Origin IGS: cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatccggtaattggtaatcacttgtcattaaagtgtgtagtcggtaattaaaccgattacacattttttttgcgaagaaccgcatgccatattttaccggttggg Mask Tandem Repeat Region ================================================ cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt Find is-nt database================================================ Query_seq: TDE1184:TDE1185|TDE1184:TDE1185:hypothetical protein:lipoprotein, putative:-><-:1211582..1211686 105 cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1184:TDE1185|TDE1184:TDE1185:hypothetical protein:lipoprotein, putative:-><-:1211582..1211686 105 cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1184:TDE1185|TDE1184:TDE1185:hypothetical protein:lipoprotein, putative:-><-:1211582..1211686 105 cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt Predict ORF larger than 30AA ================================================ cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt 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================================================ cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.6 Tail_Score: -5.75342 Start: 43 End: 72 Full_Region: cacttgtcattaaag tgtgtagtcggt aattaa accgattacaca ttttttttgcgaaga ..........................................tgtgtagtcggtaattaaaccgattacaca................................. Find igs database================================================ Query_seq: TDE1184:TDE1185|TDE1184:TDE1185:hypothetical protein:lipoprotein, putative:-><-:1211582..1211686 105 cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_002967_TDE1184_TDE1185|hypothetical protein:lipoprotein, putative|POSITIVE:NEGATIVE|[1211582,1211686]|105 HSP 1 e-value: 5.0E-39 bit: 161.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 cccaaccggtaaaatatggcatgcggttcttcgcnnnnnnnntgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt cccaaccggtaaaatatggcatgcggttcttcgcaaaaaaaatgtgtaatcggtttaattaccgactacacactttaatgacaagtgattaccaattaccggatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCAACCGGUAAAAUAUGGCAUGCGGUUCUUCGCAAAAAAAAUGUGUAAUCGGUUUAAUUACCGACUACACACUUUAAUGACAAGUGAUUACCAAUUACCGGAUU .....(((((((....(((..(((((....)))))...(((.((((((.(((((......))))).)))))).)))...............))).)))))))... (-32.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCCGGUAAUUGGUAAUCACUUGUCAUUAAAGUGUGUAGUCGGUAAUUAAACCGAUUACACAUUUUUUUUGCGAAGAACCGCAUGCCAUAUUUUACCGGUUGGG ...(((((((.(((((.............((((((((((((((((......))))))))))))))))...((((......)))))))))....)))))))..... (-40.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 36 1 124 87 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 268 53 18 48 10 NC_002967:TDE0496|5end_DNA-binding_protein,_putative_551189..551419_NEGATIVE 264 87 41 170 121 NC_002967:TDE1148|5end_hypothetical_protein_1186357..1186587_NEGATIVE 251 45 2 221 169 NC_002967:TDE2713|5end_RNA_methyltransferase,_TrmH_family_2770324..2770554_NEGATIVE 251 65 22 229 185 NC_002967:TDE1145|5end_hypothetical_protein_1184811..1185041_NEGATIVE 249 34 1 54 17 NC_002967:TDE2317|5end_hemolysin_III_2354771..2355001_NEGATIVE 249 63 24 49 16 NC_002967:TDE1384|5end_cadmium-translocating_P-type_ATPase_1422765..1422995_POSITIVE 248 34 1 200 161 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 245 34 2 229 201 NC_002967:TDE2042|5end_hypothetical_protein_2072179..2072409_NEGATIVE 243 38 5 171 134 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 241 35 1 198 166 NC_002967:TDE0016|5end_ATPase,_AAA_family_20457..20687_POSITIVE 239 34 5 114 81 NC_002967:TDE0132|5end_hypothetical_protein_152046..152276_POSITIVE 237 60 18 190 147 NC_002967:TDE0829|5end_putative_aminopeptidase_2_851477..851707_NEGATIVE 235 50 2 178 109 NC_002967:TDE2391|5end_peptidyl-prolyl_cis-trans_isomerase_2421550..2421780_NEGATIVE 235 40 3 154 124 NC_002967:TDE0063|5end_hypothetical_protein_69714..69944_POSITIVE 234 34 1 117 87 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 231 36 1 33 7 NC_002967:TDE2633|5end_hypothetical_protein_2674359..2674589_POSITIVE 231 36 4 161 130 NC_002967:TDE1036|5end_hypothetical_protein_1063805..1064035_POSITIVE 231 47 1 176 119 NC_002967:TDE0292|5end_hypothetical_protein_322014..322244_NEGATIVE 228 34 1 201 163 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 87 41 101 52 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 249 63 24 55 22 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 243 38 5 149 112 NC_002967:TDE2767|3end_flagellar_protein-related_protein_2820896..2821046_NEGATIVE 239 34 5 89 56 NC_002967:TDE0131|3end_hypothetical_protein_152101..152251_POSITIVE 237 60 18 58 15 NC_002967:TDE0830|3end_hypothetical_protein_851609..851759_NEGATIVE 231 35 3 151 123 NC_002967:TDE2426|3end_transcription_antitermination_protein_NusG_2455242..2455392_NEGATIVE 231 36 4 136 105 NC_002967:TDE1035|3end_transcriptional_regulator,_PadR_family_1063860..1064010_POSITIVE 225 72 43 48 19 NC_002967:TDE1184|3end_hypothetical_protein_1211521..1211671_POSITIVE 224 56 11 146 107 NC_002967:TDE2537|3end_hypothetical_protein_2563858..2564008_POSITIVE 224 39 1 145 97 NC_002967:TDE1959|3end_hypothetical_protein_1973805..1973955_NEGATIVE 222 36 5 60 28 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 220 53 19 77 41 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 220 53 19 73 37 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 220 53 19 104 68 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 220 53 19 78 42 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 220 53 19 78 42 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 220 53 19 69 33 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 220 53 19 87 51 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 220 53 19 73 37 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 219 69 22 76 19 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE