Origin IGS: tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat .........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 atcgaacacaaataagtctttgattaagactttaacacaaacgggaaatgccgagctcacctcattcgatgatggaaagaccggctccgtcgtgccaaagataatagttcatccgccacatgaacagatttgaccgtttgaagagatccacctcatcagaattcgagtaacatcttaaggtgctcaatattgaaaacagccttaaagaagcatttcttcacagaggccctcttttgcatggcaatatgttaagattctgagcagagttgtttttacgtactagattcaaatcaaaatgcaagcaattttcgatactctaataacttcgaacaggctcgtagaatgtgcaccggcgcgtaaaaaaaaggcttatccgaatgaattgcgtaaatttgtggcagtaaa Mask Tandem Repeat Region ================================================ tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat Find is-nt database================================================ Query_seq: PG1308:PG1310|PG1308:PG1310:hypothetical protein:exsB protein:<-->:1388819..1389223 405 tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1308:PG1310|PG1308:PG1310:hypothetical protein:exsB protein:<-->:1388819..1389223 405 tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1308:PG1310|PG1308:PG1310:hypothetical protein:exsB protein:<-->:1388819..1389223 405 tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 5 End: 112 .... M P Q I Y A I H S D K P F F Y A P V H I L R A C S K L L E Y R K L L A F ..................................................................................................................................................................................................................................................................................................... Protein_Len: 31 Strand: + Start: 93 End: 185 ............................................................................................ M E N C L H F D L N L V R K N N S A Q N L N I L P C K R G P L ............................................................................................................................................................................................................................ Protein_Len: 45 Strand: + Start: 207 End: 341 .............................................................................................................................................................................................................. M F S I L S T L R C Y S N S D E V D L F K R S N L F M W R M N Y Y L W H D G A G L S I I E ................................................................ Protein_Len: 35 Strand: + Start: 301 End: 405 ............................................................................................................................................................................................................................................................................................................ M I F G T T E P V F P S S N E V S S A F P V C V K V L I K D L F V F D Protein_Len: 37 Strand: - Start: 276 End: 386 ................................................................................................................................................................................................................................................................................... I Q E H P P H V I I K P V V S G T K G D D F S T L E A N G T Q T L T K I M ................... Protein_Len: 40 Strand: - Start: 3 End: 122 .. V A V F K R L E N P Y A K K K R A P A C E V L R N S T I L T D F I A Q M K I Q M ........................................................................................................................................................................................................................................................................................... tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat 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================================================ tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -3.4 Tail_Score: -3.63589 Start: 187 End: 199 Full_Region: AAAGAGGGCCTCTGT GAAG AAATG CTTC TTTAAGGCTGTTTTC ..........................................................................................................................................................................................GAAGAAATGCTTC.............................................................................................................................................................................................................. Find igs database================================================ Query_seq: PG1308:PG1310|PG1308:PG1310:hypothetical protein:exsB protein:<-->:1388819..1389223 405 tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat Intra-Species Hit: Count: 1 Min: 1 Max: 405 Len: 405 Subject: NC_002950_PG1308_PG1310|hypothetical protein:exsB protein|NEGATIVE:POSITIVE|[1388819,1389223]|405 HSP 1 e-value: 0.0 bit: 755.0 Len: 405 Query Start:1 Query End:405 Subject Strand: POSITIVE Subject Start: 1 Subject End: 405 tttactgccacaaatttacgcaattcattcggataagccnnnnnnnnacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat tttactgccacaaatttacgcaattcattcggataagccttttttttacgcgccggtgcacattctacgagcctgttcgaagttattagagtatcgaaaattgcttgcattttgatttgaatctagtacgtaaaaacaactctgctcagaatcttaacatattgccatgcaaaagagggcctctgtgaagaaatgcttctttaaggctgttttcaatattgagcaccttaagatgttactcgaattctgatgaggtggatctcttcaaacggtcaaatctgttcatgtggcggatgaactattatctttggcacgacggagccggtctttccatcatcgaatgaggtgagctcggcatttcccgtttgtgttaaagtcttaatcaaagacttatttgtgttcgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACUGCCACAAAUUUACGCAAUUCAUUCGGAUAAGCCUUUUUUUUACGCGCCGGUGCACAUUCUACGAGCCUGUUCGAAGUUAUUAGAGUAUCGAAAAUUGCUUGCAUUUUGAUUUGAAUCUAGUACGUAAAAACAACUCUGCUCAGAAUCUUAACAUAUUGCCAUGCAAAAGAGGGCCUCUGUGAAGAAAUGCUUCUUUAAGGCUGUUUUCAAUAUUGAGCACCUUAAGAUGUUACUCGAAUUCUGAUGAGGUGGAUCUCUUCAAACGGUCAAAUCUGUUCAUGUGGCGGAUGAACUAUUAUCUUUGGCACGACGGAGCCGGUCUUUCCAUCAUCGAAUGAGGUGAGCUCGGCAUUUCCCGUUUGUGUUAAAGUCUUAAUCAAAGACUUAUUUGUGUUCGAU ....((((((((..................((((..(((((.((((((((..(..(..((.(((...(((((...(((((..((.....))..)))))....)))))......))).))...)..)..)))))))).........((((((((.((((((.((((...))))..((((..(((..((((((...((((.....))))..)))))).....)))..))))...))))))...).))))))).)))))..)))).....(((((......)))))..))))))))..((((.........(((((((((((.((((..(((.((.((((...)))))).)))..)))).....))).))))))))(((((((.....)))))))......))))... (-104.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGAACACAAAUAAGUCUUUGAUUAAGACUUUAACACAAACGGGAAAUGCCGAGCUCACCUCAUUCGAUGAUGGAAAGACCGGCUCCGUCGUGCCAAAGAUAAUAGUUCAUCCGCCACAUGAACAGAUUUGACCGUUUGAAGAGAUCCACCUCAUCAGAAUUCGAGUAACAUCUUAAGGUGCUCAAUAUUGAAAACAGCCUUAAAGAAGCAUUUCUUCACAGAGGCCCUCUUUUGCAUGGCAAUAUGUUAAGAUUCUGAGCAGAGUUGUUUUUACGUACUAGAUUCAAAUCAAAAUGCAAGCAAUUUUCGAUACUCUAAUAACUUCGAACAGGCUCGUAGAAUGUGCACCGGCGCGUAAAAAAAAGGCUUAUCCGAAUGAAUUGCGUAAAUUUGUGGCAGUAAA ...((((......(((((((.....)))))))...(((..(((((....((((..((..((((((...)))).))..))..))))))))).)))............))))....((((((..(((..((((((...(((((.(((......))).)))))..))))))............((((((............(((((...((((.....))))...)))))..((((..(((((....))))).))))...))))))..)))...(((((((....((((((........(((.(((....(((((.............)))))...))).)))..((((((....))))))....................)))))))))))))..))))))...... (-98.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 985 80 31 171 122 NC_002950:PG1308|5end_hypothetical_protein_1388728..1388958_NEGATIVE 396 327 281 46 1 NC_002950:PG2171|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278972..2279202_NEGATIVE 382 339 291 56 6 NC_002950:PG1678|5end_hypothetical_protein_1763862..1764092_NEGATIVE 379 358 311 174 127 NC_002950:PG2097|5end_ribose-phosphate_pyrophosphokinase_2206462..2206692_NEGATIVE 378 356 311 168 116 NC_002950:PG1875|5end_hemolysin_1970621..1970851_NEGATIVE 378 79 32 56 5 NC_002950:PG1657|5end_methylmalonyl-CoA_mutase_1739344..1739574_POSITIVE 378 357 317 104 58 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 375 360 311 195 125 NC_002950:PG0359|5end_flavin_reductase_domain_protein_392851..393081_POSITIVE 371 84 52 82 45 NC_002950:PG0753|5end_protease_798301..798531_POSITIVE 360 356 311 115 58 NC_002950:PG0017|5end_sensor_histidine_kinase_18307..18537_POSITIVE 358 356 311 177 132 NC_002950:PG0776|5end_electron_transfer_flavoprotein,_alpha_subunit_830184..830414_NEGATIVE 358 370 323 149 91 NC_002950:PG0746|5end_sensor_histidine_kinase_793903..794133_NEGATIVE 357 340 291 80 32 NC_002950:PG1214|5end_hypothetical_protein_1293032..1293262_POSITIVE 356 327 281 225 164 NC_002950:PG2110|5end_thiamine_biosynthesis_protein_ThiC_2221212..2221442_NEGATIVE 356 79 37 165 124 NC_002950:PG0811|5end_Holliday_junction_DNA_helicase_motor_protein_873209..873439_NEGATIVE 355 370 321 230 165 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 354 349 311 70 31 NC_002950:PG1290|5end_branched-chain_amino_acid_aminotransferase_1368253..1368483_POSITIVE 351 356 312 198 147 NC_002950:PG2154|5end_hypothetical_protein_2260945..2261175_NEGATIVE 351 359 311 55 7 NC_002950:PG1163|5end_cobyrinic_acid_a,c-diamide_synthase_1243381..1243611_NEGATIVE 351 92 55 39 3 NC_002950:PG0770|5end_hypothetical_protein_824575..824805_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 385 209 162 121 79 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 378 359 311 126 64 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 371 84 52 98 61 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 360 356 311 104 47 NC_002950:PG0016|3end_sigma-54_dependent_DNA-binding_response_regulator_18376..18526_POSITIVE 358 366 323 149 97 NC_002950:PG1715|3end_hypothetical_protein_1803393..1803543_NEGATIVE 357 340 291 131 83 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 357 367 321 139 78 NC_002950:PG1115|3end_signal_recognition_particle_protein_1188887..1189037_POSITIVE 354 370 322 63 14 NC_002950:PG0959|3end_ATP-binding_protein,_Mrp/Nbp35_family_1020023..1020173_NEGATIVE 352 356 313 138 94 NC_002950:PG1954|3end_NAD_dependent_epimerase/reductase-related_protein_2045612..2045762_POSITIVE 352 355 317 81 37 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 347 368 322 145 95 NC_002950:PG0221|3end_hypothetical_protein_255613..255763_NEGATIVE 336 370 321 148 106 NC_002950:PG1750|3end_alpha-1,3/4-fucosidase,_putative_1837223..1837373_POSITIVE 335 364 321 58 4 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 334 368 322 49 8 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 332 370 321 130 79 NC_002950:PG0068|3end_hypothetical_protein_82079..82229_POSITIVE 331 370 321 134 82 NC_002950:PG2085|3end_tryptophanyl-tRNA_synthetase_2186595..2186745_POSITIVE 331 369 323 151 94 NC_002950:PG0747|3end_sigma-54_dependent_DNA-binding_response_regulator_793900..794050_NEGATIVE 328 348 310 50 17 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 326 369 322 131 74 NC_002950:PG0788|3end_hypothetical_protein_838043..838193_NEGATIVE 326 313 277 77 48 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE