Origin IGS: tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaccatggctgtttttctatttttactaaaaagttgatttaaatcaaaatattttttcgctctaaaatcaatcttaaagattcttttgaggtaaaaatttgctataatagaagcagacaaatttgaagggagaagaca Mask Tandem Repeat Region ================================================ tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc Find is-nt database================================================ Query_seq: SSA_1547:SSA_1548|SSA_1547:SSA_1548:HPr kinase/phosphorylase, putative:NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative:<-<-:1551071..1551208 138 tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1547:SSA_1548|SSA_1547:SSA_1548:HPr kinase/phosphorylase, putative:NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative:<-<-:1551071..1551208 138 tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1547:SSA_1548|SSA_1547:SSA_1548:HPr kinase/phosphorylase, putative:NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative:<-<-:1551071..1551208 138 tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 19 End: 138 .................. M S A S I I A N F Y L K R I F K I D F R A K K Y F D L N Q L F S K N R K T A M V tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc 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================================================ tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1547:SSA_1548|SSA_1547:SSA_1548:HPr kinase/phosphorylase, putative:NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative:<-<-:1551071..1551208 138 tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_009009_SSA_1547_SSA_1548|HPr kinase/phosphorylase, putative:NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative|NEGATIVE:NEGATIVE|[1551071,1551208]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc tgtcttctcccttcaaatttgtctgcttctattatagcaaatttttacctcaaaagaatctttaagattgattttagagcgaaaaaatattttgatttaaatcaactttttagtaaaaatagaaaaacagccatggtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUUCUCCCUUCAAAUUUGUCUGCUUCUAUUAUAGCAAAUUUUUACCUCAAAAGAAUCUUUAAGAUUGAUUUUAGAGCGAAAAAAUAUUUUGAUUUAAAUCAACUUUUUAGUAAAAAUAGAAAAACAGCCAUGGUC ...................((.(((.(((((((.(.((..((((((.((((((((.((((.....))))..)))).))).).))))))...(((((....))))).......)).).)))))))...))).))..... (-16.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACCAUGGCUGUUUUUCUAUUUUUACUAAAAAGUUGAUUUAAAUCAAAAUAUUUUUUCGCUCUAAAAUCAAUCUUAAAGAUUCUUUUGAGGUAAAAAUUUGCUAUAAUAGAAGCAGACAAAUUUGAAGGGAGAAGACA .....((..(.....((.((((((....)))))).))....)..)).....(((((((.((.((((....(((((((((....))))))))).....((((((........))))))....)))).)).))))))).. (-20.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 788 50 1 141 92 NC_009009:SSA_1547|5end_HPr_kinase/phosphorylase,_putative_1550980..1551210_NEGATIVE 294 39 1 130 86 NC_009009:SSA_0321|5end_Methylase,_putative_313867..314097_POSITIVE 293 50 10 137 100 NC_009009:SSA_2068|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_2071311..2071541_NEGATIVE 281 55 11 145 101 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 272 50 1 138 91 NC_009009:SSA_1705|5end_hypothetical_protein_1696853..1697083_NEGATIVE 252 50 1 231 173 NC_009009:SSA_0072|5end_ABC_sugar_transporter,_MsmK-like_protein,_putative_75922..76152_POSITIVE 249 46 1 117 72 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 246 61 24 140 105 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 243 49 2 133 94 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 243 47 1 130 93 NC_009009:SSA_0993|5end_hypothetical_protein_994064..994294_POSITIVE 241 39 5 128 96 NC_009009:SSA_2257|5end_DNA_mismatch_repair_protein,_putative_2253184..2253414_NEGATIVE 241 50 8 50 3 NC_009009:SSA_0109|5end_50S_ribosomal_protein_L23,_putative_109439..109669_POSITIVE 236 41 3 132 98 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 233 56 12 160 103 NC_009009:SSA_0448|5end_Excinuclease_ATPase_subunit_A,_putative_446480..446710_POSITIVE 232 49 3 133 92 NC_009009:SSA_1657|5end_hypothetical_protein_1653231..1653461_NEGATIVE 232 38 1 171 136 NC_009009:SSA_0157|5end_hypothetical_protein_153513..153743_POSITIVE 228 39 1 127 94 NC_009009:SSA_1336|5end_Conserved_ankyrin_repeat_protein,_putative_1350126..1350356_NEGATIVE 228 48 2 128 93 NC_009009:SSA_0419|5end_Alpha-galactosidase,_putative_416213..416443_POSITIVE 225 46 1 135 91 NC_009009:SSA_1270|5end_Flavodoxin_1293916..1294146_NEGATIVE 223 49 1 67 11 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 50 10 46 9 NC_009009:SSA_2069|3end_Prolyl-tRNA_synthetase,_putative_2071402..2071552_NEGATIVE 281 55 11 85 41 NC_009009:SSA_1118|3end_Peptide_methionine_sulfoxide_reductase,_putative_1144511..1144661_POSITIVE 249 46 1 120 75 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 246 61 24 40 5 NC_009009:SSA_0873|3end_ATP-dependent_DNA_helicase;_DNA_polymerase_III,_epsilon_subunit,_putative_867915..868065_POSITIVE 243 49 2 133 94 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 243 47 1 133 96 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 241 50 8 50 3 NC_009009:SSA_0108|3end_50S_ribosomal_protein_L4,_putative_109519..109669_POSITIVE 232 49 3 90 49 NC_009009:SSA_1658|3end_Cationic_amino_acid_transporter,_putative_1653274..1653424_NEGATIVE 222 38 10 30 2 NC_009009:SSA_1471|3end_hypothetical_protein_1476981..1477131_NEGATIVE 216 68 21 90 37 NC_009009:SSA_1348|3end_hypothetical_protein_1365959..1366109_POSITIVE 212 39 5 33 1 NC_009009:SSA_1424|3end_Hydrolase,_putative_1433889..1434039_NEGATIVE 212 49 1 100 49 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 209 30 1 141 112 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 207 48 3 144 96 NC_009009:SSA_0653|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_637540..637690_POSITIVE 205 38 1 134 104 NC_009009:SSA_0416|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_414222..414372_POSITIVE 204 38 1 137 89 NC_009009:SSA_0750|3end_hypothetical_protein_732255..732405_POSITIVE 202 23 3 130 110 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 202 38 1 132 83 NC_009009:SSA_0677|3end_rRNA_methylase,_putative_660361..660511_POSITIVE 200 109 64 78 34 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 200 49 8 51 3 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE