Origin IGS: tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttttcctctttctttgtcagtttctcttcgtgtaattattttgagtttaggctctgccctgggttgggacaaggccgttcagtgaatcgttgataaatgagcaaaagcactcgga Mask Tandem Repeat Region ================================================ tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac Find is-nt database================================================ Query_seq: SSA_2267:SSA_2268|SSA_2267:SSA_2268:Lactose operon transcriptional repressor, LacI family, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative:->->:2267251..2267367 117 tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2267:SSA_2268|SSA_2267:SSA_2268:Lactose operon transcriptional repressor, LacI family, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative:->->:2267251..2267367 117 tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2267:SSA_2268|SSA_2267:SSA_2268:Lactose operon transcriptional repressor, LacI family, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative:->->:2267251..2267367 117 tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac Predict ORF larger than 30AA ================================================ tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac 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================================================ tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2267:SSA_2268|SSA_2267:SSA_2268:Lactose operon transcriptional repressor, LacI family, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative:->->:2267251..2267367 117 tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_009009_SSA_2267_SSA_2268|Lactose operon transcriptional repressor, LacI family, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative|POSITIVE:POSITIVE|[2267251,2267367]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac tccgagtgcttttgctcatttatcaacgattcactgaacggccttgtcccaacccagggcagagcctaaactcaaaataattacacgaagagaaactgacaaagaaagaggaaaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGAGUGCUUUUGCUCAUUUAUCAACGAUUCACUGAACGGCCUUGUCCCAACCCAGGGCAGAGCCUAAACUCAAAAUAAUUACACGAAGAGAAACUGACAAAGAAAGAGGAAAAAC (((...(..(((((.((((((.((..((............((((((........)))))).(((......)))............))..)).))).)))))))).)...)))..... (-20.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUCCUCUUUCUUUGUCAGUUUCUCUUCGUGUAAUUAUUUUGAGUUUAGGCUCUGCCCUGGGUUGGGACAAGGCCGUUCAGUGAAUCGUUGAUAAAUGAGCAAAAGCACUCGGA ((((((.(((....((((((((...(((...(((....)))...)))....(((..(((((......))).))..))).............)))))))).))).))))))....... (-28.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 75 39 52 1 NC_009009:SSA_2020|5end_hypothetical_protein_2019284..2019514_POSITIVE 322 66 39 220 197 NC_009009:SSA_1611|5end_Era-like_GTP-binding_protein,_putative_1616032..1616262_NEGATIVE 314 68 25 179 127 NC_009009:SSA_0724|5end_ABC-type_multidrug/protein/lipid_transport_system_(pediocin_PA-1_exporter),_ATPase_and_permease_components,_putative_708652..708882_POSITIVE 312 67 28 60 24 NC_009009:SSA_0652|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_635036..635266_POSITIVE 312 67 28 186 144 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 311 60 17 231 180 NC_009009:SSA_1231|5end_hypothetical_protein_1254758..1254988_NEGATIVE 306 66 35 69 39 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 304 67 38 231 202 NC_009009:SSA_0419|5end_Alpha-galactosidase,_putative_416213..416443_POSITIVE 304 77 31 54 6 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 300 67 25 66 20 NC_009009:SSA_1428|5end_hypothetical_protein_1436348..1436578_NEGATIVE 296 69 27 180 134 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 293 66 26 185 149 NC_009009:SSA_2199|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2201108..2201338_NEGATIVE 290 60 11 53 10 NC_009009:SSA_2106|5end_Flavin_monoxygenase,_putative_2109064..2109294_NEGATIVE 290 63 34 175 138 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 286 60 12 96 55 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 284 66 26 184 142 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 284 49 4 111 65 NC_009009:SSA_1342|5end_Carbamoyl-phosphate_synthase_small_chain,_putative_1361017..1361247_NEGATIVE 283 66 30 68 35 NC_009009:SSA_0549|5end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_543556..543786_POSITIVE 279 60 12 70 24 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 278 110 62 229 170 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 50 3 49 5 NC_009009:SSA_1986|3end_Acetyltransferase,_GNAT_family,_putative_1982073..1982223_NEGATIVE 327 58 27 151 120 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 309 49 3 143 101 NC_009009:SSA_1829|3end_RNA_methyltransferase,_putative_1818959..1819109_NEGATIVE 306 66 35 69 39 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 304 67 38 122 93 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 300 67 25 59 13 NC_009009:SSA_1429|3end_hypothetical_protein_1436355..1436505_NEGATIVE 295 49 9 121 77 NC_009009:SSA_1550|3end_hypothetical_protein_1552228..1552378_NEGATIVE 286 60 12 123 82 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 284 49 4 86 40 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 279 60 12 64 18 NC_009009:SSA_0025|3end_DNA_repair_protein_recO,_putative_30547..30697_POSITIVE 278 90 47 95 54 NC_009009:SSA_0771|3end_Glutaredoxin-like_protein,_putative_751572..751722_NEGATIVE 277 66 23 150 114 NC_009009:SSA_2000|3end_hypothetical_protein_1996987..1997137_NEGATIVE 277 57 11 79 11 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 275 73 40 86 43 NC_009009:SSA_1804|3end_NADPH-flavin_oxidoreductase,_putative_1787952..1788102_NEGATIVE 275 66 40 39 2 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 271 66 27 121 82 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 269 109 83 53 25 NC_009009:SSA_1056|3end_Firmicute_fructose-1,6-bisphosphatase,_putative_1073750..1073900_POSITIVE 268 68 22 69 26 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 267 47 1 133 88 NC_009009:SSA_2111|3end_30S_ribosomal_protein_S12,_putative_2115599..2115749_NEGATIVE 266 50 1 137 71 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE