Origin IGS: aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaacaaatcctccaaattttttctgggttgataaccctaacaaatattatcatatctaaaaatagctttcaggtcaagtactaagccgctattttctaaattattatggtt Mask Tandem Repeat Region ================================================ aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa Find is-nt database================================================ Query_seq: SSA_0682:SSA_0683|SSA_0682:SSA_0683:Conserved uncharacterized protein:DNA-binding protein HU, putative:->->:664412..664523 112 aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0682:SSA_0683|SSA_0682:SSA_0683:Conserved uncharacterized protein:DNA-binding protein HU, putative:->->:664412..664523 112 aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0682:SSA_0683|SSA_0682:SSA_0683:Conserved uncharacterized protein:DNA-binding protein HU, putative:->->:664412..664523 112 aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa Predict ORF larger than 30AA ================================================ aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa 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: 87 Start: 34 End: 63 .................................CTTGACCTGAAAGCTATTTTTAGATATGAT................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0682:SSA_0683|SSA_0682:SSA_0683:Conserved uncharacterized protein:DNA-binding protein HU, putative:->->:664412..664523 112 aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_0682_SSA_0683|Conserved uncharacterized protein:DNA-binding protein HU, putative|POSITIVE:POSITIVE|[664412,664523]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa aaccataataatttagaaaatagcggcttagtacttgacctgaaagctatttttagatatgataatatttgttagggttatcaacccagaaaaaatttggaggatttgttaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCAUAAUAAUUUAGAAAAUAGCGGCUUAGUACUUGACCUGAAAGCUAUUUUUAGAUAUGAUAAUAUUUGUUAGGGUUAUCAACCCAGAAAAAAUUUGGAGGAUUUGUUAA ((((.(((((.....(((((((((...((((........))))..))))))))).(((((....)))))))))).))))......(((((.....)))))............ (-19.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAACAAAUCCUCCAAAUUUUUUCUGGGUUGAUAACCCUAACAAAUAUUAUCAUAUCUAAAAAUAGCUUUCAGGUCAAGUACUAAGCCGCUAUUUUCUAAAUUAUUAUGGUU ............(((..........((((.....)))).....................((((((((.....(((..........)))))))))))...........))).. (-12.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 66 24 79 29 NC_009009:SSA_0602|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_589918..590148_POSITIVE 276 61 22 92 53 NC_009009:SSA_2182|5end_hypothetical_protein_2181020..2181250_NEGATIVE 266 54 20 47 18 NC_009009:SSA_1227|5end_Aminoglycoside_adenylyltransferase,_putative_1252297..1252527_NEGATIVE 241 47 2 140 95 NC_009009:SSA_0877|5end_Phosphoglycolate_phosphatase,_putative_871008..871238_POSITIVE 240 65 36 96 66 NC_009009:SSA_1748|5end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1734478..1734708_NEGATIVE 235 108 61 173 127 NC_009009:SSA_2363|5end_Phosphoglycolate_phosphatase,_putative_2365632..2365862_POSITIVE 234 54 13 86 30 NC_009009:SSA_0138|5end_Metal-binding_(Zn)_permease,_putative_132533..132763_POSITIVE 231 42 2 194 154 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 229 61 21 153 120 NC_009009:SSA_1560|5end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1565194..1565424_NEGATIVE 223 49 20 36 7 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 221 110 72 65 28 NC_009009:SSA_1305|5end_hypothetical_protein_1324079..1324309_NEGATIVE 220 47 19 103 77 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 216 80 33 221 184 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 216 54 20 67 23 NC_009009:SSA_0248|5end_hypothetical_protein_241360..241590_POSITIVE 215 64 25 59 20 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 215 49 24 45 11 NC_009009:SSA_1131|5end_High-affinity_Fe_2+/Pb2+_permease,_putative_1157183..1157413_POSITIVE 215 67 21 63 18 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 214 57 17 82 39 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 214 57 11 52 8 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 211 58 21 212 177 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 66 24 69 19 NC_009009:SSA_0601|3end_Phosphorylase,_Pnp/Udp_family,_putative_589988..590138_POSITIVE 266 54 20 30 1 NC_009009:SSA_1229|3end_hypothetical_protein_1252314..1252464_NEGATIVE 236 59 15 85 40 NC_009009:SSA_1362|3end_ORFB,_transposon_ISSsa2_1378599..1378749_POSITIVE 235 108 61 121 75 NC_009009:SSA_2362|3end_L-serine_dehydratase_alpha_subunit_2365660..2365810_POSITIVE 234 54 13 76 20 NC_009009:SSA_0137|3end_ABC_transporter_(permease),_Zn_porter,_putative_132603..132753_POSITIVE 216 80 33 116 79 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 216 54 20 82 38 NC_009009:SSA_0247|3end_hypothetical_protein_241455..241605_POSITIVE 215 67 21 66 21 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 212 57 22 72 33 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 210 60 25 144 112 NC_009009:SSA_1701|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1691299..1691449_NEGATIVE 209 77 31 142 99 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 209 75 32 141 92 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 204 106 71 135 90 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 203 37 13 38 12 NC_009009:SSA_1545|3end_Conserved_uncharacterized_protein_1548812..1548962_NEGATIVE 203 52 15 48 8 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 203 90 46 68 27 NC_009009:SSA_1259|3end_Purine_nucleoside_phosphorylase,_putative_1284910..1285060_NEGATIVE 203 65 23 62 20 NC_009009:SSA_1237|3end_Uracil-DNA_glycosylase,_putative_1261713..1261863_NEGATIVE 202 43 3 142 102 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 202 55 15 93 56 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 200 41 19 143 124 NC_009009:SSA_0952|3end_hypothetical_protein_958095..958245_POSITIVE