AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0925680


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0925680 MtrunA17_Chr6g0488451 89.759 166 17 0 2 167 138 303 6.84e-107 310
Msa0925680 MtrunA17_Chr7g0256351 70.186 161 47 1 2 161 142 302 7.97e-74 226
Msa0925680 MtrunA17_Chr6g0488421 37.864 103 49 2 2 90 39 140 3.14e-14 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0925680 AT5G56780.1 40.000 155 89 2 2 152 153 307 2.01e-27 107

Find 28 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGCAACATACTTGATTTAAT+TGG 0.224850 6_2:-68964646 None:intergenic
TAAAATTTGTGGAGTGAATT+TGG 0.231337 6_2:+68964798 Msa0925680:CDS
GTTGTATCTTGAACTATCTT+AGG 0.344160 6_2:-68964751 None:intergenic
AGTGAAGGGTAGAAGTGATT+TGG 0.349328 6_2:-68964605 None:intergenic
TCGGATTTGTTATCTTTCAT+AGG 0.354876 6_2:-68964667 None:intergenic
GGAATTTGAACACGCGAGAT+AGG 0.386624 6_2:-68964717 None:intergenic
TGTTTGCAAGGCATCTCCCT+TGG 0.436980 6_2:-68964455 None:intergenic
GAGAAGAGTGGTAAAATTTG+TGG 0.450994 6_2:+68964787 Msa0925680:CDS
GCTGCCATTGTCTGCTTCAT+CGG 0.453379 6_2:-68964686 None:intergenic
ATCTGAAAATGTTCTTGTGC+TGG 0.457395 6_2:-68964578 None:intergenic
GTTAGGTGTCATGAACATAA+AGG 0.469142 6_2:+68964862 Msa0925680:CDS
TGAGTACATTTGATTATGCT+TGG 0.471865 6_2:+68964491 Msa0925680:CDS
GCTTGGAACACAATTAATAA+CGG 0.491690 6_2:+68964508 Msa0925680:CDS
CAGTTGAAATTCTGTTTGCA+AGG 0.502089 6_2:-68964467 None:intergenic
CCTTCACTCAAAAGAAAGTA+GGG 0.503569 6_2:+68964620 Msa0925680:CDS
CCCTTCACTCAAAAGAAAGT+AGG 0.510670 6_2:+68964619 Msa0925680:CDS
GAGCATTTCAAGAATATCAC+CGG 0.525607 6_2:-68964542 None:intergenic
CTATCTTAGGACGCGACCGG+TGG 0.570672 6_2:-68964738 None:intergenic
AATAACGGTCCACGGCGTCC+CGG 0.572061 6_2:+68964523 Msa0925680:CDS
CTCGCGTGTTCAAATTCCAC+CGG 0.598427 6_2:+68964722 Msa0925680:CDS
GAACTATCTTAGGACGCGAC+CGG 0.598468 6_2:-68964741 None:intergenic
TTCTATTTGTACAAAGACGC+CGG 0.623541 6_2:+68964828 Msa0925680:CDS
AGAATATCACCGGGACGCCG+TGG 0.625598 6_2:-68964532 None:intergenic
GTTGAACAGATGCAAACCAA+GGG 0.638402 6_2:+68964439 Msa0925680:intron
ACACAATTAATAACGGTCCA+CGG 0.642408 6_2:+68964515 Msa0925680:CDS
TGTTGAACAGATGCAAACCA+AGG 0.647561 6_2:+68964438 Msa0925680:intron
AGCATTTCAAGAATATCACC+GGG 0.651967 6_2:-68964541 None:intergenic
AAATCCGATGAAGCAGACAA+TGG 0.675612 6_2:+68964682 Msa0925680:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATTAGAAGCTTTAATAAT+TGG + chr6_2:68963661-68963680 Msa0925680:intron 15.0%
!! AATCTAATAGAATAAACAAT+TGG + chr6_2:68963840-68963859 Msa0925680:intron 15.0%
!!! GCATTTATATTTAATCTTTT+GGG - chr6_2:68964356-68964375 None:intergenic 15.0%
!!! TGCATTTATATTTAATCTTT+TGG - chr6_2:68964357-68964376 None:intergenic 15.0%
!!! ATATTAGAAGCTTTAATAAT+TGG + chr6_2:68963661-68963680 Msa0925680:intron 15.0%
!! AATCTAATAGAATAAACAAT+TGG + chr6_2:68963840-68963859 Msa0925680:intron 15.0%
!!! GCATTTATATTTAATCTTTT+GGG - chr6_2:68964356-68964375 None:intergenic 15.0%
!!! TGCATTTATATTTAATCTTT+TGG - chr6_2:68964357-68964376 None:intergenic 15.0%
!! TTAACAAGAAAAGTAAACAA+CGG + chr6_2:68963689-68963708 Msa0925680:intron 20.0%
!! TGTTTATTCTATTAGATTAG+AGG - chr6_2:68963838-68963857 None:intergenic 20.0%
!!! TTTTCCAATTGTTTATAGAT+GGG + chr6_2:68963927-68963946 Msa0925680:intron 20.0%
!! CAAAATGAACATATACAATA+TGG - chr6_2:68964069-68964088 None:intergenic 20.0%
!! ATAATATGTATCTCAAATCA+TGG - chr6_2:68964098-68964117 None:intergenic 20.0%
!! TTAATTAAGAGCTAAGTTAT+AGG + chr6_2:68964178-68964197 Msa0925680:intron 20.0%
!! TTAACAAGAAAAGTAAACAA+CGG + chr6_2:68963689-68963708 Msa0925680:intron 20.0%
!! TGTTTATTCTATTAGATTAG+AGG - chr6_2:68963838-68963857 None:intergenic 20.0%
!!! TTTTCCAATTGTTTATAGAT+GGG + chr6_2:68963927-68963946 Msa0925680:intron 20.0%
!! CAAAATGAACATATACAATA+TGG - chr6_2:68964069-68964088 None:intergenic 20.0%
!! ATAATATGTATCTCAAATCA+TGG - chr6_2:68964098-68964117 None:intergenic 20.0%
!! TTAATTAAGAGCTAAGTTAT+AGG + chr6_2:68964178-68964197 Msa0925680:intron 20.0%
! AAATTAAGAGACATGATTCA+AGG + chr6_2:68963904-68963923 Msa0925680:intron 25.0%
!! GTTTTCCAATTGTTTATAGA+TGG + chr6_2:68963926-68963945 Msa0925680:intron 25.0%
! TCAACTTATTAAGATCAAGA+TGG + chr6_2:68963989-68964008 Msa0925680:intron 25.0%
!! TATGAAGTAAGTATTTTCTC+TGG + chr6_2:68964233-68964252 Msa0925680:intron 25.0%
! TAAAATTTGTGGAGTGAATT+TGG + chr6_2:68964798-68964817 Msa0925680:CDS 25.0%
! AAATTAAGAGACATGATTCA+AGG + chr6_2:68963904-68963923 Msa0925680:intron 25.0%
!! GTTTTCCAATTGTTTATAGA+TGG + chr6_2:68963926-68963945 Msa0925680:intron 25.0%
! TCAACTTATTAAGATCAAGA+TGG + chr6_2:68963989-68964008 Msa0925680:intron 25.0%
!! TATGAAGTAAGTATTTTCTC+TGG + chr6_2:68964233-68964252 Msa0925680:intron 25.0%
! TAAAATTTGTGGAGTGAATT+TGG + chr6_2:68964798-68964817 Msa0925680:CDS 25.0%
!! ATGATTCTAGCTTCTTTCAT+TGG + chr6_2:68963791-68963810 Msa0925680:intron 30.0%
GTATTAAGAGACATGATTCA+AGG - chr6_2:68963870-68963889 None:intergenic 30.0%
AATGCATAGAATGTACTTAC+AGG - chr6_2:68963955-68963974 None:intergenic 30.0%
GAACATATACAATATGGTCA+AGG - chr6_2:68964063-68964082 None:intergenic 30.0%
TAAGAGCTAAGTTATAGGTT+TGG + chr6_2:68964183-68964202 Msa0925680:intron 30.0%
CACATTTGCATCTTACATAA+AGG + chr6_2:68964375-68964394 Msa0925680:intron 30.0%
TGAGTACATTTGATTATGCT+TGG + chr6_2:68964491-68964510 Msa0925680:CDS 30.0%
