Origin IGS: aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cggtatttttccgtaaaattcacgaaaatctacgaaaatgcacgaaaacaagcttgacaaatcataaaaaatatttatcattaagaaaagtctttaaaaaaggagaatctttacttt Mask Tandem Repeat Region ================================================ aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg Find is-nt database================================================ Query_seq: TDE0364:TDE0365|TDE0364:TDE0365:ABC transporter, ATP-binding protein:hypothetical protein:<-<-:411696..411812 117 aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0364:TDE0365|TDE0364:TDE0365:ABC transporter, ATP-binding protein:hypothetical protein:<-<-:411696..411812 117 aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0364:TDE0365|TDE0364:TDE0365:ABC transporter, ATP-binding protein:hypothetical protein:<-<-:411696..411812 117 aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 2 End: 100 . L L S E G K K F V K R L S L Y K K H N T L S T K T C K R L N E H M ................. aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg 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: 82 Start: 28 End: 57 ...........................CTTTTCTTAATGATAAATATTTTTTATGAT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0364:TDE0365|TDE0364:TDE0365:ABC transporter, ATP-binding protein:hypothetical protein:<-<-:411696..411812 117 aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_002967_TDE0364_TDE0365|ABC transporter, ATP-binding protein:hypothetical protein|NEGATIVE:NEGATIVE|[411696,411812]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg aaagtaaagattctccttttttaaagacttttcttaatgataaatattttttatgatttgtcaagcttgttttcgtgcattttcgtagattttcgtgaattttacggaaaaataccg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUAAAGAUUCUCCUUUUUUAAAGACUUUUCUUAAUGAUAAAUAUUUUUUAUGAUUUGUCAAGCUUGUUUUCGUGCAUUUUCGUAGAUUUUCGUGAAUUUUACGGAAAAAUACCG .((((.((((.....(((.....))).....))))..((((((((..........)))))))).))))......(((..((((((((((.(((...))).))))))))))..))).. (-15.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUAUUUUUCCGUAAAAUUCACGAAAAUCUACGAAAAUGCACGAAAACAAGCUUGACAAAUCAUAAAAAAUAUUUAUCAUUAAGAAAAGUCUUUAAAAAAGGAGAAUCUUUACUUU (((((((((..((((...............))))))))))).))......................................(((.(((((((((......)))))..)))).))). (-10.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 110 61 201 152 NC_002967:TDE0364|5end_ABC_transporter,_ATP-binding_protein_411605..411835_NEGATIVE 274 88 47 178 140 NC_002967:TDE2633|5end_hypothetical_protein_2674359..2674589_POSITIVE 268 102 63 81 39 NC_002967:TDE0929|5end_ornithine_carbamoyltransferase_952735..952965_NEGATIVE 257 46 6 155 108 NC_002967:TDE1495|5end_hypothetical_protein_1540216..1540446_NEGATIVE 256 96 53 206 158 NC_002967:TDE2119|5end_glycine_reductase_complex_selenoprotein_GrdB2_2152693..2152923_NEGATIVE 256 108 63 51 11 NC_002967:TDE0708|5end_nitroreductase_family_protein_743900..744130_POSITIVE 256 104 66 171 127 NC_002967:TDE0606|5end_ParB_family_protein_644132..644362_NEGATIVE 252 90 41 96 50 NC_002967:TDE2718|5end_magnesium_transporter_2775910..2776140_NEGATIVE 252 107 68 116 68 NC_002967:TDE0735|5end_hypothetical_protein_775003..775233_NEGATIVE 240 110 66 217 175 NC_002967:TDE2356|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2391089..2391319_POSITIVE 238 95 51 164 115 NC_002967:TDE2624|5end_hypothetical_protein_2664905..2665135_NEGATIVE 237 109 70 121 85 NC_002967:TDE1717|5end_hypothetical_protein_1771431..1771661_POSITIVE 236 107 65 153 109 NC_002967:TDE0897|5end_ABC_transporter,_ATP-binding/permease_protein_914113..914343_POSITIVE 234 98 63 208 171 NC_002967:TDE0887|5end_PIN_domain_protein_904752..904982_NEGATIVE 233 98 56 69 19 NC_002967:TDE0769|5end_ribosomal_protein_L23_807634..807864_POSITIVE 233 107 62 231 187 NC_002967:TDE0515|5end_hypothetical_protein_563783..564013_NEGATIVE 232 108 61 67 9 NC_002967:TDE1624|5end_glycine_dehydrogenase_subunit_2_1673519..1673749_NEGATIVE 232 50 8 191 138 NC_002967:TDE0229|5end_ATPase_family_protein_262746..262976_NEGATIVE 230 96 54 133 81 NC_002967:TDE2685|5end_flagellar_synthesis_regulator_FleN_2725783..2726013_NEGATIVE 229 94 52 99 49 NC_002967:TDE1169|5end_phage_DNA-binding_protein,_excisionase_family_1199724..1199954_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 107 68 119 71 NC_002967:TDE0736|3end_hypothetical_protein_775000..775150_NEGATIVE 238 95 51 144 95 NC_002967:TDE2625|3end_ABC_transporter,_ATP-binding/permease_protein_2664925..2665075_NEGATIVE 233 98 56 66 16 NC_002967:TDE0768|3end_50S_ribosomal_protein_L4_807711..807861_POSITIVE 232 108 61 67 9 NC_002967:TDE1625|3end_glycine_cleavage_system_P_protein,_subunit_1_1673519..1673669_NEGATIVE 232 50 8 138 85 NC_002967:TDE0230|3end_DNA_replication_and_repair_protein_RecF_262799..262949_NEGATIVE 230 96 54 131 79 NC_002967:TDE2686|3end_flagellar_biosynthetic_protein_FlhF_2725785..2725935_NEGATIVE 229 88 54 96 51 NC_002967:TDE0893|3end_ABC_transporter,_ATP-binding_protein_910451..910601_POSITIVE 229 96 51 104 46 NC_002967:TDE0192|3end_hypothetical_protein_227817..227967_NEGATIVE 228 98 64 44 4 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 227 109 64 130 67 NC_002967:TDE0089|3end_transglutaminase-like_domain_protein_106875..107025_NEGATIVE 225 85 44 127 81 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 223 100 57 120 70 NC_002967:TDE1148|3end_hypothetical_protein_1185974..1186124_NEGATIVE 214 107 69 137 94 NC_002967:TDE2356|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2392098..2392248_POSITIVE 213 102 61 139 101 NC_002967:TDE2264|3end_ABC_transporter,_ATP-binding/permease_protein_2300243..2300393_NEGATIVE 209 77 47 151 125 NC_002967:TDE2632|3end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2674424..2674574_POSITIVE 209 99 56 88 44 NC_002967:TDE1332|3end_hflK_protein,_putative_1369078..1369228_POSITIVE 209 98 61 146 107 NC_002967:TDE1020|3end_dicarboxylate_transporter,_periplasmic_dicarboxylate-binding_protein,_putative_1051565..1051715_NEGATIVE 207 89 59 122 94 NC_002967:TDE2295|3end_mechanosensitive_ion_channel_family_protein_2334283..2334433_POSITIVE 206 108 64 97 46 NC_002967:TDE2477|3end_selenocysteine_synthase_2500949..2501099_POSITIVE 205 97 52 147 98 NC_002967:TDE2289|3end_phosphoribulokinase/uridine_kinase_family_protein_2327496..2327646_POSITIVE