Column	Description
Sequence index	The index of the sequence
Position	The start position of predicted binding site (BS) within the sequence
Strand	The strand of the predicted BS
p-value	The p-value of the predicted BS
Binding site	The binding site as in the sequence
Adjusted binding site	The binding site in predicted orientation
Sequence annotation	The annotation of the original sequence

-----------------------------------------
pre-optimization 0
consensus: NNNGGATTAgNNNNN
score: -0.295567005150279
-----------------------------------------
pre-optimization 1
consensus: NNNNNNNGCTAATCC
score: -0.2968705301682643
-----------------------------------------
pre-optimization 2
consensus: NNNNNNNNNGGATTA
score: -0.2998645110489622
-----------------------------------------
pre-optimization 3
consensus: NNNNNNNCTACCTGN
score: -0.3087596251574336
-----------------------------------------
pre-optimization 4
consensus: NNNNNNNcTAATCCN
score: -0.29644063340606813
-----------------------------------------
pre-optimization 5
consensus: NNNNNNNcTAATCCN
score: -0.2966054557344498
-----------------------------------------
pre-optimization 6
consensus: NNNNNNGGATTAgNN
score: -0.2960250155204568
-----------------------------------------
pre-optimization 7
consensus: NNNNNNNNGGATTAG
score: -0.29700657112246615
-----------------------------------------
pre-optimization 8
consensus: NNNNNNNNGGATTAG
score: -0.2968825997973593
-----------------------------------------
pre-optimization 9
consensus: NcTAATCCNNNNNNN
score: -0.29658902318223385
-----------------------------------------
pre-optimization 10
consensus: NNNNNcTAATCCNNN
score: -0.2956125682458301
-----------------------------------------
pre-optimization 11
consensus: NNNNNNNcTAATCCN
score: -0.296571619107918
-----------------------------------------
pre-optimization 12
consensus: NNNNNNNcTAATCCN
score: -0.2962341972836779
-----------------------------------------
pre-optimization 13
consensus: NcTAATCCNNNNNNN
score: -0.29655816176857164
-----------------------------------------
pre-optimization 14
consensus: NcTAATCCNNNNNNN
score: -0.2965258452522728
-----------------------------------------
pre-optimization 15
consensus: NNNNGGATTAgNNNN
score: -0.29611726030602253
-----------------------------------------
pre-optimization 16
consensus: NNNNGGATTAgNNNN
score: -0.29582934750532014
-----------------------------------------
pre-optimization 17
consensus: NNNNGGATTAgNNNN
score: -0.2960919285853769
-----------------------------------------
pre-optimization 18
consensus: NNNNCAGGTAGNNNN
score: -0.309349126583713
-----------------------------------------
pre-optimization 19
consensus: NNNNcTAATCCNNNN
score: -0.29618438710408135
-----------------------------------------
added: NNNGGATTAgNNNNN
added: NNNNNNNCTACCTGN
number of motifs: 2
+++++++++++++++++++++++++++++++++++++++++++++++++++

finalOpt 0 -----------------------------------------
left: 3, right: -5
modified motif
consensus: GGATTAG
+++++++++++++++++++++++++++++++++++++++++++++++++++

finalOpt 1 -----------------------------------------
left: 7, right: -1
modified motif
consensus: CTACCTG

++++++++++++++++++++++++++++++++++++++++++++++

Motif model 1

motif probability: 0.906

Probabilities at position 0:

A	C	G	T
0.144	0.087	0.725	0.044

Probabilities at position 1:

A	C	G	T
0.040	0.045	0.868	0.047

Probabilities at position 2:

A	C	G	T
0.686	0.188	0.061	0.065

Probabilities at position 3:

A	C	G	T
0.048	0.120	0.052	0.781

Probabilities at position 4:

A	C	G	T
0.055	0.130	0.040	0.776

Probabilities at position 5:

A	C	G	T
0.711	0.067	0.057	0.165

Probabilities at position 6:

A	C	G	T
0.319	0.080	0.424	0.177

++++++++++++++++++++++++++++++++++++++++++++++

Motif model 2

motif probability: 0.892

Probabilities at position 0:

A	C	G	T
0.104	0.451	0.177	0.268

Probabilities at position 1:

A	C	G	T
0.063	0.032	0.152	0.753

Probabilities at position 2:

A	C	G	T
0.729	0.063	0.147	0.061

Probabilities at position 3:

A	C	G	T
0.048	0.847	0.061	0.044

Probabilities at position 4:

A	C	G	T
0.045	0.827	0.078	0.051

Probabilities at position 5:

A	C	G	T
0.046	0.078	0.105	0.771

Probabilities at position 6:

A	C	G	T
0.242	0.081	0.603	0.074