GCTTGGAACACAATTAATAA+CGG + chr6_2:68964508-68964527 Msa0925680:CDS 30.0%
GGCAACATACTTGATTTAAT+TGG - chr6_2:68964649-68964668 None:intergenic 30.0%
!! TCGGATTTGTTATCTTTCAT+AGG - chr6_2:68964670-68964689 None:intergenic 30.0%
GTTGTATCTTGAACTATCTT+AGG - chr6_2:68964754-68964773 None:intergenic 30.0%
! AATTTTACCACTCTTCTCAA+CGG - chr6_2:68964785-68964804 None:intergenic 30.0%
!! ATGATTCTAGCTTCTTTCAT+TGG + chr6_2:68963791-68963810 Msa0925680:intron 30.0%
GTATTAAGAGACATGATTCA+AGG - chr6_2:68963870-68963889 None:intergenic 30.0%
AATGCATAGAATGTACTTAC+AGG - chr6_2:68963955-68963974 None:intergenic 30.0%
GAACATATACAATATGGTCA+AGG - chr6_2:68964063-68964082 None:intergenic 30.0%
TAAGAGCTAAGTTATAGGTT+TGG + chr6_2:68964183-68964202 Msa0925680:intron 30.0%
CACATTTGCATCTTACATAA+AGG + chr6_2:68964375-68964394 Msa0925680:intron 30.0%
TGAGTACATTTGATTATGCT+TGG + chr6_2:68964491-68964510 Msa0925680:CDS 30.0%
GCTTGGAACACAATTAATAA+CGG + chr6_2:68964508-68964527 Msa0925680:CDS 30.0%
GGCAACATACTTGATTTAAT+TGG - chr6_2:68964649-68964668 None:intergenic 30.0%
!! TCGGATTTGTTATCTTTCAT+AGG - chr6_2:68964670-68964689 None:intergenic 30.0%
GTTGTATCTTGAACTATCTT+AGG - chr6_2:68964754-68964773 None:intergenic 30.0%
! AATTTTACCACTCTTCTCAA+CGG - chr6_2:68964785-68964804 None:intergenic 30.0%
!! TTCTAGCTTCTTTCATTGGA+AGG + chr6_2:68963795-68963814 Msa0925680:intron 35.0%
ATACAATATGGTCAAGGCAA+TGG - chr6_2:68964057-68964076 None:intergenic 35.0%
AGTTATAGGTTTGGAAGTCT+AGG + chr6_2:68964192-68964211 Msa0925680:intron 35.0%
CAGTTGAAATTCTGTTTGCA+AGG - chr6_2:68964470-68964489 None:intergenic 35.0%
ACACAATTAATAACGGTCCA+CGG + chr6_2:68964515-68964534 Msa0925680:CDS 35.0%
AGCATTTCAAGAATATCACC+GGG - chr6_2:68964544-68964563 None:intergenic 35.0%
GAGCATTTCAAGAATATCAC+CGG - chr6_2:68964545-68964564 None:intergenic 35.0%
ATCTGAAAATGTTCTTGTGC+TGG - chr6_2:68964581-68964600 None:intergenic 35.0%
!! CCTACTTTCTTTTGAGTGAA+GGG - chr6_2:68964622-68964641 None:intergenic 35.0%
CCTTCACTCAAAAGAAAGTA+GGG + chr6_2:68964620-68964639 Msa0925680:CDS 35.0%
GAGAAGAGTGGTAAAATTTG+TGG + chr6_2:68964787-68964806 Msa0925680:CDS 35.0%
TTCTATTTGTACAAAGACGC+CGG + chr6_2:68964828-68964847 Msa0925680:CDS 35.0%
! GTTAGGTGTCATGAACATAA+AGG + chr6_2:68964862-68964881 Msa0925680:CDS 35.0%
TCCAAGTCAGAATCAAAAAG+AGG + chr6_2:68964901-68964920 Msa0925680:CDS 35.0%
!! TCCTCTTTTTGATTCTGACT+TGG - chr6_2:68964905-68964924 None:intergenic 35.0%
CAAAAAGAGGAAATGCTTGT+AGG + chr6_2:68964914-68964933 Msa0925680:CDS 35.0%
!! TTCTAGCTTCTTTCATTGGA+AGG + chr6_2:68963795-68963814 Msa0925680:intron 35.0%
ATACAATATGGTCAAGGCAA+TGG - chr6_2:68964057-68964076 None:intergenic 35.0%
AGTTATAGGTTTGGAAGTCT+AGG + chr6_2:68964192-68964211 Msa0925680:intron 35.0%
CAGTTGAAATTCTGTTTGCA+AGG - chr6_2:68964470-68964489 None:intergenic 35.0%
ACACAATTAATAACGGTCCA+CGG + chr6_2:68964515-68964534 Msa0925680:CDS 35.0%
AGCATTTCAAGAATATCACC+GGG - chr6_2:68964544-68964563 None:intergenic 35.0%
GAGCATTTCAAGAATATCAC+CGG - chr6_2:68964545-68964564 None:intergenic 35.0%
ATCTGAAAATGTTCTTGTGC+TGG - chr6_2:68964581-68964600 None:intergenic 35.0%
!! CCTACTTTCTTTTGAGTGAA+GGG - chr6_2:68964622-68964641 None:intergenic 35.0%
CCTTCACTCAAAAGAAAGTA+GGG + chr6_2:68964620-68964639 Msa0925680:CDS 35.0%
GAGAAGAGTGGTAAAATTTG+TGG + chr6_2:68964787-68964806 Msa0925680:CDS 35.0%
TTCTATTTGTACAAAGACGC+CGG + chr6_2:68964828-68964847 Msa0925680:CDS 35.0%
! GTTAGGTGTCATGAACATAA+AGG + chr6_2:68964862-68964881 Msa0925680:CDS 35.0%
TCCAAGTCAGAATCAAAAAG+AGG + chr6_2:68964901-68964920 Msa0925680:CDS 35.0%
!! TCCTCTTTTTGATTCTGACT+TGG - chr6_2:68964905-68964924 None:intergenic 35.0%
CAAAAAGAGGAAATGCTTGT+AGG + chr6_2:68964914-68964933 Msa0925680:CDS 35.0%
AACATTTGTGTCGTGTCTCA+TGG - chr6_2:68963742-68963761 None:intergenic 40.0%
GGAGCCCATCTATAAACAAT+TGG - chr6_2:68963934-68963953 None:intergenic 40.0%
TGTTGAACAGATGCAAACCA+AGG + chr6_2:68964438-68964457 Msa0925680:intron 40.0%
GTTGAACAGATGCAAACCAA+GGG + chr6_2:68964439-68964458 Msa0925680:intron 40.0%
AGTGAAGGGTAGAAGTGATT+TGG - chr6_2:68964608-68964627 None:intergenic 40.0%
CCCTTCACTCAAAAGAAAGT+AGG + chr6_2:68964619-68964638 Msa0925680:CDS 40.0%
!! CCCTACTTTCTTTTGAGTGA+AGG - chr6_2:68964623-68964642 None:intergenic 40.0%
AAATCCGATGAAGCAGACAA+TGG + chr6_2:68964682-68964701 Msa0925680:CDS 40.0%
! GATTTTTCCGTTGAGAAGAG+TGG + chr6_2:68964775-68964794 Msa0925680:CDS 40.0%
!!! CACCTAACTCTTTTTTCGAC+CGG - chr6_2:68964850-68964869 None:intergenic 40.0%
AACATTTGTGTCGTGTCTCA+TGG - chr6_2:68963742-68963761 None:intergenic 40.0%
GGAGCCCATCTATAAACAAT+TGG - chr6_2:68963934-68963953 None:intergenic 40.0%
TGTTGAACAGATGCAAACCA+AGG + chr6_2:68964438-68964457 Msa0925680:intron 40.0%
GTTGAACAGATGCAAACCAA+GGG + chr6_2:68964439-68964458 Msa0925680:intron 40.0%
AGTGAAGGGTAGAAGTGATT+TGG - chr6_2:68964608-68964627 None:intergenic 40.0%
CCCTTCACTCAAAAGAAAGT+AGG + chr6_2:68964619-68964638 Msa0925680:CDS 40.0%
!! CCCTACTTTCTTTTGAGTGA+AGG - chr6_2:68964623-68964642 None:intergenic 40.0%
AAATCCGATGAAGCAGACAA+TGG + chr6_2:68964682-68964701 Msa0925680:CDS 40.0%
! GATTTTTCCGTTGAGAAGAG+TGG + chr6_2:68964775-68964794 Msa0925680:CDS 40.0%
!!! CACCTAACTCTTTTTTCGAC+CGG - chr6_2:68964850-68964869 None:intergenic 40.0%
GGAATTTGAACACGCGAGAT+AGG - chr6_2:68964720-68964739 None:intergenic 45.0%
