Origin IGS: gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc .........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 ggatattgaccatatctaactcatgaaagcaaatcttgtgtggtggtttgatcaatcactactagctcaggttaaataaaatataaaaagcaacagctgaaatagttgttgctttttaggtagctaggattttatcccacgttggttttgaattacagtctgnnnnnttaattaattaannnnntggaaatgtacgatttttatttggggctctctatcttttcttgatcaactgtgtctttatc Mask Tandem Repeat Region ================================================ gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Find is-nt database================================================ Query_seq: SMT_2147:SMT_2148|SMT_2147:SMT_2148:hypothetical protein:hypothetical protein:<-<-:2022986..2023230 245 gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2147:SMT_2148|SMT_2147:SMT_2148:hypothetical protein:hypothetical protein:<-<-:2022986..2023230 245 gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2147:SMT_2148|SMT_2147:SMT_2148:hypothetical protein:hypothetical protein:<-<-:2022986..2023230 245 gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Predict ORF larger than 30AA ================================================ gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc 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================================================ gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -6.3 Tail_Score: -5.34632 Start: 134 End: 156 Full_Region: CTAGCTACCTAAAAA GCAACAACT ATTTC AGCTGTTGC TTTTTATATTTTATT .....................................................................................................................................GCAACAACTATTTCAGCTGTTGC......................................................................................... TransTerm Strand: - Conf: 91 HP_score: -9.2 Tail_Score: -4.67353 Start: 134 End: 156 Full_Region: aataaaatataaaaa gcaacagctg aaa tagttgttgc tttttaggtagctag .....................................................................................................................................gcaacagctgaaatagttgttgc......................................................................................... Find igs database================================================ Query_seq: SMT_2147:SMT_2148|SMT_2147:SMT_2148:hypothetical protein:hypothetical protein:<-<-:2022986..2023230 245 gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Intra-Species Hit: Count: 6 Min: 1 Max: 245 Len: 245 Subject: smit_SMT_2147_SMT_2148|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2022986,2023230]|245 HSP 1 e-value: 1.0E-118 bit: 426.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc gataaagacacagttgatcaagaaaagatagagagccccaaataaaaatcgtacatttccannnnnttaattaattaannnnncagactgtaattcaaaaccaacgtgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_2168_SMT_2169|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[2041323,2041472]|150 HSP 1 e-value: 3.0E-73 bit: 276.0 Len: 139 Query Start:107 Query End:245 Subject Strand: POSITIVE Subject Start: 12 Subject End: 150 ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_2150_SMT_2151|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[2024966,2025115]|150 HSP 1 e-value: 3.0E-73 bit: 276.0 Len: 139 Query Start:107 Query End:245 Subject Strand: POSITIVE Subject Start: 12 Subject End: 150 ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_2146_SMT_2147|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[2022341,2022490]|150 HSP 1 e-value: 3.0E-73 bit: 276.0 Len: 139 Query Start:107 Query End:245 Subject Strand: POSITIVE Subject Start: 12 Subject End: 150 ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_2143_SMT_2144|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[2020587,2020736]|150 HSP 1 e-value: 3.0E-73 bit: 276.0 Len: 139 Query Start:107 Query End:245 Subject Strand: POSITIVE Subject Start: 12 Subject End: 150 ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_970_SMT_971|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[917856,918005]|150 HSP 1 e-value: 3.0E-73 bit: 276.0 Len: 139 Query Start:107 Query End:245 Subject Strand: POSITIVE Subject Start: 12 Subject End: 150 ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc ..........................................................................................................tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAAGACACAGUUGAUCAAGAAAAGAUAGAGAGCCCCAAAUAAAAAUCGUACAUUUCCANNNNNUUAAUUAAUUAANNNNNCAGACUGUAAUUCAAAACCAACGUGGGAUAAAAUCCUAGCUACCUAAAAAGCAACAACUAUUUCAGCUGUUGCUUUUUAUAUUUUAUUUAACCUGAGCUAGUAGUGAUUGAUCAAACCACCACACAAGAUUUGCUUUCAUGAGUUAGAUAUGGUCAAUAUCC ((((..