Origin IGS: ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccgatttttttctttata .........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 tataaagaaaaaaatcggaattgttccggttttttctatttttggaaccaaagggcttcttaattcgatatacttgtgacaattcaaccgcttttctttgtatcaaccttactaaaaatcagacaaggaataattcacaaaaaaatgctaaaagacttgcattttcatttaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Mask Tandem Repeat Region ================================================ ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccgatttttttctttata Find is-nt database================================================ Query_seq: SSA_1520:SSA_1521|SSA_1520:SSA_1521:Elongation factor Tu, putative:Phosphoenolpyruvate carboxylase, putative:<-<-:1527672..1527926 255 ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccgatttttttctttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1520:SSA_1521|SSA_1520:SSA_1521:Elongation factor Tu, putative:Phosphoenolpyruvate carboxylase, putative:<-<-:1527672..1527926 255 ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccgatttttttctttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1520:SSA_1521|SSA_1520:SSA_1521:Elongation factor Tu, putative:Phosphoenolpyruvate carboxylase, putative:<-<-:1527672..1527926 255 ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccgatttttttctttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccgatttttttctttata Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 36 End: 134 ................................... M D S R Q Y S L T F L T I L S N L N E N A S L L A F F C E L F L V ......................................................................................................................... Protein_Len: 35 Strand: + Start: 150 End: 254 ..................................................................................................................................................... M I Q R K A V E L S Q V Y R I K K P F G S K N R K N R N N S D F F L Y . Protein_Len: 38 Strand: - Start: 73 End: 186 ........................................................................ K I L N L H F H L D K L M K K H I I G Q R I K L L T S V F F L P Q I T V L M ..................................................................... Protein_Len: 60 Strand: - Start: 2 End: 235 . R V K R V I K D F K F S F A L R K A N K Q S N N R T Q N K T L N I C L F A T S N D C T Y R I L F G K P E L F L F F R F M .................... ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccgatttttttctttata 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: 81 Start: 22 End: 51 .....................ATTGCCTACTGTCTATCTATAAAATATATT............................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccgatttttttctttata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 51 HP_score: -4.9 Tail_Score: -2.91507 Start: 37 End: 59 Full_Region: aatagtaaggaaagt tagactgta ttgcc tactgtcta tctataaaatatatt ....................................tagactgtattgcctactgtcta.................................................................................................................................................................................................... TransTerm Strand: - Conf: 44 HP_score: -3.1 Tail_Score: -3.00498 Start: 39 End: 57 Full_Region: tagtaaggaaagtta gactgta ttgcc tactgtc tatctataaaatata ......................................gactgtattgcctactgtc...................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1520:SSA_1521|SSA_1520:SSA_1521:Elongation factor Tu, putative:Phosphoenolpyruvate carboxylase, putative:<-<-:1527672..1527926 255 ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccgatttttttctttata Intra-Species Hit: Count: 1 Min: 1 Max: 241 Len: 241 Subject: NC_009009_SSA_1520_SSA_1521|Elongation factor Tu, putative:Phosphoenolpyruvate carboxylase, putative|NEGATIVE:NEGATIVE|[1527672,1527926]|255 HSP 1 e-value: 1.0E-121 bit: 436.0 Len: 241 Query Start:1 Query End:241 Subject Strand: POSITIVE Subject Start: 1 Subject End: 241 ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcannnnnnngtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccga.............. ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttaaatgaaaatgcaagtcttttagcatttttttgtgaattattccttgtctgatttttagtaaggttgatacaaagaaaagcggttgaattgtcacaagtatatcgaattaagaagccctttggttccaaaaatagaaaaaaccggaacaattccga.............. Inter-species Hit: Count: 5 Min: 7 Max: 107 Len: 101 Subject: NC_007297_M5005_Spy_0507_M5005_Spy_0508|hypothetical cytosolic protein:elongation factor Tu|NEGATIVE:POSITIVE|[493933,494128]|196 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 101 Query Start:7 Query End:107 Subject Strand: NEGATIVE Subject Start: 89 Subject End: 190 ......aaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaacttt-ccttactattttatcaaatttaaatgaaaatgcaagtctttta.................................................................................................................................................... ......aaaagcctccaataaaatatattttatagatagacggtaggccatacagtctaactttaccttactattgtagcaaattacaatgaaaatgcaagtatttta.................................................................................................................................................... Subject: NC_004606_SPs1423_SPs1424|elongation factor Tu:putative cell division protein|NEGATIVE:NEGATIVE|[1422506,1422859]|354 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 101 Query Start:7 Query End:107 Subject Strand: POSITIVE Subject Start: 7 Subject End: 108 ......aaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaacttt-ccttactattttatcaaatttaaatgaaaatgcaagtctttta.................................................................................................................................................... ......aaaagcctccaataaaatatattttatagatagacggtaggccatacagtctaactttaccttactattgtagcaaattacaatgaaaatgcaagtatttta.................................................................................................................................................... Subject: NC_004070_SpyM3_0431_SpyM3_0432|putative cell division protein:elongation factor Tu|POSITIVE:POSITIVE|[473883,474236]|354 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 101 Query Start:7 Query End:107 Subject Strand: NEGATIVE Subject Start: 247 Subject End: 348 ......aaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaacttt-ccttactattttatcaaatttaaatgaaaatgcaagtctttta.................................................................................................................................................... ......aaaagcctccaataaaatatattttatagatagacggtaggccatacagtctaactttaccttactattgtagcaaattacaatgaaaatgcaagtatttta.................................................................................................................................................... Subject: NC_003485_spyM18_0677_spyM18_0678|hypothetical protein:elongation factor Tu|NEGATIVE:POSITIVE|[540478,540673]|196 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 101 Query Start:7 Query End:107 Subject Strand: NEGATIVE Subject Start: 89 Subject End: 190 ......aaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaacttt-ccttactattttatcaaatttaaatgaaaatgcaagtctttta.................................................................................................................................................... ......aaaagcctccaataaaatatattttatagatagacggtaggccatacagtctaactttaccttactattgtagcaaattacaatgaaaatgcaagtatttta.................................................................................................................................................... Subject: NC_002737_SPy0609_SPy0611|putative cell division protein:elongation factor Tu|POSITIVE:POSITIVE|[491849,492201]|353 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 101 Query Start:7 Query End:107 Subject Strand: NEGATIVE Subject Start: 246 Subject End: 347 ......aaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaacttt-ccttactattttatcaaatttaaatgaaaatgcaagtctttta.................................................................................................................................................... ......aaaagcctccaataaaatatattttatagatagacggtaggccatacagtctaactttaccttactattgtagcaaattacaatgaaaatgcaagtatttta.................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGCCUCCAAUAAAAUAUAUUUUAUAGAUAGACAGUAGGCAAUACAGUCUAACUUUCCUUACUAUUUUAUCAAAUUUAAAUGAAAAUGCAAGUCUUUUA (((((.