Origin IGS: ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgcaaaaaaaatgtcagcatt .........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 aatgctgacattttttttgcgtctaaagctcggagtgtgccgatttcgtttcgtgggctgttcaaggtggccggagggtatatgtcaaggcttcccgaaaaaatacgacttggaacgaagtggaaatgtggagattttttcaggcgaacccgaaagggcttcaggccttgacactttacccgaaggccggtttccttcgcccaaagaaaggaatcggcactccgggatcgaagacaacag Mask Tandem Repeat Region ================================================ ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgcaaaaaaaatgtcagcatt Find is-nt database================================================ Query_seq: PG1459:PG1460|PG1459:PG1460:hypothetical protein:hypothetical protein:<-->:1539860..1540099 240 ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgcaaaaaaaatgtcagcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1459:PG1460|PG1459:PG1460:hypothetical protein:hypothetical protein:<-->:1539860..1540099 240 ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgcaaaaaaaatgtcagcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1459:PG1460|PG1459:PG1460:hypothetical protein:hypothetical protein:<-->:1539860..1540099 240 ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgcaaaaaaaatgtcagcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgcaaaaaaaatgtcagcatt Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 1 End: 153 M L S S I P E C R F L S L G E G N R P S G K V S R P E A L S G S P E K I S T F P L R S K S Y F F G K P ....................................................................................... Protein_Len: 54 Strand: + Start: 77 End: 238 ............................................................................ M K P F R V R L K K S P H F H F V P S R I F S G S L D I Y P P A T L N S P R N E I G T L R A L D A K K M S A .. Protein_Len: 53 Strand: - Start: 73 End: 231 ........................................................................ P R F G K R T R R F F D G C K W K T G L R I K E P L R S M Y G G A V K F L G R F S I P V S R A K S A F F M ......... Protein_Len: 60 Strand: - Start: 3 End: 239 .. P L T D L G S A R E P E G S F I E V N G S R E L D Y K K P F G Q C I G E P W R S C G V F R F R C V G L K L R L F F T L M . Protein_Len: 40 Strand: - Start: 2 End: 121 . T T K S G P T G I G K K P R L F G A K P Y L T L A Q L G K P N A Q F F R W M E M ....................................................................................................................... ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgcaaaaaaaatgtcagcatt 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================================================ ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgcaaaaaaaatgtcagcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1459:PG1460|PG1459:PG1460:hypothetical protein:hypothetical protein:<-->:1539860..1540099 240 ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgcaaaaaaaatgtcagcatt Intra-Species Hit: Count: 1 Min: 1 Max: 222 Len: 222 Subject: NC_002950_PG1459_PG1460|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1539860,1540099]|240 HSP 1 e-value: 1.0E-122 bit: 440.0 Len: 222 Query Start:1 Query End:222 Subject Strand: POSITIVE Subject Start: 1 Subject End: 222 ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgc.................. ctgttgtcttcgatcccggagtgccgattcctttctttgggcgaaggaaaccggccttcgggtaaagtgtcaaggcctgaagccctttcgggttcgcctgaaaaaatctccacatttccacttcgttccaagtcgtattttttcgggaagccttgacatataccctccggccaccttgaacagcccacgaaacgaaatcggcacactccgagctttagacgc.................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUGUCUUCGAUCCCGGAGUGCCGAUUCCUUUCUUUGGGCGAAGGAAACCGGCCUUCGGGUAAAGUGUCAAGGCCUGAAGCCCUUUCGGGUUCGCCUGAAAAAAUCUCCACAUUUCCACUUCGUUCCAAGUCGUAUUUUUUCGGGAAGCCUUGACAUAUACCCUCCGGCCACCUUGAACAGCCCACGAAACGAAAUCGGCACACUCCGAGCUUUAGACGC .....((((.....(.((((((((((((((.((((..(((((...(....).((((...(((((..((((((((((..(((.(((....)))))).(((((((((((..(.((..................)).).)))))))))))..)))))))))).)))))...))))..........))))).)))).).)))))))..)))))).)....)))).. (-83.97) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUCUAAAGCUCGGAGUGUGCCGAUUUCGUUUCGUGGGCUGUUCAAGGUGGCCGGAGGGUAUAUGUCAAGGCUUCCCGAAAAAAUACGACUUGGAACGAAGUGGAAAUGUGGAGAUUUUUUCAGGCGAACCCGAAAGGGCUUCAGGCCUUGACACUUUACCCGAAGGCCGGUUUCCUUCGCCCAAAGAAAGGAAUCGGCACUCCGGGAUCGAAGACAACAG ..((((....((((((((..(((((((((.((((.(((((.....((((..(((((.(((((..((((((((((.((.((((((((.(.((((......)))).)..........)))))))).)).((((((....))).))).))))))))))...))))).....)))))..)))).)))))..))))))))))))))))))))).....))))..... (-98.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1114 100 51 191 142 NC_002950:PG1459|5end_hypothetical_protein_1539769..1539999_NEGATIVE 420 70 21 61 11 NC_002950:PG2188|5end_diaminopimelate_decarboxylase_2295781..2296011_NEGATIVE 414 98 51 202 140 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 403 99 51 57 3 NC_002950:PG0629|5end_inorganic_polyphosphate/ATP-NAD_kinase_683364..683594_NEGATIVE 400 59 11 136 84 NC_002950:PG0085|5end_alpha-galactosidase_99172..99402_POSITIVE 397 59 17 61 5 NC_002950:PG0377|5end_30S_ribosomal_protein_S2_406920..407150_POSITIVE 395 99 52 196 148 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 388 73 36 73 25 NC_002950:PG1385|5end_TPR_domain_protein_1466335..1466565_NEGATIVE 382 60 11 222 173 NC_002950:PG1490|5end_TraG_family_protein_1563415..1563645_POSITIVE 382 55 14 64 14 NC_002950:PG0217|5end_hypothetical_protein_252490..252720_POSITIVE 381 90 41 160 119 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 380 188 145 89 34 NC_002950:PG1482|5end_conjugative_transposon_protein_TraF_1558779..1559009_NEGATIVE 376 78 34 65 25 NC_002950:PG2182|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_A_2291155..2291385_NEGATIVE 375 60 11 81 25 NC_002950:PG1153|5end_hypothetical_protein_1235689..1235919_NEGATIVE 372 100 51 188 133 NC_002950:PG1898|5end_transporter,_putative_1997335..1997565_NEGATIVE 372 49 2 61 13 NC_002950:PG0325|5end_hypothetical_protein_359714..359944_NEGATIVE 371 48 7 50 6 NC_002950:PG1888|5end_hypothetical_protein_1985596..1985826_POSITIVE 371 56 17 187 143 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 370 99 51 77 37 NC_002950:PG1487|5end_hypothetical_protein_1561468..1561698_POSITIVE 370 60 11 62 5 NC_002950:PG0574|5end_hypothetical_protein_629018..629248_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 439 60 13 118 78 NC_002950:PG0756|3end_hypothetical_protein_804321..804471_NEGATIVE 430 69 22 145 102 NC_002950:PG1242|3end_replicative_DNA_helicase_1319101..1319251_POSITIVE 414 98 51 123 61 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 383 60 14 129 82 NC_002950:PG1364|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1444388..1444538_NEGATIVE 380 188 145 85 30 NC_002950:PG1483|3end_conjugative_transposon_protein_TraE_1558783..1558933_NEGATIVE 375 60 11 73 17 NC_002950:PG1154|3end_hypothetical_protein_1235697..1235847_NEGATIVE 372 87 45 56 8 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 371 48 7 53 9 NC_002950:PG1887|3end_rhodanese-like_domain_protein_1985679..1985829_POSITIVE 371 98 51 58 5 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 370 60 11 62 5 NC_002950:PG0573|3end_S-adenosyl-methyltransferase_MraW_629098..629248_POSITIVE 367 96 51 83 21 NC_002950:PG1760|3end_ABC_transporter,_ATP-binding_protein_1847216..1847366_POSITIVE 364 90 41 147 97 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 362 78 37 77 44 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 360 99 52 91 43 NC_002950:PG0032|3end_beta-mannosidase,_putative_37627..37777_NEGATIVE 358 70 22 79 34 NC_002950:PG1215|3end_lipoprotein_protein,_putative_1295513..1295663_POSITIVE 356 99 51 146 95 NC_002950:PG2199|3end_ABC_transporter,_ATP-binding_protein,_putative_2304786..2304936_NEGATIVE 356 59 14 54 12 NC_002950:PG1473|3end_conjugative_transposon_protein_TraQ_1549761..1549911_NEGATIVE 356 90 50 42 4 NC_002950:PG1337|3end_umuD_protein_1418318..1418468_POSITIVE 354 79 36 68 9 NC_002950:PG0216|3end_hypothetical_protein_252536..252686_POSITIVE 352 55 11 147 86 NC_002950:PG1302|3end_hypothetical_protein_1379939..1380089_NEGATIVE