Origin IGS: aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt .........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 aatctagggggagagggaaacttgttcagacgcaagtttccctctccccctaaaaccccctctcccttcaacgactgcttaggggcgcagcccctaagcacccgcatttttacaaaggttttttttcagcattgacatatttgaggctttaaagtattattataaaagaaacttatcctaaggagttttt Mask Tandem Repeat Region ================================================ aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt Find is-nt database================================================ Query_seq: TDE2419:TDE2420|TDE2419:TDE2420:hypothetical protein:DNA-directed RNA polymerase beta' subunit:<-<-:2444860..2445049 190 aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2419:TDE2420|TDE2419:TDE2420:hypothetical protein:DNA-directed RNA polymerase beta' subunit:<-<-:2444860..2445049 190 aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2419:TDE2420|TDE2419:TDE2420:hypothetical protein:DNA-directed RNA polymerase beta' subunit:<-<-:2444860..2445049 190 aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 84 End: 188 ................................................................................... M R V L R G C A P K Q S L K G E G V L G G E G N L R L N K F P S P P R .. Protein_Len: 37 Strand: - Start: 59 End: 169 .......................................................... H Q F F V K T F I R T S L P Q A G L C D N F P S P T K P P S P F K R R F M ..................... aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt 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: 89 Start: 31 End: 60 ..............................ATTGACATATTTGAGGCTTTAAAGTATTAT.................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.3 Tail_Score: -4.58685 Start: 85 End: 121 Full_Region: accccctctcccttc aacgactgcttaggggc gca gcccctaagcacccgca tttttacaaaggttt ....................................................................................aacgactgcttaggggcgcagcccctaagcacccgca..................................................................... TransTerm Strand: - Conf: 100 HP_score: -12.8 Tail_Score: -3.34488 Start: 86 End: 120 Full_Region: ccccctctcccttca acgactgcttaggggc gca gcccctaagcacccgc atttttacaaaggtt .....................................................................................acgactgcttaggggcgcagcccctaagcacccgc...................................................................... TransTerm Strand: - Conf: 100 HP_score: -16.3 Tail_Score: -2.60211 Start: 87 End: 119 Full_Region: cccctctcccttcaa cgactgcttaggggc gca gcccctaagcacccg catttttacaaaggt ......................................................................................cgactgcttaggggcgcagcccctaagcacccg....................................................................... TransTerm Strand: + Conf: 100 HP_score: -15.2 Tail_Score: -2.70932 Start: 90 End: 116 Full_Region: TTTGTAAAAATGCGG GTGCTTAGGGGC TGC GCCCCTAAGCAG TCGTTGAAGGGAGAG .........................................................................................GTGCTTAGGGGCTGCGCCCCTAAGCAG.......................................................................... Find igs database================================================ Query_seq: TDE2419:TDE2420|TDE2419:TDE2420:hypothetical protein:DNA-directed RNA polymerase beta' subunit:<-<-:2444860..2445049 190 aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: NC_002967_TDE2419_TDE2420|hypothetical protein:DNA-directed RNA polymerase beta' subunit|NEGATIVE:NEGATIVE|[2444860,2445049]|190 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgnnnnnnnncctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt aaaaactccttaggataagtttcttttataataatactttaaagcctcaaatatgtcaatgctgaaaaaaaacctttgtaaaaatgcgggtgcttaggggctgcgcccctaagcagtcgttgaagggagagggggttttagggggagagggaaacttgcgtctgaacaagtttccctctccccctagatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACUCCUUAGGAUAAGUUUCUUUUAUAAUAAUACUUUAAAGCCUCAAAUAUGUCAAUGCUGAAAAAAAACCUUUGUAAAAAUGCGGGUGCUUAGGGGCUGCGCCCCUAAGCAGUCGUUGAAGGGAGAGGGGGUUUUAGGGGGAGAGGGAAACUUGCGUCUGAACAAGUUUCCCUCUCCCCCUAGAUU .....((((((..((((.((((((((..............))))....)))).))))...............((((((.......((((.(((((((((((...))))))))))).))))))))))..))))))..((((((((((((((((((((((........)))))))))))))))))))))).. (-80.95) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUAGGGGGAGAGGGAAACUUGUUCAGACGCAAGUUUCCCUCUCCCCCUAAAACCCCCUCUCCCUUCAACGACUGCUUAGGGGCGCAGCCCCUAAGCACCCGCAUUUUUACAAAGGUUUUUUUUCAGCAUUGACAUAUUUGAGGCUUUAAAGUAUUAUUAUAAAAGAAACUUAUCCUAAGGAGUUUUU ....(((((((((((((((((((((......))))))))))))))))))))).........((((......((..(((((((((((...)))))))))))..))...........(((((((((((.(((.(..(.....)..).))).....(((....)))))))))))))).......))))..... (-74.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1091 130 81 221 172 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 573 149 105 227 184 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 479 80 31 174 127 NC_002967:TDE0902|5end_hypothetical_protein_920132..920362_NEGATIVE 446 121 85 196 161 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 441 150 103 166 111 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 426 119 71 160 109 NC_002967:TDE0617|5end_hypothetical_protein_650227..650457_NEGATIVE 415 144 103 75 29 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 399 127 83 81 29 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 395 138 92 225 176 NC_002967:TDE2600|5end_hypothetical_protein_2633958..2634188_POSITIVE 380 186 141 168 124 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 370 149 101 228 149 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 365 152 117 231 193 NC_002967:TDE2446|5end_malate_dehydrogenase_2476249..2476479_NEGATIVE 361 158 114 229 178 NC_002967:TDE2137|5end_hypothetical_protein_2166125..2166355_POSITIVE 358 136 91 57 18 NC_002967:TDE2020|5end_YD_repeat_protein_2044156..2044386_NEGATIVE 357 135 91 55 5 NC_002967:TDE1071|5end_peptide_ABC_transporter,_peptide-binding_protein_OppA_1100588..1100818_NEGATIVE 355 135 92 69 24 NC_002967:TDE0204|5end_glutamyl-tRNA_synthetase_236968..237198_POSITIVE 351 185 141 201 143 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 346 128 87 78 37 NC_002967:TDE2460|5end_aminotransferase,_class_V_2485983..2486213_POSITIVE 343 139 96 164 123 NC_002967:TDE2737|5end_hypothetical_protein_2791870..2792100_POSITIVE 340 185 141 160 110 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 590 185 141 84 40 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 527 158 111 57 6 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE 514 114 75 143 103 NC_002967:TDE1057|3end_hypothetical_protein_1086105..1086255_NEGATIVE 499 185 141 51 5 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 446 150 103 50 2 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 444 129 83 64 15 NC_002967:TDE1008|3end_flagellar_protein,_putative_1032806..1032956_POSITIVE 426 119 71 145 94 NC_002967:TDE0618|3end_hypothetical_protein_650242..650392_NEGATIVE 417 179 131 84 8 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 409 165 122 72 32 NC_002967:TDE0158|3end_hypothetical_protein_185724..185874_NEGATIVE 407 150 104 54 2 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 395 150 106 54 7 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 395 150 106 74 27 NC_002967:TDE0723|3end_hypothetical_protein_761661..761811_POSITIVE 395 150 106 54 7 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 395 150 106 54 7 NC_002967:TDE0715|3end_hypothetical_protein_750550..750700_POSITIVE 394 149 101 102 42 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 373 125 82 115 79 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 361 129 85 141 96 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 358 136 91 56 17 NC_002967:TDE2021|3end_hypothetical_protein_2044157..2044307_NEGATIVE 355 108 61 81 29 NC_002967:TDE1691|3end_hypothetical_protein_1747407..1747557_NEGATIVE 355 135 92 79 34 NC_002967:TDE0203|3end_hypothetical_protein_237058..237208_POSITIVE