Origin IGS: tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttcaaatgaaaagtaaaaaatagaaaagctaaaaattattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa .........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 ttgttatcagcctagaggcaggaattccctgtctcttttcttgtggaattggagtgttgaaaataatttttagcttttctattttttacttttcatttgaaaaggaaagtgggaaatgactaggtagacaaagaaagacagcagtataggcttttgaaggagaaagaaaaataagtggggtatagacaaaaaacaacgcccgtacttgcaattcaactcaaatagttatataataggtttgttgaaaggtgatttgtagtgattcaagttactcttttcacaataaaaatttcatgattttcataaggaggaaatcacta Mask Tandem Repeat Region ================================================ tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttcaaatgaaaagtaaaaaatagaaaagctaaaaattattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa Find is-nt database================================================ Query_seq: SMT_1096:SMT_1097|SMT_1096:SMT_1097:glyceraldehyde-3-phosphate dehydrogenase:alcohol dehydrogenase / acetaldehyde dehydrogenase:<-<-:1038467..1038786 320 tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttcaaatgaaaagtaaaaaatagaaaagctaaaaattattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1096:SMT_1097|SMT_1096:SMT_1097:glyceraldehyde-3-phosphate dehydrogenase:alcohol dehydrogenase / acetaldehyde dehydrogenase:<-<-:1038467..1038786 320 tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttcaaatgaaaagtaaaaaatagaaaagctaaaaattattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1096:SMT_1097|SMT_1096:SMT_1097:glyceraldehyde-3-phosphate dehydrogenase:alcohol dehydrogenase / acetaldehyde dehydrogenase:<-<-:1038467..1038786 320 tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttcaaatgaaaagtaaaaaatagaaaagctaaaaattattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttcaaatgaaaagtaaaaaatagaaaagctaaaaattattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 109 End: 198 ............................................................................................................ M A S T G V V F C L Y P T Y F S F S F K S L Y C C L S L S T .......................................................................................................................... Protein_Len: 41 Strand: + Start: 110 End: 232 ............................................................................................................. M Q V R A L F F V Y T P L I F L S P S K A Y T A V F L C L P S H F P L S F S N E K ........................................................................................ Protein_Len: 45 Strand: + Start: 105 End: 239 ........................................................................................................ M N C K Y G R C F L S I P H L F F F L L Q K P I L L S F F V Y L V I S H F P F Q M K S K K ................................................................................. Protein_Len: 37 Strand: - Start: 205 End: 315 ............................................................................................................................................................................................................ K G S E K E F S F Y F I S F S F I I K L V G I G C S F L C P I G A E L S M ..... tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttcaaatgaaaagtaaaaaatagaaaagctaaaaattattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa 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: 87 End: 116 ......................................................................................CTTGCAATTCAACTCAAATAGTTATATAAT............................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 236 End: 265 ...........................................................................................................................................................................................................................................GTTGAAAATAATTTTTAGCTTTTCTATTTT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttcaaatgaaaagtaaaaaatagaaaagctaaaaattattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1096:SMT_1097|SMT_1096:SMT_1097:glyceraldehyde-3-phosphate dehydrogenase:alcohol dehydrogenase / acetaldehyde dehydrogenase:<-<-:1038467..1038786 320 tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttcaaatgaaaagtaaaaaatagaaaagctaaaaattattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa Intra-Species Hit: Count: 1 Min: 1 Max: 320 Len: 320 Subject: smit_SMT_1096_SMT_1097|glyceraldehyde-3-phosphate dehydrogenase:alcohol dehydrogenase / acetaldehyde dehydrogenase|NEGATIVE:NEGATIVE|[1038467,1038786]|320 HSP 1 e-value: 1.0E-122 bit: 440.0 Len: 222 Query Start:1 Query End:222 Subject Strand: POSITIVE Subject Start: 1 Subject End: 222 tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttc.................................................................................................. tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttttgtctataccccacttatttttctttctccttcaaaagcctatactgctgtctttctttgtctacctagtcatttcccactttccttttc.................................................................................................. HSP 2 e-value: 2.0E-29 bit: 131.0 Len: 66 Query Start:255 Query End:320 Subject Strand: POSITIVE Subject Start: 255 Subject End: 320 ..............................................................................................................................................................................................................................................................ttattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa ..............................................................................................................................................................................................................................................................ttattttcaacactccaattccacaagaaaagagacagggaattcctgcctctaggctgataacaa Inter-species Hit: Count: 2 Min: 1 Max: 132 Len: 132 Subject: NC_008533_SPD_1823_SPD_1824|glyceraldehyde-3-phosphate dehydrogenase, type I:hypothetical protein|NEGATIVE:NEGATIVE|[1808494,1808669]|176 HSP 1 e-value: 2.0E-59 bit: 230.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttt............................................................................................................................................................................................ tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatacaactatttgagttgaattgcaagtatggccattgttttt............................................................................................................................................................................................ Subject: NC_003028_SP_2012_SP_2013|glyceraldehyde-3-phosphate dehydrogenase:hypothetical protein|NEGATIVE:NEGATIVE|[1919950,1920125]|176 HSP 1 e-value: 2.0E-59 bit: 230.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatataactatttgagttgaattgcaagtacgggcgttgttttt............................................................................................................................................................................................ tagtgatttcctccttatgaaaatcatgaaatttttattgtgaaaagagtaacttgaatcactacaaatcacctttcaacaaacctattatacaactatttgagttgaattgcaagtatggccattgttttt............................................................................................................................................................................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGAUUUCCUCCUUAUGAAAAUCAUGAAAUUUUUAUUGUGAAAAGAGUAACUUGAAUCACUACAAAUCACCUUUCAACAAACCUAUUAUAUAACUAUUUGAGUUGAAUUGCAAGUACGGGCGUUGUUUUU (((((((((.....(((((.....))))).....(((((.(....).)))))...))))))))).............(((((.((((((((.(((((.....))))).))....)))).))...)))))... (-18.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACAACGCCCGUACUUGCAAUUCAACUCAAAUAGUUAUAUAAUAGGUUUGUUGAAAGGUGAUUUGUAGUGAUUCAAGUUACUCUUUUCACAAUAAAAAUUUCAUGAUUUUCAUAAGGAGGAAAUCACUA ...............(((((..((..((((.....))))..))..)))))((((.(((((((((((((........)))))))).))))).))))...........((((((((.......))))))))... (-21.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 786 130 81 221 172 smit:SMT_1096|5end_glyceraldehyde-3-phosphate_dehydrogenase_1038376..1038606_NEGATIVE 260 130 86 188 144 smit:SMT_1017|5end_transcriptional_regulator,_MerR_family_954448..954678_NEGATIVE 242 123 84 44 5 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 242 123 84 44 5 smit:SMT_1321|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1290674..1290904_POSITIVE 239 50 2 136 81 smit:SMT_133|5end_L-serine_dehydratase_beta_subunit_85237..85467_NEGATIVE 234 90 41 131 79 smit:SMT_380|5end_hypothetical_protein_316376..316606_POSITIVE 234 90 41 131 79 smit:SMT_371|5end_hypothetical_protein_305248..305478_POSITIVE 229 126 103 31 7 smit:SMT_1134|5end_glutamyl-tRNA_synthetase_1076464..1076694_NEGATIVE 226 75 48 36 2 smit:SMT_969|5end_30S_ribosomal_protein_S15_914922..915152_NEGATIVE 218 100 54 136 81 smit:SMT_1295|5end_transcriptional_regulator_CtsR_1256830..1257060_POSITIVE 213 130 100 44 12 smit:SMT_1931|5end_23S_rRNA_methyltransferase_1870978..1871208_NEGATIVE 205 130 90 115 80 smit:SMT_1748|5end_anthranilate_synthase_component_I_1726685..1726915_POSITIVE 204 130 95 124 78 smit:SMT_2064|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1972182..1972412_POSITIVE 203 130 100 170 135 smit:SMT_1807|5end_putative_mucus_binding_protein_1784043..1784273_NEGATIVE 203 57 25 122 89 smit:SMT_305|5end_seryl-tRNA_synthetase_248851..249081_NEGATIVE 201 129 104 77 52 smit:SMT_1614|5end_K08998_hypothetical_protein_1601330..1601560_POSITIVE 199 77 42 196 165 smit:SMT_917|5end_hydroxymethylglutaryl-CoA_synthase_871176..871406_NEGATIVE 199 130 85 160 113 smit:SMT_179|5end_ribosomal_protein_S17_119392..119622_POSITIVE 191 35 8 83 51 smit:SMT_1246|5end_ISSag9,_transposase_1207149..1207379_NEGATIVE 190 130 97 124 92 smit:SMT_1684|5end_acetyltransferase,_GNAT_family_1667757..1667987_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 123 84 44 5 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 242 123 84 44 5 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 234 90 41 131 79 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 234 90 41 131 79 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE 201 129 104 77 52 smit:SMT_1613|3end_ribosomal_large_subunit_pseudouridine_synthase_B_1601410..1601560_POSITIVE 199 77 42 82 51 smit:SMT_918|3end_hypothetical_protein_871290..871440_NEGATIVE 199 130 85 135 88 smit:SMT_178|3end_50S_ribosomal_protein_L29_119447..119597_POSITIVE 190 130 97 124 92 smit:SMT_1685|3end_phenylalanyl-tRNA_synthetase_alpha_chain_1667757..1667907_NEGATIVE 190 99 53 115 59 smit:SMT_1229|3end_hypothetical_protein_1191494..1191644_POSITIVE 190 123 95 64 32 smit:SMT_989|3end_hypothetical_protein_932949..933099_NEGATIVE 189 86 41 80 22 smit:SMT_1150|3end_hypothetical_protein_1094288..1094438_NEGATIVE 187 74 31 48 5 smit:SMT_1523|3end_ferrochelatase_1503390..1503540_NEGATIVE 184 128 85 144 91 smit:SMT_885|3end_single-stranded-DNA-specific_exonuclease_RecJ_832340..832490_NEGATIVE 183 36 4 44 12 smit:SMT_1107|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1047989..1048139_NEGATIVE 181 128 99 143 114 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 178 72 35 47 7 smit:SMT_1667|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1657439..1657589_NEGATIVE 177 130 110 148 128 smit:SMT_195|3end_30S_ribosomal_protein_S13_127322..127472_POSITIVE 176 123 84 62 18 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 176 130 87 142 90 smit:SMT_999|3end_hypothetical_protein_predicted_by_Glimmer/Critica_941496..941646_NEGATIVE 175 128 85 49 4 smit:SMT_1580|3end_MutT/NUDIX_family_protein_1573153..1573303_POSITIVE