Origin IGS: cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaatcttaaatttaagattgccattaatctttgatggtttttaaggtgggagttttcttcccgccttaaaatcaaaacaggcggcttttaaaggagtgtgatctttggg Mask Tandem Repeat Region ================================================ cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca Find is-nt database================================================ Query_seq: TDE2216:TDE2217|TDE2216:TDE2217:galactoside ABC transporter, ATP-binding protein:galactose/glucose-binding lipoprotein:<-<-:2256744..2256853 110 cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2216:TDE2217|TDE2216:TDE2217:galactoside ABC transporter, ATP-binding protein:galactose/glucose-binding lipoprotein:<-<-:2256744..2256853 110 cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2216:TDE2217|TDE2216:TDE2217:galactoside ABC transporter, ATP-binding protein:galactose/glucose-binding lipoprotein:<-<-:2256744..2256853 110 cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca Predict ORF larger than 30AA ================================================ cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca 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================================================ cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2216:TDE2217|TDE2216:TDE2217:galactoside ABC transporter, ATP-binding protein:galactose/glucose-binding lipoprotein:<-<-:2256744..2256853 110 cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE2216_TDE2217|galactoside ABC transporter, ATP-binding protein:galactose/glucose-binding lipoprotein|NEGATIVE:NEGATIVE|[2256744,2256853]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca cccaaagatcacactcctttaaaagccgcctgttttgattttaaggcgggaagaaaactcccaccttaaaaaccatcaaagattaatggcaatcttaaatttaagattca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCAAAGAUCACACUCCUUUAAAAGCCGCCUGUUUUGAUUUUAAGGCGGGAAGAAAACUCCCACCUUAAAAACCAUCAAAGAUUAAUGGCAAUCUUAAAUUUAAGAUUCA ........................((((....((((((((((((((.((((.......)))).)))))))....))))))).....)))).((((((....))))))... (-25.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUCUUAAAUUUAAGAUUGCCAUUAAUCUUUGAUGGUUUUUAAGGUGGGAGUUUUCUUCCCGCCUUAAAAUCAAAACAGGCGGCUUUUAAAGGAGUGUGAUCUUUGGG ..(((((((....)))))))(((((((.....)))))))((((((((((((((.....)))))))))))))).((((.((.((..(((....))).)).))...)))).. (-31.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 927 50 1 141 92 NC_002967:TDE2216|5end_galactoside_ABC_transporter,_ATP-binding_protein_2256653..2256883_NEGATIVE 342 70 24 229 171 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 329 50 2 224 178 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 308 50 4 79 38 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 300 65 25 80 39 NC_002967:TDE0886|5end_hypothetical_protein_903341..903571_POSITIVE 294 51 15 83 48 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 287 62 26 223 191 NC_002967:TDE2139|5end_hypothetical_protein_2172032..2172262_POSITIVE 280 60 14 154 97 NC_002967:TDE1591|5end_inorganic_polyphosphate/ATP-NAD_kinase,_putative_1638582..1638812_POSITIVE 270 49 1 138 87 NC_002967:TDE1048|5end_30S_ribosomal_protein_S7_1074482..1074712_POSITIVE 269 54 11 140 96 NC_002967:TDE2010|5end_hypothetical_protein_2031318..2031548_POSITIVE 267 50 2 97 43 NC_002967:TDE0006|5end_Snf2_family_protein_9694..9924_NEGATIVE 266 77 44 179 144 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 265 55 11 176 131 NC_002967:TDE2660|5end_hypothetical_protein_2697517..2697747_NEGATIVE 262 69 24 66 14 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 260 68 26 83 33 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 260 67 24 194 143 NC_002967:TDE1135|5end_hypothetical_protein_1165542..1165772_NEGATIVE 260 77 33 49 4 NC_002967:TDE0872|5end_recA_protein_894841..895071_POSITIVE 259 62 22 209 172 NC_002967:TDE2597|5end_ribulose-phosphate_3-epimerase_2632665..2632895_NEGATIVE 257 56 15 144 103 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 255 51 23 66 41 NC_002967:TDE1104|5end_tRNA_pseudouridine_synthase_B_1137786..1138016_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 49 9 44 8 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 308 50 4 66 25 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 300 65 25 43 2 NC_002967:TDE0885|3end_50S_ribosomal_protein_L19_903384..903534_POSITIVE 296 68 25 139 100 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 287 67 43 51 22 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 285 69 24 113 75 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 282 66 27 105 65 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 280 60 14 113 56 NC_002967:TDE1590|3end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1638621..1638771_POSITIVE 279 62 26 64 31 NC_002967:TDE0919|3end_hypothetical_protein_939125..939275_POSITIVE 270 49 1 127 76 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 265 49 17 110 75 NC_002967:TDE0096|3end_NADH_oxidase_114137..114287_POSITIVE 258 52 25 118 80 NC_002967:TDE2060|3end_hypothetical_protein_2086843..2086993_POSITIVE 257 50 4 59 12 NC_002967:TDE2614|3end_ApbE_family_protein_2656018..2656168_NEGATIVE 255 51 23 51 26 NC_002967:TDE1105|3end_ribosome-binding_factor_A_1137801..1137951_NEGATIVE 249 47 2 62 19 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 248 52 14 122 78 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 248 58 14 68 33 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 247 49 1 58 21 NC_002967:TDE2516|3end_hypothetical_protein_2542193..2542343_POSITIVE 245 49 1 119 80 NC_002967:TDE0813|3end_ABC_transporter,_ATP-binding_protein/permease_835707..835857_POSITIVE 245 52 13 149 119 NC_002967:TDE0485|3end_hypothetical_protein_542006..542156_NEGATIVE