Origin IGS: gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctggcttgcttgatccttttctgcctgcaattttctggtgtataaaggaaattgctgtttgcgtatgtaaatgtaaaatctatctgcatataacatccatcatcggttgaagaggattgatgctagaagctgggacttactgattggtccggcttctttggtgttttggcggtgcctaaaagcttgtaaagaaagaaaatccctgcgggctcatgagggtctgcggatattttcctctttgaacttgcttttatggcctagtatcttaaggagtaatc Mask Tandem Repeat Region ================================================ gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct Find is-nt database================================================ Query_seq: SSA_1800:SSA_1801|SSA_1800:SSA_1801:UDP-N-acetylmuramate--L-alanine ligase, putative:hypothetical protein:<-<-:1782462..1782741 280 gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1800:SSA_1801|SSA_1800:SSA_1801:UDP-N-acetylmuramate--L-alanine ligase, putative:hypothetical protein:<-<-:1782462..1782741 280 gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1800:SSA_1801|SSA_1800:SSA_1801:UDP-N-acetylmuramate--L-alanine ligase, putative:hypothetical protein:<-<-:1782462..1782741 280 gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 25 End: 153 ........................ M K A S S K R K I S A D P H E P A G I F F L Y K L L G T A K T P K K P D Q S V S P S F ............................................................................................................................... Protein_Len: 32 Strand: + Start: 183 End: 278 ...................................................................................................................................................................................... M L Y A D R F Y I Y I R K Q Q F P L Y T R K L Q A E K D Q A S Q .. Protein_Len: 30 Strand: + Start: 190 End: 279 ............................................................................................................................................................................................. M Q I D F T F T Y A N S N F L Y T P E N C R Q K R I K Q A S . Protein_Len: 34 Strand: - Start: 172 End: 273 ........................................................................................................................................................................... G I I S T I H L Y I K C K C V C V A I E K I C W F I A P L F P D L M ....... Protein_Len: 60 Strand: - Start: 2 End: 184 . S R L I S P W L L L N L S S F I R L G E H A R L S K R E K C A K L C R W F V L S A P G I L L D W S R A D I R K L R H H M ................................................................................................ gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct 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================================================ gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -2.4 Tail_Score: -5.18866 Start: 69 End: 79 Full_Region: CGCAGACCCTCATGA GCCC GCA GGGA TTTTCTTTCTTTACA ....................................................................GCCCGCAGGGA......................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1800:SSA_1801|SSA_1800:SSA_1801:UDP-N-acetylmuramate--L-alanine ligase, putative:hypothetical protein:<-<-:1782462..1782741 280 gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct Intra-Species Hit: Count: 1 Min: 1 Max: 280 Len: 280 Subject: NC_009009_SSA_1800_SSA_1801|UDP-N-acetylmuramate--L-alanine ligase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1782462,1782741]|280 HSP 1 e-value: 1.0E-157 bit: 555.0 Len: 280 Query Start:1 Query End:280 Subject Strand: POSITIVE Subject Start: 1 Subject End: 280 gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct gattactccttaagatactaggccataaaagcaagttcaaagaggaaaatatccgcagaccctcatgagcccgcagggattttctttctttacaagcttttaggcaccgccaaaacaccaaagaagccggaccaatcagtaagtcccagcttctagcatcaatcctcttcaaccgatgatggatgttatatgcagatagattttacatttacatacgcaaacagcaatttcctttatacaccagaaaattgcaggcagaaaaggatcaagcaagccagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUACUCCUUAAGAUACUAGGCCAUAAAAGCAAGUUCAAAGAGGAAAAUAUCCGCAGACCCUCAUGAGCCCGCAGGGAUUUUCUUUCUUUACAAGCUUUUAGGCACCGCCAAAACACCAAAGAAGCCGGACCAAUCAGUAAGUCCCAGCUUCUAGCAUCAAUCCUCUUCAACCGAUGAUGGAUGUUAUAUGCAGAUAGAUUUUACAUUUACAUACGCAAACAGCAAUUUCCUUUAUACACCAGAAAAUUGCAGGCAGAAAAGGAUCAAGCAAGCCAGCU ......(((((..........(((.(((((((..((..((((((((((((.(((((.(.(.(....).).).)).))))))))).))))))))..))))))))))...(((..........((((((.((((..........))))..)))))).((((..((((((.((....)).)).)))).....))))..............................(((((((.((.........)).))))))).)))....)))))...(((......))) (-62.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGGCUUGCUUGAUCCUUUUCUGCCUGCAAUUUUCUGGUGUAUAAAGGAAAUUGCUGUUUGCGUAUGUAAAUGUAAAAUCUAUCUGCAUAUAACAUCCAUCAUCGGUUGAAGAGGAUUGAUGCUAGAAGCUGGGACUUACUGAUUGGUCCGGCUUCUUUGGUGUUUUGGCGGUGCCUAAAAGCUUGUAAAGAAAGAAAAUCCCUGCGGGCUCAUGAGGGUCUGCGGAUAUUUUCCUCUUUGAACUUGCUUUUAUGGCCUAGUAUCUUAAGGAGUAAUC ((((..((.(((..(((((((((.(((.((((((((((.........)))))))))).(..((.(((((((.(((.......))).)))))))..))..)......))).)))))))))..).)).)).)))).(((((........))))).(((((((.((....((((....((((((((((..(((((((..((((((..((((((((((....))))))))))..)))))).)))))..))..))))))).)))))))...)).))))))).... (-94.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1017 80 31 171 122 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 341 165 123 208 151 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 336 149 107 61 23 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 333 109 67 199 158 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 332 199 153 171 120 NC_009009:SSA_2041|5end_Leucine-rich_protein,_putative_2046682..2046912_NEGATIVE 327 146 101 84 35 NC_009009:SSA_0206|5end_hypothetical_protein_204256..204486_POSITIVE 321 180 132 73 25 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 319 187 145 52 3 NC_009009:SSA_0882|5end_Phosphoserine_phosphatase,_putative_876903..877133_POSITIVE 318 49 8 151 103 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 315 100 51 66 3 NC_009009:SSA_1982|5end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975873..1976103_NEGATIVE 315 79 34 224 169 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 314 158 118 197 144 NC_009009:SSA_1665|5end_hypothetical_protein_1665353..1665583_NEGATIVE 314 157 116 209 155 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 312 120 71 187 135 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 312 99 53 102 48 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 310 150 102 178 127 NC_009009:SSA_2089|5end_L-xylulose-5-phosphate_3-epimerase,_putative_2094339..2094569_NEGATIVE 309 149 102 143 97 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 304 100 51 61 2 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 303 127 81 71 24 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 302 166 122 71 11 NC_009009:SSA_1038|5end_Lipoprotein,_putative_1052579..1052809_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 140 94 141 93 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 336 149 107 45 7 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 327 146 101 87 38 NC_009009:SSA_2393|3end_Transcriptional_regulator,_XRE_family,_putative_204339..204489_POSITIVE 321 180 132 57 9 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 319 164 122 47 11 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 313 100 52 68 30 NC_009009:SSA_2168|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2168563..2168713_POSITIVE 300 107 63 50 5 NC_009009:SSA_1266|3end_crcB-like_protein_1,_putative_1290650..1290800_NEGATIVE 296 167 127 111 64 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 292 100 51 114 51 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 291 100 52 59 1 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE 290 77 53 140 116 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE 287 92 56 137 106 NC_009009:SSA_1357|3end_hypothetical_protein_1372077..1372227_NEGATIVE 287 110 62 64 9 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 285 166 122 58 16 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 283 88 43 87 27 NC_009009:SSA_2281|3end_hypothetical_protein_2281912..2282062_NEGATIVE 283 79 31 142 88 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 279 169 125 58 8 NC_009009:SSA_2353|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2354550..2354700_NEGATIVE 279 105 69 151 104 NC_009009:SSA_0937|3end_Arsenate_reductase,_glutaredoxin_family,_putative_946664..946814_POSITIVE 278 110 61 62 7 NC_009009:SSA_0759|3end_Acetylglutamate_kinase,_putative_742658..742808_POSITIVE 276 148 102 144 94 NC_009009:SSA_1640|3end_hypothetical_protein_1642108..1642258_NEGATIVE