Origin IGS: tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctttttactcttttaggggttagtattccgaggttataagtttttgcaatttctaatgttgtgagaaatattagtattcctccatatatagacagaacaatccactgttgcagttgaggtaaatgtttctctataacatataaagtcgttacattcggtttgaagaataacacatttatctcaaaaaaactccagaatatcaaattgataaacaatgcttttttttgcttttcagaacagcaaatcagataagaaacaaggagatatgtaaatgtggtaattgaattttcaactgacataaaaagatatatgtcagacctgttttctaaaatagacagtccaaataaaatgtgcatgaatacacacactaaattggcagtaatcaagatcttcttcatttttttgctttgaggttcaatttatctttcgttgaaaataatttacatatacttttttggtatttgctctctccgctcccgattattcttctacaagaaa Mask Tandem Repeat Region ================================================ tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag Find is-nt database================================================ Query_seq: PG1505:PG1507|PG1505:PG1507:radical SAM domain protein:hypothetical protein:->->:1583262..1583759 498 tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1505:PG1507|PG1505:PG1507:radical SAM domain protein:hypothetical protein:->->:1583262..1583759 498 tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1505:PG1507|PG1505:PG1507:radical SAM domain protein:hypothetical protein:->->:1583262..1583759 498 tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 331 End: 462 .......................................................................................................................................................................................................................................................................................................................................... M L Q T E C N D F I C Y R E T F T S T A T V D C S V Y I W R N T N I S H N I R N C K N L .................................... Protein_Len: 60 Strand: + Start: 80 End: 496 ............................................................................... M E P Q S K K M K K I L I T A N L V C V F M H I L F G L S I L E N R S D I Y L F M S V E N S I T T F T Y L L V S Y L I C .. Protein_Len: 39 Strand: - Start: 250 End: 366 ......................................................................................................................................................................................................................................................... R I Q Q E S F C F F A N N I L K I N Q L K K S I F T N N K L G F T V V K Y T M .................................................................................................................................... Protein_Len: 36 Strand: - Start: 218 End: 325 ......................................................................................................................................................................................................................... N G C K C I E K N R I Q N A T R F L L F F C Q K D I Q Y E P T K K L Y M ............................................................................................................................................................................. Protein_Len: 45 Strand: - Start: 91 End: 225 .......................................................................................... L L F I F F I K I V A L K T H T N M C M K N P S D I K S F L D S M Y R K I D T S F E I V M ................................................................................................................................................................................................................................................................................. Protein_Len: 42 Strand: - Start: 2 End: 127 . E Q L L I I P L P S L L Y W F L I H L N N E V F S L N F R L A F F H L L D Q N S G M ................................................................................................................................................................................................................................................................................................................................................................................... tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag 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: 82 Start: 226 End: 255 .................................................................................................................................................................................................................................ATTTACATATCTCCTTGTTTCTTATCTGAT................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -4.0 Tail_Score: -4.89521 Start: 134 End: 149 Full_Region: ACTGCCAATTTAGTG TGTGTA TTCA TGCACA TTTTATTTGGACTGT .....................................................................................................................................TGTGTATTCATGCACA............................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 42 HP_score: -2.4 Tail_Score: -3.1676 Start: 425 End: 446 Full_Region: aagtttttgcaattt ctaatgtt gtgaga aatattag tattcctccatatat ........................................................................................................................................................................................................................................................................................................................................................................................................................................ctaatgttgtgagaaatattag.................................................... Find igs database================================================ Query_seq: PG1505:PG1507|PG1505:PG1507:radical SAM domain protein:hypothetical protein:->->:1583262..1583759 498 tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag Intra-Species Hit: Count: 1 Min: 1 Max: 498 Len: 498 Subject: NC_002950_PG1505_PG1507|radical SAM domain protein:hypothetical protein|POSITIVE:POSITIVE|[1583262,1583759]|498 HSP 1 e-value: 0.0 bit: 856.0 Len: 498 Query Start:1 Query End:498 Subject Strand: POSITIVE Subject Start: 1 Subject End: 498 tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcnnnnnnntgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcnnnnnnnngcattgtttatcaatttgatattctggagnnnnnnngagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag tttcttgtagaagaataatcgggagcggagagagcaaataccaaaaaagtatatgtaaattattttcaacgaaagataaattgaacctcaaagcaaaaaaatgaagaagatcttgattactgccaatttagtgtgtgtattcatgcacattttatttggactgtctattttagaaaacaggtctgacatatatctttttatgtcagttgaaaattcaattaccacatttacatatctccttgtttcttatctgatttgctgttctgaaaagcaaaaaaaagcattgtttatcaatttgatattctggagtttttttgagataaatgtgttattcttcaaaccgaatgtaacgactttatatgttatagagaaacatttacctcaactgcaacagtggattgttctgtctatatatggaggaatactaatatttctcacaacattagaaattgcaaaaacttataacctcggaatactaacccctaaaagagtaaaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUGUAGAAGAAUAAUCGGGAGCGGAGAGAGCAAAUACCAAAAAAGUAUAUGUAAAUUAUUUUCAACGAAAGAUAAAUUGAACCUCAAAGCAAAAAAAUGAAGAAGAUCUUGAUUACUGCCAAUUUAGUGUGUGUAUUCAUGCACAUUUUAUUUGGACUGUCUAUUUUAGAAAACAGGUCUGACAUAUAUCUUUUUAUGUCAGUUGAAAAUUCAAUUACCACAUUUACAUAUCUCCUUGUUUCUUAUCUGAUUUGCUGUUCUGAAAAGCAAAAAAAAGCAUUGUUUAUCAAUUUGAUAUUCUGGAGUUUUUUUGAGAUAAAUGUGUUAUUCUUCAAACCGAAUGUAACGACUUUAUAUGUUAUAGAGAAACAUUUACCUCAACUGCAACAGUGGAUUGUUCUGUCUAUAUAUGGAGGAAUACUAAUAUUUCUCACAACAUUAGAAAUUGCAAAAACUUAUAACCUCGGAAUACUAACCCCUAAAAGAGUAAAAAG .(((((.(((..(((((((.(((((((..((((....((((.......))))((((((((.........(....)...(((((((..((((........(((.(((.....))).))).(((((((...(((((((((....)))))))))....))))....((((...))))...)))..((((((((........))))))))))))...))))))).....)))))))).))))..))))))).......((((((.........)))))).......)))))))......(((.(((((((..(((...(((((.((((((((((((..(((.....))).)))))..(((((((...)))))))..))))))).))))).(((((..((((((......))))))...((((((((((....)))))))).))..........))))).........)))..))))))).)))...))).)))))....... (-101.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUUACUCUUUUAGGGGUUAGUAUUCCGAGGUUAUAAGUUUUUGCAAUUUCUAAUGUUGUGAGAAAUAUUAGUAUUCCUCCAUAUAUAGACAGAACAAUCCACUGUUGCAGUUGAGGUAAAUGUUUCUCUAUAACAUAUAAAGUCGUUACAUUCGGUUUGAAGAAUAACACAUUUAUCUCAAAAAAACUCCAGAAUAUCAAAUUGAUAAACAAUGCUUUUUUUUGCUUUUCAGAACAGCAAAUCAGAUAAGAAACAAGGAGAUAUGUAAAUGUGGUAAUUGAAUUUUCAACUGACAUAAAAAGAUAUAUGUCAGACCUGUUUUCUAAAAUAGACAGUCCAAAUAAAAUGUGCAUGAAUACACACACUAAAUUGGCAGUAAUCAAGAUCUUCUUCAUUUUUUUGCUUUGAGGUUCAAUUUAUCUUUCGUUGAAAAUAAUUUACAUAUACUUUUUUGGUAUUUGCUCUCUCCGCUCCCGAUUAUUCUUCUACAAGAAA ........((((.((((((...