Origin IGS: cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag .........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 cttatttcaccccctgaatattataaaccatgtaccatagtacacggtcaagtaaattggactattttattttttcccaaagtatcactcgtatgtgattgatacttttatataatactattgattatcctaacatcccaccagaaaatccgatttaaacaccagttgtttttaaactattaagaaagtaattccactatatattccgaagacccgaaatttcatagagtagctccctagaatcatggaaaagtagtaaaaatagctg Mask Tandem Repeat Region ================================================ cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Find is-nt database================================================ Query_seq: SMT_1234:SMT_1235|SMT_1234:SMT_1235:cadmium efflux system accessory protein:transcriptional regulator, MerR family:->->:1195411..1195678 268 cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1234:SMT_1235|SMT_1234:SMT_1235:cadmium efflux system accessory protein:transcriptional regulator, MerR family:->->:1195411..1195678 268 cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1234:SMT_1235|SMT_1234:SMT_1235:cadmium efflux system accessory protein:transcriptional regulator, MerR family:->->:1195411..1195678 268 cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 170 End: 265 ......................................................................................................................................................................... D C V L S V K P F F L I T W N V Q G H V I T C P K Y Y E P P S M ... cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag 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================================================ cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 51 HP_score: -3.9 Tail_Score: -3.53444 Start: 164 End: 187 Full_Region: TAGTATTATATAAAA GTATCAATC ACATAC GAGTGATAC TTTGGGAAAAAATAA ...................................................................................................................................................................GTATCAATCACATACGAGTGATAC................................................................................. TransTerm Strand: + Conf: 82 HP_score: -8.6 Tail_Score: -4.06384 Start: 222 End: 241 Full_Region: GTCCAATTTACTTGA CCGTGTAC TATG GTACATGG TTTATAATATTCAGG .............................................................................................................................................................................................................................CCGTGTACTATGGTACATGG........................... Find igs database================================================ Query_seq: SMT_1234:SMT_1235|SMT_1234:SMT_1235:cadmium efflux system accessory protein:transcriptional regulator, MerR family:->->:1195411..1195678 268 cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Intra-Species Hit: Count: 2 Min: 1 Max: 268 Len: 268 Subject: smit_SMT_2087_SMT_2088|cadmium efflux system accessory protein:glucose-1-phosphate thymidylyltransferase|POSITIVE:POSITIVE|[1984169, 1984763]|595 HSP 1 e-value: 1.0E-150 bit: 531.0 Len: 268 Query Start:1 Query End:268 Subject Strand: POSITIVE Subject Start: 1 Subject End: 268 cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Subject: smit_SMT_1234_SMT_1235|cadmium efflux system accessory protein:transcriptional regulator, MerR family|POSITIVE:POSITIVE|[1195411,1195678]|268 HSP 1 e-value: 1.0E-150 bit: 531.0 Len: 268 Query Start:1 Query End:268 Subject Strand: POSITIVE Subject Start: 1 Subject End: 268 cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag cagctatttttactacttttccatgattctagggagctactctatgaaatttcgggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Inter-species Hit: Count: 2 Min: 54 Max: 268 Len: 215 Subject: NC_004116_SAG2024_SAG2025|mercuric resistance operon regulatory protein MerR:Mn2+/Fe2+ transporter, NRAMP family|NEGATIVE:POSITIVE|[2000942,2001646]|705 HSP 1 e-value: 1.0E-114 bit: 412.0 Len: 215 Query Start:54 Query End:268 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 216 .....................................................gggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaa-aaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag .....................................................gggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Subject: NC_004116_SAG1255_SAG1257|mercuric resistance operon regulatory protein MerR:cation-transporting ATPase, E1-E2 family|NEGATIVE:NEGATIVE|[1265349,1266611]|1263 HSP 1 e-value: 1.0E-114 bit: 412.0 Len: 215 Query Start:54 Query End:268 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 216 .....................................................gggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaa-aaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag .....................................................gggtcttcggaatatatagtggaattactttcttaatagtttaaaaacaactggtgtttaaatcggattttctggtgggatgttaggataatcaatagtattatataaaagtatcaatcacatacgagtgatactttgggaaaaaaataaaatagtccaatttacttgaccgtgtactatggtacatggtttataatattcagggggtgaaataag Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUCUUCGGAAUAUAUAGUGGAAUUACUUUCUUAAUAGUUUAAAAACAACUGGUGUUUAAAUCGGAUUUUCUGGUGGGAUGUUAGGAUAAUCAAUAGUAUUAUAUAAAAGUAUCAAUCACAUACGAGUGAUACUUUGGGAAAAAAUAAAAUAGUCCAAUUUACUUGACCGUGUACUAUGGUACAUGGUUUAUAAUAUUCAGGGGGUGAAAUAAG ...((....)).............(((((..((.................((((..((...(((((.....)))))..))..))))..........(((((((((..(((((((((.((......)).))))))))).(((.............))).........((((((((((....))))))))))))))))))).))..)))))...... (-47.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUUUCACCCCCUGAAUAUUAUAAACCAUGUACCAUAGUACACGGUCAAGUAAAUUGGACUAUUUUAUUUUUUCCCAAAGUAUCACUCGUAUGUGAUUGAUACUUUUAUAUAAUACUAUUGAUUAUCCUAACAUCCCACCAGAAAAUCCGAUUUAAACACCAGUUGUUUUUAAACUAUUAAGAAAGUAAUUCCACUAUAUAUUCCGAAGACCC ....((((.....(((..........(((.(((((....))))).)))....(((((((((.................(((((((((.(((....))).)))))))))...(((((.(....))))))....................))))))))).....)))...(((((((....))))))).....................)))).... (-30.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 93 51 56 7 smit:SMT_1934|5end_homoserine_dehydrogenase_1872402..1872632_POSITIVE 258 210 164 230 174 smit:SMT_852|5end_K03978_GTP-binding_protein_798044..798274_NEGATIVE 252 94 51 62 13 smit:SMT_2026|5end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1942432..1942662_NEGATIVE 246 87 51 213 183 smit:SMT_931|5end_cobyric_acid_synthase_884491..884721_POSITIVE 244 205 164 220 171 smit:SMT_1698|5end_CMP-binding_factor_1680092..1680322_POSITIVE 233 94 53 225 187 smit:SMT_1844|5end_hypothetical_protein_1808587..1808817_POSITIVE 230 96 51 201 153 smit:SMT_767|5end_hypothetical_protein_676454..676684_NEGATIVE 229 209 163 199 154 smit:SMT_961|5end_K02016_iron_complex_transport_system_substrate-binding_protein_907809..908039_NEGATIVE 229 87 47 60 33 smit:SMT_791|5end_thiamine_biosynthesis_protein_ThiI_702377..702607_NEGATIVE 226 208 168 100 56 smit:SMT_1880|5end_hypothetical_protein_1836854..1837084_POSITIVE 224 100 54 104 47 smit:SMT_1901|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1850537..1850767_POSITIVE 224 99 51 203 137 smit:SMT_1373|5end_K02838_ribosome_recycling_factor_1352274..1352504_NEGATIVE 223 208 164 184 148 smit:SMT_986|5end_threonyl-tRNA_synthetase_931092..931322_POSITIVE 223 208 164 46 10 smit:SMT_985|5end_guanylate_kinase_930954..931184_POSITIVE 223 208 164 184 148 smit:SMT_925|5end_DNA-directed_RNA_polymerase_omega_chain_880283..880513_NEGATIVE 216 87 63 218 193 smit:SMT_1557|5end_hypothetical_protein_1541939..1542169_POSITIVE 215 24 4 115 97 smit:SMT_2044|5end_transcriptional_activator_TipA,_putative_1955885..1956115_NEGATIVE 215 88 47 181 140 smit:SMT_1750|5end_anthranilate_phosphoribosyltransferase_1728011..1728241_POSITIVE 212 100 65 178 149 smit:SMT_514|5end_tRNA_(guanine-N(1)-)-methyltransferase_441377..441607_POSITIVE 211 88 48 72 35 smit:SMT_2171|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2042271..2042501_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 94 53 100 62 smit:SMT_1843|3end_transposase,_TnpA_1808542..1808692_POSITIVE 233 94 53 100 62 smit:SMT_1238|3end_transposase,_TnpA_1199180..1199330_POSITIVE 227 82 52 43 9 smit:SMT_2084|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1982973..1983123_NEGATIVE 224 100 54 107 50 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 210 83 48 73 42 smit:SMT_1273|3end_K02006_cobalt_transport_system_ATP-binding_protein_1237828..1237978_POSITIVE 208 80 44 56 3 smit:SMT_1359|3end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1337203..1337353_NEGATIVE 208 86 50 140 104 smit:SMT_752|3end_prephenate_dehydrogenase_655688..655838_NEGATIVE 207 92 66 122 95 smit:SMT_404|3end_hypothetical_protein_334029..334179_POSITIVE 205 85 48 133 103 smit:SMT_659|3end_hypothetical_protein_569736..569886_NEGATIVE 204 208 180 30 3 smit:SMT_434|3end_orotidine_5'-phosphate_decarboxylase_376888..377038_POSITIVE 202 191 163 57 35 smit:SMT_2075|3end_phosphoribosylamine--glycine_ligase_1977769..1977919_NEGATIVE 200 188 158 122 96 smit:SMT_1116|3end_K02244_competence_protein_ComGB_1052798..1052948_NEGATIVE 200 188 155 118 86 smit:SMT_704|3end_Cof_family_protein_614548..614698_POSITIVE 200 89 48 97 49 smit:SMT_186|3end_50S_ribosomal_protein_L18_123059..123209_POSITIVE 199 208 164 109 56 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 199 209 168 86 50 smit:SMT_777|3end_hypothetical_protein_686618..686768_NEGATIVE 198 189 146 51 10 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 197 88 48 46 5 smit:SMT_948|3end_hypothetical_protein_predicted_by_Glimmer/Critica_896655..896805_NEGATIVE 196 157 123 46 13 smit:SMT_1988|3end_two-component_sensor_kinase_YesM_1916472..1916622_NEGATIVE 196 99 51 65 12 smit:SMT_1059|3end_NAD(P)H-flavin_oxidoreductase_998172..998322_POSITIVE