Origin IGS: agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acttccactttccctacctctttcctccatctgatagacctgaagtgaaaccaagtctgaaaaatagaaaaaacacctatagcctgcagtaagctgcctgcttctaggtgttttact Mask Tandem Repeat Region ================================================ agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt Find is-nt database================================================ Query_seq: SSA_1245:SSA_1246|SSA_1245:SSA_1246:Transcriptional regulator, LysR family, putative:hypothetical protein:-><-:1269771..1269887 117 agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1245:SSA_1246|SSA_1245:SSA_1246:Transcriptional regulator, LysR family, putative:hypothetical protein:-><-:1269771..1269887 117 agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1245:SSA_1246|SSA_1245:SSA_1246:Transcriptional regulator, LysR family, putative:hypothetical protein:-><-:1269771..1269887 117 agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt Predict ORF larger than 30AA ================================================ agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt 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================================================ agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1245:SSA_1246|SSA_1245:SSA_1246:Transcriptional regulator, LysR family, putative:hypothetical protein:-><-:1269771..1269887 117 agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_009009_SSA_1245_SSA_1246|Transcriptional regulator, LysR family, putative:hypothetical protein|POSITIVE:NEGATIVE|[1269771,1269887]|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 agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt agtaaaacacctagaagcaggcagcttactgcaggctataggtgttttttctatttttcagacttggtttcacttcaggtctatcagatggaggaaagaggtagggaaagtggaagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAAACACCUAGAAGCAGGCAGCUUACUGCAGGCUAUAGGUGUUUUUUCUAUUUUUCAGACUUGGUUUCACUUCAGGUCUAUCAGAUGGAGGAAAGAGGUAGGGAAAGUGGAAGU ...((((((((((..(((..((((....))))..))).))))))))))(((((((((((..((((..((((.(((((.(.....)...))))))))).))))..))))))))))).. (-42.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUCCACUUUCCCUACCUCUUUCCUCCAUCUGAUAGACCUGAAGUGAAACCAAGUCUGAAAAAUAGAAAAAACACCUAUAGCCUGCAGUAAGCUGCCUGCUUCUAGGUGUUUUACU .....((((((.......(((.((........)).)))...))))))......................((((((((((.(((..((((....))))..)))..))))))))))... (-26.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 106 63 216 168 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 328 57 11 107 53 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 312 108 73 231 190 NC_009009:SSA_0445|5end_hypothetical_protein_444487..444717_POSITIVE 308 69 21 192 144 NC_009009:SSA_1280|5end_hypothetical_protein_1301596..1301826_NEGATIVE 294 60 16 178 117 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 294 58 13 187 148 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 291 110 64 119 75 NC_009009:SSA_0557|5end_hypothetical_protein_551900..552130_POSITIVE 290 50 8 180 137 NC_009009:SSA_1130|5end_Iron-dependent_peroxidase,_putative_1155802..1156032_POSITIVE 289 63 21 181 137 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 286 55 15 212 166 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 283 59 11 84 25 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 278 41 6 65 32 NC_009009:SSA_2189|5end_hypothetical_protein_2191097..2191327_NEGATIVE 278 48 10 88 39 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 278 44 8 52 11 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 276 106 63 211 159 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 274 40 7 226 191 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 273 60 14 175 127 NC_009009:SSA_2088|5end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2093476..2093706_NEGATIVE 273 78 39 49 7 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 272 49 1 163 122 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 272 110 63 184 128 NC_009009:SSA_0326|5end_Conserved_uncharacterized_BCR,_YbaB_family_319823..320053_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 48 4 87 43 NC_009009:SSA_1245|3end_Transcriptional_regulator,_LysR_family,_putative_1269710..1269860_POSITIVE 328 57 11 117 63 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 291 110 64 61 17 NC_009009:SSA_0556|3end_hypothetical_protein_551922..552072_POSITIVE 290 60 15 74 22 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 278 44 8 55 14 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 276 87 41 114 75 NC_009009:SSA_0193|3end_CAAX_amino_terminal_protease_family_protein,_putative_195075..195225_POSITIVE 273 110 61 81 16 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 271 55 16 47 8 NC_009009:SSA_1591|3end_Dipeptidase,_putative_1593403..1593553_NEGATIVE 270 60 13 103 43 NC_009009:SSA_0099|3end_hypothetical_protein_100134..100284_NEGATIVE 266 60 19 100 65 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 265 48 4 75 43 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE 262 52 16 40 3 NC_009009:SSA_1526|3end_hypothetical_protein_1534674..1534824_POSITIVE 262 94 54 142 97 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 261 54 15 101 59 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 260 49 6 146 103 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 260 43 9 50 21 NC_009009:SSA_0391|3end_Pyruvate_oxidase,_putative_387801..387951_POSITIVE 260 31 9 24 1 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 258 50 8 114 72 NC_009009:SSA_1586|3end_hypothetical_protein_1587730..1587880_NEGATIVE 256 48 7 92 48 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 254 92 52 128 86 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE