Origin IGS: gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttatcctattaaatcaatatgatgtaagagtcagtagcaatactggcttttatttttttaaaaatgacataaaaatctcttccnnnnnttaattaattaannnnngagtctaggacttcgcgagcgtaaacatcagtaataattgacattttttactctccttatgagttaaattttttacacctctataataccttaaaacccctcctttttcaagaaaaaacgttatctttgtgcaaattttccttaactttataaagtaatcgctttcttttgtctgttttattctaacttttatgatatactgttttc Mask Tandem Repeat Region ================================================ gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac Find is-nt database================================================ Query_seq: SMT_632:SMT_633|SMT_632:SMT_633:hypothetical protein:hypothetical protein:<-<-:537811..538124 314 gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_632:SMT_633|SMT_632:SMT_633:hypothetical protein:hypothetical protein:<-<-:537811..538124 314 gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_632:SMT_633|SMT_632:SMT_633:hypothetical protein:hypothetical protein:<-<-:537811..538124 314 gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 12 End: 200 ........... M I K V R I K Q T K E S D Y F I K L R K I C T K I T F F L E K G G V L R Y Y R G V K N L T H K E S K K C Q L L L M F T L .................................................................................................................. Protein_Len: 39 Strand: - Start: 58 End: 174 ......................................................... L T L S F K C L S L T K E Q F L L P K L T N Y L H L F N L E Y P S Y F I D I M ............................................................................................................................................ gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac 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: 87 Start: 96 End: 125 ...............................................................................................CTTGAAAAAGGAGGGGTTTTAAGGTATTAT............................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_632:SMT_633|SMT_632:SMT_633:hypothetical protein:hypothetical protein:<-<-:537811..538124 314 gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac Intra-Species Hit: Count: 1 Min: 1 Max: 314 Len: 314 Subject: smit_SMT_632_SMT_633|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[537811,538124]|314 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 314 Query Start:1 Query End:314 Subject Strand: POSITIVE Subject Start: 1 Subject End: 314 gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnnnaagagatttttatgtcatttttnnnnnnntaaaagccagtattgctactgactcttacatcatattgatttaataggataaac gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaaatgtcaattattactgatgtttacgctcgcgaagtcctagactcnnnnnttaattaattaannnnnggaagagatttttatgtcatttttaaaaaaataaaagccagtattgctactgactcttacatcatattgatttaataggataaac Inter-species Hit: Count: 3 Min: 1 Max: 163 Len: 163 Subject: NC_008533_SPD_1010_SPD_1012|hypothetical protein:phosphopyruvate hydratase|NEGATIVE:POSITIVE|[1025690,1025852]|163 HSP 1 e-value: 5.0E-85 bit: 315.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaa....................................................................................................................................................... gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaagttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaa....................................................................................................................................................... Subject: NC_003098_spr1035_spr1036|hypothetical protein:phosphopyruvate hydratase|NEGATIVE:POSITIVE|[1018159,1018321]|163 HSP 1 e-value: 5.0E-85 bit: 315.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaa....................................................................................................................................................... gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaagttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaa....................................................................................................................................................... Subject: NC_003028_SP_1127_SP_1128|hypothetical protein:phosphopyruvate hydratase|NEGATIVE:POSITIVE|[1061610,1061772]|163 HSP 1 e-value: 5.0E-85 bit: 315.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaatttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaa....................................................................................................................................................... gaaaacagtatatcataaaagttagaataaaacagacaaaagaaagcgattactttataaagttaaggaaaagttgcacaaagataacgttttttcttgaaaaaggaggggttttaaggtattatagaggtgtaaaaaatttaactcataaggagagtaaaaa....................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAACAGUAUAUCAUAAAAGUUAGAAUAAAACAGACAAAAGAAAGCGAUUACUUUAUAAAGUUAAGGAAAAUUUGCACAAAGAUAACGUUUUUUCUUGAAAAAGGAGGGGUUUUAAGGUAUUAUAGAGGUGUAAAAAAUUUAACUCAUAAGGAGAGUAAAAA .................................................(((((((....(((((((.....(((((((....((((..(((((((((....)))))........))))..))))....)))))))...))))))).......)))))))... (-20.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUACUCUCCUUAUGAGUUAAAUUUUUUACACCUCUAUAAUACCUUAAAACCCCUCCUUUUUCAAGAAAAAACGUUAUCUUUGUGCAAAUUUUCCUUAACUUUAUAAAGUAAUCGCUUUCUUUUGUCUGUUUUAUUCUAACUUUUAUGAUAUACUGUUUUC .(((.((((.......)))).))).......................((((((...........(((((.(((.((....(((((((.................)))))))....)).))).)))))...))))))........................... (-10.27) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 771 130 81 221 172 smit:SMT_632|5end_hypothetical_protein_537720..537950_NEGATIVE 242 110 65 203 150 smit:SMT_1378|5end_DNA_polymerase_III,_delta'_subunit_1356803..1357033_NEGATIVE 238 77 31 189 146 smit:SMT_1630|5end_hypothetical_protein_1617291..1617521_POSITIVE 238 77 31 189 146 smit:SMT_1241|5end_hypothetical_protein_1201040..1201270_POSITIVE 224 129 81 165 111 smit:SMT_1121|5end_hypothetical_protein_1057797..1058027_NEGATIVE 218 149 105 91 45 smit:SMT_986|5end_threonyl-tRNA_synthetase_931092..931322_POSITIVE 218 149 105 91 45 smit:SMT_925|5end_DNA-directed_RNA_polymerase_omega_chain_880283..880513_NEGATIVE 211 135 96 52 10 smit:SMT_679|5end_LicC_protein_589072..589302_NEGATIVE 206 131 103 231 198 smit:SMT_1632|5end_hypothetical_protein_1619060..1619290_NEGATIVE 203 145 104 199 145 smit:SMT_1412|5end_hypothetical_protein_1395522..1395752_POSITIVE 201 90 43 107 66 smit:SMT_241|5end_hypothetical_protein_predicted_by_Glimmer/Critica_178507..178737_POSITIVE 200 148 101 220 166 smit:SMT_1398|5end_dihydroorotase_1373204..1373434_POSITIVE 199 98 64 102 68 smit:SMT_1356|5end_fibronectin-binding_protein-like_protein_A_1332534..1332764_POSITIVE 193 132 104 97 66 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 192 68 36 224 195 smit:SMT_1015|5end_galactose_operon_repressor_951938..952168_POSITIVE 192 121 93 56 28 smit:SMT_301|5end_hypothetical_protein_244086..244316_POSITIVE 191 138 95 185 144 smit:SMT_1519|5end_DNA-binding_response_regulator_VncR_1499662..1499892_NEGATIVE 191 130 81 184 138 smit:SMT_1124|5end_pyrrolidone-carboxylate_peptidase_1060869..1061099_NEGATIVE 188 130 81 57 3 smit:SMT_1450|5end_K02057_simple_sugar_transport_system_permease_protein_1433622..1433852_NEGATIVE 188 49 9 139 101 smit:SMT_1333|5end_glycosyltransferase_1308635..1308865_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 218 149 105 66 20 smit:SMT_985|3end_guanylate_kinase_931147..931297_POSITIVE 218 149 105 66 20 smit:SMT_926|3end_guanylate_kinase_880308..880458_NEGATIVE 205 115 73 45 4 smit:SMT_1475|3end_K02004_1458661..1458811_POSITIVE 192 150 106 148 112 smit:SMT_1792|3end_K03307_solute:Na+_symporter,_SSS_family_1766575..1766725_NEGATIVE 191 138 95 42 1 smit:SMT_1520|3end_K02004_1499805..1499955_NEGATIVE 191 130 81 78 32 smit:SMT_1125|3end_K08987_putative_membrane_protein_1060975..1061125_NEGATIVE 187 110 67 63 15 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 186 128 99 51 17 smit:SMT_1764|3end_K02025_multiple_sugar_transport_system_permease_protein_1740925..1741075_POSITIVE 186 117 85 123 92 smit:SMT_1548|3end_cell_division_protein_FtsZ_1533720..1533870_POSITIVE 185 99 56 49 8 smit:SMT_1459|3end_K02037_phosphate_transport_system_permease_protein_1441519..1441669_POSITIVE 184 132 102 150 124 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 183 110 66 81 32 smit:SMT_960|3end_putative_esterase_906126..906276_NEGATIVE 182 119 88 136 109 smit:SMT_1002|3end_aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B_945149..945299_POSITIVE 179 130 82 54 1 smit:SMT_1451|3end_K02057_simple_sugar_transport_system_permease_protein_1433625..1433775_NEGATIVE 178 148 103 49 8 smit:SMT_1429|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1414936..1415086_POSITIVE 174 129 87 125 73 smit:SMT_1391|3end_dihydroxyacetone_kinase_1368589..1368739_POSITIVE 173 133 92 88 55 smit:SMT_511|3end_hypothetical_protein_predicted_by_Glimmer/Critica_440022..440172_POSITIVE 172 131 108 141 120 smit:SMT_916|3end_3-hydroxy-3-methylglutaryl-CoA_reductase_868730..868880_NEGATIVE 172 129 88 145 99 smit:SMT_689|3end_aspartate_carbamoyltransferase_600705..600855_NEGATIVE 171 100 53 71 13 smit:SMT_1272|3end_K02006_cobalt_transport_system_ATP-binding_protein_1237004..1237154_POSITIVE