AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0580980

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 128 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGCAATGCCAAGGAAAT+TGG 0.216340 4_1:+86267479 Msa0580980:CDS
CCATCACTAGAATTATAAAT+TGG 0.248930 4_1:+86267779 Msa0580980:three_prime_UTR
CAAGGAAATTGGCTTCATTA+AGG 0.318093 4_1:+86267490 Msa0580980:CDS
TCATGGGTCACTCCAACGTT+TGG 0.416385 4_1:+86266748 None:intergenic
GAACCAGGACCATAGGTCTT+GGG 0.430692 4_1:-86266780 None:intergenic
CTTAATGAAGCCAATTTCCT+TGG 0.435363 4_1:-86267489 None:intergenic
AAACATATTTACTTCCTACT+TGG 0.442515 4_1:+86267730 Msa0580980:three_prime_UTR
AGAACCAGGACCATAGGTCT+TGG 0.460388 4_1:-86266781 None:intergenic
ATTTACTTCCTACTTGGTTG+TGG 0.464265 4_1:+86267736 Msa0580980:three_prime_UTR
TAGAATTATAAATTGGATGT+TGG 0.488440 4_1:+86267786 Msa0580980:three_prime_UTR
TTCTAGTTAAAAGCTTAGAA+AGG 0.488648 4_1:-86267857 None:intergenic
CACCCCAAGACCTATGGTCC+TGG 0.491604 4_1:+86266777 Msa0580980:CDS
TTCAATAACTAAAATCATCC+TGG 0.492527 4_1:-86267640 None:intergenic
CCAATTTATAATTCTAGTGA+TGG 0.495729 4_1:-86267779 None:intergenic
AACTCTCACCCCAAGACCTA+TGG 0.505813 4_1:+86266771 Msa0580980:CDS
CCGAGCTGCAAAACGATGCC+AGG 0.511058 4_1:+86267622 Msa0580980:CDS
GATGTTGGCATCTTTGTGCA+TGG 0.537643 4_1:+86267801 Msa0580980:three_prime_UTR
CATGGATTGATCAGGAAGTA+CGG 0.572937 4_1:+86267431 Msa0580980:intron
TGTGCGAGAACCAGGACCAT+AGG 0.585453 4_1:-86266787 None:intergenic
CAATTTCCTTGGCATTGCTG+TGG 0.593734 4_1:-86267478 None:intergenic
CAACAACTCCACAACCAAGT+AGG 0.594310 4_1:-86267744 None:intergenic
AACCAGGACCATAGGTCTTG+GGG 0.607026 4_1:-86266779 None:intergenic
GTGCTTCCACAGCAATGCCA+AGG 0.623139 4_1:+86267472 Msa0580980:CDS
GGGGTGAGAGTTCCAAACGT+TGG 0.647246 4_1:-86266760 None:intergenic
TCTCCAGTCGATCAAAACCG+TGG 0.689532 4_1:-86267949 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTTTAATCTTTACAAA+TGG - chr4_1:86267918-86267937 None:intergenic 10.0%
!! TTTGTAAAGATTAAAAAAAT+AGG + chr4_1:86267918-86267937 Msa0580980:three_prime_UTR 10.0%
!! TTGTAAAGATTAAAAAAATA+GGG + chr4_1:86267919-86267938 Msa0580980:three_prime_UTR 10.0%
!!! ATTTTTTTAATCTTTACAAA+TGG - chr4_1:86267918-86267937 None:intergenic 10.0%
!! TTTGTAAAGATTAAAAAAAT+AGG + chr4_1:86267918-86267937 Msa0580980:three_prime_UTR 10.0%
!! TTGTAAAGATTAAAAAAATA+GGG + chr4_1:86267919-86267938 Msa0580980:three_prime_UTR 10.0%
!! TGATTTACTGAAACAAATTT+CGG + chr4_1:86266968-86266987 Msa0580980:intron 20.0%
!!! TCCTACTTTGAAAATAAAAT+GGG + chr4_1:86267128-86267147 Msa0580980:intron 20.0%
!! GTAAAATGATGTGAAAATTA+AGG - chr4_1:86267163-86267182 None:intergenic 20.0%
!! AAACGTTAAAAACAAAGAAT+GGG - chr4_1:86267201-86267220 None:intergenic 20.0%
!! TAGAATTATAAATTGGATGT+TGG + chr4_1:86267786-86267805 Msa0580980:three_prime_UTR 20.0%
!!! ATGATATGTAACTATTTTGT+TGG + chr4_1:86267971-86267990 Msa0580980:three_prime_UTR 20.0%
!! TGATTTACTGAAACAAATTT+CGG + chr4_1:86266968-86266987 Msa0580980:intron 20.0%
!!! TCCTACTTTGAAAATAAAAT+GGG + chr4_1:86267128-86267147 Msa0580980:intron 20.0%
!! GTAAAATGATGTGAAAATTA+AGG - chr4_1:86267163-86267182 None:intergenic 20.0%
!! AAACGTTAAAAACAAAGAAT+GGG - chr4_1:86267201-86267220 None:intergenic 20.0%
!! TAGAATTATAAATTGGATGT+TGG + chr4_1:86267786-86267805 Msa0580980:three_prime_UTR 20.0%
!!! ATGATATGTAACTATTTTGT+TGG + chr4_1:86267971-86267990 Msa0580980:three_prime_UTR 20.0%
! TGATAAATGACAGTAATCTA+TGG - chr4_1:86266926-86266945 None:intergenic 25.0%
! TCATCCAATTAACAATAAGT+TGG - chr4_1:86266951-86266970 None:intergenic 25.0%
!! GTCCTACTTTGAAAATAAAA+TGG + chr4_1:86267127-86267146 Msa0580980:intron 25.0%
!!! TCCCATTTTATTTTCAAAGT+AGG - chr4_1:86267132-86267151 None:intergenic 25.0%
! CAAACGTTAAAAACAAAGAA+TGG - chr4_1:86267202-86267221 None:intergenic 25.0%
!!! TTGTTTTTAACGTTTGTACT+TGG + chr4_1:86267206-86267225 Msa0580980:intron 25.0%
! TTCAATAACTAAAATCATCC+TGG - chr4_1:86267643-86267662 None:intergenic 25.0%
! AAACATATTTACTTCCTACT+TGG + chr4_1:86267730-86267749 Msa0580980:three_prime_UTR 25.0%
! CCAATTTATAATTCTAGTGA+TGG - chr4_1:86267782-86267801 None:intergenic 25.0%
! CCATCACTAGAATTATAAAT+TGG + chr4_1:86267779-86267798 Msa0580980:three_prime_UTR 25.0%
!! TTCTAGTTAAAAGCTTAGAA+AGG - chr4_1:86267860-86267879 None:intergenic 25.0%
! TGATAAATGACAGTAATCTA+TGG - chr4_1:86266926-86266945 None:intergenic 25.0%
! TCATCCAATTAACAATAAGT+TGG - chr4_1:86266951-86266970 None:intergenic 25.0%
!! GTCCTACTTTGAAAATAAAA+TGG + chr4_1:86267127-86267146 Msa0580980:intron 25.0%
!!! TCCCATTTTATTTTCAAAGT+AGG - chr4_1:86267132-86267151 None:intergenic 25.0%
! CAAACGTTAAAAACAAAGAA+TGG - chr4_1:86267202-86267221 None:intergenic 25.0%
!!! TTGTTTTTAACGTTTGTACT+TGG + chr4_1:86267206-86267225 Msa0580980:intron 25.0%
! TTCAATAACTAAAATCATCC+TGG - chr4_1:86267643-86267662 None:intergenic 25.0%
! AAACATATTTACTTCCTACT+TGG + chr4_1:86267730-86267749 Msa0580980:three_prime_UTR 25.0%
! CCAATTTATAATTCTAGTGA+TGG - chr4_1:86267782-86267801 None:intergenic 25.0%
! CCATCACTAGAATTATAAAT+TGG + chr4_1:86267779-86267798 Msa0580980:three_prime_UTR 25.0%
!! TTCTAGTTAAAAGCTTAGAA+AGG - chr4_1:86267860-86267879 None:intergenic 25.0%
CACACCAACTTATTGTTAAT+TGG + chr4_1:86266944-86266963 Msa0580980:intron 30.0%
! CATTAAGGTGAATATTTTGC+TGG + chr4_1:86267505-86267524 Msa0580980:intron 30.0%
! TGTCTGTTTTATGATGTGAA+TGG + chr4_1:86267824-86267843 Msa0580980:three_prime_UTR 30.0%
CACACCAACTTATTGTTAAT+TGG + chr4_1:86266944-86266963 Msa0580980:intron 30.0%
! CATTAAGGTGAATATTTTGC+TGG + chr4_1:86267505-86267524 Msa0580980:intron 30.0%
! TGTCTGTTTTATGATGTGAA+TGG + chr4_1:86267824-86267843 Msa0580980:three_prime_UTR 30.0%
GAACACAGTACTCAGAAATA+CGG - chr4_1:86266886-86266905 None:intergenic 35.0%
GGATCTGAATGAATTAGGAT+CGG - chr4_1:86267008-86267027 None:intergenic 35.0%
GAGTTGGATCTGAATGAATT+AGG - chr4_1:86267013-86267032 None:intergenic 35.0%
! ATTGGTTTCAAGAGTTGAGT+TGG - chr4_1:86267029-86267048 None:intergenic 35.0%
AAGCACATCGAAAAATGCAT+TGG - chr4_1:86267047-86267066 None:intergenic 35.0%
CTTAATGAAGCCAATTTCCT+TGG - chr4_1:86267492-86267511 None:intergenic 35.0%
! CAAGGAAATTGGCTTCATTA+AGG + chr4_1:86267490-86267509 Msa0580980:CDS 35.0%
ATTTACTTCCTACTTGGTTG+TGG + chr4_1:86267736-86267755 Msa0580980:three_prime_UTR 35.0%
AAAAATAGGGAGTTCTTCCA+CGG + chr4_1:86267932-86267951 Msa0580980:three_prime_UTR 35.0%
GAACACAGTACTCAGAAATA+CGG - chr4_1:86266886-86266905 None:intergenic 35.0%
GGATCTGAATGAATTAGGAT+CGG - chr4_1:86267008-86267027 None:intergenic 35.0%
GAGTTGGATCTGAATGAATT+AGG - chr4_1:86267013-86267032 None:intergenic 35.0%
! ATTGGTTTCAAGAGTTGAGT+TGG - chr4_1:86267029-86267048 None:intergenic 35.0%
AAGCACATCGAAAAATGCAT+TGG - chr4_1:86267047-86267066 None:intergenic 35.0%
CTTAATGAAGCCAATTTCCT+TGG - chr4_1:86267492-86267511 None:intergenic 35.0%
! CAAGGAAATTGGCTTCATTA+AGG + chr4_1:86267490-86267509 Msa0580980:CDS 35.0%
ATTTACTTCCTACTTGGTTG+TGG + chr4_1:86267736-86267755 Msa0580980:three_prime_UTR 35.0%
AAAAATAGGGAGTTCTTCCA+CGG + chr4_1:86267932-86267951 Msa0580980:three_prime_UTR 35.0%
TCGAAGAATCTTACAAGGGT+TGG - chr4_1:86266862-86266881 None:intergenic 40.0%
CGGATCGAAGAATCTTACAA+GGG - chr4_1:86266866-86266885 None:intergenic 40.0%
ACGGATCGAAGAATCTTACA+AGG - chr4_1:86266867-86266886 None:intergenic 40.0%
! TCGATGTGCTTGTACTTTTC+TGG + chr4_1:86267056-86267075 Msa0580980:intron 40.0%
! GAAACTCTCATGGATTGATC+AGG + chr4_1:86267423-86267442 Msa0580980:intron 40.0%
! CATGGATTGATCAGGAAGTA+CGG + chr4_1:86267431-86267450 Msa0580980:intron 40.0%
CATCACTTTCCACTTCTTTC+CGG + chr4_1:86267568-86267587 Msa0580980:intron 40.0%
TCGAAGAATCTTACAAGGGT+TGG - chr4_1:86266862-86266881 None:intergenic 40.0%
CGGATCGAAGAATCTTACAA+GGG - chr4_1:86266866-86266885 None:intergenic 40.0%
ACGGATCGAAGAATCTTACA+AGG - chr4_1:86266867-86266886 None:intergenic 40.0%
! TCGATGTGCTTGTACTTTTC+TGG + chr4_1:86267056-86267075 Msa0580980:intron 40.0%
! GAAACTCTCATGGATTGATC+AGG + chr4_1:86267423-86267442 Msa0580980:intron 40.0%
! CATGGATTGATCAGGAAGTA+CGG + chr4_1:86267431-86267450 Msa0580980:intron 40.0%
CATCACTTTCCACTTCTTTC+CGG + chr4_1:86267568-86267587 Msa0580980:intron 40.0%
ACAGACACGGCTACAAAACA+AGG - chr4_1:86267402-86267421 None:intergenic 45.0%
!! TTGTTTTGTAGCCGTGTCTG+TGG + chr4_1:86267401-86267420 Msa0580980:intron 45.0%
CATGAGAGTTTCCACAGACA+CGG - chr4_1:86267415-86267434 None:intergenic 45.0%
CAATTTCCTTGGCATTGCTG+TGG - chr4_1:86267481-86267500 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG + chr4_1:86267479-86267498 Msa0580980:CDS 45.0%
TTTCAGCGATACTGCAACAC+CGG - chr4_1:86267590-86267609 None:intergenic 45.0%
CAACAACTCCACAACCAAGT+AGG - chr4_1:86267747-86267766 None:intergenic 45.0%
GATGTTGGCATCTTTGTGCA+TGG + chr4_1:86267801-86267820 Msa0580980:three_prime_UTR 45.0%
ACAGACACGGCTACAAAACA+AGG - chr4_1:86267402-86267421 None:intergenic 45.0%
!! TTGTTTTGTAGCCGTGTCTG+TGG + chr4_1:86267401-86267420 Msa0580980:intron 45.0%
CATGAGAGTTTCCACAGACA+CGG - chr4_1:86267415-86267434 None:intergenic 45.0%
CAATTTCCTTGGCATTGCTG+TGG - chr4_1:86267481-86267500 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG + chr4_1:86267479-86267498 Msa0580980:CDS 45.0%
TTTCAGCGATACTGCAACAC+CGG - chr4_1:86267590-86267609 None:intergenic 45.0%
CAACAACTCCACAACCAAGT+AGG - chr4_1:86267747-86267766 None:intergenic 45.0%
GATGTTGGCATCTTTGTGCA+TGG + chr4_1:86267801-86267820 Msa0580980:three_prime_UTR 45.0%
AACTCTCACCCCAAGACCTA+TGG + chr4_1:86266771-86266790 Msa0580980:CDS 50.0%
AACCAGGACCATAGGTCTTG+GGG - chr4_1:86266782-86266801 None:intergenic 50.0%
GAACCAGGACCATAGGTCTT+GGG - chr4_1:86266783-86266802 None:intergenic 50.0%
AGAACCAGGACCATAGGTCT+TGG - chr4_1:86266784-86266803 None:intergenic 50.0%
CGTGTCTGTGGAAACTCTCA+TGG + chr4_1:86267413-86267432 Msa0580980:intron 50.0%
ACTGCAACACCGGAAAGAAG+TGG - chr4_1:86267580-86267599 None:intergenic 50.0%
!! CTTCCACGGTTTTGATCGAC+TGG + chr4_1:86267946-86267965 Msa0580980:three_prime_UTR 50.0%
TCTCCAGTCGATCAAAACCG+TGG - chr4_1:86267952-86267971 None:intergenic 50.0%
AACTCTCACCCCAAGACCTA+TGG + chr4_1:86266771-86266790 Msa0580980:CDS 50.0%
AACCAGGACCATAGGTCTTG+GGG - chr4_1:86266782-86266801 None:intergenic 50.0%
GAACCAGGACCATAGGTCTT+GGG - chr4_1:86266783-86266802 None:intergenic 50.0%
AGAACCAGGACCATAGGTCT+TGG - chr4_1:86266784-86266803 None:intergenic 50.0%
CGTGTCTGTGGAAACTCTCA+TGG + chr4_1:86267413-86267432 Msa0580980:intron 50.0%
ACTGCAACACCGGAAAGAAG+TGG - chr4_1:86267580-86267599 None:intergenic 50.0%
!! CTTCCACGGTTTTGATCGAC+TGG + chr4_1:86267946-86267965 Msa0580980:three_prime_UTR 50.0%
TCTCCAGTCGATCAAAACCG+TGG - chr4_1:86267952-86267971 None:intergenic 50.0%
GGGGTGAGAGTTCCAAACGT+TGG - chr4_1:86266763-86266782 None:intergenic 55.0%
TGTGCGAGAACCAGGACCAT+AGG - chr4_1:86266790-86266809 None:intergenic 55.0%
! ATGGTCCTGGTTCTCGCACA+TGG + chr4_1:86266790-86266809 Msa0580980:intron 55.0%
GCATACCATGTGCGAGAACC+AGG - chr4_1:86266798-86266817 None:intergenic 55.0%
GTGCTTCCACAGCAATGCCA+AGG + chr4_1:86267472-86267491 Msa0580980:CDS 55.0%
! GCATCGTTTTGCAGCTCGGA+AGG - chr4_1:86267621-86267640 None:intergenic 55.0%
! CCTGGCATCGTTTTGCAGCT+CGG - chr4_1:86267625-86267644 None:intergenic 55.0%
GGGGTGAGAGTTCCAAACGT+TGG - chr4_1:86266763-86266782 None:intergenic 55.0%
TGTGCGAGAACCAGGACCAT+AGG - chr4_1:86266790-86266809 None:intergenic 55.0%
! ATGGTCCTGGTTCTCGCACA+TGG + chr4_1:86266790-86266809 Msa0580980:intron 55.0%
GCATACCATGTGCGAGAACC+AGG - chr4_1:86266798-86266817 None:intergenic 55.0%
GTGCTTCCACAGCAATGCCA+AGG + chr4_1:86267472-86267491 Msa0580980:CDS 55.0%
! GCATCGTTTTGCAGCTCGGA+AGG - chr4_1:86267621-86267640 None:intergenic 55.0%
! CCTGGCATCGTTTTGCAGCT+CGG - chr4_1:86267625-86267644 None:intergenic 55.0%
CACCCCAAGACCTATGGTCC+TGG + chr4_1:86266777-86266796 Msa0580980:CDS 60.0%
CCGAGCTGCAAAACGATGCC+AGG + chr4_1:86267622-86267641 Msa0580980:CDS 60.0%
CACCCCAAGACCTATGGTCC+TGG + chr4_1:86266777-86266796 Msa0580980:CDS 60.0%
CCGAGCTGCAAAACGATGCC+AGG + chr4_1:86267622-86267641 Msa0580980:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 86266750 86268012 86266750 ID=Msa0580980;Name=Msa0580980
chr4_1 mRNA 86266750 86268012 86266750 ID=Msa0580980-mRNA-1;Parent=Msa0580980;Name=Msa0580980-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|0.5|0.33|1|1|1|3|332|65
chr4_1 exon 86266750 86266798 86266750 ID=Msa0580980-mRNA-1:exon:31842;Parent=Msa0580980-mRNA-1
chr4_1 exon 86267445 86267511 86267445 ID=Msa0580980-mRNA-1:exon:31843;Parent=Msa0580980-mRNA-1
chr4_1 exon 86267599 86268012 86267599 ID=Msa0580980-mRNA-1:exon:31844;Parent=Msa0580980-mRNA-1
chr4_1 CDS 86266750 86266798 86266750 ID=Msa0580980-mRNA-1:cds;Parent=Msa0580980-mRNA-1
chr4_1 CDS 86267445 86267511 86267445 ID=Msa0580980-mRNA-1:cds;Parent=Msa0580980-mRNA-1
chr4_1 CDS 86267599 86267680 86267599 ID=Msa0580980-mRNA-1:cds;Parent=Msa0580980-mRNA-1
chr4_1 three_prime_UTR 86267681 86268012 86267681 ID=Msa0580980-mRNA-1:three_prime_utr;Parent=Msa0580980-mRNA-1
Gene Sequence

>Msa0580980

ATGGGTCACTCCAACGTTTGGAACTCTCACCCCAAGACCTATGGTCCTGGAAGTACGGACTCATGTGTTGCAGACAGTGCTTCCACAGCAATGCCAAGGAAATTGGCTTCATTAAGTATCGCTGAAAAGTTGAGTCCTTCCGAGCTGCAAAACGATGCCAGGATGATTTTAGTTATTGAAGAACTTATAATTTTGTAG
Protein sequence

>Msa0580980

MGHSNVWNSHPKTYGPGSTDSCVADSASTAMPRKLASLSIAEKLSPSELQNDARMILVIEELIIL*