Origin IGS: gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatattttccttactattaactttgcgatgtttttcataagtattgaaatacttatgaaaaactcgtcggtaattgataaaaatctaataggatttttatcaattac Mask Tandem Repeat Region ================================================ gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt Find is-nt database================================================ Query_seq: TDE2504:TDE2505|TDE2504:TDE2505:O-sialoglycoprotein endopeptidase:hypothetical protein:->->:2530158..2530264 107 gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2504:TDE2505|TDE2504:TDE2505:O-sialoglycoprotein endopeptidase:hypothetical protein:->->:2530158..2530264 107 gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2504:TDE2505|TDE2504:TDE2505:O-sialoglycoprotein endopeptidase:hypothetical protein:->->:2530158..2530264 107 gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 4 End: 105 ... M D K N P I R F L S I T D E F F I S I S I L M K N I A K L I V R K I .. Protein_Len: 34 Strand: - Start: 3 End: 104 .. I S L F G I L N K D I V S S N K M L I E I S I F F M A F N I T L F M ... gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt 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================================================ gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -8.9 Tail_Score: -2.78216 Start: 38 End: 85 Full_Region: tccttactattaact ttgcgatgtttttcataagtat tgaa atacttatgaaaaactcgtcgg taattgataaaaatc .....................................ttgcgatgtttttcataagtattgaaatacttatgaaaaactcgtcgg...................... Find igs database================================================ Query_seq: TDE2504:TDE2505|TDE2504:TDE2505:O-sialoglycoprotein endopeptidase:hypothetical protein:->->:2530158..2530264 107 gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_002967_TDE2504_TDE2505|O-sialoglycoprotein endopeptidase:hypothetical protein|POSITIVE:POSITIVE|[2530158,2530264]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt gtaattgataaaaatcctattagatttttatcaattaccgacgagtttttcataagtatttcaatacttatgaaaaacatcgcaaagttaatagtaaggaaaatatt HSP 2 e-value: 4.0E-6 bit: 52.0 Len: 34 Query Start:45 Query End:78 Subject Strand: NEGATIVE Subject Start: 45 Subject End: 78 ............................................gtttttcataagtatttcaatacttatgaaaaac............................. ............................................gtttttcataagtattgaaatacttatgaaaaac............................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAUUGAUAAAAAUCCUAUUAGAUUUUUAUCAAUUACCGACGAGUUUUUCAUAAGUAUUUCAAUACUUAUGAAAAACAUCGCAAAGUUAAUAGUAAGGAAAAUAUU ((((((((((((((((......)))))))))))))))).(.((((((((((((((((((....))))))))))))))).))))........................ (-36.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUUUUCCUUACUAUUAACUUUGCGAUGUUUUUCAUAAGUAUUGAAAUACUUAUGAAAAACUCGUCGGUAAUUGAUAAAAAUCUAAUAGGAUUUUUAUCAAUUAC ........................((((.(((((((((((((((....)))))))))))))))))))..(((((((((((((((((....))))))))))))))))) (-37.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 462 89 42 230 177 NC_002967:TDE1507|5end_L-serine_dehydratase,_iron-sulfur-dependent,_beta_subunit_1555724..1555954_NEGATIVE 426 83 42 231 183 NC_002967:TDE1852|5end_ABC_transporter,_ATP-binding_protein_1881866..1882096_NEGATIVE 282 82 42 159 120 NC_002967:TDE2514|5end_serine/threonine_protein_phosphatase_family_protein_2540532..2540762_NEGATIVE 242 78 40 98 60 NC_002967:TDE1531|5end_hypothetical_protein_1575951..1576181_POSITIVE 241 100 69 30 1 NC_002967:TDE1853|5end_hypothetical_protein_1882082..1882312_NEGATIVE 230 60 15 61 21 NC_002967:TDE1472|5end_flagellar_hook-associated_protein_1520715..1520945_NEGATIVE 223 85 46 77 39 NC_002967:TDE1000|5end_3-hydroxyacid_dehydrogenase_family_protein_1026763..1026993_POSITIVE 220 50 7 53 11 NC_002967:TDE0844|5end_pyruvate_phosphate_dikinase,_putative_864886..865116_POSITIVE 215 64 31 157 124 NC_002967:TDE1762|5end_hydrolase,_haloacid_dehalogenase-like_family_1810904..1811134_NEGATIVE 214 58 16 50 3 NC_002967:TDE0338|5end_methyl-accepting_chemotaxis_protein-like_protein_377317..377547_POSITIVE 205 43 1 109 54 NC_002967:TDE0173|5end_FtsK/SpoIIIE_family_protein_203970..204200_POSITIVE 196 51 11 209 168 NC_002967:TDE0843|5end_hypothetical_protein_863850..864080_POSITIVE 193 89 43 176 136 NC_002967:TDE0156|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_183571..183801_NEGATIVE 192 46 5 131 92 NC_002967:TDE0952|5end_ABC_transporter,_ATP-binding_protein_975322..975552_POSITIVE 192 56 16 207 158 NC_002967:TDE0650|5end_hypothetical_protein_684697..684927_POSITIVE 188 60 15 152 101 NC_002967:TDE0305|5end_GTP-binding_protein_YchF_336751..336981_NEGATIVE 187 76 32 112 70 NC_002967:TDE2414|5end_hypothetical_protein_2441620..2441850_NEGATIVE 187 69 34 85 36 NC_002967:TDE0628|5end_molecular_chaperone_DnaK_660609..660839_POSITIVE 185 64 22 187 142 NC_002967:TDE0327|5end_CRISPR-associated_SAG0894_family_protein_360881..361111_POSITIVE 184 100 59 120 76 NC_002967:TDE1285|5end_flagellar_motor_switch_protein_FliG_,_putative_1320924..1321154_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 461 86 42 134 83 NC_002967:TDE1853|3end_hypothetical_protein_1881966..1882116_NEGATIVE 450 80 37 128 78 NC_002967:TDE2464|3end_hypothetical_protein_2489369..2489519_POSITIVE 374 82 42 49 9 NC_002967:TDE2504|3end_O-sialoglycoprotein_endopeptidase_2530097..2530247_POSITIVE 348 90 61 42 12 NC_002967:TDE1629|3end_dihydrolipoamide_dehydrogenase_1677153..1677303_NEGATIVE 224 90 45 54 4 NC_002967:TDE2465|3end_hypothetical_protein_2489391..2489541_NEGATIVE 216 50 16 42 4 NC_002967:TDE0843|3end_hypothetical_protein_864955..865105_POSITIVE 205 43 1 84 29 NC_002967:TDE0172|3end_undecaprenyl_pyrophosphate_phosphatase_204025..204175_POSITIVE 196 51 11 122 81 NC_002967:TDE0842|3end_cytoplasmic_filament_protein_A_863843..863993_POSITIVE 192 46 5 107 68 NC_002967:TDE0951|3end_lipoprotein,_putative_975378..975528_POSITIVE 188 60 15 113 62 NC_002967:TDE0306|3end_signal_peptide_peptidase_SppA_336790..336940_NEGATIVE 187 69 34 64 15 NC_002967:TDE0627|3end_co-chaperone_protein_GrpE_660668..660818_POSITIVE 180 64 22 129 88 NC_002967:TDE2754|3end_ornithine_cyclodeaminase_2810761..2810911_NEGATIVE 173 79 33 51 5 NC_002967:TDE2758|3end_hypothetical_protein_2814401..2814551_POSITIVE 172 60 18 120 83 NC_002967:TDE0329|3end_CRISPR-associated_protein_Cas2_366327..366477_POSITIVE 172 90 47 90 52 NC_002967:TDE0125|3end_GGDEF_domain_protein_142895..143045_NEGATIVE 171 63 40 64 41 NC_002967:TDE1997|3end_hypothetical_protein_2015256..2015406_POSITIVE 170 55 11 73 21 NC_002967:TDE1897|3end_phosphoribosylglycinamide_formyltransferase_1917525..1917675_NEGATIVE 166 54 15 68 39 NC_002967:TDE0806|3end_hypothetical_protein_828340..828490_NEGATIVE 164 60 38 77 55 NC_002967:TDE0686|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_723757..723907_POSITIVE 162 65 38 100 71 NC_002967:TDE1584|3end_lipoprotein,_putative_1632854..1633004_POSITIVE