Origin IGS: atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataacaaaaaaagaaagcctattttataagctttccttttgtkttctttttattatttacattttctatggtgaattttacactt .........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 aagtgtaaaattcaccatagaaaatgtaaataataaaaagaamacaaaaggaaagcttataaaataggctttctttttttgttatgagagctgtatttgaaaattaatataagtatataattgtataaataaaataatctattacttgattatatttttagaaagcgttataataaatccmaatatgattctaaaaaargsgtttcaaat Mask Tandem Repeat Region ================================================ atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataacaaaaaaagaaagcctattttataagctttccttttgtkttctttttattatttacattttctatggtgaattttacactt Find is-nt database================================================ Query_seq: SMT_1220:SMT_1221|SMT_1220:SMT_1221:hypothetical protein predicted by Glimmer/Critica:choline binding protein A:<-<-:1183866..1184075 210 atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataacaaaaaaagaaagcctattttataagctttccttttgtkttctttttattatttacattttctatggtgaattttacactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1220:SMT_1221|SMT_1220:SMT_1221:hypothetical protein predicted by Glimmer/Critica:choline binding protein A:<-<-:1183866..1184075 210 atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataacaaaaaaagaaagcctattttataagctttccttttgtkttctttttattatttacattttctatggtgaattttacactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1220:SMT_1221|SMT_1220:SMT_1221:hypothetical protein predicted by Glimmer/Critica:choline binding protein A:<-<-:1183866..1184075 210 atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataacaaaaaaagaaagcctattttataagctttccttttgtkttctttttattatttacattttctatggtgaattttacactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataacaaaaaaagaaagcctattttataagctttccttttgtkttctttttattatttacattttctatggtgaattttacactt Predict ORF larger than 30AA ================================================ atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataacaaaaaaagaaagcctattttataagctttccttttgtkttctttttattatttacattttctatggtgaattttacactt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 89 Start: 34 End: 63 .................................CTTGATTATATTTTTAGAAAGCGTTATAAT................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 176 End: 205 ...............................................................................................................................................................................ATTTACATTTTCTATGGTGAATTTTACACT..... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataacaaaaaaagaaagcctattttataagctttccttttgtkttctttttattatttacattttctatggtgaattttacactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1220:SMT_1221|SMT_1220:SMT_1221:hypothetical protein predicted by Glimmer/Critica:choline binding protein A:<-<-:1183866..1184075 210 atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataacaaaaaaagaaagcctattttataagctttccttttgtkttctttttattatttacattttctatggtgaattttacactt Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: smit_SMT_1220_SMT_1221|hypothetical protein predicted by Glimmer/Critica:choline binding protein A|NEGATIVE:NEGATIVE|[1183866,1184075]|210 HSP 1 e-value: 2.0E-65 bit: 249.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataac................................................................................ atttgaaacscyttttttagaatcatattkggatttattataacgctttctaaaaatataatcaagtaatagattattttatttatacaattatatacttatattaattttcaaatacagctctcataac................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUGAAACSCYUUUUUUAGAAUCAUAUUKGGAUUUAUUAUAACGCUUUCUAAAAAUAUAAUCAAGUAAUAGAUUAUUUUAUUUAUACAAUUAUAUACUUAUAUUAAUUUUCAAAUACAGCUCUCAUAAC ((((((((......((((((((.........................))))))))(((((((...(((.(((((......)))))))).)))))))............)))))))).............. (-11.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAUGAGAGCUGUAUUUGAAAAUUAAUAUAAGUAUAUAAUUGUAUAAAUAAAAUAAUCUAUUACUUGAUUAUAUUUUUAGAAAGCGUUAUAAUAAAUCCMAAUAUGAUUCUAAAAAARGSGUUUCAAAU (((((((..(((...(((((((((((((.((((((....(((((.........)))))....)))))))))).))))))))).))).))))))).................................... (-17.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 635 130 81 221 172 smit:SMT_1220|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1183775..1184005_NEGATIVE 211 93 52 96 45 smit:SMT_238|5end_hypothetical_protein_predicted_by_Glimmer/Critica_177058..177288_NEGATIVE 190 127 102 195 168 smit:SMT_1735|5end_K03596_GTP-binding_protein_LepA_1719365..1719595_POSITIVE 187 67 21 140 86 smit:SMT_1580|5end_MutT/NUDIX_family_protein_1572897..1573127_POSITIVE 176 128 108 174 153 smit:SMT_627|5end_glucose-1-phosphate_adenylyltransferase_531699..531929_POSITIVE 162 124 95 230 198 smit:SMT_1025|5end_hypothetical_protein_960557..960787_NEGATIVE 161 52 19 115 84 smit:SMT_1945|5end_putative_dihydrolipoamide_S-acetyltransferase_1879961..1880191_POSITIVE 161 50 32 146 127 smit:SMT_1285|5end_ribosomal_subunit_interface_protein_1247704..1247934_POSITIVE 160 130 90 202 152 smit:SMT_1440|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1424712..1424942_NEGATIVE 160 89 43 186 147 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 148 128 87 151 114 smit:SMT_2074|5end_dTDP-glucose_4,6-dehydratase_1977021..1977251_POSITIVE 148 128 87 47 10 smit:SMT_2073|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1976917..1977147_POSITIVE 147 130 99 108 79 smit:SMT_2020|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1937595..1937825_POSITIVE 147 130 99 108 79 smit:SMT_1317|5end_glycosyltransferase_1281921..1282151_POSITIVE 142 80 38 128 88 smit:SMT_1523|5end_ferrochelatase_1504460..1504690_NEGATIVE 140 84 49 105 69 smit:SMT_1332|5end_hypothetical_protein_1307576..1307806_NEGATIVE 138 105 61 180 130 smit:SMT_1193|5end_phosphoribosylglycinamide_formyltransferase_1152152..1152382_NEGATIVE 137 125 101 153 128 smit:SMT_1206|5end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1167043..1167273_NEGATIVE 134 52 16 191 158 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 133 83 44 129 87 smit:SMT_879|5end_hypothetical_protein_826989..827219_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 190 127 102 116 89 smit:SMT_1734|3end_serine/threonine_protein_phosphatase_1719366..1719516_POSITIVE 187 67 21 98 44 smit:SMT_1579|3end_ABC-type_sugar_transport_system,_periplasmic_component_1572935..1573085_POSITIVE 161 50 32 66 47 smit:SMT_1284|3end_predicted_amidophosphoribosyltransferase_1247704..1247854_POSITIVE 148 128 87 124 87 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 147 130 99 76 47 smit:SMT_2019|3end_dTDP-glucose_4,6-dehydratase_1937643..1937793_POSITIVE 147 130 99 76 47 smit:SMT_1316|3end_dTDP-glucose_4,6-dehydratase_1281969..1282119_POSITIVE 146 84 45 96 48 smit:SMT_759|3end_K01992_ABC-2_type_transport_system_permease_protein_664078..664228_NEGATIVE 143 127 94 111 76 smit:SMT_984|3end_transcriptional_regulator_Spx_930497..930647_NEGATIVE 140 84 49 89 53 smit:SMT_1333|3end_glycosyltransferase_1307592..1307742_NEGATIVE 137 127 90 102 66 smit:SMT_1637|3end_hypothetical_protein_1623848..1623998_POSITIVE 134 52 16 82 49 smit:SMT_480|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416765..416915_NEGATIVE 133 83 44 50 8 smit:SMT_880|3end_beta-lactam_resistance_factor_827068..827218_NEGATIVE 131 52 31 77 57 smit:SMT_217|3end_hypothetical_protein_149888..150038_POSITIVE 129 129 118 76 65 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 128 120 95 110 82 smit:SMT_2000|3end_hypothetical_protein_1922908..1923058_NEGATIVE 128 120 95 110 82 smit:SMT_1666|3end_hypothetical_protein_1656451..1656601_NEGATIVE 127 54 35 68 47 smit:SMT_129|3end_putative_glycosyltransferase_80883..81033_POSITIVE 126 126 106 127 102 smit:SMT_423|3end_sensory_transduction_protein_kinase_367531..367681_POSITIVE 125 127 98 150 120 smit:SMT_390|3end_PTS_system,_galactitol-specific_IIB_component,_putative_322679..322829_POSITIVE 124 128 106 138 120 smit:SMT_1796|3end_dihydroorotate_dehydrogenase_A_1769881..1770031_NEGATIVE