Origin IGS: ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc .........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 gagtcttcctcctttgagacatggataggaaagataagcattcaatcaagcccagcaatgttttgttgatcgaatgttagctttcatacctacagtcaaaccgctaaaaagcaaatcatgctccttagtgaaaacaagtttatttgtttattataccattttttatttaccgtcgcaaacaaagcaaaaaggctgaacattcagcc Mask Tandem Repeat Region ================================================ ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc Find is-nt database================================================ Query_seq: SSA_0583:SSA_0584|SSA_0583:SSA_0584:Nucleotidyltransferase, putative:hypothetical protein:->->:575740..575945 206 ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0583:SSA_0584|SSA_0583:SSA_0584:Nucleotidyltransferase, putative:hypothetical protein:->->:575740..575945 206 ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0583:SSA_0584|SSA_0583:SSA_0584:Nucleotidyltransferase, putative:hypothetical protein:->->:575740..575945 206 ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 7 End: 108 ...... M F S L F A L F A T V N K K W Y N K Q I N L F S L R S M I C F L A V .................................................................................................. Protein_Len: 40 Strand: - Start: 14 End: 133 ............. G K Q K T Q S P L Y F I T Y Y V F L S T K V L S C S K S K L P K V T P I F A L M ......................................................................... Protein_Len: 30 Strand: - Start: 3 End: 92 .. Q I N L R K A K N A V T F L F H Y L L C I F K N E S L L M M .................................................................................................................. ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc 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: 85 Start: 28 End: 57 ...........................TTTGCGACGGTAAATAAAAAATGGTATAAT..................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -3.3 Tail_Score: -3.72141 Start: 76 End: 106 Full_Region: CAAATAAACTTGTTT TCACTAAGGAGCA TGATT TGCTTTTTAGCGG TTTGACTGTAGGTAT ...........................................................................TCACTAAGGAGCATGATTTGCTTTTTAGCGG.................................................................................................... TransTerm Strand: + Conf: 48 HP_score: -4.6 Tail_Score: -2.82803 Start: 77 End: 105 Full_Region: AAATAAACTTGTTTT CACTAAGGAGCA TGATT TGCTTTTTAGCG GTTTGACTGTAGGTA ............................................................................CACTAAGGAGCATGATTTGCTTTTTAGCG..................................................................................................... Find igs database================================================ Query_seq: SSA_0583:SSA_0584|SSA_0583:SSA_0584:Nucleotidyltransferase, putative:hypothetical protein:->->:575740..575945 206 ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: NC_009009_SSA_0583_SSA_0584|Nucleotidyltransferase, putative:hypothetical protein|POSITIVE:POSITIVE|[575740,575945]|206 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 206 ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc ggctgaatgttcagcctttttgctttgtttgcgacggtaaataaaaaatggtataataaacaaataaacttgttttcactaaggagcatgatttgctttttagcggtttgactgtaggtatgaaagctaacattcgatcaacaaaacattgctgggcttgattgaatgcttatctttcctatccatgtctcaaaggaggaagactc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCUGAAUGUUCAGCCUUUUUGCUUUGUUUGCGACGGUAAAUAAAAAAUGGUAUAAUAAACAAAUAAACUUGUUUUCACUAAGGAGCAUGAUUUGCUUUUUAGCGGUUUGACUGUAGGUAUGAAAGCUAACAUUCGAUCAACAAAACAUUGCUGGGCUUGAUUGAAUGCUUAUCUUUCCUAUCCAUGUCUCAAAGGAGGAAGACUC ((((((....)))))).((((.((((.((((.((((...........(((((.....((((((......))))))((.((((((((((.....)))))))))).))....))))).((((.(((((.(((((((((((((((....((....)).).))))))))))).))).))))).))))..)))).)))).))))))))... (-55.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUCUUCCUCCUUUGAGACAUGGAUAGGAAAGAUAAGCAUUCAAUCAAGCCCAGCAAUGUUUUGUUGAUCGAAUGUUAGCUUUCAUACCUACAGUCAAACCGCUAAAAAGCAAAUCAUGCUCCUUAGUGAAAACAAGUUUAUUUGUUUAUUAUACCAUUUUUUAUUUACCGUCGCAAACAAAGCAAAAAGGCUGAACAUUCAGCC (((.....))).((((.(((..((.((.(((((...(((((((.(((((...((....)).....))))).)))))))..))))).))))...........((((((..((((.....))))..)))))).(((((((....)))))))......................))).))))...........((((((....)))))) (-44.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 130 89 60 13 NC_009009:SSA_0602|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_589918..590148_POSITIVE 343 158 117 180 134 NC_009009:SSA_1502|5end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1506219..1506449_NEGATIVE 327 38 1 81 35 NC_009009:SSA_1752|5end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1741875..1742105_NEGATIVE 310 180 135 225 180 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 292 32 1 202 162 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 290 139 91 205 163 NC_009009:SSA_2084|5end_Phosphotransferase_system_(PTS),_galactitol-specific_IIC_component,_putative_2089424..2089654_NEGATIVE 289 160 113 191 152 NC_009009:SSA_1953|5end_NifU_family_protein,_putative_1950079..1950309_NEGATIVE 288 199 154 71 32 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 282 159 111 214 142 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 280 128 85 57 10 NC_009009:SSA_2390|5end_hypothetical_protein_2849..3079_POSITIVE 278 120 78 226 177 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 277 195 154 174 113 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 274 37 8 212 187 NC_009009:SSA_0831|5end_Nucleotide_sugar_synthetase-like_protein,_putative_815671..815901_POSITIVE 274 186 148 95 56 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 273 200 151 148 88 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 272 37 1 209 169 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 270 118 71 60 6 NC_009009:SSA_1210|5end_GTP_pyrophosphokinase,_putative_1234655..1234885_NEGATIVE 269 187 151 225 181 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 269 200 151 171 114 NC_009009:SSA_1790|5end_SpoU_rRNA_Methylase_family_protein,_putative_1773641..1773871_NEGATIVE 267 129 81 215 171 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 130 89 50 3 NC_009009:SSA_0601|3end_Phosphorylase,_Pnp/Udp_family,_putative_589988..590138_POSITIVE 310 37 1 97 52 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 302 26 1 101 75 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 288 199 154 74 35 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 275 199 152 125 60 NC_009009:SSA_0212|3end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_209079..209229_POSITIVE 273 200 151 126 66 NC_009009:SSA_2071|3end_hypothetical_protein_2074596..2074746_NEGATIVE 267 129 81 110 66 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 264 193 153 58 20 NC_009009:SSA_0838|3end_GtfB,_putative_826829..826979_POSITIVE 264 199 152 121 65 NC_009009:SSA_0092|3end_V-type_sodium_ATPase,_subunit_B,_putative_94369..94519_POSITIVE 262 38 2 47 13 NC_009009:SSA_1224|3end_hypothetical_protein_1247251..1247401_NEGATIVE 261 128 81 102 52 NC_009009:SSA_0781|3end_Mannose-6-phosphate_isomerase,_putative_766394..766544_POSITIVE 260 158 117 143 104 NC_009009:SSA_0622|3end_Transcriptional_regulator_(XRE_family),_SOS-response_transcriptional_repressors_(RecA-mediated_autopeptidases),_putative_613742..613892_NEGATIVE 259 37 4 134 101 NC_009009:SSA_1631|3end_Sortase-like_protein,_putative_1631651..1631801_NEGATIVE 259 39 1 63 23 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE 259 200 153 58 20 NC_009009:SSA_0799|3end_hypothetical_protein_781713..781863_NEGATIVE 256 125 87 49 5 NC_009009:SSA_1145|3end_hypothetical_protein_1175694..1175844_NEGATIVE 256 37 1 45 20 NC_009009:SSA_0656|3end_Cell_division_protein_FtsZ,_putative_641516..641666_POSITIVE 254 41 1 87 48 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 253 33 1 69 17 NC_009009:SSA_1590|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1593342..1593492_POSITIVE 252 128 83 57 9 NC_009009:SSA_2168|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2168563..2168713_POSITIVE