((...((((((((........((.(((((.(((.....))).))))).))........)))))))).........((....))...)).))))). (-11.49) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGACUUGCAUUUUCAUUUAAAUUUGAUAAAAUAGUAAGGAAAGUUAGACUGUAUUGCCUACUGUCUAUCUAUAAAAUAUAUUUUAUUGGAGGCUUUU .........................((..((((((((........((.(((((.(((.....))).))))).))........))))))))..))....... (-15.89) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 756 50 1 147 98 NC_009009:SSA_1520|5end_Elongation_factor_Tu,_putative_1527581..1527811_NEGATIVE 272 74 35 117 77 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 249 79 37 105 59 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 230 79 33 227 180 NC_009009:SSA_0195|5end_hypothetical_protein_195113..195343_POSITIVE 224 66 35 80 52 NC_009009:SSA_0122|5end_50S_ribosomal_protein_L6,_putative_115427..115657_POSITIVE 222 69 28 110 55 NC_009009:SSA_1823|5end_hypothetical_protein_1812513..1812743_NEGATIVE 216 73 41 113 78 NC_009009:SSA_0130|5end_30S_ribosomal_protein_S13,_putative_120332..120562_POSITIVE 211 44 5 150 98 NC_009009:SSA_0427|5end_DNA-binding_transcriptional_activator,_SARP_family,_putative_424497..424727_POSITIVE 207 100 55 147 107 NC_009009:SSA_0865|5end_hypothetical_protein_856378..856608_POSITIVE 203 66 33 203 169 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 201 67 33 197 167 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 200 74 40 125 87 NC_009009:SSA_0250|5end_GTP_pyrophosphokinase,_putative_242167..242397_POSITIVE 198 97 57 171 130 NC_009009:SSA_1852|5end_Metal_dependent_phosphohydrolase_(HD_motif),_putative_1848482..1848712_NEGATIVE 196 65 23 107 71 NC_009009:SSA_1248|5end_hypothetical_protein_1273263..1273493_NEGATIVE 195 59 22 219 183 NC_009009:SSA_2027|5end_P-type_ATPase-metal/cation_transport_(probably_copper),_putative_2035172..2035402_NEGATIVE 194 66 28 45 10 NC_009009:SSA_0396|5end_hypothetical_protein_393595..393825_NEGATIVE 192 70 28 76 29 NC_009009:SSA_1408|5end_hypothetical_protein_1421005..1421235_NEGATIVE 192 42 4 98 59 NC_009009:SSA_1137|5end_Dihydrolipoamide_dehydrogenase,_putative_1164375..1164605_POSITIVE 192 61 28 107 75 NC_009009:SSA_1059|5end_hypothetical_protein_1076153..1076383_POSITIVE 192 65 32 214 172 NC_009009:SSA_0925|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_934749..934979_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 74 35 124 84 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 249 79 37 112 66 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 242 98 51 92 32 NC_009009:SSA_1224|3end_hypothetical_protein_1247251..1247401_NEGATIVE 230 79 33 109 62 NC_009009:SSA_0193|3end_CAAX_amino_terminal_protease_family_protein,_putative_195075..195225_POSITIVE 227 65 22 91 48 NC_009009:SSA_0796|3end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_779060..779210_POSITIVE 222 69 28 107 52 NC_009009:SSA_1824|3end_hypothetical_protein_1812516..1812666_NEGATIVE 216 73 41 95 60 NC_009009:SSA_2392|3end_50S_ribosomal_protein_L36,_putative_120394..120544_POSITIVE 205 72 31 116 80 NC_009009:SSA_1952|3end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1948212..1948362_NEGATIVE 199 57 24 34 1 NC_009009:SSA_0153|3end_hypothetical_protein_149503..149653_POSITIVE 196 65 23 95 59 NC_009009:SSA_1249|3end_hypothetical_protein_1273275..1273425_NEGATIVE 192 61 28 85 53 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 191 70 35 119 63 NC_009009:SSA_1597|3end_hypothetical_protein_1603267..1603417_NEGATIVE 189 73 39 76 41 NC_009009:SSA_1790|3end_SpoU_rRNA_Methylase_family_protein,_putative_1772901..1773051_NEGATIVE 187 63 29 107 69 NC_009009:SSA_0714|3end_hypothetical_protein_700649..700799_POSITIVE 186 42 2 139 101 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 185 100 54 92 46 NC_009009:SSA_1109|3end_ABC_transporter_ATP_binding/permease_protein,_putative_1135576..1135726_POSITIVE 185 79 33 67 32 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 184 68 22 148 98 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 184 72 39 94 64 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 184 74 32 103 64 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE