Good morning,

I've just discovered UGENE and found in the documentation that a frequency matrix can be created from a file:
"To create a position weight or frequency matrix from an alignment or a file with several sequences, press the Build new matrix button in the Weight matrix search dialog, or select the Tools ‣ Weight matrix ‣ Build weight matrix program main menu item"

Below I pasted a FASTA representation, could the frequency matrix be created for it in UGENE?
Thanks so much for any hint.
Karen

>1001
CCCACCACCCCCACCACACCACACCACCCCAAA

>1003
CTCCTTCACTTTCAATTAACAAACAACCAAAATCCATAAAAACCCAAAAACTATACCTAATAATATTCTCCCT

>1005
CCCCTCTTCCCTTCCT

>1012
AACCAAACCAAACAAAATCAAACTAATAATAAAAATCAAAACATAACAAAAAACCCTCCCCAAACCAAATCATAATCCAAAACCAACCTAAATCCTATTCCATCCACACAAACCCAAACTCAAA

>1017
CACAACACAATCAAACCAAAACAACCATCCCTCTCCATAACCAACAAACAACCAACCACCAACACAACCAAAACAAAACCACAAAAAACCAAACACAACCAAAACCACAACAACAAATCCT

>1022
CACCCACAACCCCACAACACAAACAACACACCCCACAA

>1024
AAAAAAAAACCCCAAAAACAAAAAACACCACCATCACTAATCCATCTCATACCAACCC

>1026
AAAAAAAAAACACAATCCTCCAACACAACCCACAACACAACAAAAAAACAACAAATCAATAAAAAATTTCTTCCCAAAAATTTCTAAAATCTATTTTCTTTTCTTACAAA

>1027
ATAATAACACAAAAAAAAAAAAAAACCACAAACAAAAAAACTTATTCATAATATTCCCCAAA

>1029
CCCCATCTCCCCCTCCCCCATCCCTCTCACTCCCCCCCTTTCCCTTTAAAAA

>1030
AAAAAATCCCCTTCCCCTTCCCCTTTCCTAATTATTCCCCCCCCCCCTTTTTCCCTCTTCTACACCAAATATCCCTTAAAAATCCCCTCCAAACCTTTAACCCACCACAATTCTTTATTAT

>1033
CACACACCAAAAAATCACTATACC

>1035
AAAAAAACAAACCAAAAACAC

>1037
CTCCTACACACCCCTCCTT


>1044
CCCCACAACCTCCAATCACAACCCCCC

>1052
ATCCCACATCTACTTCATACACATACAAA

>1053
CCAACTCCCTCCCTCTCCTACCCCC

>1055
AAAAAAAAAAACCTAAACCAACAAAACCAAAAACTACAACACTACCAATTTCCTTTAAATTAAACCTTACC

>1057
CACACAACAAAACACTCCAAAACTCCACCTAACACCCAATCCACACACCCAAACACAAACAAAAATAAAAAAAAAACACCAAAAAACCACAACAATCCCCAAA

>1067
CCCCAAACCCAAAAAAACCCCAAAACCCCCCCCCCCCCCTTCCTCTTATTATCCACTACCCCCAAAAATTAAATTAAAATTAATTAATATATAATCTATATTTCTTTTCCCACATTCTTTTCCCCACAAA

>1068
CACCACAACCACCACCACCCCCCACTTCATATATCAATATACAACCAACATCCTCCCTCAAACTAATCCAAAACCTCCCCCCAAAAA

>1073
CCAAAAAACAAATCAAAAATCCAATAATTCCACTTTTTAAATTACCTTCTCTATATATAACTCAAACAACA

>1088
CCCACAATCACCTCCTCCTTCTCCCTAATATACACCCCCACACCACACATCCAATCAATCATCTTTTTTTCCAAAATTTTTCCCCCAAACTAAAAACATATCCCCATACCCCCCCCCCCCCCTTATTATTTTAA

>1114
ACTCACACAAAATTCCCAATCTAAAATCACATTCACTATTCACTTTCTAATATTTCCTTAAAATACATAAAACCAAAAATCCTATTTTCACTACACAC

>1122
CAAAAACCCCAAAAACCTTTCCTTTCTTCCCCTTTAAAATAAACTCCATCAACCCTAAATAAAAATCCTCCCAAACAAAAAA

>1145
TTTCCTCTTTTTTTTTTTTTTCTCCTTTTTTTTTATTATTTATTATATATCTTAACATTTAATAATTACTTAATTTTATATTCTCTCCTTTTTTTTTTCTCTTTTTTTTAAATTTCCTAATTTTAATTATTTCACAATTCTAATTTCCACATTTATAG

>1146
CCCTACTCATACTCTCCACTACCCAACACTCCTTCAATTAAATTTAATTCATTACCTTATACTACCATTAACACCCAAAAAATTTCTCACTTTTATTTTTAATTTTTCTATCAAATTAAATCCATCCATTA

>1157
CTCTAATTTTCATCCATTTCCCACCTTTACAACAAAACCTAAAATAAAATTTCCCAATTCAACTTCCAAACAATCTCTTAATTATCTTCCAATAATACTCATTAAAAAAATTCTCCAACCAACC

>1161
ACACTCATATCCAATTTATATCTCCAAAAAACTCATATAATACCCTACATTACTTATTCCCAACCACCTACAACAAAATCTCATCATTTAAA

>1164
TCTCCTATCTTCTTATAA

>1187
AAAACCACAACAAAAAAACCAAAAAACCCAAAAACTCCCCTTCTCCTTCTCTCAATAAATCATAATTCTCCTTTTCTCCTTTCTTCTTTTTTTTTATACCATAAATATACCTAATAA

>1196
CTCCACACACTCTACAAATCATCAACTATCCCCCAACACTCTCCCTTCCCCTTCCCCCCCCTAAACTAATCCCAAAAAAAAACCCCACCACAACCCCAAAAAAAAA

>1206
CTTCAAACCCCACAAACCTACATATACCTACAAAATTCACCAACAA

Hello Karen,

thank you for using UGENE.

Usually a frequency matrix is built over sequences of the same length and without gaps. For instance, in your data, minimum sequence length is 18. So positions of a frequency matrix greater than 18 would not make sense.

You can try to cut you alignment using "Edit" context menu of MAlignment view or delete some sequences.

By the way, for what do you need the matrix? Maybe there is another way in UGENE to do that.