Origin IGS: gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggatattgaccatatctaactcatgaaagcaaatcttgtgtggtggtttgatcaatcactactagctcaggttaaataaaatataaaaagcaacagctgaaatagttgttgctttttaggtagctaggattttatcccaggttttatctc Mask Tandem Repeat Region ================================================ gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Find is-nt database================================================ Query_seq: SMT_2168:SMT_2169|SMT_2168:SMT_2169:threonyl-tRNA synthetase:hypothetical protein:-><-:2041323..2041472 150 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2168:SMT_2169|SMT_2168:SMT_2169:threonyl-tRNA synthetase:hypothetical protein:-><-:2041323..2041472 150 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2168:SMT_2169|SMT_2168:SMT_2169:threonyl-tRNA synthetase:hypothetical protein:-><-:2041323..2041472 150 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Predict ORF larger than 30AA ================================================ gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc 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================================================ gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -6.3 Tail_Score: -5.34632 Start: 39 End: 61 Full_Region: CTAGCTACCTAAAAA GCAACAACT ATTTC AGCTGTTGC TTTTTATATTTTATT ......................................GCAACAACTATTTCAGCTGTTGC......................................................................................... TransTerm Strand: - Conf: 100 HP_score: -9.2 Tail_Score: -4.67353 Start: 39 End: 61 Full_Region: aataaaatataaaaa gcaacagctg aaa tagttgttgc tttttaggtagctag ......................................gcaacagctgaaatagttgttgc......................................................................................... Find igs database================================================ Query_seq: SMT_2168:SMT_2169|SMT_2168:SMT_2169:threonyl-tRNA synthetase:hypothetical protein:-><-:2041323..2041472 150 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Intra-Species Hit: Count: 6 Min: 1 Max: 150 Len: 150 Subject: smit_SMT_2168_SMT_2169|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[2041323,2041472]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_2150_SMT_2151|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[2024966,2025115]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_2146_SMT_2147|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[2022341,2022490]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_2143_SMT_2144|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[2020587,2020736]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_970_SMT_971|threonyl-tRNA synthetase:hypothetical protein|POSITIVE:NEGATIVE|[917856,918005]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc gagataaaacctgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Subject: smit_SMT_2147_SMT_2148|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2022986,2023230]|245 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:12 Query End:150 Subject Strand: POSITIVE Subject Start: 107 Subject End: 245 ...........tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc ...........tgggataaaatcctagctacctaaaaagcaacaactatttcagctgttgctttttatattttatttaacctgagctagtagtgattgatcaaaccaccacacaagatttgctttcatgagttagatatggtcaatatcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUAAAACCUGGGAUAAAAUCCUAGCUACCUAAAAAGCAACAACUAUUUCAGCUGUUGCUUUUUAUAUUUUAUUUAACCUGAGCUAGUAGUGAUUGAUCAAACCACCACACAAGAUUUGCUUUCAUGAGUUAGAUAUGGUCAAUAUCC ..((((....(((((((...)))))))..(((.(((((((((((.((.....)).)))))))))))......(((((((((.((((.(((.(((..((.......))...)))...))).))))....).)))))))).)))...)))). (-32.