Origin IGS: agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag .........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 cttgttgtgaatatatcagggggaaaatatcggcccggccatcctgccgatggaaaaaatttcttggaaatgaagaggctctttatccgaataagccgaatgctgccataaaacaaagagagaactctcgtcctctctcatcagtcctgccggcatctccgaagagagccgaaccttatctcggaaaacttatgcacctgtgaacccgaagcatcgaccggaagcgaaaaccgcctacaccggcctcttactcttggggagct Mask Tandem Repeat Region ================================================ agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag Find is-nt database================================================ Query_seq: PG2044:PG2046|PG2044:PG2046:hypothetical protein:hypothetical protein:->->:2144226..2144488 263 agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2044:PG2046|PG2044:PG2046:hypothetical protein:hypothetical protein:->->:2144226..2144488 263 agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2044:PG2046|PG2044:PG2046:hypothetical protein:hypothetical protein:->->:2144226..2144488 263 agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 108 End: 245 ........................................................................................................... M P A G L M R E D E S S L F V L W Q H S A Y S D K E P L H F Q E I F S I G R M A G P I F S P .................. Protein_Len: 38 Strand: + Start: 148 End: 261 ................................................................................................................................................... M F Y G S I R L I R I K S L F I S K K F F P S A G W P G R Y F P P D I F T T .. Protein_Len: 34 Strand: - Start: 156 End: 257 ........................................................................................................................................................... P L M R S I R I F L R K M E L F N K G D A P H G P R Y K G G S I N M ...... Protein_Len: 60 Strand: - Start: 64 End: 249 ............................................................... M L K G L Y P E A R K P S A P L V S S L P R S N E R Q K I A A N P K N P Y L A E E N G L F K K W R C S P R A S I K G R M .............. Protein_Len: 41 Strand: - Start: 2 End: 124 . S G L L L L G T Y A T K A E P R H K P N V P A Y T K R S L T R S E E S I G A P S M ........................................................................................................................................... agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag 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================================================ agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 87 HP_score: -8.6 Tail_Score: -4.77173 Start: 127 End: 146 Full_Region: CGGCAGGACTGATGA GAGAGGAC GAGA GTTCTCTC TTTGTTTTATGGCAG ..............................................................................................................................GAGAGGACGAGAGTTCTCTC..................................................................................................................... TransTerm Strand: + Conf: 78 HP_score: -4.0 Tail_Score: -5.08824 Start: 194 End: 204 Full_Region: TAAAGAGCCTCTTCA TTTC CAA GAAA TTTTTTCCATCGGCA .................................................................................................................................................................................................TTTCCAAGAAA........................................................... Find igs database================================================ Query_seq: PG2044:PG2046|PG2044:PG2046:hypothetical protein:hypothetical protein:->->:2144226..2144488 263 agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag Intra-Species Hit: Count: 1 Min: 1 Max: 263 Len: 263 Subject: NC_002950_PG2044_PG2046|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2144226,2144488]|263 HSP 1 e-value: 1.0E-147 bit: 521.0 Len: 263 Query Start:1 Query End:263 Subject Strand: POSITIVE Subject Start: 1 Subject End: 263 agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag agctccccaagagtaagaggccggtgtaggcggttttcgcttccggtcgatgcttcgggttcacaggtgcataagttttccgagataaggttcggctctcttcggagatgccggcaggactgatgagagaggacgagagttctctctttgttttatggcagcattcggcttattcggataaagagcctcttcatttccaagaaattttttccatcggcaggatggccgggccgatattttccccctgatatattcacaacaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUCCCCAAGAGUAAGAGGCCGGUGUAGGCGGUUUUCGCUUCCGGUCGAUGCUUCGGGUUCACAGGUGCAUAAGUUUUCCGAGAUAAGGUUCGGCUCUCUUCGGAGAUGCCGGCAGGACUGAUGAGAGAGGACGAGAGUUCUCUCUUUGUUUUAUGGCAGCAUUCGGCUUAUUCGGAUAAAGAGCCUCUUCAUUUCCAAGAAAUUUUUUCCAUCGGCAGGAUGGCCGGGCCGAUAUUUUCCCCCUGAUAUAUUCACAACAAG .....(((..(((((...((((((...(((((.....)))))))))))..))))).)))....((((.....(((((((..(((((.(((...((((((.((((((...(((((...(.(((..((((((((((....))))))))))..........))))..)))))...))))))...)))))).))).)))))...))))))).....((((((.((....))..))))))........))))................ (-87.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUUGUGAAUAUAUCAGGGGGAAAAUAUCGGCCCGGCCAUCCUGCCGAUGGAAAAAAUUUCUUGGAAAUGAAGAGGCUCUUUAUCCGAAUAAGCCGAAUGCUGCCAUAAAACAAAGAGAGAACUCUCGUCCUCUCUCAUCAGUCCUGCCGGCAUCUCCGAAGAGAGCCGAACCUUAUCUCGGAAAACUUAUGCACCUGUGAACCCGAAGCAUCGACCGGAAGCGAAAACCGCCUACACCGGCCUCUUACUCUUGGGGAGCU .................(((.((......(((((.((((......))))..............(((((..(((((.....))))))))))....)))))..(((.((.........((((((.((....)).)))))).....(((.(((((((.((((....)))))))).........((((...((..........))....)))).)))..))).)).))).....)).))).....(((((((.......)))).))) (-67.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 459 150 103 59 1 NC_002950:PG1791|5end_hypothetical_protein_1881166..1881396_NEGATIVE 448 54 11 58 18 NC_002950:PG1386|5end_DNA_gyrase,_A_subunit_1468948..1469178_NEGATIVE 444 69 22 53 7 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 439 59 16 165 122 NC_002950:PG1274|5end_elongation_factor_P_1351843..1352073_POSITIVE 439 59 16 165 122 NC_002950:PG0568|5end_elongation_factor_P_624565..624795_NEGATIVE 439 60 16 226 181 NC_002950:PG0413|5end_hypothetical_protein_451781..452011_NEGATIVE 436 59 11 162 120 NC_002950:PG0344|5end_purple_acid_phosphatase_380012..380242_NEGATIVE 432 69 21 226 178 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 425 70 22 85 40 NC_002950:PG1846|5end_hypothetical_protein_1946037..1946267_POSITIVE 421 60 11 213 148 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 416 60 11 194 138 NC_002950:PG1587|5end_PAP2_superfamily_protein_1664983..1665213_POSITIVE 412 69 21 59 3 NC_002950:PG1998|5end_polyprenyl_synthetase_2088029..2088259_NEGATIVE 410 129 81 70 7 NC_002950:PG0099|5end_phenylalanyl-tRNA_synthetase_beta_subunit_118286..118516_NEGATIVE 406 58 16 223 167 NC_002950:PG1993|5end_excinuclease_ABC,_C_subunit_2083321..2083551_POSITIVE 406 69 21 51 7 NC_002950:PG1622|5end_DNA_topoisomerase_IV_subunit_A_1704114..1704344_NEGATIVE 406 138 91 228 168 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 406 60 18 62 5 NC_002950:PG0444|5end_oligopeptide_transporter,_OPT_family_483256..483486_POSITIVE 403 186 141 191 143 NC_002950:PG1961|5end_hypothetical_protein_2051153..2051383_NEGATIVE 403 70 23 163 117 NC_002950:PG1476|5end_conjugative_transposon_protein_TraM_1553219..1553449_NEGATIVE 402 60 17 60 16 NC_002950:PG1731|5end_3-dehydroquinate_dehydratase_1820103..1820333_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 448 68 22 150 98 NC_002950:PG0020|3end_transcriptional_regulator,_MarR_family_24166..24316_POSITIVE 443 70 23 112 55 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 439 137 96 111 54 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 432 69 21 125 77 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 428 63 23 146 100 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 412 70 21 127 69 NC_002950:PG0159|3end_endopeptidase_PepO_181095..181245_NEGATIVE 408 70 22 117 65 NC_002950:PG1013|3end_acetyl-CoA_hydrolase/transferase_family_protein_1073310..1073460_POSITIVE 405 47 1 85 32 NC_002950:PG1020|3end_hypothetical_protein_1083458..1083608_POSITIVE 404 70 22 102 46 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 399 60 13 80 24 NC_002950:PG1757|3end_hypothetical_protein_1843931..1844081_NEGATIVE 397 59 11 123 66 NC_002950:PG0085|3end_alpha-galactosidase_100556..100706_POSITIVE 396 46 2 148 108 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 394 58 11 114 71 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 392 65 22 141 92 NC_002950:PG1052|3end_transcriptional_regulator,_putative_1120126..1120276_POSITIVE 389 57 13 103 49 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 389 139 91 53 12 NC_002950:PG0082|3end_hypothetical_protein_97026..97176_POSITIVE 385 57 12 63 26 NC_002950:PG1724|3end_O-sialoglycoprotein_endopeptidase_1814846..1814996_POSITIVE 385 57 16 39 1 NC_002950:PG0768|3end_hypothetical_protein_821275..821425_NEGATIVE 383 58 11 71 16 NC_002950:PG2212|3end_hypothetical_protein_2324483..2324633_NEGATIVE 383 80 31 50 4 NC_002950:PG0569|3end_hypothetical_protein_624697..624847_NEGATIVE