Origin IGS: gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatgaatgaatatattgcatgtaaaaaggttttatgtcaatgagtaccgcctatttttgccaaatttctatggttttagataaagaagccctttttaaattcgttacaatatgatataatattctttctatacattaggtgattgcatattggagaagttgcgaaaaaatatgacaatagataatgcaggactcggaactataatctctacagacatagttgttctaaatgatcatgaaagaacattggtcaaatatgcttttgaacaattgaatgaagaatacaagtccactgttttggaaataggaaagaaactc Mask Tandem Repeat Region ================================================ gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa Find is-nt database================================================ Query_seq: TDE1725:TDE1726|TDE1725:TDE1726:hypothetical protein:polyA polymerase family protein:<-->:1779368..1779685 318 gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1725:TDE1726|TDE1725:TDE1726:hypothetical protein:polyA polymerase family protein:<-->:1779368..1779685 318 gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1725:TDE1726|TDE1725:TDE1726:hypothetical protein:polyA polymerase family protein:<-->:1779368..1779685 318 gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 129 End: 239 ................................................................................................................................ M H Y L L S Y F F A T S P I C N H L M Y R K N I I S Y C N E F K K G F F I ............................................................................... Protein_Len: 57 Strand: - Start: 1 End: 171 L K K G I E L V T S K Y E E N L Q E F A Y K V L T R E H D N L V V I D T S I I T G L G A N D I T M N K R L K E L M ................................................................................................................................................... gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa 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: 84 Start: 198 End: 227 .....................................................................................................................................................................................................CTTTTTAAATTCGTTACAATATGATATAAT........................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 277 End: 306 ....................................................................................................................................................................................................................................................................................ATTGACATAAAACCTTTTTACATGCAATAT............ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 140 End: 169 ...........................................................................................................................................ATTGTCATATTTTTTCGCAACTTCTCCAAT..................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -2.5 Tail_Score: -3.60323 Start: 49 End: 72 Full_Region: GTATTCTTCATTCAA TTGTTCAAA AGCATA TTTGACCAA TGTTCTTTCATGATC ................................................TTGTTCAAAAGCATATTTGACCAA...................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 43 HP_score: -2.5 Tail_Score: -3.05816 Start: 49 End: 72 Full_Region: gatcatgaaagaaca ttggtcaaa tatgct tttgaacaa ttgaatgaagaatac ................................................ttggtcaaatatgcttttgaacaa...................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TDE1725:TDE1726|TDE1725:TDE1726:hypothetical protein:polyA polymerase family protein:<-->:1779368..1779685 318 gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa Intra-Species Hit: Count: 1 Min: 1 Max: 318 Len: 318 Subject: NC_002967_TDE1725_TDE1726|hypothetical protein:polyA polymerase family protein|NEGATIVE:POSITIVE|[1779368,1779685]|318 HSP 1 e-value: 1.0E-180 bit: 630.0 Len: 318 Query Start:1 Query End:318 Subject Strand: POSITIVE Subject Start: 1 Subject End: 318 gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa gagtttctttcctatttccaaaacagtggacttgtattcttcattcaattgttcaaaagcatatttgaccaatgttctttcatgatcatttagaacaactatgtctgtagagattatagttccgagtcctgcattatctattgtcatattttttcgcaacttctccaatatgcaatcacctaatgtatagaaagaatattatatcatattgtaacgaatttaaaaagggcttctttatctaaaaccatagaaatttggcaaaaataggcggtactcattgacataaaacctttttacatgcaatatattcattcataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUUUCUUUCCUAUUUCCAAAACAGUGGACUUGUAUUCUUCAUUCAAUUGUUCAAAAGCAUAUUUGACCAAUGUUCUUUCAUGAUCAUUUAGAACAACUAUGUCUGUAGAGAUUAUAGUUCCGAGUCCUGCAUUAUCUAUUGUCAUAUUUUUUCGCAACUUCUCCAAUAUGCAAUCACCUAAUGUAUAGAAAGAAUAUUAUAUCAUAUUGUAACGAAUUUAAAAAGGGCUUCUUUAUCUAAAACCAUAGAAAUUUGGCAAAAAUAGGCGGUACUCAUUGACAUAAAACCUUUUUACAUGCAAUAUAUUCAUUCAUAA (((((((((((................(((((((.............((((.(((((......))))).))))(((((.............))))).