Origin IGS: ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc .........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 gcgcgtattttccccaaaaatcgcaccgcaatctcatcatttttcgttcgtgatttctctgtaagcgactacttttcgacggaatttcttcacctttttccatgagcggaaatatatagaatagatacatgtttgctcccttgaggcaaataataccaaagaagaatgccatccgacttgctccttgatacttgtcgccgtttcccgacagttgcggggaggtccgaatgtggaaaatcgacatggtcttttaaacttatttctcttttcctctctatttcagttgtagggtaaatcgtaaaataccatttcggagaatgggaacgatagcacctatttttcttttcaaacttttcttatgcgatcgatttatcaattactgttgtcaatactccttgcttctcttggtttcgtcgggctggaagcccaacaagccggagtagcaggtagagtattggacgaagaaggcaacccc Mask Tandem Repeat Region ================================================ ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc Find is-nt database================================================ Query_seq: PG1715:PG1718|PG1715:PG1718:hypothetical protein:hypothetical protein:<-<-:1806147..1806621 475 ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1715:PG1718|PG1715:PG1718:hypothetical protein:hypothetical protein:<-<-:1806147..1806621 475 ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1715:PG1718|PG1715:PG1718:hypothetical protein:hypothetical protein:<-<-:1806147..1806621 475 ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 5 End: 100 .... M P S S S N T L P A T P A C W A S S P T K P R E A R S I D N S N ....................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 21 End: 116 .................... M L Y L L L R L V G L P A R R N Q E K Q G V L T T V I D K S I A ....................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 100 End: 198 ................................................................................................... M I N R S H K K S L K R K I G A I V P I L R N G I L R F T L Q L K ..................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 180 End: 383 ................................................................................................................................................................................... M Y P T T E I E R K R E I S L K D H V D F P H S D L P A T V G K R R Q V S R S K S D G I L L W Y Y L P Q G S K H V S I L ............................................................................................ Protein_Len: 50 Strand: + Start: 287 End: 436 .............................................................................................................................................................................................................................................................................................. M K E Q V G W H S S L V L F A S R E Q T C I Y S I Y F R S W K K V K K F R R K V V A Y R E I T N E K ....................................... Protein_Len: 60 Strand: + Start: 232 End: 474 ....................................................................................................................................................................................................................................... M S I F H I R T S P Q L S G N G D K Y Q G A S R M A F F F G I I C L K G A N M Y L F Y I F P L M E K G E E I P S K S S R . Protein_Len: 32 Strand: - Start: 374 End: 469 ..................................................................................................................................................................................................................................................................................................................................................................................... P F L H L F E T S F Y D S V S F D R V F F S S I A T R N K P F M ...... Protein_Len: 54 Strand: - Start: 190 End: 351 ............................................................................................................................................................................................. L Q F L S S F L F L N L L G H R N E V N P G G R L Q R S V A V L I L S C T P H C E E K T N N A E L S C V H M ............................................................................................................................ Protein_Len: 42 Strand: - Start: 185 End: 310 ........................................................................................................................................................................................ G V V S I S L F L S I L K F S W T S K G C E S R G A V T P F R R C T D L L L D S P M ..................................................................................................................................................................... Protein_Len: 46 Strand: - Start: 36 End: 173 ................................... E P K N P K W G S S V L L L L S Y Q C C Y N I F R D C L F L K F L F I P A I T G M R R F P M .............................................................................................................................................................................................................................................................................................................. Protein_Len: 56 Strand: - Start: 1 End: 168 P N G E E D L V R G A V G A Q Q A E L G V F G L S A L L I S L L L Q Y I S R M L F T Q F S F Y T S D N G N E S M ................................................................................................................................................................................................................................................................................................................... ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc 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================================================ ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1715:PG1718|PG1715:PG1718:hypothetical protein:hypothetical protein:<-<-:1806147..1806621 475 ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc Intra-Species Hit: Count: 1 Min: 1 Max: 475 Len: 475 Subject: NC_002950_PG1715_PG1718|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1806147,1806621]|475 HSP 1 e-value: 0.0 bit: 942.0 Len: 475 Query Start:1 Query End:475 Subject Strand: POSITIVE Subject Start: 1 Subject End: 475 ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc ggggttgccttcttcgtccaatactctacctgctactccggcttgttgggcttccagcccgacgaaaccaagagaagcaaggagtattgacaacagtaattgataaatcgatcgcataagaaaagtttgaaaagaaaaataggtgctatcgttcccattctccgaaatggtattttacgatttaccctacaactgaaatagagaggaaaagagaaataagtttaaaagaccatgtcgattttccacattcggacctccccgcaactgtcgggaaacggcgacaagtatcaaggagcaagtcggatggcattcttctttggtattatttgcctcaagggagcaaacatgtatctattctatatatttccgctcatggaaaaaggtgaagaaattccgtcgaaaagtagtcgcttacagagaaatcacgaacgaaaaatgatgagattgcggtgcgatttttggggaaaatacgcgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGUUGCCUUCUUCGUCCAAUACUCUACCUGCUACUCCGGCUUGUUGGGCUUCCAGCCCGACGAAACCAAGAGAAGCAAGGAGUAUUGACAACAGUAAUUGAUAAAUCGAUCGCAUAAGAAAAGUUUGAAAAGAAAAAUAGGUGCUAUCGUUCCCAUUCUCCGAAAUGGUAUUUUACGAUUUACCCUACAACUGAAAUAGAGAGGAAAAGAGAAAUAAGUUUAAAAGACCAUGUCGAUUUUCCACAUUCGGACCUCCCCGCAACUGUCGGGAAACGGCGACAAGUAUCAAGGAGCAAGUCGGAUGGCAUUCUUCUUUGGUAUUAUUUGCCUCAAGGGAGCAAACAUGUAUCUAUUCUAUAUAUUUCCGCUCAUGGAAAAAGGUGAAGAAAUUCCGUCGAAAAGUAGUCGCUUACAGAGAAAUCACGAACGAAAAAUGAUGAGAUUGCGGUGCGAUUUUUGGGGAAAAUACGCGC ......((..(((.(((((((((((((...((((.(((.((.(((((((((.....)))))))))..))..))).)))).)))))))))......(..(((((....)))))..).........(((((..........((((((((((.((((((....((((((..((((..........))))..................((((((..((.....(((.....)))....))..))))))...))))))..((((.((....)).))))...(((((..((((((((((((.(((((....))).)).))))))))))))..)))))....)))))).............((((.(((.((((((....))))))...))).)))).............)))).))))))..((....)).))))).......)))))))..)).(((((((((((...)))))).))))) (-129.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGCGUAUUUUCCCCAAAAAUCGCACCGCAAUCUCAUCAUUUUUCGUUCGUGAUUUCUCUGUAAGCGACUACUUUUCGACGGAAUUUCUUCACCUUUUUCCAUGAGCGGAAAUAUAUAGAAUAGAUACAUGUUUGCUCCCUUGAGGCAAAUAAUACCAAAGAAGAAUGCCAUCCGACUUGCUCCUUGAUACUUGUCGCCGUUUCCCGACAGUUGCGGGGAGGUCCGAAUGUGGAAAAUCGACAUGGUCUUUUAAACUUAUUUCUCUUUUCCUCUCUAUUUCAGUUGUAGGGUAAAUCGUAAAAUACCAUUUCGGAGAAUGGGAACGAUAGCACCUAUUUUUCUUUUCAAACUUUUCUUAUGCGAUCGAUUUAUCAAUUACUGUUGUCAAUACUCCUUGCUUCUCUUGGUUUCGUCGGGCUGGAAGCCCAACAAGCCGGAGUAGCAGGUAGAGUAUUGGACGAAGAAGGCAACCCC ..((.(.(((((.....((((((...((((.((((....(((..((((((.((((((((((((((((((......((((((((..((((((.....(((((......))))).................((((((((.......))))))))........)))))).....)))).........)))).....))))).(((....)))..)))))))))))))))))))..)))...(((.(((((.(((((...................((((((.......)))))).......))))).))))).)))))))..(((((.(((((...))))).)))))...............))))..))))))..............(((((((((((((((.((((.(((((.((.((((.....)))).))))))))))).))))))..)))))))))..)))))).))...... (-126.17) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1067 70 21 161 112 NC_002950:PG1715|5end_hypothetical_protein_1806056..1806286_NEGATIVE 433 50 1 231 195 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 376 42 1 97 52 NC_002950:PG0955|5end_hypothetical_protein_1014832..1015062_POSITIVE 376 49 1 113 65 NC_002950:PG0065|5end_efflux_transporter,_RND_family,_MFP_subunit_81187..81417_NEGATIVE 375 59 13 214 156 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 373 300 251 178 118 NC_002950:PG1584|5end_batC_protein_1661331..1661561_POSITIVE 371 307 261 80 24 NC_002950:PG0778|5end_hypothetical_protein_831869..832099_NEGATIVE 370 49 1 197 149 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 365 309 264 143 102 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 364 297 251 149 98 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 363 338 291 200 139 NC_002950:PG0990|5end_ribosomal_protein_L35_1051356..1051586_NEGATIVE 361 86 43 51 8 NC_002950:PG0126|5end_type_I_phosphodiesterase/nucleotide_pyrophosphatase_family_protein_148018..148248_NEGATIVE 359 59 12 59 25 NC_002950:PG0714|5end_copper_homeostasis_protein_CutC_768671..768901_NEGATIVE 356 78 33 190 134 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 354 339 291 201 154 NC_002950:PG1738|5end_hypothetical_protein_1825131..1825361_NEGATIVE 354 298 252 102 29 NC_002950:PG0771|5end_hypothetical_protein_824524..824754_POSITIVE 352 78 33 65 11 NC_002950:PG1363|5end_hypothetical_protein_1443804..1444034_POSITIVE 352 279 233 166 111 NC_002950:PG0926|5end_hypothetical_protein_984634..984864_NEGATIVE 351 289 249 62 15 NC_002950:PG0226|5end_transglutaminase-related_protein_262531..262761_NEGATIVE 350 59 11 49 1 NC_002950:PG1486|5end_conjugative_transposon_protein_TraA_1561166..1561396_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 433 50 1 130 94 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 374 269 229 141 96 NC_002950:PG0731|3end_hypothetical_protein_782020..782170_NEGATIVE 369 59 14 128 83 NC_002950:PG0344|3end_purple_acid_phosphatase_378543..378693_NEGATIVE 363 338 291 122 61 NC_002950:PG0991|3end_translation_initiation_factor_IF-3_1051434..1051584_NEGATIVE 359 59 12 54 20 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 355 75 39 149 104 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 354 50 2 137 88 NC_002950:PG1276|3end_DNA-binding_protein,_histone-like_family_1353531..1353681_POSITIVE 354 50 2 137 88 NC_002950:PG0566|3end_DNA-binding_protein,_histone-like_family_622935..623085_NEGATIVE 345 283 250 62 28 NC_002950:PG0670|3end_lipoprotein,_putative_721971..722121_POSITIVE 342 50 1 147 82 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE 341 279 231 141 97 NC_002950:PG0520|3end_chaperonin_GroEL_563618..563768_NEGATIVE 339 297 260 63 19 NC_002950:PG0683|3end_ABC_transporter,_permease_protein,_putative_737701..737851_POSITIVE 337 50 1 120 45 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 337 308 261 73 21 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 335 58 12 49 1 NC_002950:PG2213|3end_nitrite_reductase-related_protein_2324848..2324998_NEGATIVE 331 77 39 67 23 NC_002950:PG1751|3end_aminotransferase,_class_V_1838490..1838640_POSITIVE 329 283 246 81 26 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 325 61 29 137 110 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 324 299 253 147 93 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 324 310 268 65 25 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE