Origin IGS: cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcaatgaaaacgcccatggggcgttttttcagcaatgaactatgaaataatccaaatatagaattttagagaaagaagaggtaggagtcatgtaaacagcagattaacaagtgataaaggataaaaatgaagaaacacttgttaaaggagaaaag Mask Tandem Repeat Region ================================================ cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat Find is-nt database================================================ Query_seq: SSA_1376:SSA_1377|SSA_1376:SSA_1377:Transport protein, putative:Asparaginyl-tRNA synthetase, putative:<-<-:1396202..1396357 156 cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1376:SSA_1377|SSA_1376:SSA_1377:Transport protein, putative:Asparaginyl-tRNA synthetase, putative:<-<-:1396202..1396357 156 cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1376:SSA_1377|SSA_1376:SSA_1377:Transport protein, putative:Asparaginyl-tRNA synthetase, putative:<-<-:1396202..1396357 156 cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat Predict ORF larger than 30AA ================================================ cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat 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: 64 End: 93 ...............................................................CATGACTCCTACCTCTTCTTTCTCTAAAAT............................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1376:SSA_1377|SSA_1376:SSA_1377:Transport protein, putative:Asparaginyl-tRNA synthetase, putative:<-<-:1396202..1396357 156 cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_009009_SSA_1376_SSA_1377|Transport protein, putative:Asparaginyl-tRNA synthetase, putative|NEGATIVE:NEGATIVE|[1396202,1396357]|156 HSP 1 e-value: 1.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat cttttctcctttaacaagtgtttcttcatttttatcctttatcacttgttaatctgctgtttacatgactcctacctcttctttctctaaaattctatatttggattatttcatagttcattgctgaaaaaacgccccatgggcgttttcattgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCUCCUUUAACAAGUGUUUCUUCAUUUUUAUCCUUUAUCACUUGUUAAUCUGCUGUUUACAUGACUCCUACCUCUUCUUUCUCUAAAAUUCUAUAUUUGGAUUAUUUCAUAGUUCAUUGCUGAAAAAACGCCCCAUGGGCGUUUUCAUUGAU ..........((((((((((......................))))))))))((.((.(((.....)))................................((((((((...))))))))..)).)).(((((((((...)))))))))....... (-25.35) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAUGAAAACGCCCAUGGGGCGUUUUUUCAGCAAUGAACUAUGAAAUAAUCCAAAUAUAGAAUUUUAGAGAAAGAAGAGGUAGGAGUCAUGUAAACAGCAGAUUAACAAGUGAUAAAGGAUAAAAAUGAAGAAACACUUGUUAAAGGAGAAAAG .(((..((((((((((...))))))))))(((....)))....))).....(((...((((..(((((................)))))..)))).........((((((((((......................)))))))))).)))...... (-28.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 90 41 181 132 NC_009009:SSA_1376|5end_Transport_protein,_putative_1396111..1396341_NEGATIVE 308 150 112 59 5 NC_009009:SSA_1937|5end_Malonyl-CoA:ACP_transacylase,_putative_1924771..1925001_NEGATIVE 292 105 62 133 87 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 284 96 53 47 2 NC_009009:SSA_0658|5end_Conserved_uncharacterized_protein_642126..642356_POSITIVE 274 96 55 125 84 NC_009009:SSA_1237|5end_Uracil-DNA_glycosylase,_putative_1262366..1262596_NEGATIVE 272 96 58 126 83 NC_009009:SSA_1400|5end_Pyridoxal_kinase,_putative_1413072..1413302_NEGATIVE 269 119 71 118 66 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 267 82 49 201 160 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 265 73 45 195 167 NC_009009:SSA_0837|5end_Glucosyltransferase,_putative_823902..824132_POSITIVE 262 87 46 70 23 NC_009009:SSA_0654|5end_Cell_division_protein_DivIB,_putative_637457..637687_POSITIVE 260 56 16 153 109 NC_009009:SSA_1622|5end_50S_ribosomal_protein_L1,_putative_1625441..1625671_NEGATIVE 260 148 109 138 107 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 258 103 63 124 88 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 257 88 43 105 49 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 256 144 102 48 1 NC_009009:SSA_1117|5end_hypothetical_protein_1142743..1142973_POSITIVE 255 148 113 54 21 NC_009009:SSA_1428|5end_hypothetical_protein_1436348..1436578_NEGATIVE 255 145 116 121 86 NC_009009:SSA_0938|5end_hypothetical_protein_946587..946817_POSITIVE 251 58 23 121 85 NC_009009:SSA_0922|5end_hypothetical_protein_932950..933180_NEGATIVE 250 145 110 72 45 NC_009009:SSA_2309|5end_Fimbrial_assembly_protein,_putative_2311886..2312116_NEGATIVE 250 116 72 149 99 NC_009009:SSA_1888|5end_hypothetical_protein_1886025..1886255_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 150 112 66 12 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 274 96 55 89 48 NC_009009:SSA_1238|3end_hypothetical_protein_1262402..1262552_NEGATIVE 274 79 35 139 95 NC_009009:SSA_0245|3end_hypothetical_protein_239608..239758_POSITIVE 267 77 46 87 52 NC_009009:SSA_1291|3end_hypothetical_protein_1308991..1309141_NEGATIVE 263 84 46 106 66 NC_009009:SSA_1803|3end_GTP-binding_protein,_putative_1786599..1786749_NEGATIVE 262 87 46 73 26 NC_009009:SSA_0653|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_637540..637690_POSITIVE 260 56 16 51 7 NC_009009:SSA_1623|3end_50S_ribosomal_protein_L11,_putative_1625543..1625693_NEGATIVE 260 148 109 87 56 NC_009009:SSA_0806|3end_hypothetical_protein_789478..789628_POSITIVE 259 149 110 57 7 NC_009009:SSA_1417|3end_SAM-dependent_methyltransferase,_putative_1427304..1427454_NEGATIVE 258 103 63 137 101 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 257 88 43 103 47 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 257 96 54 133 77 NC_009009:SSA_1149|3end_Glycosyl_hydrolase,_family_1,_putative_1179876..1180026_POSITIVE 255 148 113 47 14 NC_009009:SSA_1429|3end_hypothetical_protein_1436355..1436505_NEGATIVE 255 145 116 118 83 NC_009009:SSA_0937|3end_Arsenate_reductase,_glutaredoxin_family,_putative_946664..946814_POSITIVE 250 90 45 116 64 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 247 87 42 137 86 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 243 112 71 117 79 NC_009009:SSA_1381|3end_hypothetical_protein_1399146..1399296_NEGATIVE 240 145 113 54 22 NC_009009:SSA_0249|3end_hypothetical_protein_242115..242265_POSITIVE 239 58 17 119 74 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 236 97 52 116 54 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE