AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0574180


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0574180 MtrunA17_Chr3g0087691 37.143 70 44 0 1 70 200 269 6.29e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAAAGTGCGTAATTTAATA+TGG 0.282373 4_1:+77545609 Msa0574180:CDS
CGGGAGATTGGGGCAGTTTG+TGG 0.311118 4_1:+77545570 Msa0574180:CDS
CTTTAGATCGTGCACTGTTC+CGG 0.318558 4_1:-77546062 None:intergenic
GTGTCTTACGCCGGGAGATT+GGG 0.325199 4_1:+77545559 Msa0574180:CDS
TGTTCTGTCCACTAATGTTC+CGG 0.368591 4_1:-77546115 None:intergenic
GGTGTCTTACGCCGGGAGAT+TGG 0.369480 4_1:+77545558 Msa0574180:CDS
GGGCAGAATCAAACATGTTT+CGG 0.393461 4_1:+77546176 Msa0574180:CDS
GGGAGATTGGGGCAGTTTGT+GGG 0.396607 4_1:+77545571 Msa0574180:CDS
ATTTAATATGGAGAATTTGT+AGG 0.404420 4_1:+77545621 Msa0574180:CDS
AACTATTATGGATATTCCTC+TGG 0.407253 4_1:+77545427 None:intergenic
GGTTTGTACACTGTGCATTC+CGG 0.416558 4_1:+77545497 Msa0574180:CDS
TCGCATAATAAATCTATAAC+CGG 0.426836 4_1:-77545516 None:intergenic
ACCAACCTGATGCTTTCATA+TGG 0.443089 4_1:+77545459 Msa0574180:CDS
AGCAGAAGCCGGAACATTAG+TGG 0.475752 4_1:+77546107 Msa0574180:CDS
TCATTCCATATGAAAGCATC+AGG 0.478628 4_1:-77545464 None:intergenic
CACAAACTGCCCCAATCTCC+CGG 0.486888 4_1:-77545569 None:intergenic
AACAAAACAACAGCAGAAGC+CGG 0.495870 4_1:+77546096 Msa0574180:CDS
TATTATGCGAGGGTCTTTGA+AGG 0.516650 4_1:+77545529 Msa0574180:CDS
AACATGTTTGATTCTGCCCA+TGG 0.520894 4_1:-77546172 None:intergenic
GGAAGAGAGGTGTCTTACGC+CGG 0.527460 4_1:+77545550 Msa0574180:CDS
TGTCTTACGCCGGGAGATTG+GGG 0.530422 4_1:+77545560 Msa0574180:CDS
TTGTTCGAGCATTGATAGAG+TGG 0.537743 4_1:+77546227 Msa0574180:CDS
GAAGAGAGGTGTCTTACGCC+GGG 0.542501 4_1:+77545551 Msa0574180:CDS
GGAGATTGGGGCAGTTTGTG+GGG 0.548025 4_1:+77545572 Msa0574180:CDS
TCCATATGAAAGCATCAGGT+TGG 0.570691 4_1:-77545460 None:intergenic
GTTATAGATTTATTATGCGA+GGG 0.575166 4_1:+77545519 Msa0574180:CDS
TGATGCTTTCATATGGAATG+AGG 0.590087 4_1:+77545466 Msa0574180:CDS
CTTTCATATGGAATGAGGAG+TGG 0.601032 4_1:+77545471 Msa0574180:CDS
ATATGGAATGAGGAGTGGAA+CGG 0.603991 4_1:+77545476 Msa0574180:CDS
GGTTATAGATTTATTATGCG+AGG 0.612842 4_1:+77545518 Msa0574180:CDS
GGTTGGTCATCTATAACCAG+AGG 0.668757 4_1:-77545443 None:intergenic
GAGGGTCTTTGAAGGAAGAG+AGG 0.673662 4_1:+77545537 Msa0574180:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTAATATGGAGAATTTGT+AGG + chr4_1:77545621-77545640 Msa0574180:CDS 20.0%
!!! TTAATCTCGTTTTAATTAAG+TGG + chr4_1:77545811-77545830 Msa0574180:intron 20.0%
!!! TAATCTCGTTTTAATTAAGT+GGG + chr4_1:77545812-77545831 Msa0574180:intron 20.0%
!! ATAATAGAAATGATTGGATT+TGG + chr4_1:77545915-77545934 Msa0574180:intron 20.0%
!! ATTTAATATGGAGAATTTGT+AGG + chr4_1:77545621-77545640 Msa0574180:CDS 20.0%
!!! TTAATCTCGTTTTAATTAAG+TGG + chr4_1:77545811-77545830 Msa0574180:intron 20.0%
!!! TAATCTCGTTTTAATTAAGT+GGG + chr4_1:77545812-77545831 Msa0574180:intron 20.0%
!! ATAATAGAAATGATTGGATT+TGG + chr4_1:77545915-77545934 Msa0574180:intron 20.0%
! TCGCATAATAAATCTATAAC+CGG - chr4_1:77545519-77545538 None:intergenic 25.0%
! GTTATAGATTTATTATGCGA+GGG + chr4_1:77545519-77545538 Msa0574180:CDS 25.0%
! CTAAAGTGCGTAATTTAATA+TGG + chr4_1:77545609-77545628 Msa0574180:CDS 25.0%
!! ATTAGTATTGAATGTTAGAC+TGG + chr4_1:77545758-77545777 Msa0574180:intron 25.0%
! TTTGGCATAATAGAAATGAT+TGG + chr4_1:77545909-77545928 Msa0574180:intron 25.0%
! TCGCATAATAAATCTATAAC+CGG - chr4_1:77545519-77545538 None:intergenic 25.0%
! GTTATAGATTTATTATGCGA+GGG + chr4_1:77545519-77545538 Msa0574180:CDS 25.0%
! CTAAAGTGCGTAATTTAATA+TGG + chr4_1:77545609-77545628 Msa0574180:CDS 25.0%
!! ATTAGTATTGAATGTTAGAC+TGG + chr4_1:77545758-77545777 Msa0574180:intron 25.0%
! TTTGGCATAATAGAAATGAT+TGG + chr4_1:77545909-77545928 Msa0574180:intron 25.0%
GGTTATAGATTTATTATGCG+AGG + chr4_1:77545518-77545537 Msa0574180:CDS 30.0%
!!! ATTGACACAAGTTTTTTCCA+TGG + chr4_1:77546155-77546174 Msa0574180:CDS 30.0%
!!! TTGACACAAGTTTTTTCCAT+GGG + chr4_1:77546156-77546175 Msa0574180:CDS 30.0%
GGTTATAGATTTATTATGCG+AGG + chr4_1:77545518-77545537 Msa0574180:CDS 30.0%
!!! ATTGACACAAGTTTTTTCCA+TGG + chr4_1:77546155-77546174 Msa0574180:CDS 30.0%
!!! TTGACACAAGTTTTTTCCAT+GGG + chr4_1:77546156-77546175 Msa0574180:CDS 30.0%
!! TCATTCCATATGAAAGCATC+AGG - chr4_1:77545467-77545486 None:intergenic 35.0%
TGATGCTTTCATATGGAATG+AGG + chr4_1:77545466-77545485 Msa0574180:CDS 35.0%
!!! TCTCGTTTTAATTAAGTGGG+AGG + chr4_1:77545815-77545834 Msa0574180:intron 35.0%
!!! CTCGTTTTAATTAAGTGGGA+GGG + chr4_1:77545816-77545835 Msa0574180:intron 35.0%
!!! TCGTTTTAATTAAGTGGGAG+GGG + chr4_1:77545817-77545836 Msa0574180:intron 35.0%
TGTTAGTAGATTCTTGACGA+TGG + chr4_1:77545877-77545896 Msa0574180:intron 35.0%
! GATTGCCAATTGATCTTTTG+CGG - chr4_1:77545943-77545962 None:intergenic 35.0%
!! TCATTCCATATGAAAGCATC+AGG - chr4_1:77545467-77545486 None:intergenic 35.0%
TGATGCTTTCATATGGAATG+AGG + chr4_1:77545466-77545485 Msa0574180:CDS 35.0%
!!! TCTCGTTTTAATTAAGTGGG+AGG + chr4_1:77545815-77545834 Msa0574180:intron 35.0%
!!! CTCGTTTTAATTAAGTGGGA+GGG + chr4_1:77545816-77545835 Msa0574180:intron 35.0%
!!! TCGTTTTAATTAAGTGGGAG+GGG + chr4_1:77545817-77545836 Msa0574180:intron 35.0%
TGTTAGTAGATTCTTGACGA+TGG + chr4_1:77545877-77545896 Msa0574180:intron 35.0%
! GATTGCCAATTGATCTTTTG+CGG - chr4_1:77545943-77545962 None:intergenic 35.0%
ACCAACCTGATGCTTTCATA+TGG + chr4_1:77545459-77545478 Msa0574180:CDS 40.0%
!! TCCATATGAAAGCATCAGGT+TGG - chr4_1:77545463-77545482 None:intergenic 40.0%
CTTTCATATGGAATGAGGAG+TGG + chr4_1:77545471-77545490 Msa0574180:CDS 40.0%
ATATGGAATGAGGAGTGGAA+CGG + chr4_1:77545476-77545495 Msa0574180:CDS 40.0%
TATTATGCGAGGGTCTTTGA+AGG + chr4_1:77545529-77545548 Msa0574180:CDS 40.0%
CACATAATCCACAGTTTGTC+AGG - chr4_1:77545694-77545713 None:intergenic 40.0%
TGGAACCGCAAAAGATCAAT+TGG + chr4_1:77545935-77545954 Msa0574180:intron 40.0%
TGGCAATCAAATTCTGTGTC+TGG + chr4_1:77545955-77545974 Msa0574180:intron 40.0%
TAAGTTTAGTGCAGTCTGAC+TGG + chr4_1:77545978-77545997 Msa0574180:intron 40.0%
AACAAAACAACAGCAGAAGC+CGG + chr4_1:77546096-77546115 Msa0574180:CDS 40.0%
TGTTCTGTCCACTAATGTTC+CGG - chr4_1:77546118-77546137 None:intergenic 40.0%
AACATGTTTGATTCTGCCCA+TGG - chr4_1:77546175-77546194 None:intergenic 40.0%
GGGCAGAATCAAACATGTTT+CGG + chr4_1:77546176-77546195 Msa0574180:CDS 40.0%
ACCAACCTGATGCTTTCATA+TGG + chr4_1:77545459-77545478 Msa0574180:CDS 40.0%
!! TCCATATGAAAGCATCAGGT+TGG - chr4_1:77545463-77545482 None:intergenic 40.0%
CTTTCATATGGAATGAGGAG+TGG + chr4_1:77545471-77545490 Msa0574180:CDS 40.0%
ATATGGAATGAGGAGTGGAA+CGG + chr4_1:77545476-77545495 Msa0574180:CDS 40.0%
TATTATGCGAGGGTCTTTGA+AGG + chr4_1:77545529-77545548 Msa0574180:CDS 40.0%
CACATAATCCACAGTTTGTC+AGG - chr4_1:77545694-77545713 None:intergenic 40.0%
TGGAACCGCAAAAGATCAAT+TGG + chr4_1:77545935-77545954 Msa0574180:intron 40.0%
TGGCAATCAAATTCTGTGTC+TGG + chr4_1:77545955-77545974 Msa0574180:intron 40.0%
TAAGTTTAGTGCAGTCTGAC+TGG + chr4_1:77545978-77545997 Msa0574180:intron 40.0%
AACAAAACAACAGCAGAAGC+CGG + chr4_1:77546096-77546115 Msa0574180:CDS 40.0%
TGTTCTGTCCACTAATGTTC+CGG - chr4_1:77546118-77546137 None:intergenic 40.0%
AACATGTTTGATTCTGCCCA+TGG - chr4_1:77546175-77546194 None:intergenic 40.0%
GGGCAGAATCAAACATGTTT+CGG + chr4_1:77546176-77546195 Msa0574180:CDS 40.0%
! GGTTGGTCATCTATAACCAG+AGG - chr4_1:77545446-77545465 None:intergenic 45.0%
GGTTTGTACACTGTGCATTC+CGG + chr4_1:77545497-77545516 Msa0574180:CDS 45.0%
ACCAACACGAGACAAACTTC+AGG + chr4_1:77545652-77545671 Msa0574180:intron 45.0%
TCCTGAAGTTTGTCTCGTGT+TGG - chr4_1:77545656-77545675 None:intergenic 45.0%
AATCCACAGTTTGTCAGGCA+AGG - chr4_1:77545689-77545708 None:intergenic 45.0%
TGGTGCAAGACTGCTTTCAA+TGG + chr4_1:77545778-77545797 Msa0574180:intron 45.0%
TGTCTGTGTGCGTGAATCTA+AGG + chr4_1:77545850-77545869 Msa0574180:intron 45.0%
ACCAAAACAACAGCAGAAGC+CGG + chr4_1:77546043-77546062 Msa0574180:intron 45.0%
CTTTAGATCGTGCACTGTTC+CGG - chr4_1:77546065-77546084 None:intergenic 45.0%
! GGTTGGTCATCTATAACCAG+AGG - chr4_1:77545446-77545465 None:intergenic 45.0%
GGTTTGTACACTGTGCATTC+CGG + chr4_1:77545497-77545516 Msa0574180:CDS 45.0%
ACCAACACGAGACAAACTTC+AGG + chr4_1:77545652-77545671 Msa0574180:intron 45.0%
TCCTGAAGTTTGTCTCGTGT+TGG - chr4_1:77545656-77545675 None:intergenic 45.0%
AATCCACAGTTTGTCAGGCA+AGG - chr4_1:77545689-77545708 None:intergenic 45.0%
TGGTGCAAGACTGCTTTCAA+TGG + chr4_1:77545778-77545797 Msa0574180:intron 45.0%
TGTCTGTGTGCGTGAATCTA+AGG + chr4_1:77545850-77545869 Msa0574180:intron 45.0%
ACCAAAACAACAGCAGAAGC+CGG + chr4_1:77546043-77546062 Msa0574180:intron 45.0%
CTTTAGATCGTGCACTGTTC+CGG - chr4_1:77546065-77546084 None:intergenic 45.0%
! GAGGGTCTTTGAAGGAAGAG+AGG + chr4_1:77545537-77545556 Msa0574180:CDS 50.0%
GTTCCTTGCCTGACAAACTG+TGG + chr4_1:77545683-77545702 Msa0574180:intron 50.0%
TTAAGTGGGAGGGGTTCTGT+TGG + chr4_1:77545826-77545845 Msa0574180:intron 50.0%
AGATTCTTGACGATGGTGCG+AGG + chr4_1:77545884-77545903 Msa0574180:intron 50.0%
GATTCTTGACGATGGTGCGA+GGG + chr4_1:77545885-77545904 Msa0574180:intron 50.0%
TTTAGTGCAGTCTGACTGGC+AGG + chr4_1:77545982-77546001 Msa0574180:intron 50.0%
TTAGTGCAGTCTGACTGGCA+GGG + chr4_1:77545983-77546002 Msa0574180:intron 50.0%
!! TCCGGCTTCTGCTGTTGTTT+TGG - chr4_1:77546047-77546066 None:intergenic 50.0%
AGCAGAAGCCGGAACATTAG+TGG + chr4_1:77546107-77546126 Msa0574180:CDS 50.0%
! GAGGGTCTTTGAAGGAAGAG+AGG + chr4_1:77545537-77545556 Msa0574180:CDS 50.0%
GTTCCTTGCCTGACAAACTG+TGG + chr4_1:77545683-77545702 Msa0574180:intron 50.0%
TTAAGTGGGAGGGGTTCTGT+TGG + chr4_1:77545826-77545845 Msa0574180:intron 50.0%
AGATTCTTGACGATGGTGCG+AGG + chr4_1:77545884-77545903 Msa0574180:intron 50.0%
GATTCTTGACGATGGTGCGA+GGG + chr4_1:77545885-77545904 Msa0574180:intron 50.0%
TTTAGTGCAGTCTGACTGGC+AGG + chr4_1:77545982-77546001 Msa0574180:intron 50.0%
TTAGTGCAGTCTGACTGGCA+GGG + chr4_1:77545983-77546002 Msa0574180:intron 50.0%
!! TCCGGCTTCTGCTGTTGTTT+TGG - chr4_1:77546047-77546066 None:intergenic 50.0%
AGCAGAAGCCGGAACATTAG+TGG + chr4_1:77546107-77546126 Msa0574180:CDS 50.0%
!! GGAAGAGAGGTGTCTTACGC+CGG + chr4_1:77545550-77545569 Msa0574180:CDS 55.0%
!! GAAGAGAGGTGTCTTACGCC+GGG + chr4_1:77545551-77545570 Msa0574180:CDS 55.0%
GTGTCTTACGCCGGGAGATT+GGG + chr4_1:77545559-77545578 Msa0574180:CDS 55.0%
TGTCTTACGCCGGGAGATTG+GGG + chr4_1:77545560-77545579 Msa0574180:CDS 55.0%
CACAAACTGCCCCAATCTCC+CGG - chr4_1:77545572-77545591 None:intergenic 55.0%
GGGAGATTGGGGCAGTTTGT+GGG + chr4_1:77545571-77545590 Msa0574180:CDS 55.0%
GGAGATTGGGGCAGTTTGTG+GGG + chr4_1:77545572-77545591 Msa0574180:CDS 55.0%
TGACGATGGTGCGAGGGATT+TGG + chr4_1:77545891-77545910 Msa0574180:intron 55.0%
!! GGAAGAGAGGTGTCTTACGC+CGG + chr4_1:77545550-77545569 Msa0574180:CDS 55.0%
!! GAAGAGAGGTGTCTTACGCC+GGG + chr4_1:77545551-77545570 Msa0574180:CDS 55.0%
GTGTCTTACGCCGGGAGATT+GGG + chr4_1:77545559-77545578 Msa0574180:CDS 55.0%
TGTCTTACGCCGGGAGATTG+GGG + chr4_1:77545560-77545579 Msa0574180:CDS 55.0%
CACAAACTGCCCCAATCTCC+CGG - chr4_1:77545572-77545591 None:intergenic 55.0%
GGGAGATTGGGGCAGTTTGT+GGG + chr4_1:77545571-77545590 Msa0574180:CDS 55.0%
GGAGATTGGGGCAGTTTGTG+GGG + chr4_1:77545572-77545591 Msa0574180:CDS 55.0%
TGACGATGGTGCGAGGGATT+TGG + chr4_1:77545891-77545910 Msa0574180:intron 55.0%
GGTGTCTTACGCCGGGAGAT+TGG + chr4_1:77545558-77545577 Msa0574180:CDS 60.0%
CGGGAGATTGGGGCAGTTTG+TGG + chr4_1:77545570-77545589 Msa0574180:CDS 60.0%
GGTGTCTTACGCCGGGAGAT+TGG + chr4_1:77545558-77545577 Msa0574180:CDS 60.0%
CGGGAGATTGGGGCAGTTTG+TGG + chr4_1:77545570-77545589 Msa0574180:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 77545434 77546248 77545434 ID=Msa0574180;Name=Msa0574180
chr4_1 mRNA 77545434 77546248 77545434 ID=Msa0574180-mRNA-1;Parent=Msa0574180;Name=Msa0574180-mRNA-1;_AED=0.46;_eAED=0.50;_QI=0|0|0|1|0|0|2|0|134
chr4_1 exon 77545434 77545645 77545434 ID=Msa0574180-mRNA-1:exon:27373;Parent=Msa0574180-mRNA-1
chr4_1 exon 77546059 77546248 77546059 ID=Msa0574180-mRNA-1:exon:27374;Parent=Msa0574180-mRNA-1
chr4_1 CDS 77545434 77545645 77545434 ID=Msa0574180-mRNA-1:cds;Parent=Msa0574180-mRNA-1
chr4_1 CDS 77546059 77546248 77546059 ID=Msa0574180-mRNA-1:cds;Parent=Msa0574180-mRNA-1
Gene Sequence

>Msa0574180

ATGGATATTCCTCTGGTTATAGATGACCAACCTGATGCTTTCATATGGAATGAGGAGTGGAACGGTTTGTACACTGTGCATTCCGGTTATAGATTTATTATGCGAGGGTCTTTGAAGGAAGAGAGGTGTCTTACGCCGGGAGATTGGGGCAGTTTGTGGGGAGCTCAAGTACGTTCTAAAGTGCGTAATTTAATATGGAGAATTTGTAGGCTAAGCCGGAACAGTGCACGATCTAAAGTGATCGAAAACAACAAAACAACAGCAGAAGCCGGAACATTAGTGGACAGAACAGACAGCTGCAGTGCAGTATTGACACAAGTTTTTTCCATGGGCAGAATCAAACATGTTTCGGTTGTTGCATACGCAGAACAGAAGTCAGTTTGTTCGAGCATTGATAGAGTG

Protein sequence

>Msa0574180

MDIPLVIDDQPDAFIWNEEWNGLYTVHSGYRFIMRGSLKEERCLTPGDWGSLWGAQVRSKVRNLIWRICRLSRNSARSKVIENNKTTAEAGTLVDRTDSCSAVLTQVFSMGRIKHVSVVAYAEQKSVCSSIDRV