Origin IGS: attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcaaaacaaaactctaggcaacaaaatattgtaagtgtagtgttttagggagtgagaatgtatgtcaatacagcatcaattccactcccttttttatcataaaatagttagagagaaaaaat Mask Tandem Repeat Region ================================================ attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt Find is-nt database================================================ Query_seq: SMT_829:SMT_830|SMT_829:SMT_830:putative mucus binding protein:hypothetical protein:<-<-:765030..765153 124 attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_829:SMT_830|SMT_829:SMT_830:putative mucus binding protein:hypothetical protein:<-<-:765030..765153 124 attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_829:SMT_830|SMT_829:SMT_830:putative mucus binding protein:hypothetical protein:<-<-:765030..765153 124 attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt Predict ORF larger than 30AA ================================================ attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt 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================================================ attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -3.1 Tail_Score: -5.31275 Start: 34 End: 75 Full_Region: aagtgtagtgtttta gggagtgagaatgtatgt caataca gcatcaattccactccc ttttttatcataaaa .................................gggagtgagaatgtatgtcaatacagcatcaattccactccc................................................. Find igs database================================================ Query_seq: SMT_829:SMT_830|SMT_829:SMT_830:putative mucus binding protein:hypothetical protein:<-<-:765030..765153 124 attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: smit_SMT_829_SMT_830|putative mucus binding protein:hypothetical protein|NEGATIVE:NEGATIVE|[765030,765153]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt attttttctctctaactattttatgataaaaaagggagtggaattgatgctgtattgacatacattctcactccctaaaacactacacttacaatattttgttgcctagagttttgttttgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUUCUCUCUAACUAUUUUAUGAUAAAAAAGGGAGUGGAAUUGAUGCUGUAUUGACAUACAUUCUCACUCCCUAAAACACUACACUUACAAUAUUUUGUUGCCUAGAGUUUUGUUUUGAUU ................................((((((((((((..((((......).)))..)))).))))))))((((((..((.((..((((.....))))...)).))..)))))).... (-24.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCAAAACAAAACUCUAGGCAACAAAAUAUUGUAAGUGUAGUGUUUUAGGGAGUGAGAAUGUAUGUCAAUACAGCAUCAAUUCCACUCCCUUUUUUAUCAUAAAAUAGUUAGAGAGAAAAAAU .............((((((.(...(((((((((......))))))))).(((((((.((((..((((.......))))..))))))))))).................)))))))......... (-27.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 858 80 31 171 122 smit:SMT_829|5end_putative_mucus_binding_protein_764939..765169_NEGATIVE 246 76 34 213 159 smit:SMT_772|5end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_683300..683530_NEGATIVE 236 59 11 142 103 smit:SMT_951|5end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_900098..900328_NEGATIVE 234 76 33 181 152 smit:SMT_1924|5end_isoleucyl-tRNA_synthetase_1866188..1866418_POSITIVE 233 75 32 106 51 smit:SMT_447|5end_ABC-type_cobalt_transport_system,_permease_component_CbiQ_related_transporter_386257..386487_POSITIVE 231 88 41 69 19 smit:SMT_138|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_89262..89492_POSITIVE 230 66 33 92 69 smit:SMT_225|5end_pullulanase_163529..163759_NEGATIVE 228 75 34 192 127 smit:SMT_230|5end_hypothetical_protein_predicted_by_Glimmer/Critica_165830..166060_NEGATIVE 219 74 33 103 65 smit:SMT_900|5end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase_850616..850846_NEGATIVE 216 49 1 144 90 smit:SMT_272|5end_hypothetical_protein_213315..213545_NEGATIVE 215 78 32 110 57 smit:SMT_1451|5end_K02057_simple_sugar_transport_system_permease_protein_1434683..1434913_NEGATIVE 214 78 39 82 43 smit:SMT_1915|5end_pyridoxine_biosynthesis_protein_1860329..1860559_POSITIVE 214 74 34 89 50 smit:SMT_791|5end_thiamine_biosynthesis_protein_ThiI_702377..702607_NEGATIVE 214 79 31 171 125 smit:SMT_348|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_286456..286686_POSITIVE 213 68 32 71 36 smit:SMT_613|5end_dihydrodipicolinate_synthase_523651..523881_POSITIVE 209 71 33 226 176 smit:SMT_1753|5end_tryptophan_synthase_beta_chain_1730349..1730579_POSITIVE 207 79 33 56 3 smit:SMT_1127|5end_transcriptional_regulator,_MarR_family_1061556..1061786_NEGATIVE 205 76 35 107 73 smit:SMT_675|5end_DNA_repair_protein_582977..583207_NEGATIVE 204 46 7 143 97 smit:SMT_1389|5end_dihydroxyacetone_kinase_1366890..1367120_NEGATIVE 204 81 57 58 29 smit:SMT_882|5end_acetyl_esterase_830441..830671_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 73 31 96 63 smit:SMT_516|3end_hypothetical_protein_442527..442677_NEGATIVE 241 76 33 53 1 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 236 59 11 125 86 smit:SMT_952|3end_hypothetical_protein_900115..900265_NEGATIVE 233 75 32 104 49 smit:SMT_446|3end_ABC-type_cobalt_transport_system,_ATPase_component_386335..386485_POSITIVE 228 49 24 144 115 smit:SMT_1923|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1866244..1866394_POSITIVE 215 78 32 117 64 smit:SMT_1452|3end_ABC-type_uncharacterized_transport_system,_ATPase_component_1434676..1434826_NEGATIVE 213 80 33 150 113 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 205 76 35 64 30 smit:SMT_676|3end_DNA_helicase_II_583020..583170_NEGATIVE 204 46 7 146 100 smit:SMT_1390|3end_hypothetical_protein_1366887..1367037_NEGATIVE 200 107 63 97 56 smit:SMT_287|3end_UDP-galactopyranose_mutase_231274..231424_POSITIVE 199 54 12 132 91 smit:SMT_1446|3end_pneumococcal_vaccine_antigen_A_1428996..1429146_NEGATIVE 198 75 33 130 81 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 193 45 1 83 38 smit:SMT_1376|3end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1354675..1354825_NEGATIVE 191 74 35 109 65 smit:SMT_572|3end_fructose_repressor_491059..491209_POSITIVE 189 79 43 138 103 smit:SMT_1952|3end_hypothetical_protein_1886932..1887082_POSITIVE 186 107 63 102 62 smit:SMT_1960|3end_UDP-galactopyranose_mutase_1894094..1894244_POSITIVE 185 76 31 40 9 smit:SMT_1485|3end_exodeoxyribonuclease_1465169..1465319_NEGATIVE 185 72 34 91 47 smit:SMT_754|3end_3-dehydroquinate_synthase_657977..658127_NEGATIVE 184 79 34 108 46 smit:SMT_551|3end_K07170_GAF_domain-containing_protein_469525..469675_POSITIVE 184 74 34 105 60 smit:SMT_146|3end_sugar_transport_system_permease_protein_97382..97532_POSITIVE