Origin IGS: accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgataaaaaaacaaaataaaaacatttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca .........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 tgcgacaaatctgccgtttcgctgtaatgccgttgcaatgaaagtacagacgcatttacactcgttttcggtataagtcagaagaaaacatactgctatctaaaactttacatacttgacgttattctatgcggcgttgggcttctagccttaaaaatcaacattttagcaccattctgtaagcataaaagcagaatggtatacatatcgtgagcagtcattcaagggcgaaatgtttttattttgtttttttatcgctaaatattttgccaattcaataattatatagacctttacaccaaaatctaaccataaataaaaacaaagaaataattctatggaagaacaaatcgaagtgaaagagcttgaacacgttgtagtgttgttctctggagactcgggtgatggt Mask Tandem Repeat Region ================================================ accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgataaaaaaacaaaataaaaacatttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca Find is-nt database================================================ Query_seq: PI0178:PI0179|PI0178:PI0179:2-oxoglutarate synthase, subunit korA:hypothetical protein:->->:171488..171896 409 accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgataaaaaaacaaaataaaaacatttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0178:PI0179|PI0178:PI0179:2-oxoglutarate synthase, subunit korA:hypothetical protein:->->:171488..171896 409 accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgataaaaaaacaaaataaaaacatttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0178:PI0179|PI0178:PI0179:2-oxoglutarate synthase, subunit korA:hypothetical protein:->->:171488..171896 409 accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgataaaaaaacaaaataaaaacatttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgataaaaaaacaaaataaaaacatttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 4 End: 132 ... M T R V S R E Q H Y N V F K L F H F D L F F H R I I S L F L F M V R F W C K G L Y N Y ..................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 59 End: 241 .......................................................... M C S S I E L F L C F Y L W L D F G V K V Y I I I E L A K Y L A I K K Q N K N I S P L N D C S R Y V Y H S A F M L T E W ........................................................................................................................................................................ Protein_Len: 37 Strand: + Start: 189 End: 299 ............................................................................................................................................................................................ M T A H D M Y T I L L L C L Q N G A K M L I F K A R S P T P H R I T S S M .............................................................................................................. Protein_Len: 33 Strand: + Start: 311 End: 409 ...................................................................................................................................................................................................................................................................................................................... M A V C F L L T Y T E N E C K C V C T F I A T A L Q R N G R F V A Protein_Len: 46 Strand: - Start: 200 End: 337 ....................................................................................................................................................................................................... S I Y V M R S K H K C F P A L I N I K L A L L G V G C L I V D L I Y L K L Y C Y T K K Q S M ........................................................................ Protein_Len: 34 Strand: - Start: 124 End: 225 ........................................................................................................................... I I I S N A F Y K A I F F C F L F M E G K F S Q E R Y T Y W E A K M ........................................................................................................................................................................................ accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgataaaaaaacaaaataaaaacatttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca 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================================================ accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgataaaaaaacaaaataaaaacatttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -2.7 Tail_Score: -5.4182 Start: 70 End: 87 Full_Region: TTCGATTTGTTCTTC CATAGAA TTAT TTCTTTG TTTTTATTTATGGTT .....................................................................CATAGAATTATTTCTTTG.................................................................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: PI0178:PI0179|PI0178:PI0179:2-oxoglutarate synthase, subunit korA:hypothetical protein:->->:171488..171896 409 accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgataaaaaaacaaaataaaaacatttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca Intra-Species Hit: Count: 1 Min: 1 Max: 409 Len: 409 Subject: pint_PI0178_PI0179|2-oxoglutarate synthase, subunit korA:hypothetical protein|POSITIVE:POSITIVE|[171488,171896]|409 HSP 1 e-value: 1.0E-130 bit: 466.0 Len: 235 Query Start:175 Query End:409 Subject Strand: POSITIVE Subject Start: 175 Subject End: 409 ..............................................................................................................................................................................catttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca ..............................................................................................................................................................................catttcgcccttgaatgactgctcacgatatgtataccattctgcttttatgcttacagaatggtgctaaaatgttgatttttaaggctagaagcccaacgccgcatagaataacgtcaagtatgtaaagttttagatagcagtatgttttcttctgacttataccgaaaacgagtgtaaatgcgtctgtactttcattgcaacggcattacagcgaaacggcagatttgtcgca HSP 2 e-value: 4.0E-83 bit: 309.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgat............................................................................................................................................................................................................................................................. accatcacccgagtctccagagaacaacactacaacgtgttcaagctctttcacttcgatttgttcttccatagaattatttctttgtttttatttatggttagattttggtgtaaaggtctatataattattgaattggcaaaatatttagcgat............................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAUCACCCGAGUCUCCAGAGAACAACACUACAACGUGUUCAAGCUCUUUCACUUCGAUUUGUUCUUCCAUAGAAUUAUUUCUUUGUUUUUAUUUAUGGUUAGAUUUUGGUGUAAAGGUCUAUAUAAUUAUUGAAUUGGCAAAAUAUUUAGCGAUAAAAAAACAAAAUAAAAACAUUUCGCCCUUGAAUGACUGCUCACGAUAUGUAUACCAUUCUGCUUUUAUGCUUACAGAAUGGUGCUAAAAUGUUGAUUUUUAAGGCUAGAAGCCCAACGCCGCAUAGAAUAACGUCAAGUAUGUAAAGUUUUAGAUAGCAGUAUGUUUUCUUCUGACUUAUACCGAAAACGAGUGUAAAUGCGUCUGUACUUUCAUUGCAACGGCAUUACAGCGAAACGGCAGAUUUGUCGCA .........(((((((((.((((((((((.....(((((((..(((((.((((...(((..((((.......((((....))))((((((((..((((.(((((((.((..(((.....((.(((....))).))....))).)).))))))).))))))))))))......))))..)))....)))).))..)))...))))))).((((((((((............))))))))))......))))).)))))..(((.....)))....((((....((......))..(((((.(((((..(((((.(((........((....)).((((((((....)).)))))).)))))))).))))))).)))..)))).............)).)))))))..... (-85.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCGACAAAUCUGCCGUUUCGCUGUAAUGCCGUUGCAAUGAAAGUACAGACGCAUUUACACUCGUUUUCGGUAUAAGUCAGAAGAAAACAUACUGCUAUCUAAAACUUUACAUACUUGACGUUAUUCUAUGCGGCGUUGGGCUUCUAGCCUUAAAAAUCAACAUUUUAGCACCAUUCUGUAAGCAUAAAAGCAGAAUGGUAUACAUAUCGUGAGCAGUCAUUCAAGGGCGAAAUGUUUUUAUUUUGUUUUUUUAUCGCUAAAUAUUUUGCCAAUUCAAUAAUUAUAUAGACCUUUACACCAAAAUCUAACCAUAAAUAAAAACAAAGAAAUAAUUCUAUGGAAGAACAAAUCGAAGUGAAAGAGCUUGAACACGUUGUAGUGUUGUUCUCUGGAGACUCGGGUGAUGGU ((((.....((((...(((((.((((((...)))))).)))))...))))))))....((((((.....(((.((((((....(((.....((((((..((((((............(((((..(.....)..))))).(((.....))).............)))))).((((((((((..........))))))))))............))))))..)))...((((((((((((......((......)).....)))))))))))).................)))..))).))).................................(((((.((((.((((...(((.(((............))).)))...)))).)))).)))))...))))))..... (-86.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 400 355 70 18 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 340 396 356 60 22 pint:PI0581|5end_conserved_hypothetical_protein_525055..525285_POSITIVE 332 400 357 183 137 pint:PI0956|5end_conserved_hypothetical_protein_886077..886307_POSITIVE 332 400 356 67 30 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 323 359 311 188 127 pint:PI0522|5end_50S_ribosomal_protein_L19_479004..479234_POSITIVE 323 359 311 70 9 pint:PI0521|5end_hypothetical_protein_478886..479116_POSITIVE 315 395 358 68 26 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 309 297 261 93 49 pint:PI0750|5end_zinc_protease_677746..677976_POSITIVE 298 400 359 201 153 pint:PI0656|5end_peptidase_T_(tripeptide_aminopeptidase)_599833..600063_POSITIVE 296 400 351 161 113 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 292 274 232 230 184 pint:PI0582|5end_hypothetical_protein_524853..525083_POSITIVE 291 398 356 215 165 pint:PI0609|5end_conserved_hypothetical_protein_556519..556749_POSITIVE 287 397 353 65 20 pint:PI0958|5end_G:T/U_mismatch-specific_DNA_glycosylase_889911..890141_POSITIVE 286 240 193 144 98 pint:PI2133|5end_collagenase_2081106..2081336_POSITIVE 286 220 181 140 95 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 285 396 356 225 170 pint:PI1745|5end_conserved_hypothetical_protein_1666615..1666845_POSITIVE 281 398 355 231 186 pint:PI0046|5end_thiamine_monophosphate_synthase_(thiamine-phosphate_pyrophosphorylase)_45353..45583_POSITIVE 280 291 259 98 52 pint:PI1429|5end_L-aspartate_oxidase_1347650..1347880_POSITIVE 279 391 355 175 142 pint:PI1884|5end_conserved_hypothetical_protein_1826883..1827113_POSITIVE 279 48 2 101 51 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 400 354 141 92 pint:PI0425|3end_hypothetical_protein_389722..389872_POSITIVE 340 400 355 80 28 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 340 396 356 139 101 pint:PI0582|3end_hypothetical_protein_525214..525364_POSITIVE 332 400 357 110 64 pint:PI0955|3end_conserved_hypothetical_protein_886084..886234_POSITIVE 332 400 356 62 25 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 318 244 211 33 1 pint:PI0421|3end_hypothetical_protein_387774..387924_POSITIVE 300 392 356 97 52 pint:PI2041|3end_conserved_hypothetical_protein_1994660..1994810_POSITIVE 298 359 316 55 1 pint:PI0520|3end_hypothetical_protein_478951..479101_POSITIVE 287 397 353 61 16 pint:PI0957|3end_conserved_hypothetical_protein_889987..890137_POSITIVE 286 240 193 97 51 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 285 396 356 150 95 pint:PI1744|3end_chromosome_partitioning_protein_1666620..1666770_POSITIVE 280 291 259 63 17 pint:PI1428|3end_quinolinate_synthetase_A_1347695..1347845_POSITIVE 276 397 356 146 92 pint:PI1512|3end_hypothetical_protein_1429893..1430043_POSITIVE 275 50 1 127 90 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 274 399 355 64 21 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 273 396 357 55 12 pint:PI0526|3end_hypothetical_protein_482439..482589_POSITIVE 271 399 366 65 27 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 270 369 321 89 38 pint:PI0162|3end_ADP-ribosylglycohydrolase_(ADP-ribosyl-[dinitrogen_reductase]_hydrolase)_157001..157151_POSITIVE 269 387 342 74 31 pint:PI0917|3end_phosphoglycolate_phosphatase_847092..847242_POSITIVE 267 379 338 49 10 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE