404646_POSITIVE 146 115 78 122 77 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 145 91 56 92 62 NC_002967:TDE1125|3end_TPR_domain_protein_1156184..1156334_NEGATIVE 144 114 82 136 103 NC_002967:TDE1953|3end_transcriptional_regulator,_TetR_family_1969030..1969180_NEGATIVE 144 105 77 133 101 NC_002967:TDE1447|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_1493588..1493738_POSITIVE 144 57 12 67 16 NC_002967:TDE1171|3end_hypothetical_protein_1201058..1201208_POSITIVE 143 74 38 151 104 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 143 109 87 144 118 NC_002967:TDE1078|3end_metallo-beta-lactamase_family_protein_1111045..1111195_POSITIVE