(((.((.((((((((...............((((...........((((..((.......((((....)))).......)).))))..............))))........((((((...((((((((((((.((.....)).))))))))))))................))))))......)))))))).............((((((((....))).))))).)))))..)))). (-39.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUAUUGACCAUAUCUAACUCAUGAAAGCAAAUCUUGUGUGGUGGUUUGAUCAAUCACUACUAGCUCAGGUUAAAUAAAAUAUAAAAAGCAACAGCUGAAAUAGUUGUUGCUUUUUAGGUAGCUAGGAUUUUAUCCCACGUUGGUUUUGAAUUACAGUCUGNNNNNUUAAUUAAUUAANNNNNUGGAAAUGUACGAUUUUUAUUUGGGGCUCUCUAUCUUUUCUUGAUCAACUGUGUCUUUAUC (((((..(.((...((........)).(((....((((.(((((((((.....))))))))).....))))............((((((((((((((((...))))))))))))))))....))).)).)..)))))((((((((((..(((.((((.((((.....((((....)))).....))))..))))...........((((....))))....)))..))))))).)))........ (-52.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 818 60 11 130 81 smit:SMT_2175|5end_hypothetical_protein_2045727..2045957_NEGATIVE 818 60 11 130 81 smit:SMT_2170|5end_hypothetical_protein_2042242..2042472_NEGATIVE 818 60 11 130 81 smit:SMT_2156|5end_hypothetical_protein_predicted_by_Glimmer/Critica_2030476..2030706_NEGATIVE 818 60 11 151 102 smit:SMT_2151|5end_hypothetical_protein_2025520..2025750_NEGATIVE 818 60 11 151 102 smit:SMT_2147|5end_hypothetical_protein_2022895..2023125_NEGATIVE 468 109 67 163 121 smit:SMT_2169|5end_hypothetical_protein_2041847..2042077_NEGATIVE 426 78 36 196 154 smit:SMT_2168|5end_threonyl-tRNA_synthetase_2040991..2041221_POSITIVE 426 78 36 113 71 smit:SMT_2150|5end_threonyl-tRNA_synthetase_2024673..2024903_POSITIVE 426 78 36 113 71 smit:SMT_2146|5end_threonyl-tRNA_synthetase_2022048..2022278_POSITIVE 401 109 84 29 4 smit:SMT_968|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_914015..914245_NEGATIVE 281 150 104 53 1 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 279 189 147 77 43 smit:SMT_951|5end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_900098..900328_NEGATIVE 271 140 106 227 193 smit:SMT_942|5end_hypothetical_protein_894067..894297_NEGATIVE 263 237 199 94 53 smit:SMT_847|5end_thioredoxin_reductase_792800..793030_POSITIVE 261 41 9 52 17 smit:SMT_1487|5end_hypothetical_protein_1466361..1466591_POSITIVE 259 180 131 179 136 smit:SMT_293|5end_dTDP-4-dehydrorhamnose_reductase_235919..236149_POSITIVE 258 40 1 179 127 smit:SMT_1310|5end_D-alanine-activating_enzyme_1274237..1274467_POSITIVE 251 152 115 39 3 smit:SMT_1290|5end_autolysin_1252564..1252794_POSITIVE 251 149 102 96 43 smit:SMT_748|5end_prephenate_dehydratase_653498..653728_NEGATIVE 251 209 175 60 25 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 855 220 171 65 16 smit:SMT_2169|3end_hypothetical_protein_2041383..2041533_NEGATIVE 855 220 171 65 16 smit:SMT_2151|3end_hypothetical_protein_2025026..2025176_NEGATIVE 855 220 171 65 16 smit:SMT_2147|3end_hypothetical_protein_2022401..2022551_NEGATIVE 855 220 171 65 16 smit:SMT_2144|3end_hypothetical_protein_2020647..2020797_NEGATIVE 855 220 171 65 16 smit:SMT_971|3end_hypothetical_protein_917916..918066_NEGATIVE 818 60 11 84 35 smit:SMT_73|3end_peptidase,_M16_family_-84..66_NEGATIVE 578 240 204 85 49 smit:SMT_2175|3end_hypothetical_protein_2045212..2045362_NEGATIVE 468 109 67 133 91 smit:SMT_2170|3end_hypothetical_protein_2041877..2042027_NEGATIVE 468 109 67 125 83 smit:SMT_2156|3end_hypothetical_protein_predicted_by_Glimmer/Critica_2030297..2030447_NEGATIVE 426 78 36 94 52 smit:SMT_2149|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2024734..2024884_POSITIVE 279 189 147 60 26 smit:SMT_952|3end_hypothetical_protein_900115..900265_NEGATIVE 261 41 9 55 20 smit:SMT_1486|3end_hypothetical_protein_1466444..1466594_POSITIVE 259 180 131 113 70 smit:SMT_292|3end_dTDP-glucose_4,6-dehydratase_235933..236083_POSITIVE 251 149 102 99 46 smit:SMT_749|3end_shikimate_kinase_653495..653645_NEGATIVE 235 212 175 151 113 smit:SMT_138|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_90463..90613_POSITIVE 234 140 107 88 56 smit:SMT_1960|3end_UDP-galactopyranose_mutase_1894094..1894244_POSITIVE 234 140 107 82 50 smit:SMT_287|3end_UDP-galactopyranose_mutase_231274..231424_POSITIVE 231 132 95 131 91 smit:SMT_1760|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1735743..1735893_NEGATIVE 223 162 128 58 24 smit:SMT_2168|3end_threonyl-tRNA_synthetase_2041262..2041412_POSITIVE 223 162 128 58 24 smit:SMT_2150|3end_threonyl-tRNA_synthetase_2024905..2025055_POSITIVE