Material und Methoden; Alignment hinzugefügt

2012-08-01 03:24:07 +02:00 · 2012-08-01 03:24:07 +02:00 · 9119d1667b
commit 9119d1667b
parent f59d279abd
6 changed files with 1880 additions and 1598 deletions
--- a/misc/align_seq_ref.aln
+++ b/misc/align_seq_ref.aln
@ -0,0 +1,194 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+pETEV-16b-ppdk      ATAATTTTGTTTAACTTTAAGAAGGAGATATACCATGGGCCATCATCATCATCATCATCA
+FtPPDK-ref          ------------------------------------------------------------
+                                                                                
+
+pETEV-16b-ppdk      TCATCATCACAGCAGCGGCCATGAAAACCTGTATTTTCAGGGACATATGACCGCTAAAAA
+FtPPDK-ref          -------------------------------------------CATATGACCGCTAAAAA
+                                                               *****************
+
+pETEV-16b-ppdk      ACGCGTGTTTACGTTCGGCAAAGGTCGCTCGGAAGGCAACCGTGACATGAAATCGCTGCT
+FtPPDK-ref          ACGCGTGTTTACGTTCGGCAAAGGTCGCTCGGAAGGCAACCGTGACATGAAATCGCTGCT
+                    ************************************************************
+
+pETEV-16b-ppdk      GGGTGGCAAAGGTGCGAACCTGGCGGAAATGAGCTCTATTGGTCTGTCCGTGCCGCCGGG
+FtPPDK-ref          GGGTGGCAAAGGTGCGAACCTGGCGGAAATGAGCTCTATTGGTCTGTCCGTGCCGCCGGG
+                    ************************************************************
+
+pETEV-16b-ppdk      TCTGACCATCTCAACGGAAGCCTGCGAAGAATATCAGCAAAATGGTAAATCGCTGCCGCC
+FtPPDK-ref          TCTGACCATCTCAACGGAAGCCTGCGAAGAATATCAGCAAAATGGTAAATCGCTGCCGCC
+                    ************************************************************
+
+pETEV-16b-ppdk      GGGCCTGTGGGATGAAATCAGCGAAGGTCTGGACTACGTTCAGAAAGAAATGTCAGCCTC
+FtPPDK-ref          GGGCCTGTGGGATGAAATCAGCGAAGGTCTGGACTACGTTCAGAAAGAAATGTCAGCCTC
+                    ************************************************************
+
+pETEV-16b-ppdk      GCTGGGCGATCCGTCGAAACCGCTGCTGCTGAGCGTCCGTTCTGGTGCGGCCATTAGCAT
+FtPPDK-ref          GCTGGGCGATCCGTCGAAACCGCTGCTGCTGAGCGTCCGTTCTGGTGCGGCCATTAGCAT
+                    ************************************************************
+
+pETEV-16b-ppdk      GCCGGGCATGATGGATACCGTTCTGAACCTGGGTCTGAATGACGAAGTGGTTGCAGGTCT
+FtPPDK-ref          GCCGGGCATGATGGATACCGTTCTGAACCTGGGTCTGAATGACGAAGTGGTTGCAGGTCT
+                    ************************************************************
+
+pETEV-16b-ppdk      GGCCGGTAAATCGGGTGCTCGTTTCGCGTATGATAGCTACCGTCGCTTTCTGGACATGTT
+FtPPDK-ref          GGCCGGTAAATCGGGTGCTCGTTTCGCGTATGATAGCTACCGTCGCTTTCTGGACATGTT
+                    ************************************************************
+
+pETEV-16b-ppdk      CGGTAACGTCGTGATGGGCATCCCGCATAGCCTGTTTGATGAAAAACTGGAACAGATGAA
+FtPPDK-ref          CGGTAACGTCGTGATGGGCATCCCGCATAGCCTGTTTGATGAAAAACTGGAACAGATGAA
+                    ************************************************************
+
+pETEV-16b-ppdk      AGCCGAAAAAGGTATTCACCTGGATACCGACCTGACGGCAGCTGATCTGAAAGACCTGGT
+FtPPDK-ref          AGCCGAAAAAGGTATTCACCTGGATACCGACCTGACGGCAGCTGATCTGAAAGACCTGGT
+                    ************************************************************
+
+pETEV-16b-ppdk      GGAAAAATATAAAAACGTTTACGTCGAAGCGAAAGGCGAAAAATTCCCGACCGATCCGAA
+FtPPDK-ref          GGAAAAATATAAAAACGTTTACGTCGAAGCGAAAGGCGAAAAATTCCCGACCGATCCGAA
+                    ************************************************************
+
+pETEV-16b-ppdk      AAAACAGCTGGAACTGGCCGTCAATGCAGTGTTTGATAGTTGGGACTCCCCGCGTGCCAA
+FtPPDK-ref          AAAACAGCTGGAACTGGCCGTCAATGCAGTGTTTGATAGTTGGGACTCCCCGCGTGCCAA
+                    ************************************************************
+
+pETEV-16b-ppdk      CAAATATCGCTCCATTAATCAGATCACCGGTCTGAAAGGCACGGCAGTGAATATTCAATC
+FtPPDK-ref          CAAATATCGCTCCATTAATCAGATCACCGGTCTGAAAGGCACGGCAGTGAATATTCAATC
+                    ************************************************************
+
+pETEV-16b-ppdk      TATGGTTTTCGGTAACATGGGCAATACCAGTGGCACGGGTGTGCTGTTTACCCGTAACCC
+FtPPDK-ref          TATGGTTTTCGGTAACATGGGCAATACCAGTGGCACGGGTGTGCTGTTTACCCGTAACCC
+                    ************************************************************
+
+pETEV-16b-ppdk      GAGCACGGGCGAGAAAAAACTGTACGGCGAATTCCTGATTAATGCCCAGGGTGAAGATGT
+FtPPDK-ref          GAGCACGGGCGAGAAAAAACTGTACGGCGAATTCCTGATTAATGCCCAGGGTGAAGATGT
+                    ************************************************************
+
+pETEV-16b-ppdk      TGTCGCAGGCATCCGCACCCCGGAAGATCTGGGTACCATGGAAACGTGCATGCCGGAAGC
+FtPPDK-ref          TGTCGCAGGCATCCGCACCCCGGAAGATCTGGGTACCATGGAAACGTGCATGCCGGAAGC
+                    ************************************************************
+
+pETEV-16b-ppdk      GTATAAAGAACTGGTGGAAAACTGTGAAATTCTGGAACGTCATTACAAAGATATGATGGA
+FtPPDK-ref          GTATAAAGAACTGGTGGAAAACTGTGAAATTCTGGAACGTCATTACAAAGATATGATGGA
+                    ************************************************************
+
+pETEV-16b-ppdk      CATCGAATTCACCGTTCAGGAAAATCGCCTGTGGATGCTGCAATGTCGTACCGGTAAACG
+FtPPDK-ref          CATCGAATTCACCGTTCAGGAAAATCGCCTGTGGATGCTGCAATGTCGTACCGGTAAACG
+                    ************************************************************
+
+pETEV-16b-ppdk      CACGGGCAAAGGTGCTGTGCGTATTGCGGTTGATATGGTCAACGAAGGCCTGATTGACAC
+FtPPDK-ref          CACGGGCAAAGGTGCTGTGCGTATTGCGGTTGATATGGTCAACGAAGGCCTGATTGACAC
+                    ************************************************************
+
+pETEV-16b-ppdk      CCGTACGGCAATCAAACGCGTTGAAACCCAGCATCTGGATCAACTGCTGCACCCGCAGTT
+FtPPDK-ref          CCGTACGGCAATCAAACGCGTTGAAACCCAGCATCTGGATCAACTGCTGCACCCGCAGTT
+                    ************************************************************
+
+pETEV-16b-ppdk      CGAAGACCCGTCAGCGTATAAATCGCATGTGGTTGCCACCGGTCTGCCGGCATCCCCGGG
+FtPPDK-ref          CGAAGACCCGTCAGCGTATAAATCGCATGTGGTTGCCACCGGTCTGCCGGCATCCCCGGG
+                    ************************************************************
+
+pETEV-16b-ppdk      TGCAGCAGTGGGCCAGGTTTGCTTTTCAGCTGAAGATGCGGAAACGTGGCACGCTCAGGG
+FtPPDK-ref          TGCAGCAGTGGGCCAGGTTTGCTTTTCAGCTGAAGATGCGGAAACGTGGCACGCTCAGGG
+                    ************************************************************
+
+pETEV-16b-ppdk      TAAATCCGCGATCCTGGTGCGCACCGAAACGTCACCGGAAGATGTTGGCGGTATGCATGC
+FtPPDK-ref          TAAATCCGCGATCCTGGTGCGCACCGAAACGTCACCGGAAGATGTTGGCGGTATGCATGC
+                    ************************************************************
+
+pETEV-16b-ppdk      AGCTGCGGGCATTCTGACCGCACGTGGCGGTATGACGTCCCACGCAGCAGTCGTGGCTCG
+FtPPDK-ref          AGCTGCGGGCATTCTGACCGCACGTGGCGGTATGACGTCCCACGCAGCAGTCGTGGCTCG
+                    ************************************************************
+
+pETEV-16b-ppdk      CGGCTGGGGTAAATGCTGTGTCTCAGGTTGTGCGGATATCCGTGTGAACGATGACATGAA
+FtPPDK-ref          CGGCTGGGGTAAATGCTGTGTCTCAGGTTGTGCGGATATCCGTGTGAACGATGACATGAA
+                    ************************************************************
+
+pETEV-16b-ppdk      AATCTTCACCATCGGTGATCGCGTGATCAAAGAAGGCGACTGGCTGAGCCTGAACGGTAC
+FtPPDK-ref          AATCTTCACCATCGGTGATCGCGTGATCAAAGAAGGCGACTGGCTGAGCCTGAACGGTAC
+                    ************************************************************
+
+pETEV-16b-ppdk      CACGGGCGAAGTTATTCTGGGTAAACAGCTGCTGGCACCGCCGGCAATGTCTAATGATCT
+FtPPDK-ref          CACGGGCGAAGTTATTCTGGGTAAACAGCTGCTGGCACCGCCGGCAATGTCTAATGATCT
+                    ************************************************************
+
+pETEV-16b-ppdk      GGAAATCTTTATGAGTTGGGCTGACCAGGCGCGTCGCCTGAAAGTGATGGCTAACGCGGA
+FtPPDK-ref          GGAAATCTTTATGAGTTGGGCTGACCAGGCGCGTCGCCTGAAAGTGATGGCTAACGCGGA
+                    ************************************************************
+
+pETEV-16b-ppdk      TACCCCGAATGACGCCCTGACGGCACGTAACAATGGTGCACAGGGTATTGGTCTGTGCCG
+FtPPDK-ref          TACCCCGAATGACGCCCTGACGGCACGTAACAATGGTGCACAGGGTATTGGTCTGTGCCG
+                    ************************************************************
+
+pETEV-16b-ppdk      TACCGAACACATGTTTTTCGCTTCTGATGAACGTATTAAAGCGGTCCGCAAAATGATCAT
+FtPPDK-ref          TACCGAACACATGTTTTTCGCTTCTGATGAACGTATTAAAGCGGTCCGCAAAATGATCAT
+                    ************************************************************
+
+pETEV-16b-ppdk      GGCCGTGACGCCGGAACAGCGTAAAGTTGCTCTGGATCTGCTGCTGCCGTATCAACGTAG
+FtPPDK-ref          GGCCGTGACGCCGGAACAGCGTAAAGTTGCTCTGGATCTGCTGCTGCCGTATCAACGTAG
+                    ************************************************************
+
+pETEV-16b-ppdk      TGACTTTGAAGGTATTTTCCGCGCAATGGATGGCCTGCCGGTGACCATCCGTCTGCTGGA
+FtPPDK-ref          TGACTTTGAAGGTATTTTCCGCGCAATGGATGGCCTGCCGGTGACCATCCGTCTGCTGGA
+                    ************************************************************
+
+pETEV-16b-ppdk      TCCGCCGCTGCATGAATTTCTGCCGGAAGGTGATCTGGAACACATTGTTAACGAACTGGC
+FtPPDK-ref          TCCGCCGCTGCATGAATTTCTGCCGGAAGGTGATCTGGAACACATTGTTAACGAACTGGC
+                    ************************************************************
+
+pETEV-16b-ppdk      AGTCGATACGGGCATGAGCGCTGACGAAATCTACTCTAAAATCGAAAACCTGAGTGAAGT
+FtPPDK-ref          AGTCGATACGGGCATGAGCGCTGACGAAATCTACTCTAAAATCGAAAACCTGAGTGAAGT
+                    ************************************************************
+
+pETEV-16b-ppdk      TAATCCGATGCTGGGTTTCCGTGGCTGTCGCCTGGGTATTTCGTACCCGGAACTGACCGA
+FtPPDK-ref          TAATCCGATGCTGGGTTTCCGTGGCTGTCGCCTGGGTATTTCGTACCCGGAACTGACCGA
+                    ************************************************************
+
+pETEV-16b-ppdk      AATGCAGGTTCGTGCCATCTTTCAAGCTGCGGTCAGCATGACCAACCAGGGTGTGACGGT
+FtPPDK-ref          AATGCAGGTTCGTGCCATCTTTCAAGCTGCGGTCAGCATGACCAACCAGGGTGTGACGGT
+                    ************************************************************
+
+pETEV-16b-ppdk      TATTCCGGAAATCATGGTCCCGCTGGTTGGCACCCCGCAGGAACTGCGTCACCAAATTTC
+FtPPDK-ref          TATTCCGGAAATCATGGTCCCGCTGGTTGGCACCCCGCAGGAACTGCGTCACCAAATTTC
+                    ************************************************************
+
+pETEV-16b-ppdk      TGTTATCCGCGGCGTCGCCGCAAATGTGTTTGCGGAAATGGGTGTCACCCTGGAATATAA
+FtPPDK-ref          TGTTATCCGCGGCGTCGCCGCAAATGTGTTTGCGGAAATGGGTGTCACCCTGGAATATAA
+                    ************************************************************
+
+pETEV-16b-ppdk      AGTGGGCACGATGATTGAAATCCCGCGTGCTGCGCTGATTGCGGAAGAAATCGGTAAAGA
+FtPPDK-ref          AGTGGGCACGATGATTGAAATCCCGCGTGCTGCGCTGATTGCGGAAGAAATCGGTAAAGA
+                    ************************************************************
+
+pETEV-16b-ppdk      AGCCGATTTCTTTAGCTTTGGCACCAACGACCTGACCCAGATGACGTTCGGTTATAGTCG
+FtPPDK-ref          AGCCGATTTCTTTAGCTTTGGCACCAACGACCTGACCCAGATGACGTTCGGTTATAGTCG
+                    ************************************************************
+
+pETEV-16b-ppdk      CGATGACGTGGGCAAATTTCTGCAAATTTACCTGGCCCAGGGTATCCTGCAACATGATCC
+FtPPDK-ref          CGATGACGTGGGCAAATTTCTGCAAATTTACCTGGCCCAGGGTATCCTGCAACATGATCC
+                    ************************************************************
+
+pETEV-16b-ppdk      GTTTGAAGTTATTGACCAGAAAGGCGTCGGTCAACTGATCAAAATGGCAACCGAAAAAGG
+FtPPDK-ref          GTTTGAAGTTATTGACCAGAAAGGCGTCGGTCAACTGATCAAAATGGCAACCGAAAAAGG
+                    ************************************************************
+
+pETEV-16b-ppdk      CCGCGCCGCAAATCCGAGTCTGAAAGTGGGTATTTGCGGCGAACACGGCGGTGAACCGAG
+FtPPDK-ref          CCGCGCCGCAAATCCGAGTCTGAAAGTGGGTATTTGCGGCGAACACGGCGGTGAACCGAG
+                    ************************************************************
+
+pETEV-16b-ppdk      TTCCGTGGCGTTTTTCGATGGCGTTGGTCTGGACTACGTTAGTTGTTCCCCGTTTCGTGT
+FtPPDK-ref          TTCCGTGGCGTTTTTCGATGGCGTTGGTCTGGACTACGTTAGTTGTTCCCCGTTTCGTGT
+                    ************************************************************
+
+pETEV-16b-ppdk      CCCGATTGCCCGTCTGGCTGCCGCCCAAGTGATTGTTTAACTCGAGGATCCGGCTGCTAA
+FtPPDK-ref          CCCGATTGCCCGTCTGGCTGCCGCCCAAGTGATTGTTTAACTCGAG--------------
+                    **********************************************              
+
+pETEV-16b-ppdk      CAAAGCCCGAAAGGAAGCTGAGTTGGCTGCTGCCACCGCTGAGCAATAACTAGCATAACC
+FtPPDK-ref          ------------------------------------------------------------
+                                                                                
+
+pETEV-16b-ppdk      CCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTG
+FtPPDK-ref          -------------------------------------
+