Origin IGS: tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atggtcatcattcttttgttttaggtttcagcgcttttaatataatggatgttggcctttttgtatacactaaaatagggttggtggaaaatttccatcaaccctaaaaattatagaaccacacaaaaccctgaccagagatggccagggttttgtatttcaaaaa Mask Tandem Repeat Region ================================================ tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat Find is-nt database================================================ Query_seq: SMT_239:SMT_240|SMT_239:SMT_240:hypothetical protein:glutamate synthase small subunit, putative:->->:177849..178014 166 tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_239:SMT_240|SMT_239:SMT_240:hypothetical protein:glutamate synthase small subunit, putative:->->:177849..178014 166 tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_239:SMT_240|SMT_239:SMT_240:hypothetical protein:glutamate synthase small subunit, putative:->->:177849..178014 166 tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat Predict ORF larger than 30AA ================================================ tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat 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================================================ tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.1 Tail_Score: -4.78848 Start: 17 End: 38 Full_Region: tagaaccacacaaaa ccctgacca gaga tggccaggg ttttgtatttcaaaa ................ccctgaccagagatggccaggg................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -15.6 Tail_Score: -4.39166 Start: 61 End: 91 Full_Region: TGGTTCTATAATTTT TAGGGTTGATGGAA ATT TTCCACCAACCCTA TTTTAGTGTATACAA ............................................................TAGGGTTGATGGAAATTTTCCACCAACCCTA........................................................................... Find igs database================================================ Query_seq: SMT_239:SMT_240|SMT_239:SMT_240:hypothetical protein:glutamate synthase small subunit, putative:->->:177849..178014 166 tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: smit_SMT_239_SMT_240|hypothetical protein:glutamate synthase small subunit, putative|POSITIVE:POSITIVE|[177849,178014]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat tttttgaaatacaaaaccctggccatctctggtcagggttttgtgtggttctataatttttagggttgatggaaattttccaccaaccctattttagtgtatacaaaaaggccaacatccattatattaaaagcgctgaaacctaaaacaaaagaatgatgaccat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUGAAAUACAAAACCCUGGCCAUCUCUGGUCAGGGUUUUGUGUGGUUCUAUAAUUUUUAGGGUUGAUGGAAAUUUUCCACCAACCCUAUUUUAGUGUAUACAAAAAGGCCAACAUCCAUUAUAUUAAAAGCGCUGAAACCUAAAACAAAAGAAUGAUGACCAU ........(((((((((((((((((....)))))))))))))))))((((.(...(((((((((((((.((((.....)))).))))))).(((((((((................................)))))))))..........)))))).).)))).. (-52.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGUCAUCAUUCUUUUGUUUUAGGUUUCAGCGCUUUUAAUAUAAUGGAUGUUGGCCUUUUUGUAUACACUAAAAUAGGGUUGGUGGAAAAUUUCCAUCAACCCUAAAAAUUAUAGAACCACACAAAACCCUGACCAGAGAUGGCCAGGGUUUUGUAUUUCAAAAA ..(((((.(((((...((((..((((......))))..))))....))))).))))).(((((............(((((((((((((.....)))))))))))))................(((((((((((.(((....))).)))))))))))....))))). (-59.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 60 13 129 84 smit:SMT_1738|5end_peptidyl-prolyl_cis-trans_isomerase_1720497..1720727_POSITIVE 294 65 21 138 93 smit:SMT_1832|5end_tagatose-6-phosphate_kinase_1800438..1800668_POSITIVE 274 39 11 184 156 smit:SMT_221|5end_prolyl-tRNA_synthetase_153019..153249_POSITIVE 272 51 19 64 30 smit:SMT_2064|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1972182..1972412_POSITIVE 269 89 43 223 174 smit:SMT_141|5end_K03495_glucose_inhibited_division_protein_A_91408..91638_POSITIVE 263 122 85 169 128 smit:SMT_139|5end_hypothetical_protein_90523..90753_POSITIVE 260 58 17 227 180 smit:SMT_1538|5end_two-component_response_regulator_YvqC_1523301..1523531_NEGATIVE 258 46 19 57 22 smit:SMT_2164|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2037861..2038091_POSITIVE 258 41 18 86 62 smit:SMT_1640|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1626321..1626551_NEGATIVE 257 49 10 165 110 smit:SMT_370|5end_acetyltransferase,_GNAT_family_304688..304918_POSITIVE 256 143 109 52 21 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 256 59 19 190 141 smit:SMT_1489|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468892..1469122_POSITIVE 253 47 16 189 153 smit:SMT_1977|5end_endopeptidase_O_1907832..1908062_POSITIVE 251 49 4 228 182 smit:SMT_738|5end_hypothetical_protein_predicted_by_Glimmer/Critica_643042..643272_NEGATIVE 250 69 21 225 191 smit:SMT_2044|5end_transcriptional_activator_TipA,_putative_1955885..1956115_NEGATIVE 250 69 21 210 176 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 250 69 21 183 149 smit:SMT_2008|5end_K07485_transposase_1928662..1928892_NEGATIVE 250 69 21 52 18 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 250 69 21 201 167 smit:SMT_2001|5end_membrane_protease_protein_family_1923387..1923617_POSITIVE 250 69 21 146 112 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 499 46 6 82 40 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 306 60 13 150 105 smit:SMT_1737|3end_peptidyl-prolyl_cis-trans_isomerase_1720598..1720748_POSITIVE 294 65 21 127 82 smit:SMT_1831|3end_galactose-6-phosphate_isomerase_1800507..1800657_POSITIVE 267 52 18 57 20 smit:SMT_1641|3end_arginyl-tRNA_synthetase_1626562..1626712_NEGATIVE 263 64 22 115 78 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE 261 52 19 35 4 smit:SMT_317|3end_K03625_N_utilization_substance_protein_B_257475..257625_NEGATIVE 251 52 15 74 35 smit:SMT_1523|3end_ferrochelatase_1503390..1503540_NEGATIVE 251 64 28 34 1 smit:SMT_1013|3end_galactose-1-phosphate_uridylyltransferase_949601..949751_NEGATIVE 248 60 12 86 41 smit:SMT_1934|3end_homoserine_dehydrogenase_1873150..1873300_POSITIVE 248 67 29 100 45 smit:SMT_853|3end_ATP-dependent_endopeptidase_clp_ATP-binding_subunit_ClpX_798053..798203_NEGATIVE 248 53 12 134 77 smit:SMT_670|3end_aminotransferase_(class_V),_putative_580324..580474_POSITIVE 242 73 35 147 109 smit:SMT_323|3end_amino_acid_transport_ATP-binding_protein_261519..261669_NEGATIVE 241 49 2 143 89 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 239 52 17 61 11 smit:SMT_754|3end_3-dehydroquinate_synthase_657977..658127_NEGATIVE 235 90 42 78 28 smit:SMT_1142|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1086897..1087047_POSITIVE 234 40 14 151 119 smit:SMT_1664|3end_hypothetical_protein_1653176..1653326_NEGATIVE 232 53 17 61 21 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 232 45 5 69 23 smit:SMT_593|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_510317..510467_POSITIVE 231 50 17 46 3 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 229 120 87 41 3 smit:SMT_815|3end_hypothetical_protein_723677..723827_NEGATIVE