Origin IGS: tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcatgattttaaaaatttagaagaggttatcagaaggttatcacaaagctatttgagctcaaaaatcgacaaaaaagcactttgcaaaatttttgcaaagtgctttgaaacgttgatataatcgtattga Mask Tandem Repeat Region ================================================ tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat Find is-nt database================================================ Query_seq: SMT_1226:SMT_1227|SMT_1226:SMT_1227:ribosomal protein S9:site-specific recombinase, phage integrase family:-><-:1189270..1189400 131 tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1226:SMT_1227|SMT_1226:SMT_1227:ribosomal protein S9:site-specific recombinase, phage integrase family:-><-:1189270..1189400 131 tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1226:SMT_1227|SMT_1226:SMT_1227:ribosomal protein S9:site-specific recombinase, phage integrase family:-><-:1189270..1189400 131 tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 9 End: 98 ........ M I S T F Q S T L Q K F C K V L F C R F L S S N S F V I T F ................................. Protein_Len: 30 Strand: - Start: 13 End: 102 ............ I L T E F C K A F I K C L A K K D I K S S L Y S Q S L R R M ............................. tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat 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================================================ tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -16.8 Tail_Score: -3.58037 Start: 28 End: 54 Full_Region: aaaatcgacaaaaaa gcactttgcaaa att tttgcaaagtgc tttgaaacgttgata ...........................gcactttgcaaaatttttgcaaagtgc............................................................................. Find igs database================================================ Query_seq: SMT_1226:SMT_1227|SMT_1226:SMT_1227:ribosomal protein S9:site-specific recombinase, phage integrase family:-><-:1189270..1189400 131 tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: smit_SMT_1226_SMT_1227|ribosomal protein S9:site-specific recombinase, phage integrase family|POSITIVE:NEGATIVE|[1189270,1189400]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat tcaatacgattatatcaacgtttcaaagcactttgcaaaaattttgcaaagtgcttttttgtcgatttttgagctcaaatagctttgtgataaccttctgataacctcttctaaatttttaaaatcatgat HSP 2 e-value: 7.0E-8 bit: 58.0 Len: 33 Query Start:25 Query End:57 Subject Strand: NEGATIVE Subject Start: 25 Subject End: 57 ........................aaagcactttgcaaaaattttgcaaagtgcttt.......................................................................... ........................aaagcactttgcaaaatttttgcaaagtgcttt.......................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAUACGAUUAUAUCAACGUUUCAAAGCACUUUGCAAAAAUUUUGCAAAGUGCUUUUUUGUCGAUUUUUGAGCUCAAAUAGCUUUGUGAUAACCUUCUGAUAACCUCUUCUAAAUUUUUAAAAUCAUGAU ............(((((.......((((((((((((((.....)))))))))))))).((((((......(((((.....)))))..)))))).....)))))............................ (-28.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUGAUUUUAAAAAUUUAGAAGAGGUUAUCAGAAGGUUAUCACAAAGCUAUUUGAGCUCAAAAAUCGACAAAAAAGCACUUUGCAAAAUUUUUGCAAAGUGCUUUGAAACGUUGAUAUAAUCGUAUUGA ...((((((..............(((....(((((.((((.......)))).))))).)))....((((((...((((((((((((((.....)))))))))))))).....))))))..))))))..... (-35.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 110 61 141 87 smit:SMT_609|5end_laminin-binding_surface_protein_521286..521516_POSITIVE 296 120 73 64 15 smit:SMT_756|5end_3-dehydroquinate_dehydratase_660584..660814_NEGATIVE 272 98 51 222 184 smit:SMT_797|5end_hypothetical_protein_705164..705394_POSITIVE 271 66 27 77 36 smit:SMT_1916|5end_glutamine_amidotransferase_1860539..1860769_POSITIVE 271 118 75 88 43 smit:SMT_1699|5end_purine_operon_repressor_1681138..1681368_POSITIVE 270 102 68 214 169 smit:SMT_301|5end_hypothetical_protein_244086..244316_POSITIVE 263 64 23 163 119 smit:SMT_182|5end_50S_ribosomal_protein_L5_120454..120684_POSITIVE 242 109 61 65 21 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 232 99 52 165 118 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 232 59 11 153 101 smit:SMT_1165|5end_sensor_protein_CiaH_1111820..1112050_NEGATIVE 232 59 11 153 101 smit:SMT_539|5end_sensor_histidine_kinase_CiaH_455752..455982_POSITIVE 227 85 44 225 192 smit:SMT_753|5end_chorismate_synthase_657967..658197_NEGATIVE 226 120 71 115 67 smit:SMT_275|5end_transcriptional_activator-exopolysaccharide_biosynthesis_217369..217599_POSITIVE 225 108 62 103 54 smit:SMT_370|5end_acetyltransferase,_GNAT_family_304688..304918_POSITIVE 224 100 51 139 92 smit:SMT_2127|5end_exodeoxyribonuclease_V_alpha_chain_2009306..2009536_POSITIVE 224 97 53 85 35 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 223 76 34 65 23 smit:SMT_591|5end_K02029_polar_amino_acid_transport_system_permease_protein_508108..508338_POSITIVE 222 95 52 221 173 smit:SMT_723|5end_hypothetical_protein_629475..629705_NEGATIVE 221 108 62 113 63 smit:SMT_1361|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1341402..1341632_NEGATIVE 219 99 53 159 110 smit:SMT_1497|5end_acetyltransferase,_GNAT_family_1481432..1481662_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 415 57 15 66 19 smit:SMT_1226|3end_ribosomal_protein_S9_1189209..1189359_POSITIVE 308 60 17 44 1 smit:SMT_1239|3end_site-specific_recombinase,_phage_integrase_family_1199639..1199789_NEGATIVE 308 60 17 44 1 smit:SMT_248|3end_site-specific_recombinase,_phage_integrase_family_183716..183866_NEGATIVE 296 120 73 67 18 smit:SMT_757|3end_K06969_putative_SAM-dependent_methyltransferase_660581..660731_NEGATIVE 271 66 27 76 35 smit:SMT_1915|3end_pyridoxine_biosynthesis_protein_1860618..1860768_POSITIVE 263 64 23 139 95 smit:SMT_181|3end_50S_ribosomal_protein_L24_120510..120660_POSITIVE 235 110 61 62 12 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 232 89 42 36 2 smit:SMT_821|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_734060..734210_POSITIVE 229 100 53 85 38 smit:SMT_2046|3end_choline_binding_protein_C_1957280..1957430_NEGATIVE 224 100 51 119 72 smit:SMT_2126|3end_indole-3-glycerol_phosphate_synthase_2009366..2009516_POSITIVE 224 97 53 92 42 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 221 108 62 101 51 smit:SMT_1362|3end_chaperone_protein_hscC_1341414..1341564_NEGATIVE 219 99 53 84 36 smit:SMT_336|3end_hypothetical_protein_275622..275772_POSITIVE 218 75 36 89 49 smit:SMT_1274|3end_K02008_cobalt_transport_system_permease_protein_1238615..1238765_POSITIVE 217 101 61 135 90 smit:SMT_161|3end_putative_folyl-polyglutamate_synthetase_106586..106736_POSITIVE 216 107 66 125 78 smit:SMT_1644|3end_3-isopropylmalate_dehydrogenase_1631821..1631971_POSITIVE 215 100 52 64 18 smit:SMT_1256|3end_ketol-acid_reductoisomerase_1221855..1222005_NEGATIVE 215 100 52 149 106 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 215 100 52 141 73 smit:SMT_424|3end_transcriptional_regulatory_protein_368108..368258_POSITIVE 213 85 44 69 28 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE