Origin IGS: gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacaggcctcctttcataaaatgcaaagggtactccaacaatcaaaatgattgctgtcggctacagatacaaaaagtatctcattatttattcatatatctaagactcatctcgaaatcttaagatacagtctgctctgaaaaagataaacctcctttcttcatttttctttgtctatatagtaagcgcttacttttcgaaagaatc Mask Tandem Repeat Region ================================================ gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt Find is-nt database================================================ Query_seq: SSA_1136:SSA_1137|SSA_1136:SSA_1137:ATPases with chaperone activity, ATP-binding subunit, putative:Dihydrolipoamide dehydrogenase, putative:->->:1164308..1164514 207 gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1136:SSA_1137|SSA_1136:SSA_1137:ATPases with chaperone activity, ATP-binding subunit, putative:Dihydrolipoamide dehydrogenase, putative:->->:1164308..1164514 207 gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1136:SSA_1137|SSA_1136:SSA_1137:ATPases with chaperone activity, ATP-binding subunit, putative:Dihydrolipoamide dehydrogenase, putative:->->:1164308..1164514 207 gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 88 End: 192 ....................................................................................... S K S I L R L Y I F L Y H S V K Q I Q L R C C D N Q N N S Y G K C K M ............... gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt 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================================================ gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 50 HP_score: -4.3 Tail_Score: -3.11784 Start: 128 End: 142 Full_Region: ttgctgtcggctaca gatac aaaaa gtatc tcattatttattcat ...............................................................................................................................gatacaaaaagtatc................................................................. Find igs database================================================ Query_seq: SSA_1136:SSA_1137|SSA_1136:SSA_1137:ATPases with chaperone activity, ATP-binding subunit, putative:Dihydrolipoamide dehydrogenase, putative:->->:1164308..1164514 207 gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt Intra-Species Hit: Count: 1 Min: 1 Max: 207 Len: 207 Subject: NC_009009_SSA_1136_SSA_1137|ATPases with chaperone activity, ATP-binding subunit, putative:Dihydrolipoamide dehydrogenase, putative|POSITIVE:POSITIVE|[1164308,1164514]|207 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 207 Query Start:1 Query End:207 Subject Strand: POSITIVE Subject Start: 1 Subject End: 207 gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt gattctttcgaaaagtaagcgcttactatatagacaaagaaaaatgaagaaaggaggtttatctttttcagagcagactgtatcttaagatttcgagatgagtcttagatatatgaataaataatgagatactttttgtatctgtagccgacagcaatcattttgattgttggagtaccctttgcattttatgaaaggaggcctgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUCUUUCGAAAAGUAAGCGCUUACUAUAUAGACAAAGAAAAAUGAAGAAAGGAGGUUUAUCUUUUUCAGAGCAGACUGUAUCUUAAGAUUUCGAGAUGAGUCUUAGAUAUAUGAAUAAAUAAUGAGAUACUUUUUGUAUCUGUAGCCGACAGCAAUCAUUUUGAUUGUUGGAGUACCCUUUGCAUUUUAUGAAAGGAGGCCUGUU ..((((((((...(((((....))))).............((((((...(((((.((((.........(((((((((..((((((((((((((......))))))))....(((......)))...))))))..))))).)))).))))..((((((((.....))))))))......))))).)))))).))))))))........ (-47.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGGCCUCCUUUCAUAAAAUGCAAAGGGUACUCCAACAAUCAAAAUGAUUGCUGUCGGCUACAGAUACAAAAAGUAUCUCAUUAUUUAUUCAUAUAUCUAAGACUCAUCUCGAAAUCUUAAGAUACAGUCUGCUCUGAAAAAGAUAAACCUCCUUUCUUCAUUUUUCUUUGUCUAUAUAGUAAGCGCUUACUUUUCGAAAGAAUC ....((((.((((((((...))).)))))......((.(((((.....))))).))..))))..((((((.....)))))).....((((((.(((((....(((((.((((..(....)..))))..))))).....((((((((..((......))..)).))))))......))))))))))).........(((....))).. (-35.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 179 138 141 101 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 284 186 143 228 187 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 281 190 141 148 91 NC_009009:SSA_0205|5end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_202722..202952_POSITIVE 272 180 132 73 28 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 270 100 52 181 135 NC_009009:SSA_1686|5end_hypothetical_protein_1679176..1679406_POSITIVE 268 189 144 65 24 NC_009009:SSA_1602|5end_Exoribonuclease,_VacB/Rnb_family,_putative_1609370..1609600_NEGATIVE 268 105 63 194 157 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 266 179 133 53 3 NC_009009:SSA_1899|5end_hypothetical_protein_1894739..1894969_NEGATIVE 264 70 27 142 103 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 264 179 132 171 126 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 264 200 161 230 182 NC_009009:SSA_0070|5end_Acetylxylan_esterase,_putative_73833..74063_POSITIVE 263 185 144 170 129 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 260 186 141 228 180 NC_009009:SSA_0167|5end_Hypothetical_protein_(Asparagine/proline-rich)_165254..165484_POSITIVE 255 183 144 80 31 NC_009009:SSA_2187|5end_Conserved_hypothetical_membrane_associated_protein_2188026..2188256_POSITIVE 255 106 63 207 166 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 255 187 141 61 16 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 253 185 142 168 123 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 253 199 151 75 15 NC_009009:SSA_0013|5end_Cell_cycle_control_ATPase,_PP-loop_superfamily,_putative_11196..11426_POSITIVE 251 80 31 195 146 NC_009009:SSA_2000|5end_hypothetical_protein_1997469..1997699_NEGATIVE 250 107 61 208 162 NC_009009:SSA_0666|5end_hypothetical_protein_649788..650018_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 180 131 149 96 NC_009009:SSA_1053|3end_Pyruvate_phosphate_dikinase,_putative_1067447..1067597_NEGATIVE 275 102 63 147 109 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 272 180 132 76 31 NC_009009:SSA_0338|3end_Hydroxymethylglutaryl-CoA_synthase,_putative_332160..332310_NEGATIVE 270 171 131 103 60 NC_009009:SSA_1244|3end_hypothetical_protein_1268465..1268615_NEGATIVE 264 70 27 60 21 NC_009009:SSA_1298|3end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1316627..1316777_POSITIVE 264 200 161 114 66 NC_009009:SSA_0069|3end_Hypothetical_protein,_possibly_membrane-associated_73797..73947_POSITIVE 259 185 142 143 103 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE 259 179 132 63 12 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 257 97 52 125 84 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE 253 199 151 78 18 NC_009009:SSA_0012|3end_Beta-lactamase_class_A,_putative_11279..11429_POSITIVE 252 58 33 55 30 NC_009009:SSA_0062|3end_Aldose_1-epimerase,_putative_64858..65008_POSITIVE 248 179 140 42 1 NC_009009:SSA_1900|3end_N_utilization_substance_protein_A,_putative_1894750..1894900_NEGATIVE 247 50 2 64 17 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 245 87 47 125 78 NC_009009:SSA_1685|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1678390..1678540_NEGATIVE 244 85 45 86 38 NC_009009:SSA_1559|3end_Conserved_uncharacterized_protein_1560862..1561012_NEGATIVE 242 186 141 125 82 NC_009009:SSA_2212|3end_Possible_polysaccharide_transport_protein,_putative_2212627..2212777_NEGATIVE 242 106 62 66 29 NC_009009:SSA_0476|3end_Precorrin-2_C20-methyltransferase,_putative_479281..479431_POSITIVE 236 160 125 151 116 NC_009009:SSA_1096|3end_Methyltransferase,_putative_1114099..1114249_POSITIVE 231 47 3 145 97 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 226 85 41 113 50 NC_009009:SSA_2290|3end_hypothetical_protein_2292964..2293114_POSITIVE