Origin IGS: taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctcctattatgcgttttattttaagatatgtcaatggaaggtgaattgaatttgtaataatactataaaaataccctagtcaacagctcttgtttgtgatataataagaaaatatcctttccttggaggaggtatgaaaaaattattttctatgttaatttcgtta Mask Tandem Repeat Region ================================================ taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga Find is-nt database================================================ Query_seq: TDE2671:TDE2672|TDE2671:TDE2672:hypothetical protein:TPR domain protein:<-->:2710183..2710349 167 taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2671:TDE2672|TDE2671:TDE2672:hypothetical protein:TPR domain protein:<-->:2710183..2710349 167 taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2671:TDE2672|TDE2671:TDE2672:hypothetical protein:TPR domain protein:<-->:2710183..2710349 167 taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga Predict ORF larger than 30AA ================================================ taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga 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: 88 Start: 132 End: 161 ...................................................................................................................................ATTGACATATCTTAAAATAAAACGCATAAT...... PromScan Matrix: RpoD-17 Strand: - Score: 87 Start: 62 End: 91 .............................................................CTAGTCAACAGCTCTTGTTTGTGATATAAT............................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -2.9 Tail_Score: -3.24804 Start: 17 End: 31 Full_Region: ccttggaggaggtat gaaaa aatta ttttc tatgttaatttcgtt ................gaaaaaattattttc........................................................................................................................................ Find igs database================================================ Query_seq: TDE2671:TDE2672|TDE2671:TDE2672:hypothetical protein:TPR domain protein:<-->:2710183..2710349 167 taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_002967_TDE2671_TDE2672|hypothetical protein:TPR domain protein|NEGATIVE:POSITIVE|[2710183,2710349]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga taacgaaattaacatagaaaataattttttcatacctcctccaaggaaaggatattttcttattatatcacaaacaagagctgttgactagggtatttttatagtattattacaaattcaattcaccttccattgacatatcttaaaataaaacgcataataggaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGAAAUUAACAUAGAAAAUAAUUUUUUCAUACCUCCUCCAAGGAAAGGAUAUUUUCUUAUUAUAUCACAAACAAGAGCUGUUGACUAGGGUAUUUUUAUAGUAUUAUUACAAAUUCAAUUCACCUUCCAUUGACAUAUCUUAAAAUAAAACGCAUAAUAGGAGA ................(((((.....)))))....(((((..(((((((.....)))))))..............((((..(((..(..(((((.........(((....)))...........)))))...)..)))..)))).................))))). (-22.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCCUAUUAUGCGUUUUAUUUUAAGAUAUGUCAAUGGAAGGUGAAUUGAAUUUGUAAUAAUACUAUAAAAAUACCCUAGUCAACAGCUCUUGUUUGUGAUAUAAUAAGAAAAUAUCCUUUCCUUGGAGGAGGUAUGAAAAAAUUAUUUUCUAUGUUAAUUUCGUUA .........................((.((....(((((((((((......((((((.......)))))).(((((............(((((((........))))))).....(((((......)))))))))).......)))))))))))....)).)).... (-24.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 803 80 31 171 122 NC_002967:TDE2671|5end_hypothetical_protein_2710092..2710322_NEGATIVE 268 53 11 117 71 NC_002967:TDE1637|5end_DNA_polymerase_I_1686072..1686302_POSITIVE 248 69 21 133 83 NC_002967:TDE0119|5end_flagellar_protein_FliS_137498..137728_NEGATIVE 242 140 91 92 49 NC_002967:TDE2662|5end_lipoprotein,_putative_2698650..2698880_NEGATIVE 240 62 23 122 81 NC_002967:TDE2288|5end_hypothetical_protein_2325644..2325874_NEGATIVE 227 42 4 106 53 NC_002967:TDE0106|5end_hypothetical_protein_126546..126776_NEGATIVE 226 51 31 109 89 NC_002967:TDE2145|5end_hypothetical_protein_2182925..2183155_NEGATIVE 225 60 22 123 79 NC_002967:TDE1652|5end_ABC_transporter,_ATP-binding/permease_protein_1700524..1700754_NEGATIVE 223 119 78 106 69 NC_002967:TDE1590|5end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1637516..1637746_POSITIVE 216 47 2 118 60 NC_002967:TDE1171|5end_hypothetical_protein_1200175..1200405_POSITIVE 214 159 126 125 96 NC_002967:TDE1854|5end_nucleotidyltransferase_family_protein_1882715..1882945_NEGATIVE 211 52 29 26 2 NC_002967:TDE1990|5end_ATP-dependent_helicase,_DinG_family_2008496..2008726_NEGATIVE 210 53 25 121 95 NC_002967:TDE2473|5end_30S_ribosomal_protein_S21_2496298..2496528_POSITIVE 208 61 34 184 157 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 207 42 22 185 162 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 207 102 66 152 120 NC_002967:TDE0409|5end_hypothetical_protein_461577..461807_POSITIVE 206 42 2 102 60 NC_002967:TDE2030|5end_lipoprotein,_RlpA_family_2058254..2058484_POSITIVE 205 80 31 149 89 NC_002967:TDE2325|5end_hypothetical_protein_2359952..2360182_POSITIVE 205 84 41 46 1 NC_002967:TDE1221|5end_glycosyl_hydrolase,_family_3_1254796..1255026_POSITIVE 204 69 21 128 78 NC_002967:TDE0708|5end_nitroreductase_family_protein_743900..744130_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 99 52 128 80 NC_002967:TDE1959|3end_hypothetical_protein_1973805..1973955_NEGATIVE 245 88 41 119 65 NC_002967:TDE2306|3end_hypothetical_protein_2344138..2344288_NEGATIVE 242 140 91 126 83 NC_002967:TDE2663|3end_isoleucyl-tRNA_synthetase_2698616..2698766_NEGATIVE 238 108 62 116 65 NC_002967:TDE1062|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1090387..1090537_POSITIVE 235 93 53 137 92 NC_002967:TDE2357|3end_iron_compound_ABC_transporter,_permease_protein_2393101..2393251_POSITIVE 223 119 78 100 63 NC_002967:TDE1589|3end_purine-binding_chemotaxis_protein_1637590..1637740_POSITIVE 222 70 36 58 19 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 220 112 75 139 108 NC_002967:TDE2469|3end_hexokinase_family_protein_2491236..2491386_NEGATIVE 216 47 2 105 47 NC_002967:TDE1170|3end_DNA-binding_protein_1200242..1200392_POSITIVE 214 94 53 52 14 NC_002967:TDE1050|3end_hypothetical_protein_1078150..1078300_POSITIVE 204 69 21 88 38 NC_002967:TDE0707|3end_hypothetical_protein_743940..744090_POSITIVE 202 84 51 32 3 NC_002967:TDE1220|3end_hypothetical_protein_1254862..1255012_POSITIVE 200 100 54 150 111 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 195 157 118 53 7 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 194 100 66 43 10 NC_002967:TDE1051|3end_hypothetical_protein_1078212..1078362_NEGATIVE 194 114 76 57 24 NC_002967:TDE0958|3end_patatin_family_protein_982031..982181_POSITIVE 193 99 52 86 28 NC_002967:TDE0735|3end_hypothetical_protein_774746..774896_NEGATIVE 193 90 49 131 81 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 193 98 76 26 3 NC_002967:TDE0275|3end_CAAX_amino_terminal_protease_family_protein_307378..307528_POSITIVE 192 61 35 151 131 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE