Origin IGS: tgaaagaagctgatactgaatctgacgaccgtattttggatcgtacgattgaggaactggacttgtctgtgcgttcatacaactgtttgaaacgtgccggtatcaatactgtgcatgatttgacagaaaaatctgaagcagagatgatgaaagtacgaaatcttggacgcaagagtttggaagaagtgaaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa .........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 ttattcctcctttatttatcttttaatccaagacccaaatcaatgagtttgagtttcacttcttccaaactcttgcgtccaagatttcgtactttcatcatctctgcttcagatttttctgtcaaatcatgcacagtattgataccggcacgtttcaaacagttgtatgaacgcacagacaagtccagttcctcaatcgtacgatccaaaatacggtcgtcagattcagtatcagcttctttca Mask Tandem Repeat Region ================================================ tgaaagaagctgatactgaatctgacgaccgtattttggatcgtacgattgaggaactggacttgtctgtgcgttcatacaactgtttgaaacgtgccggtatcaatactgtgcatgatttgacagaaaaatctgaagcagagatgatgaaagtacgaaatcttggacgcaagagtttggaagaagtgaaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa Find is-nt database================================================ Query_seq: SMT_197:SMT_198|SMT_197:SMT_198:DNA-directed RNA polymerase, alpha subunit:50S ribosomal protein L17:->->:128528..128771 244 tgaaagaagctgatactgaatctgacgaccgtattttggatcgtacgattgaggaactggacttgtctgtgcgttcatacaactgtttgaaacgtgccggtatcaatactgtgcatgatttgacagaaaaatctgaagcagagatgatgaaagtacgaaatcttggacgcaagagtttggaagaagtgaaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_197:SMT_198|SMT_197:SMT_198:DNA-directed RNA polymerase, alpha subunit:50S ribosomal protein L17:->->:128528..128771 244 tgaaagaagctgatactgaatctgacgaccgtattttggatcgtacgattgaggaactggacttgtctgtgcgttcatacaactgtttgaaacgtgccggtatcaatactgtgcatgatttgacagaaaaatctgaagcagagatgatgaaagtacgaaatcttggacgcaagagtttggaagaagtgaaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 27 Max: 188 Len: 162 Subject: gi|89110715|ref|AP_004495.1| RNA polymerase, alpha subunit [Escherichia coli W3110] HSP 1 e-value: 2.0E-9 bit: 57.4 Len: 162 Query Start:27 Query End:188 Subject Strand: null Subject Start: 250 Subject End: 303 .......................... D R I L D R T I E E L D L S V R S Y N C L K R A G I N T V H D L T E K S E A E M M K V R N L G R K S L E E V ........................................................ .......................... D P I L L R P V D D L E L T V R S A N C L K A E A I H Y I G D L V Q R T E V E L L K T P N L G K K S L T E I ........................................................ Find nr database================================================ Query_seq: SMT_197:SMT_198|SMT_197:SMT_198:DNA-directed RNA polymerase, alpha subunit:50S ribosomal protein L17:->->:128528..128771 244 tgaaagaagctgatactgaatctgacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaagaagctgatactgaatctgacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 33 End: 230 ................................ M L D R T I E E L D L S V R S Y N C L K R A G I N T V H D L T E K S E A E M M K V R N L G R K S L E E V K L K L I D L G .............. Protein_Len: 43 Strand: - Start: 78 End: 206 ............................................................................. V V T Q F T G T D I S H M I Q C F F R F C L H H F Y S I K S A L T Q F F H F E F E N M ...................................... Protein_Len: 60 Strand: - Start: 2 End: 202 . S S R I K S R V I S S S S K D T R E Y L Q K F R A P I L V T C S K V S F D S A S I I F T R F R P R L L K S S T F S L S M .......................................... tgaaagaagctgatactgaatctgacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa 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: 81 Start: 119 End: 148 ......................................................................................................................TTTGACAGAAAAATCTGAAGCAGAGATGAT................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaaagaagctgatactgaatctgacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -5.4 Tail_Score: -4.9792 Start: 132 End: 142 Full_Region: cgtactttcatcatc tctg ctt caga tttttctgtcaaatc ...................................................................................................................................tctgcttcaga...................................................................................................... Find igs database================================================ Query_seq: SMT_197:SMT_198|SMT_197:SMT_198:DNA-directed RNA polymerase, alpha subunit:50S ribosomal protein L17:->->:128528..128771 244 tgaaagaagctgatactgaatctgacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa Intra-Species Hit: Count: 1 Min: 1 Max: 244 Len: 244 Subject: smit_SMT_197_SMT_198|DNA-directed RNA polymerase, alpha subunit:50S ribosomal protein L17|POSITIVE:POSITIVE|[128528,128771]|244 HSP 1 e-value: 1.0E-23 bit: 111.0 Len: 56 Query Start:189 Query End:244 Subject Strand: POSITIVE Subject Start: 189 Subject End: 244 ............................................................................................................................................................................................aaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa ............................................................................................................................................................................................aaactcaaactcattgatttgggtcttggattaaaagataaataaaggaggaataa HSP 2 e-value: 9.0E-6 bit: 52.0 Len: 26 Query Start:1 Query End:26 Subject Strand: POSITIVE Subject Start: 1 Subject End: 26 tgaaagaagctgatactgaatctgac.......................................................................................................................................................................................................................... tgaaagaagctgatactgaatctgac.......................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAGAAGCUGAUACUGAAUCUGACGACCGUAUUUUGGAUCGUACGAUUGAGGAACUGGACUUGUCUGUGCGUUCAUACAACUGUUUGAAACGUGCCGGUAUCAAUACUGUGCAUGAUUUGACAGAAAAAUCUGAAGCAGAGAUGAUGAAAGUACGAAAUCUUGGACGCAAGAGUUUGGAAGAAGUGAAACUCAAACUCAUUGAUUUGGGUCUUGGAUUAAAAGAUAAAUAAAGGAGGAAUAA ...............((.((((..(((((((.....))).))))..)))).))...((..(.((((((((((.(((((....((((((....((((((((((....))))).)))))......((((....)))))))))).....))))).))))..(((((.((((.(((((((((((............))))))))......))).)))).)))))...)))))).)..))......... (-61.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUCCUCCUUUAUUUAUCUUUUAAUCCAAGACCCAAAUCAAUGAGUUUGAGUUUCACUUCUUCCAAACUCUUGCGUCCAAGAUUUCGUACUUUCAUCAUCUCUGCUUCAGAUUUUUCUGUCAAAUCAUGCACAGUAUUGAUACCGGCACGUUUCAAACAGUUGUAUGAACGCACAGACAAGUCCAGUUCCUCAAUCGUACGAUCCAAAAUACGGUCGUCAGAUUCAGUAUCAGCUUCUUUCA ........................((((...((((.....(((.(((((((((........))..))))))))))...........((((((...........(((.....(((((.(((((....((((((((.((.((((.((......)).)))))).).)))))))....))))).))))))))..........))))))..........))))....)))).................. (-40.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 58 12 135 81 smit:SMT_585|5end_ATP_synthase_gamma_chain_501569..501799_POSITIVE 300 59 19 54 8 smit:SMT_1257|5end_acetolactate_synthase_small_subunit_1223173..1223403_NEGATIVE 292 99 56 158 105 smit:SMT_1914|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1859486..1859716_POSITIVE 290 104 62 46 7 smit:SMT_1422|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1407467..1407697_NEGATIVE 290 104 62 171 132 smit:SMT_1421|5end_K02003_1407342..1407572_NEGATIVE 282 68 24 66 4 smit:SMT_183|5end_30S_ribosomal_protein_S14_121014..121244_POSITIVE 279 99 57 119 76 smit:SMT_2121|5end_putative_mucus_binding_protein_2007145..2007375_NEGATIVE 279 99 57 119 76 smit:SMT_2068|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1974482..1974712_NEGATIVE 269 69 28 191 154 smit:SMT_732|5end_K07467_phage_replication_initiation_protein_639409..639639_NEGATIVE 266 56 15 217 180 smit:SMT_2067|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1973432..1973662_POSITIVE 266 110 62 203 133 smit:SMT_2037|5end_lysine_decarboxylase_1948260..1948490_NEGATIVE 266 56 15 65 27 smit:SMT_1172|5end_hypothetical_protein_1124506..1124736_NEGATIVE 265 174 139 137 89 smit:SMT_1793|5end_inosine-5'-monophosphate_dehydrogenase_1767985..1768215_POSITIVE 265 67 21 176 120 smit:SMT_1065|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1004341..1004571_POSITIVE 264 100 51 165 119 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 264 100 51 81 32 smit:SMT_778|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_686870..687100_POSITIVE 262 69 21 188 137 smit:SMT_920|5end_serine/threonine_protein_kinase_874501..874731_NEGATIVE 259 98 52 53 3 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 259 69 23 136 77 smit:SMT_2023|5end_tryptophan_synthase,_alpha_subunit_1939315..1939545_POSITIVE 259 69 23 136 77 smit:SMT_1818|5end_tryptophan_synthase,_alpha_subunit_1792190..1792420_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 58 12 119 65 smit:SMT_584|3end_ATP_synthase_alpha_chain_501633..501783_POSITIVE 301 59 13 61 1 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 271 98 59 73 34 smit:SMT_948|3end_hypothetical_protein_predicted_by_Glimmer/Critica_896655..896805_NEGATIVE 266 56 15 51 14 smit:SMT_2066|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973346..1973496_POSITIVE 260 110 63 127 68 smit:SMT_242|3end_PTS_system,_mannose-specific_IID_component_179163..179313_NEGATIVE 259 98 52 56 6 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 258 44 8 149 105 smit:SMT_2099|3end_putative_zinc-binding_dehydrogenase_1992263..1992413_POSITIVE 257 180 132 69 23 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 257 117 76 63 12 smit:SMT_1250|3end_hypothetical_protein_1210788..1210938_NEGATIVE 254 99 56 66 12 smit:SMT_1630|3end_hypothetical_protein_1618141..1618291_POSITIVE 253 100 54 123 72 smit:SMT_524|3end_methionyl-tRNA_synthetase_450882..451032_POSITIVE 251 100 56 68 15 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 249 105 61 59 19 smit:SMT_780|3end_peptidase_family_U32_688752..688902_NEGATIVE 246 99 57 68 7 smit:SMT_1972|3end_uncharacterized_conserved_phage_related_protein_1904440..1904590_POSITIVE 245 117 71 74 23 smit:SMT_1947|3end_lysine_decarboxylase_1882313..1882463_NEGATIVE 245 97 51 56 2 smit:SMT_1840|3end_6-phosphogluconate_dehydrogenase,_decarboxylating_1806007..1806157_NEGATIVE 244 59 15 54 18 smit:SMT_1632|3end_hypothetical_protein_1618371..1618521_NEGATIVE 244 99 58 71 35 smit:SMT_531|3end_hypothetical_protein_predicted_by_Glimmer/Critica_453075..453225_POSITIVE 242 105 61 56 8 smit:SMT_2015|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1932839..1932989_POSITIVE 242 125 85 59 18 smit:SMT_632|3end_hypothetical_protein_537274..537424_NEGATIVE