Origin IGS: ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagactctcctctttatttttctatctttaattataccatattttttataaaagtccagctatttacgtatagtttgacaggttcgcagtcttgacaaaattttttttctcaaataaactttaagttaagataaattttaagagatatagctttctctatggaggaaaa Mask Tandem Repeat Region ================================================ ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt Find is-nt database================================================ Query_seq: TDE2288:TDE2289|TDE2288:TDE2289:hypothetical protein:phosphoribulokinase/uridine kinase family protein:<-->:2325735..2325903 169 ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2288:TDE2289|TDE2288:TDE2289:hypothetical protein:phosphoribulokinase/uridine kinase family protein:<-->:2325735..2325903 169 ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2288:TDE2289|TDE2288:TDE2289:hypothetical protein:phosphoribulokinase/uridine kinase family protein:<-->:2325735..2325903 169 ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt Predict ORF larger than 30AA ================================================ ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt 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: 85 Start: 50 End: 79 .................................................CTTGACAAAATTTTTTTTCTCAAATAAACT.......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2288:TDE2289|TDE2288:TDE2289:hypothetical protein:phosphoribulokinase/uridine kinase family protein:<-->:2325735..2325903 169 ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: NC_002967_TDE2288_TDE2289|hypothetical protein:phosphoribulokinase/uridine kinase family protein|NEGATIVE:POSITIVE|[2325735,2325903]|169 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagnnnnnnnnttttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt ttttcctccatagagaaagctatatctcttaaaatttatcttaacttaaagtttatttgagaaaaaaaattttgtcaagactgcgaacctgtcaaactatacgtaaatagctggacttttataaaaaatatggtataattaaagatagaaaaataaagaggagagtctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCUCCAUAGAGAAAGCUAUAUCUCUUAAAAUUUAUCUUAACUUAAAGUUUAUUUGAGAAAAAAAAUUUUGUCAAGACUGCGAACCUGUCAAACUAUACGUAAAUAGCUGGACUUUUAUAAAAAAUAUGGUAUAAUUAAAGAUAGAAAAAUAAAGAGGAGAGUCUU ((((((((...(((((........))))).....((((((((........((...(((((.((((....)))).)))))...))..(((.(((...((((......))))...)))...(((.....))).))).......))))))))........)))))))).... (-29.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGACUCUCCUCUUUAUUUUUCUAUCUUUAAUUAUACCAUAUUUUUUAUAAAAGUCCAGCUAUUUACGUAUAGUUUGACAGGUUCGCAGUCUUGACAAAAUUUUUUUUCUCAAAUAAACUUUAAGUUAAGAUAAAUUUUAAGAGAUAUAGCUUUCUCUAUGGAGGAAAA .......((((((.........((((((.((((..(((.(((.....)))...(((.((((((......)))))).))).)))........((((.((((....)))).))))..........)))))))))).......(((((........)))))..))))))... (-28.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 852 120 71 211 162 NC_002967:TDE2288|5end_hypothetical_protein_2325644..2325874_NEGATIVE 234 111 81 55 24 NC_002967:TDE2629|5end_peptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_2669329..2669559_POSITIVE 228 104 69 170 137 NC_002967:TDE1188|5end_NAD(P)_transhydrogenase,_beta_subunit_1216622..1216852_NEGATIVE 223 118 79 218 169 NC_002967:TDE1140|5end_hypothetical_protein_1169845..1170075_NEGATIVE 222 114 71 168 106 NC_002967:TDE1350|5end_rod_shape-determining_protein_MreC_1390327..1390557_POSITIVE 222 118 72 200 149 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 220 48 1 151 97 NC_002967:TDE2364|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398949..2399179_NEGATIVE 219 115 76 74 34 NC_002967:TDE1037|5end_hypothetical_protein_1064470..1064700_POSITIVE 213 117 72 179 140 NC_002967:TDE1213|5end_flagellar_basal_body_rod_protein_1245817..1246047_POSITIVE 210 138 94 152 110 NC_002967:TDE1939|5end_hypothetical_protein_1954627..1954857_POSITIVE 210 39 1 115 81 NC_002967:TDE1331|5end_anaerobic_ribonucleoside_triphosphate_reductase_1365868..1366098_POSITIVE 207 114 71 182 125 NC_002967:TDE2404|5end_RNA_polymerase_sigma-54_factor,_putative_2430704..2430934_NEGATIVE 205 101 81 203 183 NC_002967:TDE0507|5end_hypothetical_protein_558992..559222_NEGATIVE 204 103 69 174 135 NC_002967:TDE0889|5end_hypothetical_protein_905090..905320_POSITIVE 203 114 77 172 132 NC_002967:TDE1030|5end_hypothetical_protein_1059114..1059344_POSITIVE 202 112 78 230 199 NC_002967:TDE1002|5end_hypothetical_protein_1029137..1029367_NEGATIVE 201 86 55 168 133 NC_002967:TDE2255|5end_hypothetical_protein_2291591..2291821_POSITIVE 200 123 106 176 159 NC_002967:TDE2287|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2325058..2325288_NEGATIVE 199 122 84 181 142 NC_002967:TDE2670|5end_glycosyl_transferase,_group_4_family_protein_2708034..2708264_NEGATIVE 197 118 75 181 129 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 117 80 91 58 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 222 118 72 123 72 NC_002967:TDE0571|3end_hypothetical_protein_603497..603647_POSITIVE 221 119 78 97 60 NC_002967:TDE1004|3end_flagellar_filament_core_protein_1029276..1029426_NEGATIVE 219 115 76 77 37 NC_002967:TDE1036|3end_hypothetical_protein_1064553..1064703_POSITIVE 210 39 1 81 47 NC_002967:TDE1330|3end_conserved_hypothetical_protein_TIGR00244_1365914..1366064_POSITIVE 205 114 74 125 89 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 204 113 72 150 116 NC_002967:TDE1212|3end_flagellar_basal-body_rod_protein_FlgB_1245873..1246023_POSITIVE 203 113 74 151 115 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 203 114 77 72 32 NC_002967:TDE1029|3end_Hsp20/alpha_crystallin_family_protein_1059094..1059244_POSITIVE 200 123 106 72 55 NC_002967:TDE2288|3end_hypothetical_protein_2325162..2325312_NEGATIVE 200 117 91 80 56 NC_002967:TDE0460|3end_transporter,_putative_515274..515424_NEGATIVE 199 122 84 72 33 NC_002967:TDE2671|3end_hypothetical_protein_2708143..2708293_NEGATIVE 199 120 76 151 104 NC_002967:TDE2180|3end_tRNA_modification_GTPase_2210590..2210740_NEGATIVE 197 118 75 109 57 NC_002967:TDE2236|3end_methylaspartate_mutase,_E_subunit_2274660..2274810_NEGATIVE 196 117 73 150 110 NC_002967:TDE1091|3end_hypothetical_protein_1123017..1123167_NEGATIVE 195 117 71 55 17 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 194 100 81 151 132 NC_002967:TDE0508|3end_hypothetical_protein_559043..559193_NEGATIVE 193 104 66 134 93 NC_002967:TDE1480|3end_hypothetical_protein_1525162..1525312_NEGATIVE 192 118 84 116 79 NC_002967:TDE1079|3end_DNA-binding_protein/PTS_system,_IIA_component_1111805..1111955_POSITIVE 190 122 81 144 99 NC_002967:TDE2603|3end_DNA_mismatch_repair_protein_2644231..2644381_POSITIVE