Origin IGS: taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcttcctccatacttgctcttattatatgctagaaagcctcaccattgctagaatatttctcaactgtcagttttctactctaaaatgcaaaaaagtttgacgcaagtatcccttacatcaaactttta Mask Tandem Repeat Region ================================================ taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga Find is-nt database================================================ Query_seq: SMT_1494:SMT_1495|SMT_1494:SMT_1495:nucleoside diphosphate kinase:hypothetical protein:->->:1480282..1480410 129 taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1494:SMT_1495|SMT_1494:SMT_1495:nucleoside diphosphate kinase:hypothetical protein:->->:1480282..1480410 129 taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1494:SMT_1495|SMT_1494:SMT_1495:nucleoside diphosphate kinase:hypothetical protein:->->:1480282..1480410 129 taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga Predict ORF larger than 30AA ================================================ taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga 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================================================ taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1494:SMT_1495|SMT_1494:SMT_1495:nucleoside diphosphate kinase:hypothetical protein:->->:1480282..1480410 129 taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: smit_SMT_1494_SMT_1495|nucleoside diphosphate kinase:hypothetical protein|POSITIVE:POSITIVE|[1480282,1480410]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga taaaagtttgatgtaagggatacttgcgtcaaacttttttgcattttagagtagaaaactgacagttgagaaatattctagcaatggtgaggctttctagcatataataagagcaagtatggaggaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGUUUGAUGUAAGGGAUACUUGCGUCAAACUUUUUUGCAUUUUAGAGUAGAAAACUGACAGUUGAGAAAUAUUCUAGCAAUGGUGAGGCUUUCUAGCAUAUAAUAAGAGCAAGUAUGGAGGAAGA .((((((((((((((((.....))))))))))))))))...((((((((((((...(((.....)))......)))))))).))))......((((((..(((((...........))))).)))))). (-35.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUCCUCCAUACUUGCUCUUAUUAUAUGCUAGAAAGCCUCACCAUUGCUAGAAUAUUUCUCAACUGUCAGUUUUCUACUCUAAAAUGCAAAAAAGUUUGACGCAAGUAUCCCUUACAUCAAACUUUUA .........((((((((((..(((...(((((((((((...((..(((..(((.....))))))..))..)))))))).........)))....)))..)).))))))))................... (-18.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 92 58 41 8 smit:SMT_1369|5end_alanine_dehydrogenase_1348280..1348510_POSITIVE 271 43 1 49 7 smit:SMT_705|5end_hypothetical_protein_615336..615566_NEGATIVE 246 104 76 178 146 smit:SMT_1873|5end_K02006_cobalt_transport_system_ATP-binding_protein_1831936..1832166_POSITIVE 242 42 4 229 195 smit:SMT_1520|5end_K02004_1501184..1501414_NEGATIVE 241 118 81 66 30 smit:SMT_1738|5end_peptidyl-prolyl_cis-trans_isomerase_1720497..1720727_POSITIVE 241 115 76 88 49 smit:SMT_869|5end_hypothetical_protein_817698..817928_NEGATIVE 240 104 63 192 155 smit:SMT_303|5end_hypothetical_protein_245364..245594_POSITIVE 236 59 15 48 4 smit:SMT_822|5end_putative_mucus_binding_protein_740574..740804_NEGATIVE 232 42 5 209 168 smit:SMT_2096|5end_ATP-dependent_exonuclease_RexB_1990380..1990610_NEGATIVE 228 119 76 197 146 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 226 100 59 214 166 smit:SMT_754|5end_3-dehydroquinate_synthase_659044..659274_NEGATIVE 225 120 76 42 7 smit:SMT_1974|5end_high-affinity_zinc_uptake_system_protein_ZnuA_precursor_/_hypothetical_exported_protein_1905506..1905736_POSITIVE 223 100 53 229 179 smit:SMT_1477|5end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1460376..1460606_NEGATIVE 222 114 78 38 4 smit:SMT_2106|5end_unknown,_predicted_membrane_protein_(TMS5)_1997163..1997393_POSITIVE 222 104 63 92 40 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 222 114 78 38 4 smit:SMT_1771|5end_unknown,_predicted_membrane_protein_(TMS5)_1747437..1747667_POSITIVE 219 102 74 108 79 smit:SMT_1938|5end_zinc_metalloprotease_ZmpB,_putative_1875374..1875604_POSITIVE 218 103 62 205 159 smit:SMT_2166|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2039569..2039799_POSITIVE 218 104 79 224 200 smit:SMT_1985|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1914571..1914801_NEGATIVE 218 104 64 90 37 smit:SMT_1977|5end_endopeptidase_O_1907832..1908062_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 38 2 89 53 smit:SMT_1494|3end_nucleoside_diphosphate_kinase_1480221..1480371_POSITIVE 279 94 51 59 9 smit:SMT_913|3end_putative_sucrose-specific_PTS_permease,_enzyme_II_863923..864073_NEGATIVE 271 43 1 68 26 smit:SMT_706|3end_hypothetical_protein_615317..615467_NEGATIVE 241 118 81 87 51 smit:SMT_1737|3end_peptidyl-prolyl_cis-trans_isomerase_1720598..1720748_POSITIVE 241 115 76 86 47 smit:SMT_870|3end_hypothetical_protein_817700..817850_NEGATIVE 240 104 63 67 30 smit:SMT_302|3end_K07444_putative_N6-adenine-specific_DNA_methylase_245319..245469_POSITIVE 235 93 51 48 5 smit:SMT_124|3end_hypothetical_protein_75590..75740_NEGATIVE 234 94 51 52 2 smit:SMT_764|3end_alanyl-tRNA_synthetase_669495..669645_NEGATIVE 232 42 5 114 73 smit:SMT_2097|3end_type_I_restriction_enzyme_M_protein_1990475..1990625_NEGATIVE 228 65 22 46 2 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 227 82 48 78 42 smit:SMT_412|3end_hypothetical_protein_predicted_by_Glimmer/Critica_356436..356586_NEGATIVE 222 102 86 77 61 smit:SMT_1991|3end_K03706_transcriptional_pleiotropic_repressor_1917770..1917920_NEGATIVE 219 102 74 76 47 smit:SMT_1937|3end_glycosyl_transferase,_family_2_1875422..1875572_POSITIVE 216 50 6 52 5 smit:SMT_1785|3end_phenylalanyl-tRNA_synthetase_beta_chain_1762327..1762477_NEGATIVE 215 93 51 54 11 smit:SMT_1912|3end_D-alanyl-D-alanine_carboxypeptidase_1857807..1857957_NEGATIVE 215 93 51 54 11 smit:SMT_868|3end_D-alanyl-D-alanine_carboxypeptidase_816509..816659_NEGATIVE 211 118 88 35 4 smit:SMT_1302|3end_hypothetical_protein_1264649..1264799_POSITIVE 209 70 25 131 94 smit:SMT_171|3end_50S_ribosomal_protein_L4_116260..116410_POSITIVE 205 50 3 95 39 smit:SMT_1272|3end_K02006_cobalt_transport_system_ATP-binding_protein_1237004..1237154_POSITIVE 205 115 75 45 12 smit:SMT_198|3end_50S_ribosomal_protein_L17_129281..129431_POSITIVE