Origin IGS: cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttgaaaaaatctgtgatttactctctaaaatagaaaatcatttatggaaaataaaaaagtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattgattgtttcattttgccttatgcggtgtatgccgtaaaaggcaggatgaaacttttttattttccataaatgattttctattttagagagtaaatcacagattttttcaaagaaaataggatatttcttgtataataggaatatctaaaaagatttggagttagaagaag Mask Tandem Repeat Region ================================================ cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttgaaaaaatctgtgatttactctctaaaatagaaaatcatttatggaaaataaaaaagtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta Find is-nt database================================================ Query_seq: SMT_1362:SMT_1363|SMT_1362:SMT_1363:chaperone protein hscC:50S ribosomal protein L20:<-<-:1343169..1343343 175 cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttgaaaaaatctgtgatttactctctaaaatagaaaatcatttatggaaaataaaaaagtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1362:SMT_1363|SMT_1362:SMT_1363:chaperone protein hscC:50S ribosomal protein L20:<-<-:1343169..1343343 175 cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttgaaaaaatctgtgatttactctctaaaatagaaaatcatttatggaaaataaaaaagtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1362:SMT_1363|SMT_1362:SMT_1363:chaperone protein hscC:50S ribosomal protein L20:<-<-:1343169..1343343 175 cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttgaaaaaatctgtgatttactctctaaaatagaaaatcatttatggaaaataaaaaagtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttgaaaaaatctgtgatttactctctaaaatagaaaatcatttatggaaaataaaaaagtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 27 End: 173 .......................... M F L L Y K K Y P I F F E K I C D L L S K I E N H L W K I K K F H P A F Y G I H R I R Q N E T I N .. cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttgaaaaaatctgtgatttactctctaaaatagaaaatcatttatggaaaataaaaaagtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta 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================================================ cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttgaaaaaatctgtgatttactctctaaaatagaaaatcatttatggaaaataaaaaagtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1362:SMT_1363|SMT_1362:SMT_1363:chaperone protein hscC:50S ribosomal protein L20:<-<-:1343169..1343343 175 cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttgaaaaaatctgtgatttactctctaaaatagaaaatcatttatggaaaataaaaaagtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: smit_SMT_1362_SMT_1363|chaperone protein hscC:50S ribosomal protein L20|NEGATIVE:NEGATIVE|[1343169,1343343]|175 HSP 1 e-value: 5.0E-28 bit: 125.0 Len: 63 Query Start:1 Query End:63 Subject Strand: POSITIVE Subject Start: 1 Subject End: 63 cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttg................................................................................................................ cttcttctaactccaaatctttttagatattcctattatacaagaaatatcctattttctttg................................................................................................................ HSP 2 e-value: 2.0E-24 bit: 113.0 Len: 57 Query Start:119 Query End:175 Subject Strand: POSITIVE Subject Start: 119 Subject End: 175 ......................................................................................................................gtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta ......................................................................................................................gtttcatcctgccttttacggcatacaccgcataaggcaaaatgaaacaatcaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUUCUAACUCCAAAUCUUUUUAGAUAUUCCUAUUAUACAAGAAAUAUCCUAUUUUCUUUGAAAAAAUCUGUGAUUUACUCUCUAAAAUAGAAAAUCAUUUAUGGAAAAUAAAAAAGUUUCAUCCUGCCUUUUACGGCAUACACCGCAUAAGGCAAAAUGAAACAAUCAAUUA .........................((((((.((........)).)))))).((((((((.(((........(((((((....((((...)))))))))))))).)))))))).....(((((((..((((((...(((......)))...))))))..)))))))......... (-32.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUGAUUGUUUCAUUUUGCCUUAUGCGGUGUAUGCCGUAAAAGGCAGGAUGAAACUUUUUUAUUUUCCAUAAAUGAUUUUCUAUUUUAGAGAGUAAAUCACAGAUUUUUUCAAAGAAAAUAGGAUAUUUCUUGUAUAAUAGGAAUAUCUAAAAAGAUUUGGAGUUAGAAGAAG .........(((((((((((((((.((((((....)))))).)))))))))))))))(((((((..(((((......((((((((...)))))))).((((....((((((.....)))))).((((((((((........)))))))))).....))))))))).))))))).. (-51.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 749 140 91 231 182 smit:SMT_1362|5end_chaperone_protein_hscC_1343078..1343308_NEGATIVE 294 158 121 190 147 smit:SMT_2015|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1932655..1932885_POSITIVE 284 158 120 141 86 smit:SMT_1697|5end_hypothetical_protein_1678846..1679076_POSITIVE 265 156 121 218 177 smit:SMT_1021|5end_K05846_osmoprotectant_transport_system_permease_protein_957999..958229_NEGATIVE 263 160 111 66 7 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 251 158 127 72 37 smit:SMT_1613|5end_ribosomal_large_subunit_pseudouridine_synthase_B_1600608..1600838_POSITIVE 246 147 118 213 172 smit:SMT_2164|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2037861..2038091_POSITIVE 246 147 118 136 95 smit:SMT_2152|5end_cell_division_protein_2025649..2025879_POSITIVE 243 149 130 210 189 smit:SMT_2154|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2027454..2027684_POSITIVE 243 149 130 198 177 smit:SMT_2140|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2017620..2017850_POSITIVE 237 163 126 154 104 smit:SMT_1115|5end_K02245_competence_protein_ComGC_1052796..1053026_NEGATIVE 231 157 138 21 1 smit:SMT_2034|5end_hydrolase,_haloacid_dehalogenase-like_family_1946671..1946901_POSITIVE 231 149 118 52 19 smit:SMT_1752|5end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1729772..1730002_POSITIVE 228 156 121 138 105 smit:SMT_1954|5end_6-phospho-beta-glucosidase_1888548..1888778_POSITIVE 225 166 126 136 99 smit:SMT_320|5end_alcohol_dehydrogenase,_zinc-containing_259492..259722_NEGATIVE 224 156 119 132 84 smit:SMT_893|5end_leucine_rich_protein_841311..841541_NEGATIVE 222 168 129 222 181 smit:SMT_1331|5end_hypothetical_protein_1306236..1306466_NEGATIVE 220 155 120 95 54 smit:SMT_1981|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912261..1912491_POSITIVE 220 156 123 37 1 smit:SMT_909|5end_type_I_restriction_enzyme_M_protein_858827..859057_NEGATIVE 217 159 118 121 84 smit:SMT_1458|5end_K02040_phosphate_transport_system_substrate-binding_protein_1440277..1440507_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 158 120 139 84 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 263 160 111 69 10 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 251 158 127 85 50 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 236 158 117 90 35 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 231 149 118 65 32 smit:SMT_1751|3end_indole-3-glycerol_phosphate_synthase_1729865..1730015_POSITIVE 230 155 118 151 105 smit:SMT_1073|3end_L-asparaginase_1012251..1012401_POSITIVE 224 156 119 128 80 smit:SMT_894|3end_hypothetical_protein_841315..841465_NEGATIVE 221 162 126 151 102 smit:SMT_1116|3end_K02244_competence_protein_ComGB_1052798..1052948_NEGATIVE 220 155 120 54 13 smit:SMT_2023|3end_tryptophan_synthase,_alpha_subunit_1939997..1940147_POSITIVE 220 155 120 81 40 smit:SMT_1970|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903032..1903182_POSITIVE 220 156 123 37 1 smit:SMT_910|3end_type_I_restriction_enzyme_R_protein_858827..858977_NEGATIVE 219 157 127 145 109 smit:SMT_322|3end_hypothetical_protein_261346..261496_POSITIVE 215 170 121 59 1 smit:SMT_1674|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1660361..1660511_NEGATIVE 212 47 1 68 24 smit:SMT_1743|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1725058..1725208_NEGATIVE 206 156 124 135 103 smit:SMT_1650|3end_ribonuclease_III_1637087..1637237_POSITIVE 204 149 101 72 13 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 204 143 105 109 66 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 202 140 98 104 59 smit:SMT_2119|3end_mercuric_reductase_2006145..2006295_POSITIVE 202 155 125 40 3 smit:SMT_2015|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1932839..1932989_POSITIVE 202 158 129 39 15 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE