Origin IGS: acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttttataggagattcgataaacagttcggcagaaattcagccttactgtttatctttcgagttttgtgctttgcacaaaatatcgtgttataggagaatgt Mask Tandem Repeat Region ================================================ acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac Find is-nt database================================================ Query_seq: TDE1849:TDE1850|TDE1849:TDE1850:hypothetical protein:ABC transporter, permease protein, putative:<-<-:1878214..1878316 103 acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1849:TDE1850|TDE1849:TDE1850:hypothetical protein:ABC transporter, permease protein, putative:<-<-:1878214..1878316 103 acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1849:TDE1850|TDE1849:TDE1850:hypothetical protein:ABC transporter, permease protein, putative:<-<-:1878214..1878316 103 acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 2 End: 97 . M R R Y C S I K H L A C F E F S L C Y P Q I E A S S N I S D G M ...... acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac 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================================================ acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -8.6 Tail_Score: -3.21593 Start: 17 End: 44 Full_Region: ttactgtttatcttt cgagttttgtgc ttt gcacaaaatatcg tgttataggagaatg ................cgagttttgtgctttgcacaaaatatcg........................................................... TransTerm Strand: - Conf: 77 HP_score: -10.4 Tail_Score: -2.94726 Start: 22 End: 40 Full_Region: tgtttatctttcgag ttttgtgc ttt gcacaaaa tatcgtgttatagga .....................ttttgtgctttgcacaaaa............................................................... Find igs database================================================ Query_seq: TDE1849:TDE1850|TDE1849:TDE1850:hypothetical protein:ABC transporter, permease protein, putative:<-<-:1878214..1878316 103 acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002967_TDE1849_TDE1850|hypothetical protein:ABC transporter, permease protein, putative|NEGATIVE:NEGATIVE|[1878214,1878316]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac acattctcctataacacgatattttgtgcaaagcacaaaactcgaaagataaacagtaaggctgaatttctgccgaactgtttatcgaatctcctataaaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUCUCCUAUAACACGAUAUUUUGUGCAAAGCACAAAACUCGAAAGAUAAACAGUAAGGCUGAAUUUCUGCCGAACUGUUUAUCGAAUCUCCUAUAAAAAC ................(((..((((((((...)))))))).)))...((((((((((..(((.(.....).)))..))))))))))................. (-28.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUAUAGGAGAUUCGAUAAACAGUUCGGCAGAAAUUCAGCCUUACUGUUUAUCUUUCGAGUUUUGUGCUUUGCACAAAAUAUCGUGUUAUAGGAGAAUGU .(((((((((.......((((((((((..(((.(.....).)))..))))))))))...((((((((((((...))))))))).)))..)))))))))..... (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 869 80 31 171 122 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 770 80 31 172 124 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 770 80 31 62 14 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 722 80 31 175 127 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 700 99 51 159 111 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 698 87 41 168 122 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 696 80 31 174 126 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 692 100 51 204 155 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 692 100 51 103 54 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 683 100 51 79 30 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 666 80 33 83 36 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 664 86 41 189 144 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 642 67 22 231 187 NC_002967:TDE0064|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_72651..72881_NEGATIVE 630 97 51 157 111 NC_002967:TDE1210|5end_ATP-dependent_protease_peptidase_subunit_1243329..1243559_POSITIVE 614 80 33 134 88 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 605 89 42 152 106 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 600 98 51 140 93 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 587 86 48 151 113 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 584 86 48 151 113 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 573 89 45 151 107 NC_002967:TDE2220|5end_prolyl-tRNA_synthetase_2260885..2261115_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 773 80 31 73 25 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 755 80 31 76 27 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 722 80 31 73 25 NC_002967:TDE1299|3end_hypothetical_protein_1335417..1335567_NEGATIVE 707 87 41 83 37 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 692 100 51 83 34 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 683 100 51 64 15 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 671 96 52 45 1 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 664 86 41 78 33 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 664 86 41 72 27 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 662 87 41 76 31 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 636 87 41 62 17 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 630 97 51 90 44 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 615 100 51 86 37 NC_002967:TDE0642|3end_hypothetical_protein_678460..678610_NEGATIVE 614 80 33 66 20 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 605 89 42 79 33 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 600 98 51 64 17 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 599 68 22 151 106 NC_002967:TDE1235|3end_hypothetical_protein_1269557..1269707_POSITIVE 593 80 35 67 22 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 587 86 48 139 101 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 555 86 41 67 22 NC_002967:TDE1130|3end_methyltransferase,_putative_1163240..1163390_POSITIVE