GGAATTTGAACACGCGAGAT+AGG - chr6_2:68964720-68964739 None:intergenic 45.0%
! TGTTTGCAAGGCATCTCCCT+TGG - chr6_2:68964458-68964477 None:intergenic 50.0%
GCTGCCATTGTCTGCTTCAT+CGG - chr6_2:68964689-68964708 None:intergenic 50.0%
CTCGCGTGTTCAAATTCCAC+CGG + chr6_2:68964722-68964741 Msa0925680:CDS 50.0%
GAACTATCTTAGGACGCGAC+CGG - chr6_2:68964744-68964763 None:intergenic 50.0%
CGCCGGTCGAAAAAAGAGTT+AGG + chr6_2:68964845-68964864 Msa0925680:CDS 50.0%
! TGTTTGCAAGGCATCTCCCT+TGG - chr6_2:68964458-68964477 None:intergenic 50.0%
GCTGCCATTGTCTGCTTCAT+CGG - chr6_2:68964689-68964708 None:intergenic 50.0%
CTCGCGTGTTCAAATTCCAC+CGG + chr6_2:68964722-68964741 Msa0925680:CDS 50.0%
GAACTATCTTAGGACGCGAC+CGG - chr6_2:68964744-68964763 None:intergenic 50.0%
CGCCGGTCGAAAAAAGAGTT+AGG + chr6_2:68964845-68964864 Msa0925680:CDS 50.0%
AATAACGGTCCACGGCGTCC+CGG + chr6_2:68964523-68964542 Msa0925680:CDS 60.0%
AGAATATCACCGGGACGCCG+TGG - chr6_2:68964535-68964554 None:intergenic 60.0%
CTATCTTAGGACGCGACCGG+TGG - chr6_2:68964741-68964760 None:intergenic 60.0%
AATAACGGTCCACGGCGTCC+CGG + chr6_2:68964523-68964542 Msa0925680:CDS 60.0%
AGAATATCACCGGGACGCCG+TGG - chr6_2:68964535-68964554 None:intergenic 60.0%
CTATCTTAGGACGCGACCGG+TGG - chr6_2:68964741-68964760 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 68963640 68964942 68963640 ID=Msa0925680;Name=Msa0925680
chr6_2 mRNA 68963640 68964942 68963640 ID=Msa0925680-mRNA-1;Parent=Msa0925680;Name=Msa0925680-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|0|0|0.5|0|0.5|2|0|167
chr6_2 exon 68963640 68963648 68963640 ID=Msa0925680-mRNA-1:exon:11068;Parent=Msa0925680-mRNA-1
chr6_2 exon 68964448 68964942 68964448 ID=Msa0925680-mRNA-1:exon:11069;Parent=Msa0925680-mRNA-1
chr6_2 CDS 68963640 68963648 68963640 ID=Msa0925680-mRNA-1:cds;Parent=Msa0925680-mRNA-1
chr6_2 CDS 68964448 68964942 68964448 ID=Msa0925680-mRNA-1:cds;Parent=Msa0925680-mRNA-1
Gene Sequence

>Msa0925680

ATGGCAAAAATGCAAACCAAGGGAGATGCCTTGCAAACAGAATTTCAACTGTTGAGTACATTTGATTATGCTTGGAACACAATTAATAACGGTCCACGGCGTCCCGGTGATATTCTTGAAATGCTCAACAAAATATCTTCCAGCACAAGAACATTTTCAGATGTAGCCAAATCACTTCTACCCTTCACTCAAAAGAAAGTAGGGATACCAATTAAATCAAGTATGTTGCCTATGAAAGATAACAAATCCGATGAAGCAGACAATGGCAGCTACAATTTCCTATCTCGCGTGTTCAAATTCCACCGGTCGCGTCCTAAGATAGTTCAAGATACAACTGATTTTTCCGTTGAGAAGAGTGGTAAAATTTGTGGAGTGAATTTGGATAATAGTTCTATTTGTACAAAGACGCCGGTCGAAAAAAGAGTTAGGTGTCATGAACATAAAGGAATGAGAATAAGAACATCCAAGTCAGAATCAAAAAGAGGAAATGCTTGTAGGTACTAA

Protein sequence

>Msa0925680

MAKMQTKGDALQTEFQLLSTFDYAWNTINNGPRRPGDILEMLNKISSSTRTFSDVAKSLLPFTQKKVGIPIKSSMLPMKDNKSDEADNGSYNFLSRVFKFHRSRPKIVQDTTDFSVEKSGKICGVNLDNSSICTKTPVEKRVRCHEHKGMRIRTSKSESKRGNACRY*