AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0636670

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0636670 MtrunA17_Chr4g0019551 54.386 114 31 1 1 93 1 114 5.80e-31 110
Msa0636670 MtrunA17_Chr4g0019481 48.182 110 36 2 1 89 1 110 1.22e-23 91.3
Msa0636670 MtrunA17_Chr4g0019471 43.548 124 35 2 1 89 1 124 1.33e-21 86.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 40 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCGAATCTAATATTAAATT+TGG 0.129441 4_3:+27544293 None:intergenic
AAATAATTTACAAGATGATA+TGG 0.212103 4_3:-27544066 Msa0636670:CDS
GGTGGTTGAGGATGGTTATT+TGG 0.221703 4_3:+27544254 None:intergenic
TGTGGTTGAGGCTGGTTATT+TGG 0.223810 4_3:+27544233 None:intergenic
GCTTTCTGATAAGTGCTTCT+TGG 0.258496 4_3:+27543964 None:intergenic
TGCCATTTCCTCTTGCTTCC+TGG 0.265597 4_3:+27543896 None:intergenic
GGAGGCTGGCTCAAGTTAAT+TGG 0.275027 4_3:+27544164 None:intergenic
AGGTTCAAAGCTCGAACATT+AGG 0.361025 4_3:+27544143 None:intergenic
TGACTCGTATGCACAATAGA+AGG 0.372588 4_3:+27544113 None:intergenic
TATCAGAAAGCAAGAAGCTT+TGG 0.383471 4_3:-27543952 Msa0636670:CDS
GGCTGGTTATTTGGTGGTTG+AGG 0.391961 4_3:+27544242 None:intergenic
GGTTATTTGGTGGTTGAGGA+TGG 0.406136 4_3:+27544246 None:intergenic
TACCAGGAAGCAAGAGGAAA+TGG 0.421313 4_3:-27543898 Msa0636670:CDS
GGATGGTTATTTGGTGGTAG+AGG 0.431093 4_3:+27544263 None:intergenic
AAGTGAAGATGGAGCAGAAA+AGG 0.463976 4_3:-27543998 Msa0636670:CDS
AAGTTAATTGGCTGCACATG+TGG 0.509287 4_3:+27544176 None:intergenic
AATAATTTACAAGATGATAT+GGG 0.509595 4_3:-27544065 Msa0636670:CDS
GTTGCTTCTTCATCATCTCA+AGG 0.532802 4_3:+27543781 None:intergenic
GGTTGAGGCTGGTTATTTGG+TGG 0.533930 4_3:+27544236 None:intergenic
GACTCGTATGCACAATAGAA+GGG 0.537355 4_3:+27544114 None:intergenic
GAGAATGCAACAACAACACT+TGG 0.542875 4_3:-27543925 Msa0636670:CDS
GAGCAATCTAAGACAAATGC+TGG 0.544449 4_3:-27543816 Msa0636670:CDS
AACATGCACTGCTAAAACAT+GGG 0.552835 4_3:+27544331 None:intergenic
AAGCTCGAACATTAGGAGGC+TGG 0.553043 4_3:+27544150 None:intergenic
ACTGCATAAGAATTCTAGCT+TGG 0.557073 4_3:+27544379 None:intergenic
GGTTGAGGATGGTTATTTGG+TGG 0.557091 4_3:+27544257 None:intergenic
TAACATGCACTGCTAAAACA+TGG 0.569150 4_3:+27544330 None:intergenic
TCAACTGTTAGAAGTGAAGA+TGG 0.576254 4_3:-27544009 Msa0636670:CDS
TTCAAAGCTCGAACATTAGG+AGG 0.585789 4_3:+27544146 None:intergenic
ACTGCTAAAACATGGGGAGA+TGG 0.597465 4_3:+27544338 None:intergenic
GGAAACTACCAGGAAGCAAG+AGG 0.631081 4_3:-27543904 Msa0636670:CDS
GAAACAACATGAGGAGACAA+TGG 0.637862 4_3:-27543841 Msa0636670:CDS
AACAACACTTGGAAACTACC+AGG 0.641183 4_3:-27543914 Msa0636670:CDS
ACTCGTATGCACAATAGAAG+GGG 0.645441 4_3:+27544115 None:intergenic
CTCGTATGCACAATAGAAGG+GGG 0.684292 4_3:+27544116 None:intergenic
TTAATTGGCTGCACATGTGG+AGG 0.687081 4_3:+27544179 None:intergenic
ACATGCACTGCTAAAACATG+GGG 0.693010 4_3:+27544332 None:intergenic
AAACATGCAGAAACAACATG+AGG 0.696986 4_3:-27543850 Msa0636670:CDS
TGTGGAGGTGATGCATTGTG+TGG 0.709748 4_3:+27544194 None:intergenic
GCATACGAGTCAAGATCCTG+AGG 0.710797 4_3:-27544102 Msa0636670:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAATTTACAAGATGATA+TGG - chr4_3:27544087-27544106 Msa0636670:CDS 15.0%
!! AATAATTTACAAGATGATAT+GGG - chr4_3:27544088-27544107 Msa0636670:CDS 15.0%
!! CTCGAATCTAATATTAAATT+TGG + chr4_3:27543863-27543882 None:intergenic 20.0%
! TTTTGAACGATAATAACCTC+AGG + chr4_3:27544070-27544089 None:intergenic 30.0%
! ACTGCATAAGAATTCTAGCT+TGG + chr4_3:27543777-27543796 None:intergenic 35.0%
AACATGCACTGCTAAAACAT+GGG + chr4_3:27543825-27543844 None:intergenic 35.0%
TAACATGCACTGCTAAAACA+TGG + chr4_3:27543826-27543845 None:intergenic 35.0%
TCAACTGTTAGAAGTGAAGA+TGG - chr4_3:27544144-27544163 Msa0636670:CDS 35.0%
TATCAGAAAGCAAGAAGCTT+TGG - chr4_3:27544201-27544220 Msa0636670:CDS 35.0%
AAACATGCAGAAACAACATG+AGG - chr4_3:27544303-27544322 Msa0636670:CDS 35.0%
ACATGCACTGCTAAAACATG+GGG + chr4_3:27543824-27543843 None:intergenic 40.0%
! TGTGTTGCATTTTGTGGTTG+AGG + chr4_3:27543935-27543954 None:intergenic 40.0%
AAGTTAATTGGCTGCACATG+TGG + chr4_3:27543980-27543999 None:intergenic 40.0%
TTCAAAGCTCGAACATTAGG+AGG + chr4_3:27544010-27544029 None:intergenic 40.0%
AGGTTCAAAGCTCGAACATT+AGG + chr4_3:27544013-27544032 None:intergenic 40.0%
ACTCGTATGCACAATAGAAG+GGG + chr4_3:27544041-27544060 None:intergenic 40.0%
GACTCGTATGCACAATAGAA+GGG + chr4_3:27544042-27544061 None:intergenic 40.0%
TGACTCGTATGCACAATAGA+AGG + chr4_3:27544043-27544062 None:intergenic 40.0%
AAGTGAAGATGGAGCAGAAA+AGG - chr4_3:27544155-27544174 Msa0636670:CDS 40.0%
GCTTTCTGATAAGTGCTTCT+TGG + chr4_3:27544192-27544211 None:intergenic 40.0%
GAGAATGCAACAACAACACT+TGG - chr4_3:27544228-27544247 Msa0636670:CDS 40.0%
AACAACACTTGGAAACTACC+AGG - chr4_3:27544239-27544258 Msa0636670:CDS 40.0%
GAAACAACATGAGGAGACAA+TGG - chr4_3:27544312-27544331 Msa0636670:CDS 40.0%
! GAGCAATCTAAGACAAATGC+TGG - chr4_3:27544337-27544356 Msa0636670:CDS 40.0%
GTTGCTTCTTCATCATCTCA+AGG + chr4_3:27544375-27544394 None:intergenic 40.0%
ACTGCTAAAACATGGGGAGA+TGG + chr4_3:27543818-27543837 None:intergenic 45.0%
! GGATGGTTATTTGGTGGTAG+AGG + chr4_3:27543893-27543912 None:intergenic 45.0%
GGTTGAGGATGGTTATTTGG+TGG + chr4_3:27543899-27543918 None:intergenic 45.0%
GGTGGTTGAGGATGGTTATT+TGG + chr4_3:27543902-27543921 None:intergenic 45.0%
! GGTTATTTGGTGGTTGAGGA+TGG + chr4_3:27543910-27543929 None:intergenic 45.0%
! TGTGGTTGAGGCTGGTTATT+TGG + chr4_3:27543923-27543942 None:intergenic 45.0%
! TTGCATTTTGTGGTTGAGGC+TGG + chr4_3:27543931-27543950 None:intergenic 45.0%
! GGTCGATGTGTTGCATTTTG+TGG + chr4_3:27543941-27543960 None:intergenic 45.0%
TTAATTGGCTGCACATGTGG+AGG + chr4_3:27543977-27543996 None:intergenic 45.0%
GCACAATAGAAGGGGGATTA+AGG + chr4_3:27544033-27544052 None:intergenic 45.0%
CTCGTATGCACAATAGAAGG+GGG + chr4_3:27544040-27544059 None:intergenic 45.0%
TACCAGGAAGCAAGAGGAAA+TGG - chr4_3:27544255-27544274 Msa0636670:CDS 45.0%
! GGCTGGTTATTTGGTGGTTG+AGG + chr4_3:27543914-27543933 None:intergenic 50.0%
! GGTTGAGGCTGGTTATTTGG+TGG + chr4_3:27543920-27543939 None:intergenic 50.0%
TGTGGAGGTGATGCATTGTG+TGG + chr4_3:27543962-27543981 None:intergenic 50.0%
! GGAGGCTGGCTCAAGTTAAT+TGG + chr4_3:27543992-27544011 None:intergenic 50.0%
AAGCTCGAACATTAGGAGGC+TGG + chr4_3:27544006-27544025 None:intergenic 50.0%
GCATACGAGTCAAGATCCTG+AGG - chr4_3:27544051-27544070 Msa0636670:CDS 50.0%
GGAAACTACCAGGAAGCAAG+AGG - chr4_3:27544249-27544268 Msa0636670:CDS 50.0%
! TGCCATTTCCTCTTGCTTCC+TGG + chr4_3:27544260-27544279 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 27543770 27544405 27543770 ID=Msa0636670;Name=Msa0636670
chr4_3 mRNA 27543770 27544405 27543770 ID=Msa0636670-mRNA-1;Parent=Msa0636670;Name=Msa0636670-mRNA-1;_AED=0.31;_eAED=0.31;_QI=0|-1|0|1|-1|1|1|0|211
chr4_3 exon 27543770 27544405 27543770 ID=Msa0636670-mRNA-1:exon:6813;Parent=Msa0636670-mRNA-1
chr4_3 CDS 27543770 27544405 27543770 ID=Msa0636670-mRNA-1:cds;Parent=Msa0636670-mRNA-1
Gene Sequence

>Msa0636670

ATGACCAAGCTAGAATTCTTATGCAGTGATTGTGACGCAAAGTTTCCATCTCCCCATGTTTTAGCAGTGCATGTTATCGAACAACATCATCCAAATTTAATATTAGATTCGAGTGCAAATCCTCTACCACCAAATAACCATCCTCAACCACCAAATAACCAGCCTCAACCACAAAATGCAACACATCGACCACACAATGCATCACCTCCACATGTGCAGCCAATTAACTTGAGCCAGCCTCCTAATGTTCGAGCTTTGAACCTTAATCCCCCTTCTATTGTGCATACGAGTCAAGATCCTGAGGTTATTATCGTTCAAAATAATTTACAAGATGATATGGGAAATCAGAAGCTGACAACAGAAGTTGTGCAAGCTCAACTGTTAGAAGTGAAGATGGAGCAGAAAAGGCAGAATGATATCCAAGAAGCACTTATCAGAAAGCAAGAAGCTTTGGAAAAGAGAATGCAACAACAACACTTGGAAACTACCAGGAAGCAAGAGGAAATGGCAAAGAAGCAAGAAGAACTTGAAAGAAACATGCAGAAACAACATGAGGAGACAATGGCTGAGCAATCTAAGACAAATGCTGGCATTGCTGCTATCCTTGAGATGATGAAGAAGCAACAACAACCTTAA
Protein sequence

>Msa0636670

MTKLEFLCSDCDAKFPSPHVLAVHVIEQHHPNLILDSSANPLPPNNHPQPPNNQPQPQNATHRPHNASPPHVQPINLSQPPNVRALNLNPPSIVHTSQDPEVIIVQNNLQDDMGNQKLTTEVVQAQLLEVKMEQKRQNDIQEALIRKQEALEKRMQQQHLETTRKQEEMAKKQEELERNMQKQHEETMAEQSKTNAGIAAILEMMKKQQQP*