Origin IGS: atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaccgcatttgataattgctctctaagttcataaaaagcaaatctgggactcgttctcagatttttttgtgaggtggaatatgtcatatttttggggtttgacaacatttaagagcgctcattttatgatataataaaaacaatttgaatacagaaagaaaaatat Mask Tandem Repeat Region ================================================ atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg Find is-nt database================================================ Query_seq: SSA_1314:SSA_1315|SSA_1314:SSA_1315:Fe-S-cluster oxidoreductase, putative:hypothetical protein:<-<-:1331331..1331497 167 atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1314:SSA_1315|SSA_1314:SSA_1315:Fe-S-cluster oxidoreductase, putative:hypothetical protein:<-<-:1331331..1331497 167 atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1314:SSA_1315|SSA_1314:SSA_1315:Fe-S-cluster oxidoreductase, putative:hypothetical protein:<-<-:1331331..1331497 167 atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 59 End: 166 .......................................................... M L S N P K N M T Y S T S Q K N L R T S P R F A F Y E L R E Q L S N A V . Protein_Len: 30 Strand: - Start: 36 End: 125 ................................... I M F H A S K F T T L G W F Y S M N W R V F F D S F S D W M .......................................... atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg 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: 83 Start: 17 End: 46 ................ATTCAAATTGTTTTTATTATATCATAAAAT......................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 88 HP_score: -5.3 Tail_Score: -5.626 Start: 106 End: 124 Full_Region: ttcataaaaagcaaa tctggga ctcgt tctcaga tttttttgtgaggtg .........................................................................................................tctgggactcgttctcaga........................................... Find igs database================================================ Query_seq: SSA_1314:SSA_1315|SSA_1314:SSA_1315:Fe-S-cluster oxidoreductase, putative:hypothetical protein:<-<-:1331331..1331497 167 atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_009009_SSA_1314_SSA_1315|Fe-S-cluster oxidoreductase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1331331,1331497]|167 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacnnnnnnntctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg atatttttctttctgtattcaaattgtttttattatatcataaaatgagcgctcttaaatgttgtcaaaccccaaaaatatgacatattccacctcacaaaaaaatctgagaacgagtcccagatttgctttttatgaacttagagagcaattatcaaatgcggttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUUUUCUUUCUGUAUUCAAAUUGUUUUUAUUAUAUCAUAAAAUGAGCGCUCUUAAAUGUUGUCAAACCCCAAAAAUAUGACAUAUUCCACCUCACAAAAAAAUCUGAGAACGAGUCCCAGAUUUGCUUUUUAUGAACUUAGAGAGCAAUUAUCAAAUGCGGUUG ............(((((((..((((((((((......(((((((..((((.......(((((.((((.............))))))))).............(((((((.((.....)).)))))))))))))))))).....))))))))))....)))))))... (-29.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACCGCAUUUGAUAAUUGCUCUCUAAGUUCAUAAAAAGCAAAUCUGGGACUCGUUCUCAGAUUUUUUUGUGAGGUGGAAUAUGUCAUAUUUUUGGGGUUUGACAACAUUUAAGAGCGCUCAUUUUAUGAUAUAAUAAAAACAAUUUGAAUACAGAAAGAAAAAUAU .....(.(((..(..((((...((((..((((((((((...(((((((((.....))))))))))))))))))).)))).(((((((((....((((((((............)))).))))...))))))))).......)))))..))).).............. (-35.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 875 130 81 221 172 NC_009009:SSA_1314|5end_Fe-S-cluster_oxidoreductase,_putative_1331240..1331470_NEGATIVE 288 134 93 194 150 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 263 96 51 173 131 NC_009009:SSA_2189|5end_hypothetical_protein_2191097..2191327_NEGATIVE 249 50 9 145 102 NC_009009:SSA_1181|5end_Hydrolase,_alpha/beta_superfamily,_putative_1209416..1209646_NEGATIVE 242 135 93 66 27 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 242 140 94 220 178 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 242 119 84 77 46 NC_009009:SSA_0395|5end_6-phospho-beta-glucosidase,_putative_391061..391291_POSITIVE 241 140 95 206 157 NC_009009:SSA_2032|5end_Integrase/recombinase,_phage_integrase_family,_putative_2038006..2038236_POSITIVE 239 120 71 124 73 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 238 135 93 141 100 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 238 119 81 126 86 NC_009009:SSA_1138|5end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1165731..1165961_POSITIVE 236 140 92 189 136 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 235 67 28 163 119 NC_009009:SSA_2242|5end_hypothetical_protein_2238663..2238893_NEGATIVE 235 115 84 125 89 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 233 86 44 200 159 NC_009009:SSA_1939|5end_Acyl_carrier_protein,_putative_1926099..1926329_NEGATIVE 232 132 95 159 119 NC_009009:SSA_0876|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870233..870463_POSITIVE 232 150 103 44 3 NC_009009:SSA_0594|5end_Transcriptional_regulator,_AraC_family,_putative_585630..585860_POSITIVE 230 158 114 205 158 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 229 68 22 174 125 NC_009009:SSA_1585|5end_hypothetical_protein_1587604..1587834_NEGATIVE 228 157 114 178 142 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 134 93 89 45 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 239 120 71 127 76 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 238 135 93 93 52 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 238 119 81 110 70 NC_009009:SSA_1137|3end_Dihydrolipoamide_dehydrogenase,_putative_1165795..1165945_POSITIVE 236 127 98 89 56 NC_009009:SSA_1206|3end_A/G-specific_adenine_glycosylase,_putative_1230071..1230221_NEGATIVE 235 67 28 57 13 NC_009009:SSA_2243|3end_Conserved_uncharacterized_protein_2238769..2238919_NEGATIVE 233 86 44 144 103 NC_009009:SSA_1940|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1926155..1926305_NEGATIVE 232 132 95 86 46 NC_009009:SSA_0875|3end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_870240..870390_POSITIVE 232 132 93 79 29 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 231 150 104 66 24 NC_009009:SSA_1964|3end_conserved_uncharacterized_protein_1960996..1961146_NEGATIVE 230 142 107 97 66 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 224 129 91 144 105 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 219 130 81 87 33 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 216 122 90 71 47 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 215 110 61 57 4 NC_009009:SSA_0422|3end_Phosphoglycerate_mutase_family_protein,_putative_420839..420989_POSITIVE 214 139 94 78 22 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 211 135 94 87 41 NC_009009:SSA_1630|3end_hypothetical_protein_1631508..1631658_POSITIVE 211 97 51 68 28 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 210 145 109 95 58 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 209 73 46 38 14 NC_009009:SSA_0566|3end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560885..561035_POSITIVE