Origin IGS: tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc .........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 ggaggagacgacggacaggtgtcccgcttcggtgggggattgaaccctgctacgatcctccagaacgagtacgtagctgtctgcattattttccatatactactgcgattataaggttatcgcagcaaagatacgcgaggcaaacaggaatgatgaagatgggtttcttagcgtttcttagaatggattagaatggaaaagccgtgtatctgttccaatttctggcttgccggatgcagatttatgttgactgcagaaagaagactgtagtaatgaatgaatatcttaaaaatggaccgcgctatggggaaggaaaccagctacggcaaaaagacaaagcaataccatgccaatggctgtaatgctatatcggacgagtgga Mask Tandem Repeat Region ================================================ tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc Find is-nt database================================================ Query_seq: PG1493:PG1494|PG1493:PG1494:hypothetical protein:hypothetical protein:->->:1569599..1569980 382 tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1493:PG1494|PG1493:PG1494:hypothetical protein:hypothetical protein:->->:1569599..1569980 382 tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1493:PG1494|PG1493:PG1494:hypothetical protein:hypothetical protein:->->:1569599..1569980 382 tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 101 End: 202 .................................................................................................... M H S L L Q S S F C S Q H K S A S G K P E I G T D T R L F H S N P F .................................................................................................................................................................................... Protein_Len: 50 Strand: + Start: 63 End: 212 .............................................................. M V S F P I A R S I F K I F I H Y Y S L L S A V N I N L H P A S Q K L E Q I H G F S I L I H S K K R .......................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 199 End: 294 ...................................................................................................................................................................................................... M L R N A K K P I F I I P V C L A Y L C C D N L I I A V V Y G K ........................................................................................ Protein_Len: 32 Strand: + Start: 285 End: 380 ............................................................................................................................................................................................................................................................................................ M W K I M Q T A T Y S F W R I V A G F N P P P K R D T C P S S P .. Protein_Len: 32 Strand: + Start: 287 End: 382 .............................................................................................................................................................................................................................................................................................. M E N N A D S Y V L V L E D R S R V Q S P T E A G H L S V V S S Protein_Len: 31 Strand: - Start: 272 End: 364 ............................................................................................................................................................................................................................................................................... L R L L I H F I I C V A V Y E N Q L I T A P N L G G G F R S M .................. Protein_Len: 34 Strand: - Start: 205 End: 306 ............................................................................................................................................................................................................ S V S L F G D E D N R N A E R I K A A I V K Y D C Y Y I S F L A S M ............................................................................ Protein_Len: 50 Strand: - Start: 195 End: 344 .................................................................................................................................................................................................. D M R L F A L F G M K M M G T Q R A Y R Q Q S L R I I A T T Y P F Y H L C S R V R E P P D Y C P E M ...................................... Protein_Len: 52 Strand: - Start: 24 End: 179 ....................... L W Q C P I A K D K Q R L Q N G E G Y R P G N K L Y E N M V V T K K R C D V Y I Q M R C A L F Q F L Y M ........................................................................................................................................................................................................... Protein_Len: 35 Strand: - Start: 2 End: 106 . W E D S I A N C G N A H Y Q K T K K G Y S T E K G M A R D M K L I N M .................................................................................................................................................................................................................................................................................... tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc 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================================================ tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -4.6 Tail_Score: -2.8805 Start: 255 End: 283 Full_Region: TTGCCTCGCGTATCT TTGCTGCGATAA CCTTA TAATCGCAGTAG TATATGGAAAATAAT ..............................................................................................................................................................................................................................................................TTGCTGCGATAACCTTATAATCGCAGTAG................................................................................................... TransTerm Strand: + Conf: 53 HP_score: -6.3 Tail_Score: -2.6927 Start: 258 End: 280 Full_Region: CCTCGCGTATCTTTG CTGCGATAA CCTTA TAATCGCAG TAGTATATGGAAAAT .................................................................................................................................................................................................................................................................CTGCGATAACCTTATAATCGCAG...................................................................................................... TransTerm Strand: - Conf: 47 HP_score: -3.9 Tail_Score: -2.99842 Start: 306 End: 334 Full_Region: gggggattgaaccct gctacgatcctc cagaac gagtacgtagc tgtctgcattatttt .................................................................................................................................................................................................................................................................................................................gctacgatcctccagaacgagtacgtagc................................................ Find igs database================================================ Query_seq: PG1493:PG1494|PG1493:PG1494:hypothetical protein:hypothetical protein:->->:1569599..1569980 382 tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc Intra-Species Hit: Count: 1 Min: 1 Max: 382 Len: 382 Subject: NC_002950_PG1493_PG1494|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1569599,1569980]|382 HSP 1 e-value: 0.0 bit: 757.0 Len: 382 Query Start:1 Query End:382 Subject Strand: POSITIVE Subject Start: 1 Subject End: 382 tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc tccactcgtccgatatagcattacagccattggcatggtattgctttgtctttttgccgtagctggtttccttccccatagcgcggtccatttttaagatattcattcattactacagtcttctttctgcagtcaacataaatctgcatccggcaagccagaaattggaacagatacacggcttttccattctaatccattctaagaaacgctaagaaacccatcttcatcattcctgtttgcctcgcgtatctttgctgcgataaccttataatcgcagtagtatatggaaaataatgcagacagctacgtactcgttctggaggatcgtagcagggttcaatcccccaccgaagcgggacacctgtccgtcgtctcctcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCACUCGUCCGAUAUAGCAUUACAGCCAUUGGCAUGGUAUUGCUUUGUCUUUUUGCCGUAGCUGGUUUCCUUCCCCAUAGCGCGGUCCAUUUUUAAGAUAUUCAUUCAUUACUACAGUCUUCUUUCUGCAGUCAACAUAAAUCUGCAUCCGGCAAGCCAGAAAUUGGAACAGAUACACGGCUUUUCCAUUCUAAUCCAUUCUAAGAAACGCUAAGAAACCCAUCUUCAUCAUUCCUGUUUGCCUCGCGUAUCUUUGCUGCGAUAACCUUAUAAUCGCAGUAGUAUAUGGAAAAUAAUGCAGACAGCUACGUACUCGUUCUGGAGGAUCGUAGCAGGGUUCAAUCCCCCACCGAAGCGGGACACCUGUCCGUCGUCUCCUCC ...........((((.((((.(((.(((...)))...))).)))).)))).......((((((((.(((((.........(((((..........................................(((((...........)))))...(((((((..(((..(((((.((........)).)))))..........((((.((.....)).))))..............)))..))))))).)))))....((((((((((.........)))))))))).....)))))..........))))))))..........((((((.((..(((((......((((.(......).))))..)))))....))..)))))) (-96.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGGAGACGACGGACAGGUGUCCCGCUUCGGUGGGGGAUUGAACCCUGCUACGAUCCUCCAGAACGAGUACGUAGCUGUCUGCAUUAUUUUCCAUAUACUACUGCGAUUAUAAGGUUAUCGCAGCAAAGAUACGCGAGGCAAACAGGAAUGAUGAAGAUGGGUUUCUUAGCGUUUCUUAGAAUGGAUUAGAAUGGAAAAGCCGUGUAUCUGUUCCAAUUUCUGGCUUGCCGGAUGCAGAUUUAUGUUGACUGCAGAAAGAAGACUGUAGUAAUGAAUGAAUAUCUUAAAAAUGGACCGCGCUAUGGGGAAGGAAACCAGCUACGGCAAAAAGACAAAGCAAUACCAUGCCAAUGGCUGUAAUGCUAUAUCGGACGAGUGGA ((((((..((..((.(((((.((((((....)))))).)......)))))).)).)))))).(..(((...((((((((....(....((..(((((.....(((((((.........)))))))........((((.(((((.(((((((....((((.(.(((....))).).)))).((((((((....((((.....))))..))))))))..)))))))..))))).((((...((((((....(((((((........))))))).))))))...))))............)))).)))))..)).)....))))))))............((((.(((...(((...))).))).))))...)))..)....... (-118.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 379 335 210 163 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 407 94 56 83 39 NC_002950:PG1473|5end_conjugative_transposon_protein_TraQ_1550225..1550455_NEGATIVE 407 86 44 68 23 NC_002950:PG1313|5end_dipeptidase-related_protein_1392282..1392512_POSITIVE 404 380 331 112 41 NC_002950:PG0605|5end_hypothetical_protein_662406..662636_NEGATIVE 402 370 322 182 123 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 397 377 331 74 34 NC_002950:PG0604|5end_4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase_660262..660492_POSITIVE 396 360 314 222 162 NC_002950:PG0431|5end_hypothetical_protein_468978..469208_POSITIVE 391 376 331 226 170 NC_002950:PG1523|5end_naphthoate_synthase_1600988..1601218_NEGATIVE 380 90 42 219 163 NC_002950:PG0923|5end_ribosome-binding_factor_A_982814..983044_NEGATIVE 370 379 332 215 151 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 364 87 41 79 27 NC_002950:PG0546|5end_hypothetical_protein_600391..600621_NEGATIVE 364 49 6 223 174 NC_002950:PG0025|5end_fumarylacetoacetate_hydrolase_family_protein_28457..28687_POSITIVE 361 60 15 141 97 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 361 346 302 96 39 NC_002950:PG1753|5end_selenide,_water_dikinase_1838615..1838845_POSITIVE 358 50 1 216 162 NC_002950:PG0002|5end_hexapeptide_transferase_family_protein_1295..1525_POSITIVE 356 159 111 73 22 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 356 340 300 77 38 NC_002950:PG1858|5end_flavodoxin_1957035..1957265_NEGATIVE 354 375 332 91 42 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 352 359 311 160 112 NC_002950:PG1538|5end_undecaprenol_kinase,_putative_1617631..1617861_POSITIVE 350 369 325 182 140 NC_002950:PG1488|5end_hypothetical_protein_1561747..1561977_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 94 56 70 26 NC_002950:PG1474|3end_conjugative_transposon_protein_TraO_1550238..1550388_NEGATIVE 397 377 331 77 37 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 395 373 338 47 1 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 387 379 333 129 83 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 384 360 314 130 85 NC_002950:PG0771|3end_hypothetical_protein_824867..825017_POSITIVE 372 380 332 70 3 NC_002950:PG0545|3end_hypothetical_protein_600228..600378_POSITIVE 371 77 34 98 52 NC_002950:PG0068|3end_hypothetical_protein_82079..82229_POSITIVE 370 379 332 114 50 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 361 346 302 99 42 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 361 380 335 67 2 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 356 159 111 54 3 NC_002950:PG1960|3end_ribosomal_protein_L28_2048424..2048574_NEGATIVE 356 43 6 143 105 NC_002950:PG0024|3end_redox-sensing_transcriptional_repressor_Rex_28468..28618_POSITIVE 352 359 311 52 4 NC_002950:PG1537|3end_hypothetical_protein_1617603..1617753_POSITIVE 349 379 334 73 16 NC_002950:PG0243|3end_hypothetical_protein_278976..279126_NEGATIVE 342 170 121 125 61 NC_002950:PG1600|3end_hypothetical_protein_1679959..1680109_NEGATIVE 342 380 332 56 6 NC_002950:PG0315|3end_50S_ribosomal_protein_L27_348417..348567_POSITIVE 342 360 315 84 36 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 342 360 315 77 20 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 341 369 322 63 3 NC_002950:PG0703|3end_cobalamin_(5'-phosphate)_synthase,_putative_759006..759156_POSITIVE 341 347 306 70 21 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE