Origin IGS: tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctcttcgatgaattacgaaccgaaaatgctcggattgtggtctgtaaatcctgagaaaacggcgcgagatttttttcgctgtggttccaaaaaattttaattctcgcgccaaaacgaaaaaattctcgcgccacgtttttacgaatgctgatcaggtaatttcccgaaccaaaacgcaaaacaactcctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg .........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.........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 cagtggattattagggtatcggtcagaaaaaagccttccgaatccgacaaagatagtagaaagagagtgcatctgaaaacagatcattcgaggattatcgatcaactgaaaaggcaggagttgttttgcgttttggttcgggaaattacctgatcagcattcgtaaaaacgtggcgcgagaattttttcgttttggcgcgagaattaaaattttttggaaccacagcgaaaaaaatctcgcgccgttttctcaggatttacagaccacaatccgagcattttcggttcgtaattcatcgaagagacaggttttacctgaaatcagagagagaatatccgtagtccaacggttcatccttatatcagaggttaaaagatatggtacgctcatcgaggagctgattggcttagtaggtgagactttcttaagagacctatcggcacctacaggaagttcatggcacacaaggcaaaggaggcaatcttcgcagaccggactcatatcaaaaggatgaaacgacttttccatacgacaaccaaatagccgtctacggtagacgaatgcaaacccaatatgaggccatcaatcaatccgaatgacagcttttgggcaatatattatgcatattttgattcgcgtttaaaggaaaagtgcatatatttgcgattgtggtatttctttcggtttctatgtgaattttgtctcccaagaagactttataatgcataaatacagaaggggtactacacagtaaaatcatattctaatttcatcaaa Mask Tandem Repeat Region ================================================ tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctcttcgatgaattacgaaccgaaaatgctcggattgtggtctgtaaatcctgagaaaacggcgcgagatttttttcgctgtggttccaaaaaattttaattctcgcgccaaaacgaaaaaattctcgcgccacgtttttacgaatgctgatcaggtaatttcccgaaccaaaacgcaaaacaactcctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg Find is-nt database================================================ Query_seq: PG2024:PG2026|PG2024:PG2026:hemagglutinin protein HagE:phosphoglycerate mutase family protein:<-->:2124294..2125071 778 tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctcttcgatgaattacgaaccgaaaatgctcggattgtggtctgtaaatcctgagaaaacggcgcgagatttttttcgctgtggttccaaaaaattttaattctcgcgccaaaacgaaaaaattctcgcgccacgtttttacgaatgctgatcaggtaatttcccgaaccaaaacgcaaaacaactcctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2024:PG2026|PG2024:PG2026:hemagglutinin protein HagE:phosphoglycerate mutase family protein:<-->:2124294..2125071 778 tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctcttcgatgaattacgaaccgaaaatgctcggattgtggtctgtaaatcctgagaaaacggcgcgagatttttttcgctgtggttccaaaaaattttaattctcgcgccaaaacgaaaaaattctcgcgccacgtttttacgaatgctgatcaggtaatttcccgaaccaaaacgcaaaacaactcctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2024:PG2026|PG2024:PG2026:hemagglutinin protein HagE:phosphoglycerate mutase family protein:<-->:2124294..2125071 778 tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctcttcgatgaattacgaaccgaaaatgctcggattgtggtctgtaaatcctgagaaaacggcgcgagatttttttcgctgtggttccaaaaaattttaattctcgcgccaaaacgaaaaaattctcgcgccacgtttttacgaatgctgatcaggtaatttcccgaaccaaaacgcaaaacaactcctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 4 Min: 479 Max: 661 Len: 183 Subject: UniRef90_Q7MU89 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 8.0E-8 bit: 60.1 Len: 162 Query Start:489 Query End:650 Subject Strand: null Subject Start: 13 Subject End: 66 ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ T N R K C S D C G L * I L R K R R E I F F A V V P K N F N S R A K T K K F S R H V F T N A D Q V I S R T K T ................................................................................................................................ ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ T N Q K S S D C G S C F L K K W R E I F F V L A C K F F N C R A K T K K F S R H V F V G N K C E N S G T Q T ................................................................................................................................ Subject: UniRef90_Q7MTB1 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 1.0E-7 bit: 59.3 Len: 132 Query Start:482 Query End:613 Subject Strand: null Subject Start: 4 Subject End: 47 ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. K T W R E N F F V L A R E L K F F G T T A K K I S R R F L R I Y R P Q S E H F R F V I H ..................................................................................................................................................................... ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. K T W R E N F F V L V R E V K N L R A T A K K I S R H F F R K Y E P Q P G V F W F V F H ..................................................................................................................................................................... Subject: UniRef90_Q7MXG1 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 3.0E-7 bit: 58.2 Len: 183 Query Start:479 Query End:661 Subject Strand: null Subject Start: 67 Subject End: 127 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. S M N Y E P K M L G L W S V N P E K T A R D F F R C G S K K F * F S R Q N E K I L A P R F Y E C * S G N F P N Q N A K Q L ..................................................................................................................... .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. S E D Y E P K T V G L R C V F W R K H A R E I F R F G S K N F Y F S R H N E K I F A P R L F Q P Y S G F F S N D K R E K V ..................................................................................................................... Subject: UniRef90_Q7MWR8 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 9.0E-7 bit: 56.6 Len: 135 Query Start:488 Query End:622 Subject Strand: null Subject Start: 18 Subject End: 62 ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... A F V K T W R E N F F V L A R E L K F F G T T A K K I S R R F L R I Y R P Q S E H F R F V ............................................................................................................................................................ ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... S F V K T W R E K I F A L A R K F F V S R T K T E K I S R V F S R I Y E P Q S E H F R R V ............................................................................................................................................................ tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 18 End: 188 ................. M I L L C S T P S V F M H Y K V F L G D K I H I E T E R N T T I A N I C T F P L N A N Q N M H N I L P K S C H S D .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 38 Strand: + Start: 164 End: 277 ................................................................................................................................................................... M A Q K L S F G L I D G L I L G L H S S T V D G Y L V V V W K S R F I L L I ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 205 End: 525 ............................................................................................................................................................................................................ M G F A F V Y R R R L F G C R M E K S F H P F D M S P V C E D C L L C L V C H E L P V G A D R S L K K V S P T K P I S S ............................................................................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 482 End: 571 ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. M N Y E P K M L G L W S V N P E K T A R D F F R C G S K K F ............................................................................................................................................................................................................... Protein_Len: 51 Strand: + Start: 522 End: 674 ......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M L R K R R E I F F A V V P K N F N S R A K T K K F S R H V F T N A D Q V I S R T K T Q N N S C L F S ........................................................................................................ Protein_Len: 39 Strand: + Start: 662 End: 778 ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M P F Q L I D N P R M I C F Q M H S L S T I F V G F G R L F S D R Y P N N P L Protein_Len: 48 Strand: - Start: 629 End: 772 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... T I E R V L V C F L E Q R K L Q D I I R S H D T K L H V R K R S D K D S E S P K K R V S V R I M ...... Protein_Len: 49 Strand: - Start: 440 End: 586 ....................................................................................................................................................................................................................................................................................................................................................................................................................................................... P Y E R E S K L Y F R D R R H I V F R F H E S Q P R Y I R L F R R S I K K A T T G F F K L E R A M ................................................................................................................................................................................................ Protein_Len: 60 Strand: - Start: 267 End: 653 .......................................................................................................................................................................................................................................................................... R K S S N R V S F A R I T T Q L D Q S F P A L N K E S H N W F I K I R A G F R F F E R A V N K R I S I L Y N G S G F R M ............................................................................................................................. Protein_Len: 35 Strand: - Start: 238 End: 342 ............................................................................................................................................................................................................................................. K T T T H F L R K M R K I H T R D A F I A E K A K H A M F K R Y T G M .................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 51 Strand: - Start: 52 End: 204 ................................................... A N Y L R R P L C F E C L F R F F Y W L R L Y I C K E K L R S D F Y A Y Y I A W F S D N P N I S P R M .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 31 Strand: - Start: 27 End: 119 .......................... Q T T G R R Y K H M I F D E Q S V F N V Y F G F S I G C D C M ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg 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================================================ tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 40 HP_score: -2.2 Tail_Score: -2.70528 Start: 490 End: 511 Full_Region: CTCTTCGATGAATTA CGAACCGA AAATGC TCGGATTG TGGTCTGTAAATCCT .........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CGAACCGAAAATGCTCGGATTG........................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG2024:PG2026|PG2024:PG2026:hemagglutinin protein HagE:phosphoglycerate mutase family protein:<-->:2124294..2125071 778 tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg Intra-Species Hit: Count: 1 Min: 1 Max: 778 Len: 778 Subject: NC_002950_PG2024_PG2026|hemagglutinin protein HagE:phosphoglycerate mutase family protein|NEGATIVE:POSITIVE|[2124294,2125071]|778 HSP 1 e-value: 0.0 bit: 948.0 Len: 478 Query Start:1 Query End:478 Subject Strand: POSITIVE Subject Start: 1 Subject End: 478 tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctct............................................................................................................................................................................................................................................................................................................ tttgatgaaattagaatatgattttactgtgtagtaccccttctgtatttatgcattataaagtcttcttgggagacaaaattcacatagaaaccgaaagaaataccacaatcgcaaatatatgcacttttcctttaaacgcgaatcaaaatatgcataatatattgcccaaaagctgtcattcggattgattgatggcctcatattgggtttgcattcgtctaccgtagacggctatttggttgtcgtatggaaaagtcgtttcatccttttgatatgagtccggtctgcgaagattgcctcctttgccttgtgtgccatgaacttcctgtaggtgccgataggtctcttaagaaagtctcacctactaagccaatcagctcctcgatgagcgtaccatatcttttaacctctgatataaggatgaaccgttggactacggatattctctctctgatttcaggtaaaacctgtctct............................................................................................................................................................................................................................................................................................................ HSP 2 e-value: 1.0E-59 bit: 232.0 Len: 117 Query Start:662 Query End:778 Subject Strand: POSITIVE Subject Start: 662 Subject End: 778 .....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg .....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ctgccttttcagttgatcgataatcctcgaatgatctgttttcagatgcactctctttctactatctttgtcggattcggaaggcttttttctgaccgataccctaataatccactg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAUGAAAUUAGAAUAUGAUUUUACUGUGUAGUACCCCUUCUGUAUUUAUGCAUUAUAAAGUCUUCUUGGGAGACAAAAUUCACAUAGAAACCGAAAGAAAUACCACAAUCGCAAAUAUAUGCACUUUUCCUUUAAACGCGAAUCAAAAUAUGCAUAAUAUAUUGCCCAAAAGCUGUCAUUCGGAUUGAUUGAUGGCCUCAUAUUGGGUUUGCAUUCGUCUACCGUAGACGGCUAUUUGGUUGUCGUAUGGAAAAGUCGUUUCAUCCUUUUGAUAUGAGUCCGGUCUGCGAAGAUUGCCUCCUUUGCCUUGUGUGCCAUGAACUUCCUGUAGGUGCCGAUAGGUCUCUUAAGAAAGUCUCACCUACUAAGCCAAUCAGCUCCUCGAUGAGCGUACCAUAUCUUUUAACCUCUGAUAUAAGGAUGAACCGUUGGACUACGGAUAUUCUCUCUCUGAUUUCAGGUAAAACCUGUCUCUUCGAUGAAUUACGAACCGAAAAUGCUCGGAUUGUGGUCUGUAAAUCCUGAGAAAACGGCGCGAGAUUUUUUUCGCUGUGGUUCCAAAAAAUUUUAAUUCUCGCGCCAAAACGAAAAAAUUCUCGCGCCACGUUUUUACGAAUGCUGAUCAGGUAAUUUCCCGAACCAAAACGCAAAACAACUCCUGCCUUUUCAGUUGAUCGAUAAUCCUCGAAUGAUCUGUUUUCAGAUGCACUCUCUUUCUACUAUCUUUGUCGGAUUCGGAAGGCUUUUUUCUGACCGAUACCCUAAUAAUCCACUG ...((((....(((((...(((((((..(((((((((.......))))...)))))..))))))).(((..(((.(((................(....)....((((((((((((((((((((((..(((..(((......)))...)))..))))).)))).))))......(((((((.((.....)).)))))))..(((.((.((((((.(((((((..((((((((((((....))))))).)))))..(((((..(((((((((...((((.((...(((..((((((........))))))...(((((((((((.......(((((((..(((...(((....)))..))).)))))))..(((......)))..)).))).))))))...........))).)).)))))))))))))((((......)))).............)))))((((.....)))).......)))))))..)))))).)).)))....))))))))).)))...)))..)))....(((((((((.((((((((...((((......................))))...)))))))).))))))))).........(((..(((((..(((((..............................)))))..)))))...))).........((.(((((((....))))).)).))...))))).))))..((((((..(((((((.....)))))))))))))................ (-195.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUGGAUUAUUAGGGUAUCGGUCAGAAAAAAGCCUUCCGAAUCCGACAAAGAUAGUAGAAAGAGAGUGCAUCUGAAAACAGAUCAUUCGAGGAUUAUCGAUCAACUGAAAAGGCAGGAGUUGUUUUGCGUUUUGGUUCGGGAAAUUACCUGAUCAGCAUUCGUAAAAACGUGGCGCGAGAAUUUUUUCGUUUUGGCGCGAGAAUUAAAAUUUUUUGGAACCACAGCGAAAAAAAUCUCGCGCCGUUUUCUCAGGAUUUACAGACCACAAUCCGAGCAUUUUCGGUUCGUAAUUCAUCGAAGAGACAGGUUUUACCUGAAAUCAGAGAGAGAAUAUCCGUAGUCCAACGGUUCAUCCUUAUAUCAGAGGUUAAAAGAUAUGGUACGCUCAUCGAGGAGCUGAUUGGCUUAGUAGGUGAGACUUUCUUAAGAGACCUAUCGGCACCUACAGGAAGUUCAUGGCACACAAGGCAAAGGAGGCAAUCUUCGCAGACCGGACUCAUAUCAAAAGGAUGAAACGACUUUUCCAUACGACAACCAAAUAGCCGUCUACGGUAGACGAAUGCAAACCCAAUAUGAGGCCAUCAAUCAAUCCGAAUGACAGCUUUUGGGCAAUAUAUUAUGCAUAUUUUGAUUCGCGUUUAAAGGAAAAGUGCAUAUAUUUGCGAUUGUGGUAUUUCUUUCGGUUUCUAUGUGAAUUUUGUCUCCCAAGAAGACUUUAUAAUGCAUAAAUACAGAAGGGGUACUACACAGUAAAAUCAUAUUCUAAUUUCAUCAAA .............((((.((((((.(((....((((.((....((.((.......)).........((((.(((((.......((.(((((((((((.(((...((((((((.((..(((...(((((((..(((((.((((......)))))))))....)))))))....(((((((((.((((((((((.(((..(.((((........)))).)..))).)))))))))).))))))))).....))).(((((..........)))))..)).))))))))))))))))).)))))))..((((.....))))...)))))....((((.(((..((.((((((((((..((((......))))......(((..((....)).)))...)))))).))))))..(((((((.((.((((....))))....))..))))))).))).))))...))))....))....))))))....)))...))))))))))..........(((((((..((((((((................((((....))))....((((((...((((....(((((..(((.((.....)).)))..)))))))))(((.((((.....)))).)))....))))))...)))))))).......(((((...((((((((..((((..((...(((((.......((((.......))))........)))))...)).))))..))))))))..)))))............)))))))... (-222.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 80 31 171 122 NC_002950:PG2024|5end_hemagglutinin_protein_HagE_2124203..2124433_NEGATIVE 584 614 575 83 44 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 568 617 575 117 78 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 537 614 575 85 46 NC_002950:PG0313|5end_hypothetical_protein_347366..347596_POSITIVE 527 621 583 39 1 NC_002950:PG0524|5end_hypothetical_protein_568599..568829_POSITIVE 524 614 575 119 80 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 505 614 573 176 136 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 495 558 519 41 2 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 443 617 575 124 80 NC_002950:PG0174|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_197628..197858_NEGATIVE 431 580 531 107 56 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 430 268 225 189 141 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 418 620 576 86 42 NC_002950:PG0080|5end_hypothetical_protein_93832..94062_NEGATIVE 414 619 579 194 155 NC_002950:PG2063|5end_hypothetical_protein_2160596..2160826_NEGATIVE 405 340 291 81 31 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 393 310 261 87 40 NC_002950:PG0428|5end_hypothetical_protein_465977..466207_NEGATIVE 391 759 712 208 142 NC_002950:PG0226|5end_transglutaminase-related_protein_262531..262761_NEGATIVE 375 317 279 191 133 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 375 270 230 60 7 NC_002950:PG0656|5end_50S_ribosomal_protein_L34_707097..707327_NEGATIVE 373 417 371 73 29 NC_002950:PG0452|5end_hypothetical_protein_492879..493109_POSITIVE 371 339 291 111 53 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 562 615 573 59 16 NC_002950:PG0542|3end_hypothetical_protein_595377..595527_NEGATIVE 461 619 573 96 51 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE 391 759 712 146 80 NC_002950:PG0227|3end_DNA_repair_protein_RadA_262593..262743_NEGATIVE 381 600 551 151 102 NC_002950:PG1718|3end_hypothetical_protein_1806532..1806682_NEGATIVE 350 349 307 80 35 NC_002950:PG0523|3end_inositol-5-monophosphate_dehydrogenase_566898..567048_NEGATIVE 341 606 575 39 8 NC_002950:PG0155|3end_riboflavin_biosynthesis_protein_RibD_177861..178011_NEGATIVE 340 562 524 83 45 NC_002950:PG1875|3end_hemolysin_1969647..1969797_NEGATIVE 340 227 182 51 3 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 340 720 672 127 76 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 337 759 711 129 83 NC_002950:PG0610|3end_hypothetical_protein_663604..663754_NEGATIVE 335 340 291 121 75 NC_002950:PG0424|3end_hypothetical_protein_463213..463363_POSITIVE 333 750 701 49 1 NC_002950:PG1269|3end_delta-1-pyrroline-5-carboxylate_dehydrogenase_1347570..1347720_NEGATIVE 333 229 183 134 81 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 332 318 276 118 74 NC_002950:PG1382|3end_hypothetical_protein_1462550..1462700_POSITIVE 330 260 214 72 25 NC_002950:PG1760|3end_ABC_transporter,_ATP-binding_protein_1847216..1847366_POSITIVE 329 340 295 67 13 NC_002950:PG0915|3end_hypothetical_protein_977057..977207_POSITIVE 324 540 493 58 12 NC_002950:PG2213|3end_nitrite_reductase-related_protein_2324848..2324998_NEGATIVE 322 330 285 120 68 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 322 260 211 64 17 NC_002950:PG1173|3end_YkgG_family_protein_1253129..1253279_POSITIVE 322 318 273 72 33 NC_002950:PG0561|3end_peptidase,_M20/M25/M40_family_617700..617850_NEGATIVE