Origin IGS: nnnnnaagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaaggctcatttctttatgattataaaaactcatggtctctctccaattttgtgatgttactattataccccattttgagggaatttggsctcggtctattctatacttttctaatttaccttgctctagaatttttaaactgctatacttataacaaaaacccttnnnnn Mask Tandem Repeat Region ================================================ nnnnnaagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa Find is-nt database================================================ Query_seq: SMT_212:SMT_213|SMT_212:SMT_213:Holliday junction DNA helicase RuvB:leucyl-tRNA synthetase:->->:145360..145531 172 nnnnnaagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_212:SMT_213|SMT_212:SMT_213:Holliday junction DNA helicase RuvB:leucyl-tRNA synthetase:->->:145360..145531 172 nnnnnaagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_212:SMT_213|SMT_212:SMT_213:Holliday junction DNA helicase RuvB:leucyl-tRNA synthetase:->->:145360..145531 172 nnnnnaagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 nnnnnaagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 39 End: 170 ...................................... M L E Q G K L E K Y R I D R X Q I P S K W G I I V T S Q N W R E T M S F Y N H K E M S L .. Protein_Len: 40 Strand: - Start: 20 End: 139 ................... L Y L L K F I R S C P L N S F Y L I S R X W I G E F H P I I T V D C F Q L S V M ................................. Protein_Len: 40 Strand: - Start: 1 End: 120 X X P N K N Y T Y C N L F E L A L Y I L F T Y F L G L G F E R L I P Y L L L M M .................................................... nnnnnaagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa 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================================================ nnnnnaagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_212:SMT_213|SMT_212:SMT_213:Holliday junction DNA helicase RuvB:leucyl-tRNA synthetase:->->:145360..145531 172 nnnnnaagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa Intra-Species Hit: Count: 2 Min: 6 Max: 172 Len: 167 Subject: smit_SMT_212_SMT_213|Holliday junction DNA helicase RuvB:leucyl-tRNA synthetase|POSITIVE:POSITIVE|[145360,145531]|172 HSP 1 e-value: 3.0E-89 bit: 328.0 Len: 167 Query Start:6 Query End:172 Subject Strand: POSITIVE Subject Start: 6 Subject End: 172 .....aagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa .....aagggtttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagaccatgagtttttataatcataaagaaatgagccttaa Subject: smit_SMT_207_SMT_208|putative two-component sensor histidine kinase:leucyl-tRNA synthetase|NEGATIVE:POSITIVE|[139970,140116]|147 HSP 1 e-value: 1.0E-49 bit: 197.0 Len: 127 Query Start:11 Query End:137 Subject Strand: POSITIVE Subject Start: 22 Subject End: 147 ..........tttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagacc................................... ..........tttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaa-atggtataatagtaacatcacaaaattggagagagacc................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGGUUUUUGUUAUAAGUAUAGCAGUUUAAAAAUUCUAGAGCAAGGUAAAUUAGAAAAGUAUAGAAUAGACCGAGSCCAAAUUCCCUCAAAAUGGGGUAUAAUAGUAACAUCACAAAAUUGGAGAGAGACCAUGAGUUUUUAUAAUCAUAAAGAAAUGAGCCUUAA .((((((((((((((....)))))))..(((((((((.....(..(((..(((..(......)..)))..)))....((((..((((.......)))).......((......))....)))).....).....)))))))))...............))))))).. (-24.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAGGCUCAUUUCUUUAUGAUUAUAAAAACUCAUGGUCUCUCUCCAAUUUUGUGAUGUUACUAUUAUACCCCAUUUUGAGGGAAUUUGGSCUCGGUCUAUUCUAUACUUUUCUAAUUUACCUUGCUCUAGAAUUUUUAAACUGCUAUACUUAUAACAAAAACCCUU ..((((....(((..((((((.((((......((...((((((........(((((((....))))))).........))))))...))....((((..((((((.......................))))))......)))).)))).))))))..)))..)))) (-17.63) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 702 50 1 157 107 smit:SMT_207|5end_putative_two-component_sensor_histidine_kinase_139879..140109_NEGATIVE 321 130 85 207 160 smit:SMT_954|5end_cation-transporting_ATPase,_E1-E2_family_904025..904255_NEGATIVE 251 108 62 65 1 smit:SMT_1025|5end_hypothetical_protein_960557..960787_NEGATIVE 222 89 52 196 152 smit:SMT_1719|5end_DNA_mismatch_repair_protein_1706842..1707072_NEGATIVE 216 96 52 223 169 smit:SMT_590|5end_tetratricopeptide_repeat_family_protein_506737..506967_POSITIVE 215 142 123 60 40 smit:SMT_178|5end_50S_ribosomal_protein_L29_119161..119391_POSITIVE 212 126 82 146 101 smit:SMT_1073|5end_L-asparaginase_1011209..1011439_POSITIVE 209 99 54 195 148 smit:SMT_937|5end_dipeptidase_889579..889809_POSITIVE 209 99 54 195 148 smit:SMT_932|5end_tellurite_resistance_protein_885065..885295_POSITIVE 208 130 82 155 92 smit:SMT_1039|5end_tRNA_(uracil-5-)_-methyltransferase_982698..982928_NEGATIVE 204 109 63 40 1 smit:SMT_1341|5end_putative_cell_division_protein_1319115..1319345_NEGATIVE 204 137 96 204 162 smit:SMT_993|5end_hypothetical_protein_935476..935706_NEGATIVE 203 98 71 154 127 smit:SMT_596|5end_K03976_putative_transcription_regulator_513075..513305_NEGATIVE 202 140 96 159 120 smit:SMT_2024|5end_hypothetical_protein_1940359..1940589_POSITIVE 202 139 91 142 92 smit:SMT_1582|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1573732..1573962_POSITIVE 202 140 96 159 120 smit:SMT_724|5end_hypothetical_protein_630060..630290_NEGATIVE 201 100 52 76 25 smit:SMT_1884|5end_hypothetical_protein_1838964..1839194_POSITIVE 201 100 52 76 25 smit:SMT_1875|5end_hypothetical_protein_1832965..1833195_POSITIVE 201 89 42 70 12 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 201 90 41 77 31 smit:SMT_547|5end_branched-chain_amino_acid_aminotransferase_463947..464177_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 216 49 1 71 20 smit:SMT_1655|3end_glucose-6-phosphate_1-dehydrogenase_1643534..1643684_NEGATIVE 215 142 123 50 30 smit:SMT_177|3end_K02878_large_subunit_ribosomal_protein_L16_119231..119381_POSITIVE 209 99 54 67 20 smit:SMT_936|3end_cobyric_acid_synthase_889531..889681_POSITIVE 209 99 54 67 20 smit:SMT_931|3end_cobyric_acid_synthase_885017..885167_POSITIVE 209 50 1 71 25 smit:SMT_697|3end_glucose-inhibited_division_protein_B_608282..608432_POSITIVE 207 80 36 72 16 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 207 98 69 142 110 smit:SMT_330|3end_membrane-associated_phospholipid_phosphatase_266187..266337_POSITIVE 205 48 7 45 1 smit:SMT_635|3end_ribonucleoside-diphosphate_reductase_alpha_chain_541043..541193_POSITIVE 199 95 71 146 127 smit:SMT_597|3end_K08974_putative_membrane_protein_513075..513225_NEGATIVE 196 88 41 63 10 smit:SMT_581|3end_ATP_synthase_A_chain_499069..499219_POSITIVE 195 98 51 73 33 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 194 89 48 128 87 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 193 70 21 134 94 smit:SMT_2118|3end_putative_two-component_sensor_histidine_kinase_2004725..2004875_NEGATIVE 189 44 2 39 1 smit:SMT_1491|3end_capsular_polysaccharide_biosynthesis_protein,_putative_1471967..1472117_POSITIVE 188 147 114 39 4 smit:SMT_190|3end_preprotein_translocase,_SecY_subunit_125675..125825_POSITIVE 187 90 45 57 16 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 182 87 45 151 110 smit:SMT_941|3end_hypothetical_protein_892863..893013_NEGATIVE 179 76 35 123 79 smit:SMT_1274|3end_K02008_cobalt_transport_system_permease_protein_1238615..1238765_POSITIVE 176 87 44 81 40 smit:SMT_236|3end_ribosomal_small_subunit_pseudouridine_synthase_A_175211..175361_POSITIVE 175 142 103 69 32 smit:SMT_1220|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1180509..1180659_NEGATIVE