Origin IGS: ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaattaaaaatgaaaaaacaggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattaaaagaaagttgttcatatttttctcttgcaggacaaatttgtcctgttttttcatttttaattacgaatagataagtaggagcgagtttctcatgacaaaagaaacagattgagaaacagaacttcgcttgagtaaaaaaaattttttaagaattttgcataa Mask Tandem Repeat Region ================================================ ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaattaaaaatgaaaaaacaggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc Find is-nt database================================================ Query_seq: SSA_2192:SSA_2193|SSA_2192:SSA_2193:Conserved uncharacterized protein:ADP-ribose pyrophosphatase, putative:<-<-:2193933..2194100 168 ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaattaaaaatgaaaaaacaggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2192:SSA_2193|SSA_2192:SSA_2193:Conserved uncharacterized protein:ADP-ribose pyrophosphatase, putative:<-<-:2193933..2194100 168 ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaattaaaaatgaaaaaacaggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2192:SSA_2193|SSA_2192:SSA_2193:Conserved uncharacterized protein:ADP-ribose pyrophosphatase, putative:<-<-:2193933..2194100 168 ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaattaaaaatgaaaaaacaggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaattaaaaatgaaaaaacaggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 10 End: 99 ......... M L K K F F L L K R S S V S Q S V S F V M R N S L L L I Y S ..................................................................... Protein_Len: 49 Strand: + Start: 21 End: 167 .................... M F F T Q A K F C F S I C F F C H E K L A P T Y L F V I K N E K T G Q I C P A R E K Y E Q L S F N . ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaattaaaaatgaaaaaacaggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc 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================================================ ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaattaaaaatgaaaaaacaggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2192:SSA_2193|SSA_2192:SSA_2193:Conserved uncharacterized protein:ADP-ribose pyrophosphatase, putative:<-<-:2193933..2194100 168 ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaattaaaaatgaaaaaacaggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: NC_009009_SSA_2192_SSA_2193|Conserved uncharacterized protein:ADP-ribose pyrophosphatase, putative|NEGATIVE:NEGATIVE|[2193933,2194100]|168 HSP 1 e-value: 4.0E-38 bit: 159.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 ttatgcaaaattcttaaaaaannnnnnnnactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaatt................................................................ ttatgcaaaattcttaaaaaattttttttactcaagcgaagttctgtttctcaatctgtttcttttgtcatgagaaactcgctcctacttatctattcgtaatt................................................................ HSP 2 e-value: 7.0E-21 bit: 101.0 Len: 51 Query Start:118 Query End:168 Subject Strand: POSITIVE Subject Start: 118 Subject End: 168 .....................................................................................................................caggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc .....................................................................................................................caggacaaatttgtcctgcaagagaaaaatatgaacaactttcttttaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUGCAAAAUUCUUAAAAAAUUUUUUUUACUCAAGCGAAGUUCUGUUUCUCAAUCUGUUUCUUUUGUCAUGAGAAACUCGCUCCUACUUAUCUAUUCGUAAUUAAAAAUGAAAAAACAGGACAAAUUUGUCCUGCAAGAGAAAAAUAUGAACAACUUUCUUUUAAUC ...(((........((((((....)))))).....)))..((((..((((((.....(((((((.......))))))).................(((((........)))))....(((((((....)))))))...)))))).....))))............... (-27.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAAAAGAAAGUUGUUCAUAUUUUUCUCUUGCAGGACAAAUUUGUCCUGUUUUUUCAUUUUUAAUUACGAAUAGAUAAGUAGGAGCGAGUUUCUCAUGACAAAAGAAACAGAUUGAGAAACAGAACUUCGCUUGAGUAAAAAAAAUUUUUUAAGAAUUUUGCAUAA ..........(((((((((.(((((.(((...((((((((....))))))))...(((............))).))).))))).))))..((((((((.................))))))))..))))).((..((.((((((....))))))....))..)).... (-31.53) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 90 41 181 132 NC_009009:SSA_2192|5end_Conserved_uncharacterized_protein_2193842..2194072_NEGATIVE 318 92 55 113 77 NC_009009:SSA_0667|5end_Transcriptional_regulator,_putative_649778..650008_POSITIVE 308 74 34 231 195 NC_009009:SSA_1693|5end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1686811..1687041_NEGATIVE 291 90 43 62 3 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 290 105 63 86 47 NC_009009:SSA_1717|5end_Modification_methylase_DpnIIB,_putative_1704958..1705188_NEGATIVE 281 70 32 69 28 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 280 80 31 100 44 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 268 95 51 207 153 NC_009009:SSA_1423|5end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1433783..1434013_NEGATIVE 264 70 35 207 172 NC_009009:SSA_1484|5end_DNA_ligase,_putative_1492188..1492418_NEGATIVE 262 62 21 187 144 NC_009009:SSA_2177|5end_hypothetical_protein_2176215..2176445_NEGATIVE 257 85 41 139 96 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 253 75 35 204 164 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 253 86 47 106 68 NC_009009:SSA_0107|5end_50S_ribosomal_protein_L3,_putative_108165..108395_POSITIVE 251 99 55 42 9 NC_009009:SSA_2246|5end_Competence-damage_protein,_putative_2242496..2242726_NEGATIVE 251 43 4 137 87 NC_009009:SSA_1135|5end_Na+-driven_multidrug_efflux_pump,_putative_1160352..1160582_POSITIVE 245 80 32 160 103 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 245 70 35 74 43 NC_009009:SSA_0858|5end_DTDP-L-rhamnose_synthase,_putative_845512..845742_POSITIVE 244 72 31 92 39 NC_009009:SSA_0927|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936049..936279_POSITIVE 244 85 42 126 75 NC_009009:SSA_0165|5end_hypothetical_protein_163938..164168_POSITIVE 243 98 51 117 66 NC_009009:SSA_0751|5end_Oligoendopeptidase_F,_putative_732367..732597_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 105 63 93 54 NC_009009:SSA_1718|3end_Site-specific_DNA-methyltransferase,_putative_1704951..1705101_NEGATIVE 281 70 32 72 31 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 268 95 51 101 47 NC_009009:SSA_1424|3end_Hydrolase,_putative_1433889..1434039_NEGATIVE 264 70 35 101 66 NC_009009:SSA_1485|3end_Citrulline_cluster-linked_gene,_putative_1492294..1492444_NEGATIVE 262 62 21 114 71 NC_009009:SSA_2178|3end_hypothetical_protein_2176288..2176438_NEGATIVE 252 90 44 148 104 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 249 54 21 68 20 NC_009009:SSA_1810|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1794707..1794857_NEGATIVE 247 84 41 109 68 NC_009009:SSA_1087|3end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1106472..1106622_POSITIVE 244 85 42 105 54 NC_009009:SSA_0164|3end_hypothetical_protein_163997..164147_POSITIVE 240 70 26 141 89 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 238 89 41 95 39 NC_009009:SSA_0918|3end_Conserved_uncharacterized_protein_930945..931095_POSITIVE 233 99 56 102 64 NC_009009:SSA_1416|3end_hypothetical_protein_1426520..1426670_NEGATIVE 233 86 45 57 22 NC_009009:SSA_1285|3end_hypothetical_protein_1304993..1305143_NEGATIVE 233 59 35 148 127 NC_009009:SSA_1251|3end_Hydrolase,_HD_superfamily,_putative_1274493..1274643_NEGATIVE 232 100 57 120 70 NC_009009:SSA_1331|3end_Conserved_uncharacterized_protein_1346473..1346623_NEGATIVE 231 98 56 118 68 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 230 85 43 150 104 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 230 89 41 73 32 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 230 72 35 141 106 NC_009009:SSA_1179|3end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1206640..1206790_NEGATIVE 229 87 45 111 64 NC_009009:SSA_1907|3end_hypothetical_protein_1900813..1900963_POSITIVE