Origin IGS: atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagtgaattatcctcctttaagctagatccattatagcacagttaggtataaaaagatagggatatcaactccatagcttagaaatgaaaaaagaggctcatggtgaacctcttgatgat Mask Tandem Repeat Region ================================================ atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt Find is-nt database================================================ Query_seq: SSA_1044:SSA_1045|SSA_1044:SSA_1045:Homoserine kinase, putative:hypothetical protein:->->:1060860..1060980 121 atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1044:SSA_1045|SSA_1044:SSA_1045:Homoserine kinase, putative:hypothetical protein:->->:1060860..1060980 121 atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1044:SSA_1045|SSA_1044:SSA_1045:Homoserine kinase, putative:hypothetical protein:->->:1060860..1060980 121 atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt Predict ORF larger than 30AA ================================================ atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt 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================================================ atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1044:SSA_1045|SSA_1044:SSA_1045:Homoserine kinase, putative:hypothetical protein:->->:1060860..1060980 121 atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: NC_009009_SSA_1044_SSA_1045|Homoserine kinase, putative:hypothetical protein|POSITIVE:POSITIVE|[1060860,1060980]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt atcatcaagaggttcaccatgagcctcttttttcatttctaagctatggagttgatatccctatctttttatacctaactgtgctataatggatctagcttaaaggaggataattcacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUCAAGAGGUUCACCAUGAGCCUCUUUUUUCAUUUCUAAGCUAUGGAGUUGAUAUCCCUAUCUUUUUAUACCUAACUGUGCUAUAAUGGAUCUAGCUUAAAGGAGGAUAAUUCACUUU ......(((((((((.....)))))))))(((((.....(((((((.(((.......)))..((((..(((((.(.......).))))).)))).)))))))...)))))........... (-24.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUGAAUUAUCCUCCUUUAAGCUAGAUCCAUUAUAGCACAGUUAGGUAUAAAAAGAUAGGGAUAUCAACUCCAUAGCUUAGAAAUGAAAAAAGAGGCUCAUGGUGAACCUCUUGAUGAU .......((((((....(((((((((......(((((.(.......).)))))...((((....)))).......)))))))))........((((((.((.....)).)))))))))))) (-24.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 59 11 127 75 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 309 51 13 121 79 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 299 50 1 205 160 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 275 70 24 146 101 NC_009009:SSA_2004|5end_Zinc_metalloprotease_zmpB_precursor,_putative_2004930..2005160_NEGATIVE 270 65 23 156 115 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 270 56 11 225 182 NC_009009:SSA_0738|5end_Ornithine_carbamoyltransferase,_catabolic,_putative_719904..720134_POSITIVE 261 70 23 64 15 NC_009009:SSA_1818|5end_Very_short_patch_repair_endonuclease,_putative_1806110..1806340_NEGATIVE 253 50 6 117 73 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 253 40 1 197 152 NC_009009:SSA_0532|5end_Propanediol_utilization_protein_PduB,_putative_528244..528474_POSITIVE 252 99 52 67 24 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 249 27 1 145 113 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 247 110 61 175 134 NC_009009:SSA_1569|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571891..1572121_POSITIVE 247 40 4 109 76 NC_009009:SSA_0149|5end_hypothetical_protein_143574..143804_POSITIVE 243 25 1 171 151 NC_009009:SSA_0943|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_950846..951076_POSITIVE 240 56 23 63 24 NC_009009:SSA_2066|5end_DNA_polymerase_III_polC-type,_putative_2070137..2070367_NEGATIVE 239 109 63 138 97 NC_009009:SSA_0322|5end_Transcriptional_activator,_TipA_family,_putative_314717..314947_POSITIVE 238 50 4 85 29 NC_009009:SSA_2081|5end_hypothetical_protein_2085309..2085539_POSITIVE 238 60 16 129 87 NC_009009:SSA_1988|5end_ABC-type_transport_system_(uncharacterized),_permease_component,_putative_1984188..1984418_NEGATIVE 238 47 7 198 145 NC_009009:SSA_1732|5end_Uracil_phosphoribosyltransferase,_putative_1717545..1717775_NEGATIVE 237 59 11 130 82 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 59 11 117 65 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 310 50 7 90 54 NC_009009:SSA_2108|3end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2111457..2111607_NEGATIVE 299 50 1 145 100 NC_009009:SSA_1118|3end_Peptide_methionine_sulfoxide_reductase,_putative_1144511..1144661_POSITIVE 278 100 55 125 72 NC_009009:SSA_2052|3end_Thioredoxin,_putative_2057193..2057343_NEGATIVE 268 60 16 126 70 NC_009009:SSA_0146|3end_DNA_repair_ATPase,_putative_142159..142309_POSITIVE 249 27 1 145 113 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 240 50 7 107 62 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 239 60 11 148 84 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 238 60 16 127 85 NC_009009:SSA_1989|3end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1984190..1984340_NEGATIVE 238 47 7 100 47 NC_009009:SSA_1734|3end_Cation_(Mg/Ni_uptake)_transport_ATPase,_putative_1717643..1717793_NEGATIVE 237 59 11 115 67 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 237 51 22 29 3 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 237 60 14 139 91 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 236 80 31 86 36 NC_009009:SSA_2314|3end_hypothetical_protein_2315886..2316036_NEGATIVE 236 60 14 136 91 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 234 50 4 131 73 NC_009009:SSA_1743|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1731005..1731155_POSITIVE 233 33 7 57 35 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 233 41 5 89 48 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 232 100 51 143 97 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 231 49 3 99 38 NC_009009:SSA_0427|3end_DNA-binding_transcriptional_activator,_SARP_family,_putative_427615..427765_POSITIVE