Origin IGS: agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actcattcataatattttaactaaatatagtattgacacaatgaaatatagtatgatattatcataaatatagttagattgacctgtttaaagacaggtgtacagaaccaatttaacattttcaacaaaaaaataattgcaatgtaaaaaggtattgcaaaaaggaaggtttagact Mask Tandem Repeat Region ================================================ agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt Find is-nt database================================================ Query_seq: TDE0439:TDE0440|TDE0439:TDE0440:hypothetical protein:DNA-binding protein:<-->:495914..496090 177 agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0439:TDE0440|TDE0439:TDE0440:hypothetical protein:DNA-binding protein:<-->:495914..496090 177 agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0439:TDE0440|TDE0439:TDE0440:hypothetical protein:DNA-binding protein:<-->:495914..496090 177 agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 23 End: 154 ...................... M P F Y I A I I F L L K M L N W F C T P V F K Q V N L T I F M I I S Y Y I S L C Q Y Y I ....................... agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt 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================================================ agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0439:TDE0440|TDE0439:TDE0440:hypothetical protein:DNA-binding protein:<-->:495914..496090 177 agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_002967_TDE0439_TDE0440|hypothetical protein:DNA-binding protein|NEGATIVE:POSITIVE|[495914,496090]|177 HSP 1 e-value: 2.0E-83 bit: 309.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 agtctaaaccttcctttttgcaatacctttttacattgcaattannnnnnngttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt agtctaaaccttcctttttgcaatacctttttacattgcaattatttttttgttgaaaatgttaaattggttctgtacacctgtctttaaacaggtcaatctaactatatttatgataatatcatactatatttcattgtgtcaatactatatttagttaaaatattatgaatgagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUAAACCUUCCUUUUUGCAAUACCUUUUUACAUUGCAAUUAUUUUUUUGUUGAAAAUGUUAAAUUGGUUCUGUACACCUGUCUUUAAACAGGUCAAUCUAACUAUAUUUAUGAUAAUAUCAUACUAUAUUUCAUUGUGUCAAUACUAUAUUUAGUUAAAAUAUUAUGAAUGAGU .(((((((..........((((..(((..((((((((((((........))))....)))).))))..)))..)))).((((((......)))))).............)))).)))........(((....(((((.((((....((((....))))....)))).)))))..))) (-27.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCAUUCAUAAUAUUUUAACUAAAUAUAGUAUUGACACAAUGAAAUAUAGUAUGAUAUUAUCAUAAAUAUAGUUAGAUUGACCUGUUUAAAGACAGGUGUACAGAACCAAUUUAACAUUUUCAACAAAAAAAUAAUUGCAAUGUAAAAAGGUAUUGCAAAAAGGAAGGUUUAGACU ....................((((((...............(((((.....((((((...))))))......((((((((((((((((....))))))).........)))))))))..)))))............((((((((........))))))))........))))))... (-31.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 778 110 61 201 152 NC_002967:TDE0439|5end_hypothetical_protein_495823..496053_NEGATIVE 417 105 66 200 158 NC_002967:TDE1818|5end_hypothetical_protein_1853791..1854021_NEGATIVE 365 96 57 171 128 NC_002967:TDE1956|5end_hypothetical_protein_1971114..1971344_POSITIVE 279 160 119 229 189 NC_002967:TDE0442|5end_hypothetical_protein_497723..497953_NEGATIVE 234 89 42 221 171 NC_002967:TDE2049|5end_bacterial_extracellular_solute-binding_proteins,_family_5_2077865..2078095_POSITIVE 226 54 11 126 80 NC_002967:TDE0379|5end_hypothetical_protein_432458..432688_POSITIVE 219 109 71 131 95 NC_002967:TDE0941|5end_NLP/P60_family_protein_964102..964332_NEGATIVE 217 43 13 50 22 NC_002967:TDE0999|5end_formate/nitrite_transporter_1025870..1026100_POSITIVE 211 49 3 144 97 NC_002967:TDE2585|5end_methyl-accepting_chemotaxis_domain/unknown_domain_protein_2620303..2620533_NEGATIVE 211 159 114 69 20 NC_002967:TDE1835|5end_hypothetical_protein_1868317..1868547_NEGATIVE 211 159 114 69 20 NC_002967:TDE1779|5end_hypothetical_protein_1821996..1822226_NEGATIVE 211 130 82 91 40 NC_002967:TDE0113|5end_Tpl_protein_132615..132845_POSITIVE 209 51 13 128 94 NC_002967:TDE0918|5end_hypothetical_protein_935277..935507_POSITIVE 207 95 72 229 203 NC_002967:TDE0988|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1015082..1015312_POSITIVE 200 98 69 82 50 NC_002967:TDE0847|5end_hypothetical_protein_870894..871124_POSITIVE 199 55 11 193 154 NC_002967:TDE1598|5end_ABC_transporter,_ATP-binding_protein_1648910..1649140_NEGATIVE 199 59 11 140 87 NC_002967:TDE1342|5end_hypothetical_protein_1378442..1378672_POSITIVE 193 69 28 50 6 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 192 108 67 201 153 NC_002967:TDE1228|5end_pentapeptide_repeat_family_protein_1261889..1262119_POSITIVE 192 86 44 185 150 NC_002967:TDE0953|5end_branched-chain_amino_acid_ABC_transporter,_permease_protein_976863..977093_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 54 11 104 58 NC_002967:TDE0378|3end_hypothetical_protein_432516..432666_POSITIVE 211 130 82 80 29 NC_002967:TDE0112|3end_hypothetical_protein_132684..132834_POSITIVE 209 98 72 151 118 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 199 59 11 143 90 NC_002967:TDE1341|3end_hypothetical_protein_1378525..1378675_POSITIVE 191 96 59 100 69 NC_002967:TDE2060|3end_hypothetical_protein_2086843..2086993_POSITIVE 186 92 74 24 4 NC_002967:TDE2244|3end_hypothetical_protein_2284320..2284470_POSITIVE 185 78 34 101 52 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 185 40 9 149 114 NC_002967:TDE1267|3end_phosphoribosylamine--glycine_ligase_1301627..1301777_NEGATIVE 183 39 1 78 32 NC_002967:TDE1995|3end_magnesium_chelatase_family_protein_2014244..2014394_POSITIVE 183 82 47 145 105 NC_002967:TDE1435|3end_hypothetical_protein_1479543..1479693_POSITIVE 183 38 2 142 106 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 183 96 53 71 16 NC_002967:TDE1185|3end_lipoprotein,_putative_1211597..1211747_NEGATIVE 182 98 62 71 40 NC_002967:TDE1226|3end_zinc_ABC_transporter,_periplasmic_zinc-binding_protein_1259545..1259695_NEGATIVE 182 50 1 63 24 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 182 49 10 57 22 NC_002967:TDE0023|3end_acetyltransferase,_GNAT_family_28523..28673_NEGATIVE 181 47 9 139 95 NC_002967:TDE0868|3end_oxidoreductase,_FAD/FMN-binding_891472..891622_POSITIVE 180 103 63 149 109 NC_002967:TDE1211|3end_ATP-dependent_protease_ATP-binding_subunit_1245402..1245552_POSITIVE 179 31 8 122 93 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 179 28 1 114 85 NC_002967:TDE1070|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1097700..1097850_NEGATIVE 178 88 51 98 59 NC_002967:TDE1441|3end_dTDP-glucose_4,6-dehydratase_1487415..1487565_POSITIVE