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUAUUGACCAUAUCUAACUCAUGAAAGCAAAUCUUGUGUGGUGGUUUGAUCAAUCACUACUAGCUCAGGUUAAAUAAAAUAUAAAAAGCAACAGCUGAAAUAGUUGUUGCUUUUUAGGUAGCUAGGAUUUUAUCCCAGGUUUUAUCUC (((((..((((................(((....((((.(((((((((.....))))))))).....))))............((((((((((((((((...))))))))))))))))....))).((((...))))..)))).))))). (-41.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 545 45 5 231 186 smit:SMT_2147|5end_hypothetical_protein_2022895..2023125_NEGATIVE 279 94 52 77 43 smit:SMT_951|5end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_900098..900328_NEGATIVE 263 142 104 94 53 smit:SMT_847|5end_thioredoxin_reductase_792800..793030_POSITIVE 254 98 52 193 140 smit:SMT_293|5end_dTDP-4-dehydrorhamnose_reductase_235919..236149_POSITIVE 253 60 13 88 36 smit:SMT_521|5end_K02005_HlyD_family_secretion_protein_445566..445796_POSITIVE 251 57 20 39 3 smit:SMT_1290|5end_autolysin_1252564..1252794_POSITIVE 251 114 80 60 25 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 247 114 78 83 53 smit:SMT_1797|5end_threonine_dehydratase_1772684..1772914_NEGATIVE 245 140 93 211 150 smit:SMT_986|5end_threonyl-tRNA_synthetase_931092..931322_POSITIVE 245 140 93 73 12 smit:SMT_985|5end_guanylate_kinase_930954..931184_POSITIVE 245 45 12 227 194 smit:SMT_942|5end_hypothetical_protein_894067..894297_NEGATIVE 245 140 93 211 150 smit:SMT_925|5end_DNA-directed_RNA_polymerase_omega_chain_880283..880513_NEGATIVE 244 98 52 78 31 smit:SMT_1160|5end_K03152_4-methyl-5(b-hydroxyethyl)-thiazole_monophosphate_biosynthesis_1105174..1105404_NEGATIVE 240 55 22 53 17 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 237 150 104 93 47 smit:SMT_2123|5end_hypothetical_protein_2008201..2008431_POSITIVE 236 122 82 177 134 smit:SMT_1552|5end_RNA_binding_protein_1535119..1535349_POSITIVE 234 89 44 175 128 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 234 89 44 175 128 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 234 89 44 175 128 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 234 45 12 72 40 smit:SMT_288|5end_hypothetical_protein_231184..231414_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 876 130 81 70 21 smit:SMT_2151|3end_hypothetical_protein_2025026..2025176_NEGATIVE 876 130 81 70 21 smit:SMT_2148|3end_hypothetical_protein_2023141..2023291_NEGATIVE 876 130 81 70 21 smit:SMT_2147|3end_hypothetical_protein_2022401..2022551_NEGATIVE 876 130 81 70 21 smit:SMT_2144|3end_hypothetical_protein_2020647..2020797_NEGATIVE 876 130 81 70 21 smit:SMT_971|3end_hypothetical_protein_917916..918066_NEGATIVE 674 150 109 90 49 smit:SMT_2175|3end_hypothetical_protein_2045212..2045362_NEGATIVE 279 94 52 60 26 smit:SMT_952|3end_hypothetical_protein_900115..900265_NEGATIVE 254 98 52 127 74 smit:SMT_292|3end_dTDP-glucose_4,6-dehydratase_235933..236083_POSITIVE 244 98 52 67 20 smit:SMT_1161|3end_K05837_rod_shape_determining_protein_RodA_1105185..1105335_NEGATIVE 236 117 74 151 107 smit:SMT_138|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_90463..90613_POSITIVE 234 89 44 60 13 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 234 45 12 88 56 smit:SMT_1960|3end_UDP-galactopyranose_mutase_1894094..1894244_POSITIVE 234 89 44 60 13 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 234 89 44 60 13 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 234 45 12 82 50 smit:SMT_287|3end_UDP-galactopyranose_mutase_231274..231424_POSITIVE 223 67 33 58 24 smit:SMT_2168|3end_threonyl-tRNA_synthetase_2041262..2041412_POSITIVE 223 67 33 58 24 smit:SMT_2150|3end_threonyl-tRNA_synthetase_2024905..2025055_POSITIVE 223 67 33 58 24 smit:SMT_2146|3end_threonyl-tRNA_synthetase_2022280..2022430_POSITIVE 223 67 33 58 24 smit:SMT_2143|3end_threonyl-tRNA_synthetase_2020526..2020676_POSITIVE 223 67 33 58 24 smit:SMT_970|3end_threonyl-tRNA_synthetase_917795..917945_POSITIVE