(((((((((....))).))))))..))))))).((((((...((((.((((((................))))))))))....))))))...))))))).........((((((((.......(((((((((((......((((......)))).....))).......(.((((....)))).)......))))))))..))))))))....)))).... (-50.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUGAAUGAAUAUAUUGCAUGUAAAAAGGUUUUAUGUCAAUGAGUACCGCCUAUUUUUGCCAAAUUUCUAUGGUUUUAGAUAAAGAAGCCCUUUUUAAAUUCGUUACAAUAUGAUAUAAUAUUCUUUCUAUACAUUAGGUGAUUGCAUAUUGGAGAAGUUGCGAAAAAAUAUGACAAUAGAUAAUGCAGGACUCGGAACUAUAAUCUCUACAGACAUAGUUGUUCUAAAUGAUCAUGAAAGAACAUUGGUCAAAUAUGCUUUUGAACAAUUGAAUGAAGAAUACAAGUCCACUGUUUUGGAAAUAGGAAAGAAACUC ...(((((((((.....(((...(((.((((..(((........)))..)))).))).)))...........((((((.......))))))........))))))).)).............((((((((...(((((....((((((((((................)))))).))))...)))))((((((..(((.((......(((.((....(((((((((.(((((((((((......)).)))))).......))).)))))))))..)).))).....)))))...))))))......)))))))).... (-54.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 849 140 91 231 182 NC_002967:TDE1725|5end_hypothetical_protein_1779277..1779507_NEGATIVE 288 188 144 147 100 NC_002967:TDE0518|5end_hypothetical_protein_565263..565493_NEGATIVE 277 170 122 111 75 NC_002967:TDE1589|5end_purine-binding_chemotaxis_protein_1637004..1637234_POSITIVE 265 146 106 84 42 NC_002967:TDE2552|5end_ABC_transporter,_ATP-binding/permease_protein_2578944..2579174_NEGATIVE 262 149 101 59 17 NC_002967:TDE0714|5end_capsular_polysaccharide_biosynthesis_protein_747633..747863_POSITIVE 261 165 123 89 43 NC_002967:TDE0982|5end_dihydroorotate_dehydrogenase/oxidoreductase,_FAD-binding_1006477..1006707_POSITIVE 261 150 101 216 171 NC_002967:TDE0459|5end_hypothetical_protein_514382..514612_POSITIVE 254 156 111 198 143 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 250 77 31 209 162 NC_002967:TDE0673|5end_hypothetical_protein_711990..712220_POSITIVE 250 129 81 101 58 NC_002967:TDE0052|5end_flagellar_biosynthetic_protein_FliQ_61305..61535_POSITIVE 248 295 257 67 30 NC_002967:TDE0042|5end_phosphate_acetyltransferase_48676..48906_POSITIVE 244 155 118 99 60 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 243 56 11 65 24 NC_002967:TDE2644|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2683651..2683881_POSITIVE 241 135 101 112 67 NC_002967:TDE1978|5end_hypothetical_protein_1991758..1991988_NEGATIVE 240 129 81 67 20 NC_002967:TDE1454|5end_sugar_transporter_1501438..1501668_POSITIVE 240 169 121 56 9 NC_002967:TDE0519|5end_hypothetical_protein_565989..566219_NEGATIVE 240 86 54 73 34 NC_002967:TDE0452|5end_hypothetical_protein_510143..510373_NEGATIVE 232 139 95 224 182 NC_002967:TDE1590|5end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1637516..1637746_POSITIVE 231 147 102 76 34 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 231 180 137 65 21 NC_002967:TDE1210|5end_ATP-dependent_protease_peptidase_subunit_1243329..1243559_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 133 101 34 1 NC_002967:TDE0603|3end_hypothetical_protein_641885..642035_POSITIVE 273 49 1 135 77 NC_002967:TDE1584|3end_lipoprotein,_putative_1632854..1633004_POSITIVE 269 144 102 151 99 NC_002967:TDE0754|3end_hypothetical_protein_794507..794657_POSITIVE 262 149 101 62 20 NC_002967:TDE0713|3end_transcription_antitermination_protein,_NusG_family_747716..747866_POSITIVE 261 165 123 67 21 NC_002967:TDE0981|3end_hypothetical_protein_1006535..1006685_POSITIVE 250 77 31 150 103 NC_002967:TDE0672|3end_hypothetical_protein_712011..712161_POSITIVE 243 56 11 68 27 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 241 135 101 115 70 NC_002967:TDE1979|3end_hypothetical_protein_1991755..1991905_NEGATIVE 240 129 81 65 18 NC_002967:TDE1453|3end_alpha-galactosidase_1501516..1501666_POSITIVE 240 86 54 73 34 NC_002967:TDE0453|3end_hypothetical_protein_510143..510293_NEGATIVE 239 148 103 52 8 NC_002967:TDE1252|3end_lipoprotein,_putative_1287094..1287244_POSITIVE 237 145 118 134 105 NC_002967:TDE2545|3end_hypothetical_protein_2571170..2571320_NEGATIVE 232 156 113 151 106 NC_002967:TDE2071|3end_hypothetical_protein_2098593..2098743_POSITIVE 231 30 10 21 1 NC_002967:TDE2553|3end_lysyl-tRNA_synthetase_2579047..2579197_NEGATIVE 231 147 102 86 44 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 229 146 104 77 29 NC_002967:TDE1204|3end_cell_division_protein_FtsZ_1237666..1237816_POSITIVE 229 168 122 62 2 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE 228 166 122 133 95 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 228 139 92 145 101 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 225 55 12 105 53 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE