Origin IGS: ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacaaaccataacggatatacnnnnnttaattaattaannnnnagcaggtctagctctagcggcatgcgggtcatctcaatcaagcaatgctgacaagacatactcttatatctttgtcagcaaccctgatacc Mask Tandem Repeat Region ================================================ ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta Find is-nt database================================================ Query_seq: SMT_1815:SMT_1816|SMT_1815:SMT_1816:K02035 peptide/nickel transport system substrate-binding protein:K02026 multiple sugar transport system permease protein:<-->:1790819..1790952 134 ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1815:SMT_1816|SMT_1815:SMT_1816:K02035 peptide/nickel transport system substrate-binding protein:K02026 multiple sugar transport system permease protein:<-->:1790819..1790952 134 ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1815:SMT_1816|SMT_1815:SMT_1816:K02035 peptide/nickel transport system substrate-binding protein:K02026 multiple sugar transport system permease protein:<-->:1790819..1790952 134 ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta Predict ORF larger than 30AA ================================================ ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta 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================================================ ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1815:SMT_1816|SMT_1815:SMT_1816:K02035 peptide/nickel transport system substrate-binding protein:K02026 multiple sugar transport system permease protein:<-->:1790819..1790952 134 ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: smit_SMT_1815_SMT_1816|K02035 peptide/nickel transport system substrate-binding protein:K02026 multiple sugar transport system permease protein|NEGATIVE:POSITIVE|[1790819,1790952]|134 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta ggtatcagggttgctgacaaagatataagagtatgtcttgtcagcattgcttgattgagatgacccgcatgccgctagagctagacctgctnnnnnttaattaattaannnnngtatatccgttatggtttgta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAUCAGGGUUGCUGACAAAGAUAUAAGAGUAUGUCUUGUCAGCAUUGCUUGAUUGAGAUGACCCGCAUGCCGCUAGAGCUAGACCUGCUNNNNNUUAAUUAAUUAANNNNNGUAUAUCCGUUAUGGUUUGUA (((((..(((((((((((((.((((((....))))))))))))))....(((....)))..)))))..)))))......((.(((((.((...............................))...))))))). (-32.58) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAAACCAUAACGGAUAUACNNNNNUUAAUUAAUUAANNNNNAGCAGGUCUAGCUCUAGCGGCAUGCGGGUCAUCUCAAUCAAGCAAUGCUGACAAGACAUACUCUUAUAUCUUUGUCAGCAACCCUGAUACC ......((.....))..............................((((....((....)).((.((.(((....)))...)).))..(((((((((((.(((....))).)).)))))))))..))))..... (-23.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1055 90 41 181 132 smit:SMT_1815|5end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1790728..1790958_NEGATIVE 358 90 44 46 3 smit:SMT_151|5end_K02073_D-methionine_transport_system_substrate-binding_protein_99474..99704_POSITIVE 335 82 43 227 187 smit:SMT_152|5end_sensor_histidine_kinase,_putative_100759..100989_POSITIVE 329 90 42 55 13 smit:SMT_1208|5end_choline_binding_protein_PcpA_1169690..1169920_NEGATIVE 316 90 43 72 13 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 297 90 44 197 160 smit:SMT_1353|5end_GTP-binding_protein_1331589..1331819_NEGATIVE 297 53 13 48 6 smit:SMT_221|5end_prolyl-tRNA_synthetase_153019..153249_POSITIVE 296 90 41 211 160 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 296 90 43 125 67 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 295 91 53 201 168 smit:SMT_1461|5end_putative_phosphate_ABC_transporter_(ATP-binding_protein)_1442324..1442554_POSITIVE 292 88 41 56 1 smit:SMT_848|5end_hypothetical_protein_795153..795383_NEGATIVE 292 89 42 213 176 smit:SMT_118|5end_K02026_multiple_sugar_transport_system_permease_protein_69430..69660_POSITIVE 291 90 43 230 171 smit:SMT_2044|5end_transcriptional_activator_TipA,_putative_1955885..1956115_NEGATIVE 291 90 43 215 156 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 291 90 43 188 129 smit:SMT_2008|5end_K07485_transposase_1928662..1928892_NEGATIVE 291 90 43 206 147 smit:SMT_2001|5end_membrane_protease_protein_family_1923387..1923617_POSITIVE 291 90 43 151 92 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 291 90 43 151 92 smit:SMT_1961|5end_K07485_transposase_1894206..1894436_POSITIVE 291 90 43 151 92 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 291 90 43 195 136 smit:SMT_1954|5end_6-phospho-beta-glucosidase_1888548..1888778_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 78 33 78 18 smit:SMT_2075|3end_phosphoribosylamine--glycine_ligase_1977769..1977919_NEGATIVE 293 91 60 65 32 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE 293 50 4 83 34 smit:SMT_772|3end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_682143..682293_NEGATIVE 292 88 41 59 4 smit:SMT_849|3end_hypothetical_protein_795150..795300_NEGATIVE 289 108 67 65 15 smit:SMT_2003|3end_serine_protease_1924693..1924843_NEGATIVE 289 90 48 80 30 smit:SMT_923|3end_methionyl-tRNA_formyltransferase_876559..876709_NEGATIVE 281 78 36 54 4 smit:SMT_1789|3end_hypothetical_protein_1765511..1765661_POSITIVE 280 37 1 144 109 smit:SMT_1049|3end_hypothetical_protein_989213..989363_POSITIVE 279 90 43 132 81 smit:SMT_137|3end_hypothetical_protein_88137..88287_NEGATIVE 277 89 43 44 2 smit:SMT_302|3end_K07444_putative_N6-adenine-specific_DNA_methylase_245319..245469_POSITIVE 275 45 1 56 12 smit:SMT_1401|3end_pyruvate_dehydrogenase_E1_component_beta_subunit_1378085..1378235_POSITIVE 275 87 42 77 26 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 274 91 51 150 105 smit:SMT_1803|3end_K03693_penicillin_binding_protein_1779346..1779496_POSITIVE 272 85 49 48 1 smit:SMT_944|3end_PhnA_protein_894768..894918_NEGATIVE 270 79 38 147 105 smit:SMT_1690|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1673370..1673520_NEGATIVE 270 78 31 149 105 smit:SMT_1646|3end_3-isopropylmalate_dehydratase_large_subunit_1633473..1633623_POSITIVE 270 89 47 46 5 smit:SMT_955|3end_acyltransferase_family_protein_904703..904853_POSITIVE 265 73 32 145 92 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 264 108 61 102 41 smit:SMT_1557|3end_hypothetical_protein_1543650..1543800_POSITIVE 261 91 60 73 37 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE