Origin IGS: atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatttttgacaattgcttacttgtttctactgggaaaaagatgaatgcaatcgtgtccatctttttctttttatggtaaaatagagaaataatatggtgaaaagccttgagggagtgaccgat Mask Tandem Repeat Region ================================================ atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc Find is-nt database================================================ Query_seq: SMT_1079:SMT_1080|SMT_1079:SMT_1080:dihydropteroate synthase:CAAX amino terminal protease family protein:<-<-:1017750..1017872 123 atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1079:SMT_1080|SMT_1079:SMT_1080:dihydropteroate synthase:CAAX amino terminal protease family protein:<-<-:1017750..1017872 123 atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1079:SMT_1080|SMT_1079:SMT_1080:dihydropteroate synthase:CAAX amino terminal protease family protein:<-<-:1017750..1017872 123 atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 1 End: 123 M G H S L K A F H H I I S L F Y H K K K K M D T I A F I F F P V E T S K Q L S K I atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc 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: 81 Start: 22 End: 51 .....................TTTCACCATATTATTTCTCTATTTTACCAT........................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 42 End: 71 .........................................GTGTCCATCTTTTTCTTTTTATGGTAAAAT.................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -8.3 Tail_Score: -4.91511 Start: 57 End: 90 Full_Region: acttgtttctactgg gaaaaagatgaatgc aatc gtgtccatctttttc tttttatggtaaaat ........................................................gaaaaagatgaatgcaatcgtgtccatctttttc................................. Find igs database================================================ Query_seq: SMT_1079:SMT_1080|SMT_1079:SMT_1080:dihydropteroate synthase:CAAX amino terminal protease family protein:<-<-:1017750..1017872 123 atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: smit_SMT_1079_SMT_1080|dihydropteroate synthase:CAAX amino terminal protease family protein|NEGATIVE:NEGATIVE|[1017750,1017872]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc atcggtcactccctcaaggcttttcaccatattatttctctattttaccataaaaagaaaaagatggacacgattgcattcatctttttcccagtagaaacaagtaagcaattgtcaaaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGGUCACUCCCUCAAGGCUUUUCACCAUAUUAUUUCUCUAUUUUACCAUAAAAAGAAAAAGAUGGACACGAUUGCAUUCAUCUUUUUCCCAGUAGAAACAAGUAAGCAAUUGUCAAAAAUC ...(((.....((....))......)))...((((((.((((((............((((((((((((..(....)..))))))))))))..))))))...))))))................ (-16.34) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUUGACAAUUGCUUACUUGUUUCUACUGGGAAAAAGAUGAAUGCAAUCGUGUCCAUCUUUUUCUUUUUAUGGUAAAAUAGAGAAAUAAUAUGGUGAAAAGCCUUGAGGGAGUGACCGAU .........((.((.((((.((((((((.((((((((((((((.((((....)))).))))))))))).............)))))))))))...(((.....))).)))).)).))...... (-25.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 858 50 1 141 92 smit:SMT_1079|5end_dihydropteroate_synthase_1017659..1017889_NEGATIVE 292 50 2 119 65 smit:SMT_246|5end_alcohol_dehydrogenase_183004..183234_NEGATIVE 269 46 1 159 116 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 265 44 9 203 157 smit:SMT_455|5end_cation_transport_ATPase_391670..391900_POSITIVE 261 99 63 112 65 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 251 50 5 132 92 smit:SMT_843|5end_hypothetical_protein_789638..789868_NEGATIVE 248 39 2 68 33 smit:SMT_1836|5end_cytidine/deoxycytidylate_deaminase_family_protein_1804498..1804728_NEGATIVE 244 45 3 162 119 smit:SMT_1697|5end_hypothetical_protein_1678846..1679076_POSITIVE 240 77 31 230 185 smit:SMT_900|5end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase_850616..850846_NEGATIVE 239 49 21 161 131 smit:SMT_705|5end_hypothetical_protein_615336..615566_NEGATIVE 238 50 1 131 90 smit:SMT_1474|5end_K02003_1455170..1455400_POSITIVE 236 110 66 228 183 smit:SMT_1576|5end_ribose_ABC_transporter_protein_RbsD_1568950..1569180_POSITIVE 235 49 3 206 157 smit:SMT_929|5end_hypothetical_protein_883342..883572_NEGATIVE 230 43 2 156 113 smit:SMT_1992|5end_carboxynorspermidine_decarboxylase_1919207..1919437_NEGATIVE 230 43 2 156 113 smit:SMT_1415|5end_carboxynorspermidine_decarboxylase_1399570..1399800_NEGATIVE 229 109 62 65 16 smit:SMT_1388|5end_hypothetical_protein_1365214..1365444_POSITIVE 227 33 2 222 185 smit:SMT_1971|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1903282..1903512_POSITIVE 226 48 1 140 82 smit:SMT_726|5end_ImpB/MucB/SamB_family_protein_631827..632057_NEGATIVE 225 118 74 61 7 smit:SMT_1269|5end_hypothetical_protein_1233440..1233670_POSITIVE 222 32 1 124 96 smit:SMT_2035|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1947167..1947397_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 50 4 113 67 smit:SMT_1124|3end_pyrrolidone-carboxylate_peptidase_1060225..1060375_NEGATIVE 251 50 5 58 18 smit:SMT_844|3end_putative_phospho-sugar_mutase_789712..789862_NEGATIVE 226 48 1 137 79 smit:SMT_727|3end_phage_transcriptional_repressor_631830..631980_NEGATIVE 222 32 1 134 106 smit:SMT_2034|3end_hydrolase,_haloacid_dehalogenase-like_family_1947257..1947407_POSITIVE 218 38 2 145 113 smit:SMT_1993|3end_hypothetical_protein_1919207..1919357_NEGATIVE 218 38 2 145 113 smit:SMT_1416|3end_hypothetical_protein_1399570..1399720_NEGATIVE 218 49 4 105 40 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 214 104 62 53 4 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE 214 110 64 140 86 smit:SMT_1061|3end_hypothetical_protein_999915..1000065_POSITIVE 213 117 75 69 31 smit:SMT_1082|3end_Cof_family_protein_1020877..1021027_POSITIVE 213 108 62 59 2 smit:SMT_141|3end_K03495_glucose_inhibited_division_protein_A_93401..93551_POSITIVE 211 41 12 100 75 smit:SMT_1554|3end_isoleucyl-tRNA_synthetase_1539912..1540062_POSITIVE 211 109 66 67 16 smit:SMT_147|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_98016..98166_POSITIVE 210 71 32 72 29 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 210 48 1 137 80 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 210 48 1 137 80 smit:SMT_407|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_353166..353316_POSITIVE 209 103 64 70 37 smit:SMT_1718|3end_Holliday_junction_DNA_helicase_RuvA_1704284..1704434_NEGATIVE 208 116 76 80 39 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 208 48 3 94 48 smit:SMT_1646|3end_3-isopropylmalate_dehydratase_large_subunit_1633473..1633623_POSITIVE 208 49 1 85 26 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE