Origin IGS: tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgctttttttgctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcaaaaaaagcggtgtgaccgcttttttctatgcttttaaaatcaattgtggactgtattagatctcttagatgaactccagtttcatctgcatctgttcaacatattaaatcttggagta Mask Tandem Repeat Region ================================================ tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgctttttttgctta Find is-nt database================================================ Query_seq: SSA_0916:SSA_0917|SSA_0916:SSA_0917:2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, putative:Cobalamin-independent methionine synthase II, putative:-><-:929053..929176 124 tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgctttttttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0916:SSA_0917|SSA_0916:SSA_0917:2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, putative:Cobalamin-independent methionine synthase II, putative:-><-:929053..929176 124 tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgctttttttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0916:SSA_0917|SSA_0916:SSA_0917:2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, putative:Cobalamin-independent methionine synthase II, putative:-><-:929053..929176 124 tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgctttttttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgctttttttgctta Predict ORF larger than 30AA ================================================ tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgctttttttgctta 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================================================ tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgctttttttgctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0916:SSA_0917|SSA_0916:SSA_0917:2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, putative:Cobalamin-independent methionine synthase II, putative:-><-:929053..929176 124 tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgctttttttgctta Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_0916_SSA_0917|2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate hydrolase, putative:Cobalamin-independent methionine synthase II, putative|POSITIVE:NEGATIVE|[929053,929176]|124 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgc............ tactccaagatttaatatgttgaacagatgcagatgaaactggagttcatctaagagatctaatacagtccacaattgattttaaaagcatagaaaaaagcggtcacaccgc............ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUCCAAGAUUUAAUAUGUUGAACAGAUGCAGAUGAAACUGGAGUUCAUCUAAGAGAUCUAAUACAGUCCACAAUUGAUUUUAAAAGCAUAGAAAAAAGCGGUCACACCGC ..........(((..((((((..........(((((((.(....))))))))..((((((.................))))))...))))))..)))..((((.....)))) (-18.13) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGGUGUGACCGCUUUUUUCUAUGCUUUUAAAAUCAAUUGUGGACUGUAUUAGAUCUCUUAGAUGAACUCCAGUUUCAUCUGCAUCUGUUCAACAUAUUAAAUCUUGGAGUA ((((.....)))).........((((((..........((((...((...(((((....(((((((((....).)))))))).)))))..)).)))).........)))))) (-21.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 80 31 183 140 NC_009009:SSA_0920|5end_hypothetical_protein_930896..931126_POSITIVE 255 110 66 204 165 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 251 50 3 91 33 NC_009009:SSA_0391|5end_Pyruvate_oxidase,_putative_385946..386176_POSITIVE 236 89 46 224 172 NC_009009:SSA_1954|5end_Aminotransferase,_class-V,_putative_1951298..1951528_NEGATIVE 236 68 21 82 33 NC_009009:SSA_1847|5end_RRNA_methyltransferase_RsmB,_putative_1842004..1842234_NEGATIVE 231 74 34 157 119 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 227 46 3 55 2 NC_009009:SSA_0860|5end_N-acetylmuramidase/lysin,_putative_847615..847845_POSITIVE 221 89 41 55 17 NC_009009:SSA_2343|5end_hypothetical_protein_2346126..2346356_NEGATIVE 221 45 4 171 132 NC_009009:SSA_0724|5end_ABC-type_multidrug/protein/lipid_transport_system_(pediocin_PA-1_exporter),_ATPase_and_permease_components,_putative_708652..708882_POSITIVE 220 110 68 148 113 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 218 53 17 230 191 NC_009009:SSA_0663|5end_Acetyltransferase,_putative_648352..648582_POSITIVE 215 43 3 39 5 NC_009009:SSA_0790|5end_hypothetical_protein_773047..773277_POSITIVE 212 57 25 117 70 NC_009009:SSA_1275|5end_hypothetical_protein_1297606..1297836_NEGATIVE 211 70 25 164 120 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 211 70 25 64 18 NC_009009:SSA_0735|5end_Integral_membrane_protein,_putative_717103..717333_POSITIVE 210 50 3 145 101 NC_009009:SSA_0518|5end_Ethanolamine_utilization_protein_EutA,_putative_516610..516840_POSITIVE 209 68 21 62 3 NC_009009:SSA_0877|5end_Phosphoglycolate_phosphatase,_putative_871008..871238_POSITIVE 205 61 30 74 46 NC_009009:SSA_2132|5end_Ure_cluster_protein,_putative_2134170..2134400_POSITIVE 205 50 17 210 186 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 205 105 68 225 187 NC_009009:SSA_1219|5end_Sortase,_putative_1241337..1241567_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 70 25 68 19 NC_009009:SSA_0037|3end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_45614..45764_POSITIVE 246 76 31 144 109 NC_009009:SSA_0918|3end_Conserved_uncharacterized_protein_930945..931095_POSITIVE 220 110 68 151 116 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE 211 70 25 77 31 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 205 61 30 71 43 NC_009009:SSA_2131|3end_DNA-binding_protein,_putative_2134247..2134397_POSITIVE 205 75 32 74 25 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 204 33 4 143 107 NC_009009:SSA_0458|3end_Formylmethionine_deformylase,_putative_462099..462249_POSITIVE 203 58 15 60 23 NC_009009:SSA_2156|3end_Conserved_uncharacterized_protein_2156216..2156366_NEGATIVE 201 105 66 54 5 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 200 94 59 74 37 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 198 110 64 78 40 NC_009009:SSA_2014|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014019..2014169_NEGATIVE 198 70 29 141 100 NC_009009:SSA_1072|3end_Glutamate_5-kinase,_putative_1090944..1091094_POSITIVE 198 106 66 71 38 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 197 47 3 86 45 NC_009009:SSA_2069|3end_Prolyl-tRNA_synthetase,_putative_2071402..2071552_NEGATIVE 197 104 67 141 97 NC_009009:SSA_0726|3end_FmtA-like_protein,_putative_712784..712934_POSITIVE 196 59 19 104 56 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE 195 64 40 85 64 NC_009009:SSA_1235|3end_Dihydroorotase,_putative_1259959..1260109_NEGATIVE 194 89 42 70 38 NC_009009:SSA_1158|3end_hypothetical_protein_1187187..1187337_POSITIVE 194 70 21 130 81 NC_009009:SSA_0841|3end_hypothetical_protein_827236..827386_POSITIVE 193 75 33 64 32 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE