Origin IGS: acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtatagcaggcggactcaatccccgcagagggaaaccatgaattttagggggtgcgataaacagttcggcagaaattcagcctcactgtttatctgccgagtttgcctttcggcaaacgtcgcattattgt Mask Tandem Repeat Region ================================================ acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac Find is-nt database================================================ Query_seq: TDE2394:TDE2395|TDE2394:TDE2395:hypothetical protein:Jag protein, putative:<-<-:2422703..2422833 131 acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2394:TDE2395|TDE2394:TDE2395:hypothetical protein:Jag protein, putative:<-<-:2422703..2422833 131 acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2394:TDE2395|TDE2394:TDE2395:hypothetical protein:Jag protein, putative:<-<-:2422703..2422833 131 acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 2 End: 94 . L L A V N A S L C V R C I F L S A S N R G F Q K D C G R F N M ..................................... Protein_Len: 30 Strand: - Start: 1 End: 90 C Y H S T Q R F A F E A S L C H P Q I E A S S N I A G G L M ......................................... acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac 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================================================ acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 63 HP_score: -5.8 Tail_Score: -3.84451 Start: 31 End: 67 Full_Region: gggtgcgataaacag ttcggcagaaattcag cctca ctgtttatctgccgag tttgcctttcggcaa ..............................ttcggcagaaattcagcctcactgtttatctgccgag................................................................ TransTerm Strand: - Conf: 56 HP_score: -7.1 Tail_Score: -2.90349 Start: 32 End: 66 Full_Region: ggtgcgataaacagt tcggcagaaattcag cctca ctgtttatctgccga gtttgcctttcggca ...............................tcggcagaaattcagcctcactgtttatctgccga................................................................. Find igs database================================================ Query_seq: TDE2394:TDE2395|TDE2394:TDE2395:hypothetical protein:Jag protein, putative:<-<-:2422703..2422833 131 acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_002967_TDE2394_TDE2395|hypothetical protein:Jag protein, putative|NEGATIVE:NEGATIVE|[2422703,2422833]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac acaataatgcgacgtttgccgaaaggcaaactcggcagataaacagtgaggctgaatttctgccgaactgtttatcgcaccccctaaaattcatggtttccctctgcggggattgagtccgcctgctatac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAUAAUGCGACGUUUGCCGAAAGGCAAACUCGGCAGAUAAACAGUGAGGCUGAAUUUCUGCCGAACUGUUUAUCGCACCCCCUAAAAUUCAUGGUUUCCCUCUGCGGGGAUUGAGUCCGCCUGCUAUAC ........((...(((((((....)))))))..(((.((((((((((..(((.(.....).)))..))))))))))............(((((....(((((.....))))).)))))..))).))..... (-49.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUAGCAGGCGGACUCAAUCCCCGCAGAGGGAAACCAUGAAUUUUAGGGGGUGCGAUAAACAGUUCGGCAGAAAUUCAGCCUCACUGUUUAUCUGCCGAGUUUGCCUUUCGGCAAACGUCGCAUUAUUGU .......((((((((((.((((((.((..((....)).)).......))))))((((((((((((..(((.(.....).)))..)))))))))).)).))))))))))..((((....))))......... (-49.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1016 130 81 221 172 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 958 70 21 183 134 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 958 70 21 184 135 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 958 70 21 83 34 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 940 50 1 224 175 NC_002967:TDE1903|5end_hypothetical_protein_1922417..1922647_POSITIVE 884 50 1 84 35 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 884 50 1 224 175 NC_002967:TDE1693|5end_hypothetical_protein_1749226..1749456_NEGATIVE 864 50 1 224 175 NC_002967:TDE0641|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_678282..678512_NEGATIVE 851 76 31 65 20 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 769 50 3 63 16 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 762 77 31 179 134 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 762 77 31 69 24 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 750 80 31 184 136 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 747 77 31 178 132 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 742 76 31 89 44 NC_002967:TDE1131|5end_hypothetical_protein_1163182..1163412_POSITIVE 741 50 3 230 185 NC_002967:TDE2018|5end_lipoprotein,_putative_2040550..2040780_NEGATIVE 714 77 31 182 137 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 675 40 1 231 192 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 673 50 1 222 173 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 673 50 1 54 5 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 958 70 21 72 23 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 958 70 21 63 14 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 958 70 21 66 17 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 873 60 11 56 7 NC_002967:TDE0642|3end_hypothetical_protein_678460..678610_NEGATIVE 851 76 31 50 5 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 772 70 21 55 7 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 771 76 31 82 37 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 769 50 3 48 1 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 761 77 31 83 37 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 747 77 31 74 28 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 742 76 31 67 22 NC_002967:TDE1130|3end_methyltransferase,_putative_1163240..1163390_POSITIVE 731 76 31 79 35 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 721 70 25 69 25 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 714 77 31 80 35 NC_002967:TDE1299|3end_hypothetical_protein_1335417..1335567_NEGATIVE 698 76 31 73 28 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 670 78 38 144 101 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 659 76 38 79 41 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 619 76 37 76 37 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 613 86 41 62 17 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 594 90 49 44 1 NC_002967:TDE0467|3end_hypothetical_protein_519006..519156_NEGATIVE