Origin IGS: atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct .........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 agatcttcctttcttttgctagtaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgattagggctgtaaaagctgatgaaatcagcgtaatagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagactcaagttccttttctctgat Mask Tandem Repeat Region ================================================ atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct Find is-nt database================================================ Query_seq: SSA_1008:SSA_1009|SSA_1008:SSA_1009:Galactokinase, putative:Galactose-1-phosphate-uridylyltransferase, putative:->->:1011175..1011393 219 atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1008:SSA_1009|SSA_1008:SSA_1009:Galactokinase, putative:Galactose-1-phosphate-uridylyltransferase, putative:->->:1011175..1011393 219 atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1008:SSA_1009|SSA_1008:SSA_1009:Galactokinase, putative:Galactose-1-phosphate-uridylyltransferase, putative:->->:1011175..1011393 219 atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 85 End: 198 .................................................................................... M G S I T L I S S A F T A L I N C A E V G R R N R I L T N Y R F L S H S L Y ..................... Protein_Len: 57 Strand: + Start: 48 End: 218 ............................................... M V F G L S S K T Q W L S G L Y Y A D F I S F Y S P N Q L C G G G T T K S N S N E L P I S V P L S L L A K E R K I . Protein_Len: 38 Strand: - Start: 48 End: 161 ............................................... N D K S Q R A L R L P Q T P E I V S I E D A K V A R I L Q A S T P R R F R M .......................................................... atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct 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================================================ atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -8.6 Tail_Score: -4.08945 Start: 99 End: 113 Full_Region: AGTGGGCTCTATTAC GCTGAT TTC ATCAGC TTTTACAGCCCTAAT ..................................................................................................GCTGATTTCATCAGC.......................................................................................................... Find igs database================================================ Query_seq: SSA_1008:SSA_1009|SSA_1008:SSA_1009:Galactokinase, putative:Galactose-1-phosphate-uridylyltransferase, putative:->->:1011175..1011393 219 atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct Intra-Species Hit: Count: 2 Min: 1 Max: 219 Len: 219 Subject: NC_009009_SSA_1008_SSA_1009|Galactokinase, putative:Galactose-1-phosphate-uridylyltransferase, putative|POSITIVE:POSITIVE|[1011175,1011393]|219 HSP 1 e-value: 1.0E-121 bit: 434.0 Len: 219 Query Start:1 Query End:219 Subject Strand: POSITIVE Subject Start: 1 Subject End: 219 atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct atcagagaaaaggaacttgagtctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctctttactagcaaaagaaaggaagatct Subject: NC_009009_SSA_0205_SSA_2393|NisK (sensor-receptor histidine kinase domain), putative:Transcriptional regulator, XRE family, putative|POSITIVE:POSITIVE|[203900,204195]|296 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 174 Query Start:23 Query End:196 Subject Strand: NEGATIVE Subject Start: 25 Subject End: 198 ......................ctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctcttt....................... ......................ctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctactacgctgatttcatcagcttttacagccctactcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctcttt....................... Inter-species Hit: Count: 1 Min: 79 Max: 191 Len: 113 Subject: NC_004116_SAG0025_SAG0026|phosphoribosylformylglycinamidine synthase, putative:amidophosphoribosyltransferase|POSITIVE:POSITIV E|[40309,40719]|411 HSP 1 e-value: 6.0E-13 bit: 75.8 Len: 113 Query Start:79 Query End:191 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 112 ..............................................................................ggttgagtgggctctattacgctgatttcatcagcttttacagccctaatcaactgtgcggaggtgggacgacgaaatcgaattc-taacgaattaccgatttctgtcccactc............................ ..............................................................................ggttgagtgggctctaattcgctgataa-atcaactcttacagccccactcaactgtgcggagg-gggacgacaaaatcgaattcctttggaattaccgatttttgtcccactc............................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUGAGUGGGCUCUAUUACGCUGAUUUCAUCAGCUUUUACAGCCCUAAUCAACUGUGCGGAGGUGGGACGACGAAAUCGAAUUCUAACGAAUUACCGAUUUCUGUCCCACUC ((((((..(((((.((..(.((((((...)))))))..)).)))))...)))))).......(((((((((..((((((((((((....)))))..)))))))))))))))). (-48.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUGGGACAGAAAUCGGUAAUUCGUUAGAAUUCGAUUUCGUCGUCCCACCUCCGCACAGUUGAUUAGGGCUGUAAAAGCUGAUGAAAUCAGCGUAAUAGAGCCCACUCAACC (((((((((.((((((((..((((....))))))))))))...)))))).)))......(((((...(((((.((...((((((...))))))....)).)))))..))))). (-46.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 437 70 21 193 144 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 326 62 21 72 36 NC_009009:SSA_1925|5end_Seryl-tRNA_synthetase,_putative_1913508..1913738_POSITIVE 322 90 43 229 183 NC_009009:SSA_2213|5end_Nucleotide_sugar_dehydratase,_putative_2215111..2215341_NEGATIVE 322 74 42 220 182 NC_009009:SSA_0292|5end_Transcriptional_regulator,_AraC_family_(arabinose_operon_control),_putative_286208..286438_POSITIVE 317 99 58 42 10 NC_009009:SSA_1111|5end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1136532..1136762_POSITIVE 316 90 53 67 27 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 316 70 21 59 3 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 316 57 11 57 1 NC_009009:SSA_0637|5end_Tryptophan_synthase_beta_chain,_putative_625719..625949_POSITIVE 315 60 11 66 16 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 309 55 15 181 135 NC_009009:SSA_2362|5end_L-serine_dehydratase_alpha_subunit_2364708..2364938_POSITIVE 307 36 1 45 14 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 305 79 31 187 135 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 300 74 31 206 157 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 293 63 21 224 189 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 292 71 31 231 183 NC_009009:SSA_0114|5end_50S_ribosomal_protein_L16,_putative_111979..112209_POSITIVE 291 66 21 193 134 NC_009009:SSA_0124|5end_30S_ribosomal_protein_S5,_putative_116422..116652_POSITIVE 290 75 34 215 160 NC_009009:SSA_0848|5end_Pyruvate_kinase_I,_fructose-stimulated,_putative_834439..834669_POSITIVE 290 44 1 89 37 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 288 46 1 89 47 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 286 89 41 214 167 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 931 110 61 58 9 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 316 57 11 67 11 NC_009009:SSA_0636|3end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625809..625959_POSITIVE 315 67 22 142 97 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 312 67 23 71 21 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 311 76 33 132 82 NC_009009:SSA_0712|3end_P-type_ATPase-metal_cation_transport_(calcium_efflux),_putative_696761..696911_NEGATIVE 307 60 11 146 87 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 307 36 1 45 14 NC_009009:SSA_0996|3end_cGMP-specific_phosphodiesterase,_putative_996859..997009_POSITIVE 300 74 31 132 83 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 295 75 34 65 30 NC_009009:SSA_0445|3end_hypothetical_protein_444776..444926_POSITIVE 292 46 1 147 109 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 290 44 1 85 33 NC_009009:SSA_0493|3end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_494483..494633_POSITIVE 288 46 1 116 74 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 287 76 31 55 8 NC_009009:SSA_2007|3end_Chaperone_protein_dnaK/HSP70,_putative_2007443..2007593_NEGATIVE 281 61 21 37 6 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 281 69 21 57 12 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 274 46 1 81 36 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 274 44 7 50 7 NC_009009:SSA_1281|3end_Uracil-DNA_glycosylase,_putative_1301608..1301758_NEGATIVE 272 100 55 43 1 NC_009009:SSA_1946|3end_Oligopeptide_transport_system_permease_protein,_putative_1937698..1937848_NEGATIVE 271 67 22 122 49 NC_009009:SSA_2110|3end_30S_ribosomal_protein_S7,_putative_2115109..2115259_NEGATIVE 269 47 4 148 104 NC_009009:SSA_2042|3end_hypothetical_protein_2046669..2046819_NEGATIVE