Origin IGS: agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcaaaagcacctccataaatttcgattcgatgcctctagacacagagacaacaattataagtcagactatctcagtataacatttgtagcggatttttgcaagtgtgaaaaacgct Mask Tandem Repeat Region ================================================ agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Find is-nt database================================================ Query_seq: SMT_191:SMT_192|SMT_191:SMT_192:adenylate kinase:translation initiation factor IF-1:->->:126524..126639 116 agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_191:SMT_192|SMT_191:SMT_192:adenylate kinase:translation initiation factor IF-1:->->:126524..126639 116 agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_191:SMT_192|SMT_191:SMT_192:adenylate kinase:translation initiation factor IF-1:->->:126524..126639 116 agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Predict ORF larger than 30AA ================================================ agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc 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: 14 End: 43 .............CTTGCAAAAATCCGCTACAAATGTTATACT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_191:SMT_192|SMT_191:SMT_192:adenylate kinase:translation initiation factor IF-1:->->:126524..126639 116 agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: smit_SMT_191_SMT_192|adenylate kinase:translation initiation factor IF-1|POSITIVE:POSITIVE|[126524,126639]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Inter-species Hit: Count: 2 Min: 1 Max: 116 Len: 116 Subject: NC_003028_SP_0231_SP_0232|adenylate kinase:translation initiation factor IF-1|POSITIVE:POSITIVE|[205200,205315]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Subject: NC_008533_SPD_0214_SPD_0215|adenylate kinase:translation initiation factor IF-1|POSITIVE:POSITIVE|[207709,207824]|116 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 agcgtttttcacacttgcaaaaatccgctacaaatgttatactgagatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc agcgtttttcacacttgcaaaaatccgctacaaatgttatactgaaatagtctgacttataattgttgtctctgtgtctagaggcatcgaatcgaaatttatggaggtgcttttgc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGUUUUUCACACUUGCAAAAAUCCGCUACAAAUGUUAUACUGAGAUAGUCUGACUUAUAAUUGUUGUCUCUGUGUCUAGAGGCAUCGAAUCGAAAUUUAUGGAGGUGCUUUUGC ................((((((..((.(((.((((((((.((((...)))).))))......(((.((((((((....)))))))).)))......)))).))).))...)))))) (-22.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAAAGCACCUCCAUAAAUUUCGAUUCGAUGCCUCUAGACACAGAGACAACAAUUAUAAGUCAGACUAUCUCAGUAUAACAUUUGUAGCGGAUUUUUGCAAGUGUGAAAAACGCU (((((((....(((..............(.((.((((......)))).)).)..((((((((...(((.....))).....)))))))).)))))))))).(((((.....))))) (-19.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 90 47 54 8 smit:SMT_761|5end_prephenate_dehydrogenase_667150..667380_NEGATIVE 300 90 47 54 8 smit:SMT_752|5end_prephenate_dehydrogenase_656791..657021_NEGATIVE 284 109 73 138 98 smit:SMT_1990|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1917565..1917795_POSITIVE 274 90 45 148 101 smit:SMT_1709|5end_aminopeptidase_P_1695450..1695680_NEGATIVE 265 110 63 228 186 smit:SMT_1630|5end_hypothetical_protein_1617291..1617521_POSITIVE 265 110 63 228 186 smit:SMT_1241|5end_hypothetical_protein_1201040..1201270_POSITIVE 264 110 71 191 142 smit:SMT_110|5end_alpha-L-fucosidase_57445..57675_POSITIVE 258 110 65 94 45 smit:SMT_2164|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2037861..2038091_POSITIVE 256 90 42 104 61 smit:SMT_732|5end_K07467_phage_replication_initiation_protein_639409..639639_NEGATIVE 255 89 44 181 140 smit:SMT_1677|5end_transcription-repair_coupling_factor_1662112..1662342_NEGATIVE 244 84 42 59 19 smit:SMT_2020|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1937595..1937825_POSITIVE 244 84 42 59 19 smit:SMT_1317|5end_glycosyltransferase_1281921..1282151_POSITIVE 240 61 23 224 192 smit:SMT_1090|5end_K07485_transposase_1025089..1025319_POSITIVE 236 97 56 86 44 smit:SMT_2171|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2042271..2042501_POSITIVE 236 95 68 66 24 smit:SMT_2039|5end_malolactic_enzyme_1950427..1950657_NEGATIVE 235 86 42 42 3 smit:SMT_126|5end_hypothetical_membrane_associated_protein_78250..78480_NEGATIVE 230 54 17 155 125 smit:SMT_1304|5end_hypothetical_protein_1266630..1266860_POSITIVE 229 29 3 109 83 smit:SMT_1589|5end_hypothetical_protein_1578332..1578562_POSITIVE 228 110 61 201 146 smit:SMT_1797|5end_threonine_dehydratase_1772684..1772914_NEGATIVE 227 108 68 176 137 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 95 62 53 10 smit:SMT_753|3end_chorismate_synthase_656801..656951_NEGATIVE 258 110 65 70 21 smit:SMT_2163|3end_cell_division_protein_FtsA_2037917..2038067_POSITIVE 256 90 42 101 58 smit:SMT_733|3end_hypothetical_protein_639412..639562_NEGATIVE 239 67 23 106 60 smit:SMT_1811|3end_hypothetical_protein_1786366..1786516_POSITIVE 235 86 42 55 16 smit:SMT_127|3end_transcriptional_regulator,_PadR_family_78237..78387_NEGATIVE 229 29 3 122 96 smit:SMT_1588|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1578425..1578575_POSITIVE 229 90 50 89 51 smit:SMT_561|3end_putative_translation_elongation_factor_EF-Tu_480687..480837_POSITIVE 228 110 61 67 12 smit:SMT_1798|3end_exonuclease_RexA_1772818..1772968_NEGATIVE 223 76 42 49 12 smit:SMT_1703|3end_recombination_protein_RecR_1687336..1687486_POSITIVE 222 110 66 136 76 smit:SMT_1555|3end_hypothetical_protein_1540223..1540373_NEGATIVE 221 109 79 51 6 smit:SMT_456|3end_pyruvate_oxidase_396091..396241_POSITIVE 220 87 41 86 41 smit:SMT_1879|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836567..1836717_NEGATIVE 219 95 61 66 27 smit:SMT_1729|3end_exodeoxyribonuclease_VII_small_subunit_1714858..1715008_POSITIVE 217 109 69 141 98 smit:SMT_448|3end_K03707_transcriptional_activator_TenA_387690..387840_POSITIVE 215 84 43 119 77 smit:SMT_1649|3end_GMP_reductase_1636068..1636218_POSITIVE 215 109 69 150 107 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 212 46 23 63 42 smit:SMT_1032|3end_putative_biotin_operon_repressor_969759..969909_POSITIVE 211 89 43 150 100 smit:SMT_1990|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1917677..1917827_POSITIVE 211 44 1 82 47 smit:SMT_1461|3end_putative_phosphate_ABC_transporter_(ATP-binding_protein)_1443207..1443357_POSITIVE 211 107 74 144 102 smit:SMT_1158|3end_DNA_gyrase_subunit_B_1102011..1102161_NEGATIVE