BISMA results:

Reference sequence (original) : GGGCCCATCAATGTCAGATGCAGCCACGTGGACAAAGAACACTCCCTGAGCACAAGACACGAAAGAACCCGGTCTCCAGTGTCACAAACAGGCCTGCCCAGCAGGGTCTGCCCCTGCCCACCTCCTCCAGCCTAGGTAAGGCCACAAAGCCCTGCCCTAGTGCTGACAGCGTGGGAGGGGCCACTGTTGGCCCAGCCCCACCCCCAACCAAGATCCCTTTGCCAGGGATTCAGAGGTAGCCCTGATGCCTGGCTGGCCTGGCCTCCTAATCCAAGGCCCGCCCCTTGGCCCGCCCCTGGCCTGGGTGGGGTGACCCCCTACAAAAGCTCAGAATTTCCAGCAGCGGCTCCTTCCTCCAGGAGTCTCTGGTGCAG
Reference sequence (converted): GGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
Number CpG in Reference sequence: 7

Parameters used:

Alignment mode: pairwise alignment of reference sequence and experimental sequences
Lower threshold conversion rate: 95%
Lower threshold sequence identity: 90%
Upper threshold of N-sites at cytosine positions: 20%
Upper threshold insertions/deletions: 20%

Final sequence alignment of the sequences included:

                                                                                                                                                                                                                                                                                                                                                                                           
                                                                                                   1                   1                   1                   1                   1                   2                   2                   2                   2                   2                   3                   3                   3                     3                 
                   2                   4                   6                   8                   0                   2                   4                   6                   8                   0                   2                   4                   6                   8                   0                   2                   4                     6                 
Number Sequence_id                    0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                     0                 
Reference GGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT--AGGAGTTTTTGGTGTAG
116-Hyal12C1-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT-TAGGAGTTTTTGGTGTAG
217-Hyal12C2-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT--AGGAGTTTTTGGTGTAG
318-Hyal12C3-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGGGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTANAATTTTTAGTAGTGGTTTTTTTTTTT--AGGAGTTTTTGGTGTAN
423-Hyal12C8-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT--AGGAGTTTTTGGTGTAG
527-Hyal12C12-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTTTAGGAGTTTTTGGTGTAG
621-Hyal12C6-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTCATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT--AGGAGTTTTTGGTGTAG
722-Hyal12C7-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTATAATTTTTAGTAGTGGTTTTTTTTTTT--AGGAGTTTTTGGTGTAG
825-Hyal12C10-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTT---AGGAGTTTTTGGTGTAG
928-Hyal12C13-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT--AGGAGTTTTTGGTGTAG
1019-Hyal12C4-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTT---AGGAGTTTTTGGTGTAG
1126-Hyal12C11-M13R.ab1selectionGGGTTTATTAATGTTANATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT-TAGGAGTTTTTGGTGTAG
1229-Hyal12C14-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTCAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT--AGGAGTTTTTGGTGTAG
1330-Hyal12C15-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT--AGGAGTTTTTGGTGTAG
Legend: methylated CpG position unmethylated CpG position unconverted cytosine cytosine at unexpected position

Methylation pattern in subclones:

methylated  , unmethylated  , unknown 

Methylation status of CpG-sites cytosine in the sequence context


Methylation pattern



Average methylation for each CpG site:

CpG site 1 2 3 4 5 6 7
CpG position 27 60 70 170 279 291 344
Methylation [%] 7.7 30.8 61.5 7.7 0.0 0.0 0.0


CG site No.

7.7%30.8%61.5%7.7%0.0%0.0%0.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 84.6% (77 cases)
Methylated CpGs: 15.4% (14 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (91 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
16-Hyal12C1-M13R.ab1selection 28.6
17-Hyal12C2-M13R.ab1selection 28.6
18-Hyal12C3-M13R.ab1selection 28.6
23-Hyal12C8-M13R.ab1selection 28.6
27-Hyal12C12-M13R.ab1selection 28.6
21-Hyal12C6-M13R.ab1selection 14.3
22-Hyal12C7-M13R.ab1selection 14.3
25-Hyal12C10-M13R.ab1selection 14.3
28-Hyal12C13-M13R.ab1selection 14.3
19-Hyal12C4-M13R.ab1selection 0
26-Hyal12C11-M13R.ab1selection 0
29-Hyal12C14-M13R.ab1selection 0
30-Hyal12C15-M13R.ab1selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 1/16/14
Tissue CTPE
Gene or position Hyal1 #2