Origin IGS: aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttcctcctgctgggaaaaacagtcccagcgatttttcttctatataatgagcagcaagagctcacaagataccgtatgattttaccaaaaaaacttctatctgtcacggggtatgatataatgtaacagacaaatccaaatggaggaatt Mask Tandem Repeat Region ================================================ aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac Find is-nt database================================================ Query_seq: SSA_0103:SSA_0104|SSA_0103:SSA_0104:Integral membrane protein, putative:Queuine tRNA-ribosyltransferase, putative:<-->:105581..105732 152 aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0103:SSA_0104|SSA_0103:SSA_0104:Integral membrane protein, putative:Queuine tRNA-ribosyltransferase, putative:<-->:105581..105732 152 aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0103:SSA_0104|SSA_0103:SSA_0104:Integral membrane protein, putative:Queuine tRNA-ribosyltransferase, putative:<-->:105581..105732 152 aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 2 End: 151 . M P P F G F V C Y I I S Y P V T D R S F F G K I I R Y L V S S C C S L Y R R K I A G T V F P S R R K . Protein_Len: 39 Strand: - Start: 28 End: 144 ........................... M I D Y G T V S L L K K P L I M R Y R T L E Q Q E N Y L L F I A P V T K G L M ........ aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac 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: 85 Start: 43 End: 72 ..........................................CGTGACAGATAGAAGTTTTTTTGGTAAAAT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0103:SSA_0104|SSA_0103:SSA_0104:Integral membrane protein, putative:Queuine tRNA-ribosyltransferase, putative:<-->:105581..105732 152 aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_009009_SSA_0103_SSA_0104|Integral membrane protein, putative:Queuine tRNA-ribosyltransferase, putative|NEGATIVE:POSITIVE|[105581,105732]|152 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagnnnnnnnggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac aattcctccatttggatttgtctgttacattatatcataccccgtgacagatagaagtttttttggtaaaatcatacggtatcttgtgagctcttgctgctcattatatagaagaaaaatcgctgggactgtttttcccagcaggaggaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCCUCCAUUUGGAUUUGUCUGUUACAUUAUAUCAUACCCCGUGACAGAUAGAAGUUUUUUUGGUAAAAUCAUACGGUAUCUUGUGAGCUCUUGCUGCUCAUUAUAUAGAAGAAAAAUCGCUGGGACUGUUUUUCCCAGCAGGAGGAAAC ..(((((((.......((((((((((((...............)))))))))))).((((((((.(((......))).((((...((((((.......)))))).))))...)))))))).(((((((.......))))))).))))))).. (-47.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUCCUCCUGCUGGGAAAAACAGUCCCAGCGAUUUUUCUUCUAUAUAAUGAGCAGCAAGAGCUCACAAGAUACCGUAUGAUUUUACCAAAAAAACUUCUAUCUGUCACGGGGUAUGAUAUAAUGUAACAGACAAAUCCAAAUGGAGGAAUU ..(((((((.(((((((.......)))))))(((((.(((..(((((..(((((.......)))))....(((((.(.((((......................)))).).)))))......)))))..))).))))).....))))))).. (-42.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 896 130 81 221 172 NC_009009:SSA_0103|5end_Integral_membrane_protein,_putative_105490..105720_NEGATIVE 334 100 52 221 170 NC_009009:SSA_0164|5end_hypothetical_protein_162478..162708_POSITIVE 321 116 77 148 105 NC_009009:SSA_1969|5end_Acetolactate_synthase_small_subunit,_putative_1965222..1965452_NEGATIVE 293 108 63 74 18 NC_009009:SSA_1058|5end_Thiamine_biosynthesis_protein,_putative_1074917..1075147_POSITIVE 292 136 95 192 147 NC_009009:SSA_2087|5end_Conserved_uncharacterized_protein_2092657..2092887_NEGATIVE 281 100 54 231 170 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 279 124 86 43 4 NC_009009:SSA_1506|5end_Lipopolysaccharide_biosynthesis_protein,_putative_1511222..1511452_NEGATIVE 274 129 82 75 24 NC_009009:SSA_1449|5end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1451931..1452161_NEGATIVE 273 127 83 73 13 NC_009009:SSA_0932|5end_hypothetical_protein_941453..941683_POSITIVE 272 87 42 196 152 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 272 130 82 77 40 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 267 148 113 60 22 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 265 148 123 130 108 NC_009009:SSA_0057|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_60762..60992_POSITIVE 264 129 82 59 21 NC_009009:SSA_1122|5end_Thioredoxin_family_protein,_putative_1147871..1148101_POSITIVE 261 147 123 40 13 NC_009009:SSA_1279|5end_Oxidoreductase,_putative_1300832..1301062_NEGATIVE 260 138 97 219 172 NC_009009:SSA_1745|5end_General_stress_response_protein_CsbD,_putative_1732191..1732421_NEGATIVE 258 102 61 58 1 NC_009009:SSA_1453|5end_hypothetical_protein_1460208..1460438_NEGATIVE 258 106 64 189 152 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 256 126 81 58 21 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 253 128 81 48 4 NC_009009:SSA_1217|5end_Conserved_uncharacterized_protein_1238964..1239194_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 146 112 45 13 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 293 108 63 70 14 NC_009009:SSA_1057|3end_Aminotransferase,_class-V,_putative_1074993..1075143_POSITIVE 292 136 95 83 38 NC_009009:SSA_2088|3end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2092766..2092916_NEGATIVE 274 107 64 147 98 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 272 130 82 66 29 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 267 148 113 75 37 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 265 148 123 118 96 NC_009009:SSA_0056|3end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_60830..60980_POSITIVE 264 129 82 44 6 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 264 142 112 65 33 NC_009009:SSA_0808|3end_hypothetical_protein_791012..791162_POSITIVE 263 146 115 59 33 NC_009009:SSA_1529|3end_Lysyl-tRNA_synthetase,_putative_1537441..1537591_POSITIVE 261 142 108 60 30 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 260 138 97 118 71 NC_009009:SSA_1746|3end_hypothetical_protein_1732292..1732442_NEGATIVE 253 145 108 85 47 NC_009009:SSA_0505|3end_Conserved_protein/domain_typically_associated_with_flavoprotein_oxygenases,_DIM6/NTAB_family,_putative_504427..504577_POSITIVE 251 138 93 74 27 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 249 123 81 100 62 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 247 142 113 38 11 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 247 103 62 139 103 NC_009009:SSA_1179|3end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1206640..1206790_NEGATIVE 247 129 81 147 103 NC_009009:SSA_1053|3end_Pyruvate_phosphate_dikinase,_putative_1067447..1067597_NEGATIVE 246 128 81 138 82 NC_009009:SSA_1005|3end_Sugar_ABC_transporter,_permease_protein,_putative_1006941..1007091_POSITIVE 244 142 108 70 38 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE