Origin IGS: gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaaacatgaaatcgctatttcataaataattgcttcaaatctattgcttttgcctactatttttgatatgatagtaggcggtattgtttaccccatttgtaaggccccggaacctttcaaataactcgcggaccggaacatccgccctgtaaacaaaaacgatattcataggagaaatc Mask Tandem Repeat Region ================================================ gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc Find is-nt database================================================ Query_seq: SSA_2034:SSA_2035|SSA_2034:SSA_2035:50S ribosomal protein L13, putative:Conserved uncharacterized protein:<-<-:2039335..2039514 180 gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2034:SSA_2035|SSA_2034:SSA_2035:50S ribosomal protein L13, putative:Conserved uncharacterized protein:<-<-:2039335..2039514 180 gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2034:SSA_2035|SSA_2034:SSA_2035:50S ribosomal protein L13, putative:Conserved uncharacterized protein:<-<-:2039335..2039514 180 gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 2 End: 136 . M S P M N I V F V Y R A D V P V R E L F E R F R G L T N G V N N T A Y Y H I K N S R Q K Q ............................................ Protein_Len: 32 Strand: - Start: 59 End: 154 .......................................................... K F P E P A K C I P Y V I G G V I M D F I T P L L L L N S A I M .......................... gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc 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: 83 Start: 108 End: 137 ...........................................................................................................ATTGCTTTTGCCTACTATTTTTGATATGAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2034:SSA_2035|SSA_2034:SSA_2035:50S ribosomal protein L13, putative:Conserved uncharacterized protein:<-<-:2039335..2039514 180 gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_009009_SSA_2034_SSA_2035|50S ribosomal protein L13, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2039335,2039514]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc gatttctcctatgaatatcgtttttgtttacagggcggatgttccggtccgcgagttatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaaatagtaggcaaaagcaatagatttgaagcaattatttatgaaatagcgatttcatgttttc Inter-species Hit: Count: 3 Min: 18 Max: 119 Len: 102 Subject: NC_007432_SAK_0275_SAK_0276|hypothetical protein:50S ribosomal protein L13|POSITIVE:POSITIVE|[239943,240358]|416 HSP 1 e-value: 1.0E-28 bit: 127.0 Len: 102 Query Start:18 Query End:119 Subject Strand: NEGATIVE Subject Start: 295 Subject End: 398 .................tcgtttttgtttacagg-gcggatgttccggtccgcgagt-tatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaa............................................................. .................tcgtttttgtttacaggtgtggatgttccggtccacgagagtatttgaaaggttccggggccttacaaatggggtaaacaataccgcttataatcatatcaaaa............................................................. Subject: NC_004368_gbs0208_gbs0209|hypothetical protein:50S ribosomal protein L13|NEGATIVE:POSITIVE|[231624,231908]|285 HSP 1 e-value: 1.0E-28 bit: 127.0 Len: 102 Query Start:18 Query End:119 Subject Strand: NEGATIVE Subject Start: 164 Subject End: 267 .................tcgtttttgtttacagg-gcggatgttccggtccgcgagt-tatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaa............................................................. .................tcgtttttgtttacaggtgtggatgttccggtccacgagagtatttgaaaggttccggggccttacaaatggggtaaacaataccgcttataatcatatcaaaa............................................................. Subject: NC_004116_SAG0213_SAG0214|hypothetical protein:50S ribosomal protein L13|POSITIVE:POSITIVE|[230393,230808]|416 HSP 1 e-value: 1.0E-28 bit: 127.0 Len: 102 Query Start:18 Query End:119 Subject Strand: NEGATIVE Subject Start: 295 Subject End: 398 .................tcgtttttgtttacagg-gcggatgttccggtccgcgagt-tatttgaaaggttccggggccttacaaatggggtaaacaataccgcctactatcatatcaaaa............................................................. .................tcgtttttgtttacaggtgtggatgttccggtccacgagagtatttgaaaggttccggggccttacaaatggggtaaacaataccgcttataatcatatcaaaa............................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUUUUUGUUUACAGGGCGGAUGUUCCGGUCCGCGAGUUAUUUGAAAGGUUCCGGGGCCUUACAAAUGGGGUAAACAAUACCGCCUACUAUCAUAUCAAAA .((...((((((((...((((((......))))))...(((((((.((((((....)))))).))))))).))))))))...)).................. (-29.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGAUAUGAUAGUAGGCGGUAUUGUUUACCCCAUUUGUAAGGCCCCGGAACCUUUCAAAUAACUCGCGGACCGGAACAUCCGCCCUGUAAACAAAAACGA (((((.....((((..(((((...(((((...(((((((.((((........)))).))))).......))....))))).)))))))))...))))).... (-22.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1070 60 11 168 119 NC_009009:SSA_2034|5end_50S_ribosomal_protein_L13,_putative_2039244..2039474_NEGATIVE 369 59 12 186 135 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 366 59 14 165 118 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 353 58 13 205 151 NC_009009:SSA_1180|5end_hypothetical_protein_1208559..1208789_NEGATIVE 339 60 13 184 136 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 337 60 11 98 19 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 333 57 15 223 169 NC_009009:SSA_2329|5end_hypothetical_protein_2332262..2332492_POSITIVE 323 60 13 55 22 NC_009009:SSA_1044|5end_Homoserine_kinase,_putative_1059853..1060083_POSITIVE 321 59 18 197 165 NC_009009:SSA_1588|5end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1591905..1592135_NEGATIVE 318 59 11 204 157 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 313 44 2 223 179 NC_009009:SSA_0628|5end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_617892..618122_POSITIVE 312 60 15 171 118 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 310 50 1 158 110 NC_009009:SSA_2392|5end_50S_ribosomal_protein_L36,_putative_120198..120428_POSITIVE 305 60 12 58 10 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 303 60 12 175 129 NC_009009:SSA_1790|5end_SpoU_rRNA_Methylase_family_protein,_putative_1773641..1773871_NEGATIVE 303 58 15 83 37 NC_009009:SSA_1362|5end_ORFB,_transposon_ISSsa2_1377911..1378141_POSITIVE 303 58 15 83 37 NC_009009:SSA_0266|5end_ORFB,_transposon_ISSsa1_260134..260364_POSITIVE 300 57 17 67 30 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 300 59 11 155 110 NC_009009:SSA_0018|5end_Cell-shape_determining_protein_MreD,_putative_23628..23858_POSITIVE 299 59 15 210 165 NC_009009:SSA_2171|5end_hypothetical_protein_2170760..2170990_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 59 12 68 17 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 327 42 6 42 5 NC_009009:SSA_2380|3end_hypothetical_protein_2385665..2385815_NEGATIVE 323 60 13 53 20 NC_009009:SSA_1043|3end_Homoserine_dehydrogenase,_putative_1059931..1060081_POSITIVE 313 59 15 50 9 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 310 50 1 135 87 NC_009009:SSA_0129|3end_Translation_initiation_factor_IF-1,_putative_120255..120405_POSITIVE 302 59 17 106 58 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 301 59 14 83 33 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 297 57 20 86 47 NC_009009:SSA_0416|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_414222..414372_POSITIVE 291 60 13 62 13 NC_009009:SSA_1431|3end_hypothetical_protein_1438047..1438197_NEGATIVE 286 59 15 89 45 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 282 59 15 57 10 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 281 50 3 138 57 NC_009009:SSA_2293|3end_hypothetical_protein_2295955..2296105_POSITIVE 277 59 17 76 34 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 276 59 15 62 29 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 274 99 55 93 39 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 273 60 14 51 9 NC_009009:SSA_0353|3end_Conserved_uncharacterized_protein_346310..346460_POSITIVE 271 40 1 143 96 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 268 76 32 42 2 NC_009009:SSA_1092|3end_Dihydrofolate_reductase,_putative_1110191..1110341_POSITIVE 267 60 11 57 6 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 266 50 9 72 24 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE