Origin IGS: acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagaccaaagatagcggatattttaccctatcgatacagaaccatgccgatccatttccttttcactgcactctttgtcgaaacgagttggtataggaggcgaatctctattttcaggccgacaaattccaatgaaagatattcgctgacacgcacgacctccaagttcaccggacagcaataattagataccggatctttggtccagaaaccaactattgtccttagctcctcttgcctaaaaaagaaaggctgccgaagtttttatacccggacagccttgcctattggagtaaccctattccgattcggataatatcagctcctgaaaacgaaataagggaaaaagatgt Mask Tandem Repeat Region ================================================ acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta Find is-nt database================================================ Query_seq: PG1085:PG1087|PG1085:PG1087:hypothetical protein:radical SAM protein, TIGR01212 family:->->:1153592..1153944 353 acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1085:PG1087|PG1085:PG1087:hypothetical protein:radical SAM protein, TIGR01212 family:->->:1153592..1153944 353 acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1085:PG1087|PG1085:PG1087:hypothetical protein:radical SAM protein, TIGR01212 family:->->:1153592..1153944 353 acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 135 End: 323 ...................................................................................................................................... M V G F W T K D P V S N Y C C P V N L E V V R V S E Y L S L E F V G L K I E I R L L Y Q L V S T K S A V K R K W I G M V .............................. Protein_Len: 52 Strand: + Start: 173 End: 328 ............................................................................................................................................................................ M L S G E L G G R A C Q R I S F I G I C R P E N R D S P P I P T R F D K E C S E K E M D R H G S V S I G ......................... Protein_Len: 43 Strand: - Start: 208 End: 336 ............................................................................................................................................................................................................... R I D K M P I Q R G S F L S E G G I G V R K S L S H L S F S I S R C P E T D I P Y F M ................. Protein_Len: 57 Strand: - Start: 173 End: 343 ............................................................................................................................................................................ Q Q G T F K S T T R T L S Y R E N S N T P R F I S I R R R Y W S T E V F L A T F L F H I P M T R Y R Y P L I D A M .......... Protein_Len: 38 Strand: - Start: 41 End: 154 ........................................ G F R F L T V G I P L A T R T Y F S R C G K K K L C S S S L V I T P K Q V M ....................................................................................................................................................................................................... Protein_Len: 39 Strand: - Start: 3 End: 119 .. D K E R I E N E P A S I I R I P I P N S W Y A L S D P Y L F K P L R E K K P M .......................................................................................................................................................................................................................................... acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta 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================================================ acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -4.8 Tail_Score: -5.00616 Start: 70 End: 107 Full_Region: GGGTTACTCCAATAG GCAAGGCTGTCCGGGT ATAAAA ACTTCGGCAGCCTTTC TTTTTTAGGCAAGAG .....................................................................GCAAGGCTGTCCGGGTATAAAAACTTCGGCAGCCTTTC...................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 76 HP_score: -4.2 Tail_Score: -5.04249 Start: 74 End: 103 Full_Region: TACTCCAATAGGCAA GGCTGTCCGGGT ATAAAA ACTTCGGCAGCC TTTCTTTTTTAGGCA .........................................................................GGCTGTCCGGGTATAAAAACTTCGGCAGCC.......................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG1085:PG1087|PG1085:PG1087:hypothetical protein:radical SAM protein, TIGR01212 family:->->:1153592..1153944 353 acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta Intra-Species Hit: Count: 1 Min: 1 Max: 353 Len: 353 Subject: NC_002950_PG1085_PG1087|hypothetical protein:radical SAM protein, TIGR01212 family|POSITIVE:POSITIVE|[1153592,1153944]|353 HSP 1 e-value: 0.0 bit: 700.0 Len: 353 Query Start:1 Query End:353 Subject Strand: POSITIVE Subject Start: 1 Subject End: 353 acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta acatctttttcccttatttcgttttcaggagctgatattatccgaatcggaatagggttactccaataggcaaggctgtccgggtataaaaacttcggcagcctttcttttttaggcaagaggagctaaggacaatagttggtttctggaccaaagatccggtatctaattattgctgtccggtgaacttggaggtcgtgcgtgtcagcgaatatctttcattggaatttgtcggcctgaaaatagagattcgcctcctataccaactcgtttcgacaaagagtgcagtgaaaaggaaatggatcggcatggttctgtatcgatagggtaaaatatccgctatctttggtcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUCUUUUUCCCUUAUUUCGUUUUCAGGAGCUGAUAUUAUCCGAAUCGGAAUAGGGUUACUCCAAUAGGCAAGGCUGUCCGGGUAUAAAAACUUCGGCAGCCUUUCUUUUUUAGGCAAGAGGAGCUAAGGACAAUAGUUGGUUUCUGGACCAAAGAUCCGGUAUCUAAUUAUUGCUGUCCGGUGAACUUGGAGGUCGUGCGUGUCAGCGAAUAUCUUUCAUUGGAAUUUGUCGGCCUGAAAAUAGAGAUUCGCCUCCUAUACCAACUCGUUUCGACAAAGAGUGCAGUGAAAAGGAAAUGGAUCGGCAUGGUUCUGUAUCGAUAGGGUAAAAUAUCCGCUAUCUUUGGUCUA ...((((((((((((((((((..(((.(((..........)))))).)))))))))).(((((....((((.((((((((..(((......)))..))))))))(((((((((((((..((.(((....((.((((((((((...(((((.......)))))...)))))))))))).(((((((((...(((..((((........))))...)))))))))))).))).)).))))))))).))))....))))...........(((...)))....)))))....))))))))..((((((.(((......)))...(((((((........)).)))))...)))))) (-105.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACCAAAGAUAGCGGAUAUUUUACCCUAUCGAUACAGAACCAUGCCGAUCCAUUUCCUUUUCACUGCACUCUUUGUCGAAACGAGUUGGUAUAGGAGGCGAAUCUCUAUUUUCAGGCCGACAAAUUCCAAUGAAAGAUAUUCGCUGACACGCACGACCUCCAAGUUCACCGGACAGCAAUAAUUAGAUACCGGAUCUUUGGUCCAGAAACCAACUAUUGUCCUUAGCUCCUCUUGCCUAAAAAAGAAAGGCUGCCGAAGUUUUUAUACCCGGACAGCCUUGCCUAUUGGAGUAACCCUAUUCCGAUUCGGAUAAUAUCAGCUCCUGAAAACGAAAUAAGGGAAAAAGAUGU ....((...(((((.((........))))))).....................(((((.((((((..((.....(((((....((((((((.(((((.(((((((.(((...((((....((.....))...))))))).)))))))............((((((.......((((((........((((.....))))(((((......)))))...))))))...((...((((........))))((((((((((..((......)).))).)))))))))...))))))....))))).))))))))))))).....))...)))))).)))))..))........... (-84.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 273 233 172 134 NC_002950:PG0316|5end_seryl-tRNA_synthetase_348437..348667_POSITIVE 391 210 162 79 22 NC_002950:PG1566|5end_glutamyl-tRNA_synthetase_1647401..1647631_NEGATIVE 377 276 231 186 142 NC_002950:PG2003|5end_deoxyguanosinetriphosphate_triphosphohydrolase_2092991..2093221_NEGATIVE 375 216 171 221 170 NC_002950:PG2204|5end_hypothetical_protein_2310381..2310611_POSITIVE 366 199 155 231 183 NC_002950:PG0922|5end_hypothetical_protein_982451..982681_NEGATIVE 356 196 151 139 88 NC_002950:PG0572|5end_hypothetical_protein_627571..627801_NEGATIVE 352 109 61 159 102 NC_002950:PG0248|5end_translation_initation_factor_SUI1,_putative_281842..282072_NEGATIVE 351 106 63 53 16 NC_002950:PG1038|5end_ATP-dependent_DNA_helicase_UvrD/PcrA/Rep_Family_1102744..1102974_POSITIVE 351 75 31 62 18 NC_002950:PG0963|5end_hypothetical_protein_1024332..1024562_NEGATIVE 346 318 271 153 101 NC_002950:PG1757|5end_hypothetical_protein_1844962..1845192_NEGATIVE 346 86 41 112 68 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 345 220 173 205 153 NC_002950:PG0451|5end_CBS_domain_protein_491519..491749_POSITIVE 343 187 143 115 71 NC_002950:PG0722|5end_hypothetical_protein_774891..775121_NEGATIVE 341 110 62 68 23 NC_002950:PG1659|5end_hypothetical_protein_1743747..1743977_NEGATIVE 337 87 44 48 2 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 337 99 52 157 98 NC_002950:PG1805|5end_V-type_ATP_synthase_subunit_D_1899589..1899819_POSITIVE 334 209 161 205 142 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 333 227 181 52 2 NC_002950:PG1988|5end_hypothetical_protein_2078867..2079097_NEGATIVE 332 289 250 196 155 NC_002950:PG1683|5end_hypothetical_protein_1769644..1769874_POSITIVE 332 350 301 46 3 NC_002950:PG0903|5end_hypothetical_protein_969640..969870_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 273 233 72 34 NC_002950:PG0315|3end_50S_ribosomal_protein_L27_348417..348567_POSITIVE 433 109 66 43 1 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 430 190 142 67 22 NC_002950:PG1268|3end_hypothetical_protein_1347549..1347699_POSITIVE 360 250 203 149 89 NC_002950:PG1999|3end_hypothetical_protein_2088183..2088333_NEGATIVE 357 210 173 57 7 NC_002950:PG1410|3end_hypothetical_protein_1493436..1493586_POSITIVE 352 109 61 62 5 NC_002950:PG0249|3end_oxaloacetate_decarboxylase,_putative_281939..282089_NEGATIVE 351 106 63 53 16 NC_002950:PG1037|3end_hypothetical_protein_1102824..1102974_POSITIVE 348 106 63 69 20 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 345 103 65 46 8 NC_002950:PG2124|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2231264..2231414_POSITIVE 341 110 62 71 26 NC_002950:PG1660|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1743744..1743894_NEGATIVE 338 106 61 50 1 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 337 99 52 141 82 NC_002950:PG1804|3end_V-type_ATP_synthase_subunit_B_1899653..1899803_POSITIVE 336 211 173 124 78 NC_002950:PG1659|3end_hypothetical_protein_1743355..1743505_NEGATIVE 331 118 74 56 11 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 331 206 175 135 100 NC_002950:PG0343|3end_methionine_gamma-lyase_377181..377331_NEGATIVE 327 105 69 69 29 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 326 237 191 55 23 NC_002950:PG1010|3end_ABC_transporter,_ATP-binding_protein_1068509..1068659_NEGATIVE 325 276 234 99 41 NC_002950:PG1851|3end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1949954..1950104_NEGATIVE 324 107 75 141 104 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 323 196 151 56 11 NC_002950:PG1079|3end_enoyl-CoA_hydratase/isomerase_family_protein_1147399..1147549_POSITIVE