Origin IGS: attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtcaaaatttttataaaaaaattcatatttatacttgacataatattatattttatataatatataaatataaataatatactaaatagtattatataatatcagatatagcaaggaggttaacggg .........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 cccgttaacctccttgctatatctgatattatataatactatttagtatattatttatatttatatattatataaaatataatattatgtcaagtataaatatgaatttttttataaaaattttgacaaaatttttaatatatgatagtatgggtgataattatttatattgattggcggcttaataggtgccttgattctataaaaattgaatatatttggaggtaaaat Mask Tandem Repeat Region ================================================ attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtcaaaatttttataaaaaaattcatatttatacttgacataatattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncagatatagcaaggaggttaacggg Find is-nt database================================================ Query_seq: TDE1857:TDE1858|TDE1857:TDE1858:hypothetical protein:transcriptional regulator, PadR family:<-->:1884541..1884771 231 attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtcaaaatttttataaaaaaattcatatttatacttgacataatattatattttatataatatataaatataaataatatactaaatagtattatataatatcagatatagcaaggaggttaacggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1857:TDE1858|TDE1857:TDE1858:hypothetical protein:transcriptional regulator, PadR family:<-->:1884541..1884771 231 attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtcaaaatttttataaaaaaattcatatttatacttgacataatattatattttatataatatataaatataaataatatactaaatagtattatataatatcagatatagcaaggaggttaacggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1857:TDE1858|TDE1857:TDE1858:hypothetical protein:transcriptional regulator, PadR family:<-->:1884541..1884771 231 attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtcaaaatttttataaaaaaattcatatttatacttgacataatattatattttatataatatataaatataaataatatactaaatagtattatataatatcagatatagcaaggaggttaacggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtcaaaatttttataaaaaaattcatatttatacttgacataatattatattttatataatatataaatataaataatatactaaatagtattatataatatcagatatagcaaggaggttaacggg Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 1 End: 117 M L P P N I F N F Y R I K A P I K P P I N I N N Y H P Y Y H I L K I L S K F L .................................................................................................................. Protein_Len: 46 Strand: - Start: 62 End: 199 ............................................................. Y L Y N D G M S D Y I L F K T L I K I F F N M N I S S M I N Y K I Y Y I F I F L I S F L I M ................................ attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtcaaaatttttataaaaaaattcatatttatacttgacataatattatattttatataatatataaatataaataatatactaaatagtattatataatatcagatatagcaaggaggttaacggg 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: 81 End: 110 ................................................................................TTTGACAAAATTTTTAATATATGATAGTAT......................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 138 End: 167 .........................................................................................................................................CTTGACATAATATTATATTTTATATAATAT................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 71 End: 100 ......................................................................TTTTTAATATATGATAGTATGGGTGATAAT................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 144 End: 173 ...............................................................................................................................................ATTTATATATTATATAAAATATAATATTAT.......................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 190 End: 219 .............................................................................................................................................................................................CTTGCTATATCTGATATTATATAATACTAT............ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtcaaaatttttataaaaaaattcatatttatacttgacataatattatattttatataatatataaatataaataatatactaaatagtattatataatatcagatatagcaaggaggttaacggg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1857:TDE1858|TDE1857:TDE1858:hypothetical protein:transcriptional regulator, PadR family:<-->:1884541..1884771 231 attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtcaaaatttttataaaaaaattcatatttatacttgacataatattatattttatataatatataaatataaataatatactaaatagtattatataatatcagatatagcaaggaggttaacggg Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_002967_TDE1857_TDE1858|hypothetical protein:transcriptional regulator, PadR family|NEGATIVE:POSITIVE|[1884541,1884771]|231 HSP 1 e-value: 4.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtc............................................................................................................................ attttacctccaaatatattcaatttttatagaatcaaggcacctattaagccgccaatcaatataaataattatcacccatactatcatatattaaaaattttgtc............................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUACCUCCAAAUAUAUUCAAUUUUUAUAGAAUCAAGGCACCUAUUAAGCCGCCAAUCAAUAUAAAUAAUUAUCACCCAUACUAUCAUAUAUUAAAAAUUUUGUC .....................((((((((((.......(((..((....))..)))......)))))).)))).................................. ( -5.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAAAAUUUUUAAUAUAUGAUAGUAUGGGUGAUAAUUAUUUAUAUUGAUUGGCGGCUUAAUAGGUGCCUUGAUUCUAUAAAAAUUGAAUAUAUUUGGAGGUAAAAU ......(((((((((((((..((((((((((((...))))))))))))...((((.((....)).))))...................))))).))))))))..... (-17.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 839 80 31 171 122 NC_002967:TDE1857|5end_hypothetical_protein_1884450..1884680_NEGATIVE 235 79 39 110 78 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 234 58 34 164 139 NC_002967:TDE0988|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1015082..1015312_POSITIVE 228 53 27 213 188 NC_002967:TDE2276|5end_hypothetical_protein_2312676..2312906_NEGATIVE 221 88 41 99 58 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 215 89 43 90 45 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 212 87 51 91 48 NC_002967:TDE2739|5end_hypothetical_protein_2794673..2794903_POSITIVE 212 46 5 90 56 NC_002967:TDE1783|5end_hypothetical_protein_1823605..1823835_NEGATIVE 209 88 44 97 55 NC_002967:TDE2085|5end_uridylate_kinase_2114182..2114412_POSITIVE 209 58 37 37 6 NC_002967:TDE1001|5end_orotate_phosphoribosyltransferase_1027653..1027883_POSITIVE 208 64 39 21 2 NC_002967:TDE1501|5end_pyruvate_phosphate_dikinase_1548041..1548271_POSITIVE 207 63 23 80 33 NC_002967:TDE0958|5end_patatin_family_protein_981040..981270_POSITIVE 205 69 31 54 20 NC_002967:TDE1263|5end_hypothetical_protein_1297304..1297534_POSITIVE 202 56 18 230 203 NC_002967:TDE1876|5end_glycosyl_transferase,_WecB/TagA/CpsF_family_1897679..1897909_NEGATIVE 201 84 45 114 75 NC_002967:TDE2426|5end_transcription_antitermination_protein_NusG_2455799..2456029_NEGATIVE 199 56 30 198 171 NC_002967:TDE2121|5end_hypothetical_protein_2154729..2154959_NEGATIVE 199 61 22 205 160 NC_002967:TDE0445|5end_amino_acid_permease_499744..499974_POSITIVE 198 78 42 172 125 NC_002967:TDE2365|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399949..2400179_NEGATIVE 198 56 19 67 26 NC_002967:TDE0300|5end_leucyl_aminopeptidase_330843..331073_POSITIVE 197 55 17 209 175 NC_002967:TDE0852|5end_50S_ribosomal_protein_L13_875019..875249_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 55 32 40 16 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 234 58 34 79 54 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 227 38 3 120 83 NC_002967:TDE0036|3end_hypothetical_protein_42135..42285_NEGATIVE 212 46 5 114 80 NC_002967:TDE1784|3end_transcriptional_activator,_AraC_family_1823581..1823731_NEGATIVE 209 62 33 48 21 NC_002967:TDE2403|3end_metallo-beta-lactamase_family_protein_2428641..2428791_NEGATIVE 209 88 44 64 22 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE 201 84 45 110 71 NC_002967:TDE2427|3end_preprotein_translocase,_SecE_subunit_2455803..2455953_NEGATIVE 196 88 50 95 46 NC_002967:TDE2768|3end_flagellar_hook_protein_2821119..2821269_NEGATIVE 196 56 12 70 17 NC_002967:TDE0949|3end_enolase_973391..973541_POSITIVE 194 64 35 149 123 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 192 56 24 126 95 NC_002967:TDE2725|3end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2782240..2782390_NEGATIVE 192 65 24 122 80 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 192 55 30 46 15 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 190 42 1 100 55 NC_002967:TDE2201|3end_hypothetical_protein_2238492..2238642_NEGATIVE 186 63 24 133 101 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 186 73 44 81 50 NC_002967:TDE0504|3end_hypothetical_protein_557469..557619_NEGATIVE 185 39 1 144 99 NC_002967:TDE2472|3end_ISTde1,_transposase_2496226..2496376_POSITIVE 185 39 1 144 99 NC_002967:TDE2033|3end_ISTde1,_transposase_2060292..2060442_NEGATIVE 185 57 22 149 107 NC_002967:TDE0444|3end_glutamine_amidotransferase_class-I_domain_protein_499771..499921_POSITIVE 185 39 1 144 99 NC_002967:TDE0039|3end_ISTde1,_transposase_44489..44639_NEGATIVE