((((((.((((...(((.((((..((((.......))))..))))...))).....))))(((((..((((((..((((((((..(((((.(((((((((((((.......((((..........)))).((((........))))...))))))))))))).....((((....((((.....)))).....((((...(((((.....))))).)))).................))))...)))))..))))..)))).........((((((((........))))))))..))))))((((...)))).............)))))...))))))........((((((.(((................((((((..((...(((((.......)))))..)).))))))......((.(((((.....))))).))........))).))))))...)))))).)))).. (-95.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 36 4 66 32 NC_002950:PG0200|5end_hypothetical_protein_238351..238581_NEGATIVE 328 420 375 176 121 NC_002950:PG0903|5end_hypothetical_protein_969640..969870_NEGATIVE 323 406 361 50 4 NC_002950:PG1824|5end_phosphopyruvate_hydratase_1919430..1919660_NEGATIVE 310 40 4 54 28 NC_002950:PG1773|5end_PAP2_superfamily_protein_1859815..1860045_POSITIVE 298 42 4 54 12 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 285 49 1 67 20 NC_002950:PG2155|5end_lipoprotein,_putative_2261862..2262092_NEGATIVE 283 277 231 202 148 NC_002950:PG1383|5end_amino_acid_exporter,_putative_1462669..1462899_POSITIVE 276 274 236 52 9 NC_002950:PG1726|5end_PDZ_domain_protein_1815281..1815511_POSITIVE 274 34 4 174 136 NC_002950:PG1648|5end_RelA/SpoT_family_protein_1727762..1727992_POSITIVE 269 67 21 145 101 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 265 185 144 127 87 NC_002950:PG1184|5end_alginate_O-acetyltransferase,_putative_1266870..1267100_NEGATIVE 264 420 380 80 45 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 262 29 6 42 16 NC_002950:PG2038|5end_N-acetylmuramoyl-L-alanine_amidase,_putative_2138207..2138437_NEGATIVE 262 37 9 135 104 NC_002950:PG1712|5end_alpha-1,2-mannosidase_family_protein_1801325..1801555_NEGATIVE 259 42 19 198 174 NC_002950:PG1052|5end_transcriptional_regulator,_putative_1119690..1119920_POSITIVE 256 50 2 106 46 NC_002950:PG0470|5end_hypothetical_protein_511883..512113_NEGATIVE 255 430 381 57 2 NC_002950:PG2222|5end_acyltransferase,_HtrB/MsbB_family_2336757..2336987_POSITIVE 252 146 109 213 173 NC_002950:PG2002|5end_dihydrodipicolinate_reductase_2091587..2091817_NEGATIVE 252 138 93 166 112 NC_002950:PG1724|5end_O-sialoglycoprotein_endopeptidase_1813741..1813971_POSITIVE 252 274 237 182 146 NC_002950:PG1316|5end_hypothetical_protein_1396771..1397001_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 36 4 60 26 NC_002950:PG0201|3end_ribonuclease_P_238357..238507_NEGATIVE 298 42 4 73 31 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 286 421 382 146 99 NC_002950:PG1239|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_1313623..1313773_NEGATIVE 281 42 4 150 117 NC_002950:PG1812|3end_2-oxoglutarate_ferredoxin_oxidoreductase_1907046..1907196_NEGATIVE 278 405 366 56 14 NC_002950:PG0005|3end_hypothetical_protein_3797..3947_NEGATIVE 277 39 5 116 68 NC_002950:PG1458|3end_hypothetical_protein_1539682..1539832_POSITIVE 274 34 4 106 68 NC_002950:PG1647|3end_cardiolipin_synthetase_1727774..1727924_POSITIVE 274 39 1 101 66 NC_002950:PG1323|3end_PhoH_family_protein_1402844..1402994_POSITIVE 269 67 21 105 61 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 265 185 144 105 65 NC_002950:PG1185|3end_hypothetical_protein_1266892..1267042_NEGATIVE 262 37 9 53 22 NC_002950:PG1713|3end_lipoprotein,_putative_1801407..1801557_NEGATIVE 259 42 19 133 109 NC_002950:PG1051|3end_hypothetical_protein_1119705..1119855_POSITIVE 259 36 5 67 31 NC_002950:PG0158|3end_competence_protein_F-related_protein_180995..181145_POSITIVE 258 36 19 127 110 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 255 430 381 60 5 NC_002950:PG2221|3end_MiaB-like_tRNA_modifying_enzyme_2336840..2336990_POSITIVE 255 42 4 68 24 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 247 420 373 137 83 NC_002950:PG1467|3end_methlytransferase,_UbiE/COQ5_family_1543901..1544051_POSITIVE 246 420 380 147 98 NC_002950:PG0470|3end_hypothetical_protein_511737..511887_NEGATIVE 243 150 114 123 88 NC_002950:PG2070|3end_hypothetical_protein_2166547..2166697_POSITIVE 242 272 235 68 24 NC_002950:PG1431|3end_DNA-binding_response_regulator,_LuxR_family_1515986..1516136_NEGATIVE