AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1230010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1230010 MtrunA17_Chr8g0337781 98.630 73 1 0 1 73 1 73 1.16e-46 142
Msa1230010 MtrunA17_Chr8g0337711 65.753 73 25 0 1 73 1 73 4.95e-30 100
Msa1230010 MtrunA17_Chr6g0458744 62.162 74 26 2 1 73 37 109 1.80e-22 82.8
Msa1230010 MtrunA17_Chr6g0458644 62.162 74 26 2 1 73 37 109 1.80e-22 82.8
Msa1230010 MtrunA17_Chr8g0337731 56.757 74 31 1 1 73 1 74 2.80e-22 81.3
Msa1230010 MtrunA17_Chr6g0458787 60.811 74 27 2 1 73 1 73 4.18e-22 80.9
Msa1230010 MtrunA17_Chr6g0458701 60.811 74 27 2 1 73 37 109 6.75e-22 81.3
Msa1230010 MtrunA17_Chr8g0337741 57.353 68 29 0 6 73 5 72 5.06e-21 78.2
Msa1230010 MtrunA17_Chr6g0458807 59.459 74 28 2 1 73 1 73 5.93e-21 77.8
Msa1230010 MtrunA17_Chr8g0337061 49.315 73 36 1 1 72 9 81 1.43e-20 77.4
Msa1230010 MtrunA17_Chr8g0337721 55.405 74 32 1 1 73 1 74 2.47e-20 76.3
Msa1230010 MtrunA17_Chr8g0337771 50.000 72 35 1 1 71 1 72 3.61e-20 75.9
Msa1230010 MtrunA17_Chr8g0337761 56.250 48 21 0 1 48 1 48 1.19e-12 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTCTGGGATTCTATAAAT+TGG 0.233803 8_2:+5976757 Msa1230010:five_prime_UTR
CGGATAACAATTTAAATTCA+TGG 0.303955 8_2:+5976718 Msa1230010:five_prime_UTR
AACAATGTGGTTATCTTTGC+AGG 0.321948 8_2:+5977619 Msa1230010:CDS
TCATAGCTAGATTATGTTCA+TGG 0.337702 8_2:+5977765 Msa1230010:three_prime_UTR
ATTAATTCTCTTCTCACTAA+AGG 0.349308 8_2:-5977813 None:intergenic
GCTAGCATGTGCTTCTTTGT+GGG 0.371494 8_2:+5976657 Msa1230010:five_prime_UTR
TGCTAGCATGTGCTTCTTTG+TGG 0.371716 8_2:+5976656 Msa1230010:five_prime_UTR
TTCTTCAGTGGTGCATGTAT+TGG 0.373930 8_2:+5977582 Msa1230010:CDS
TGGTCTTATCACTTTGACTA+AGG 0.375528 8_2:+5976603 Msa1230010:five_prime_UTR
TTAATTCTCTTCTCACTAAA+GGG 0.376554 8_2:-5977812 None:intergenic
TGCAAAGATAACCACATTGT+TGG 0.420533 8_2:-5977617 None:intergenic
GTCTTCTAAAATAATGTAAG+TGG 0.421980 8_2:-5976813 None:intergenic
ATTTATAGAATCCCAGAAGT+TGG 0.448278 8_2:-5976754 None:intergenic
GGTGCATGTATTGGTTCATC+TGG 0.472404 8_2:+5977591 Msa1230010:CDS
TGACTAAGGAGTAACATTCA+TGG 0.478114 8_2:+5976617 Msa1230010:five_prime_UTR
ATTAGTGACTAAATGTAGTT+CGG 0.485444 8_2:+5976698 Msa1230010:five_prime_UTR
GCACCACTGAAGAATTTACT+TGG 0.486888 8_2:-5977573 None:intergenic
GAAGAGAATTAATTAACATA+TGG 0.491793 8_2:+5977823 Msa1230010:three_prime_UTR
TTCTCTTCTCACTAAAGGGA+AGG 0.492137 8_2:-5977808 None:intergenic
TCATAGTGGAGATGTTCAAC+AGG 0.492350 8_2:-5977694 None:intergenic
TTAGTTCTGTTACACTATGT+TGG 0.496955 8_2:-5977942 None:intergenic
CTAGCATGTGCTTCTTTGTG+GGG 0.519231 8_2:+5976658 Msa1230010:five_prime_UTR
TATCTTTGCAGGAGAGGAGA+AGG 0.525618 8_2:+5977630 Msa1230010:CDS
TAACAATTTAAATTCATGGT+GGG 0.538768 8_2:+5976722 Msa1230010:five_prime_UTR
AGAAGCAGTGGTGCAAATTG+AGG 0.543400 8_2:+5977539 Msa1230010:CDS
TCTCTTCTCACTAAAGGGAA+GGG 0.551142 8_2:-5977807 None:intergenic
GGAAATTTCAGAAGAAGCAG+TGG 0.578102 8_2:+5977527 Msa1230010:intron
TGTGGTTATCTTTGCAGGAG+AGG 0.610983 8_2:+5977624 Msa1230010:CDS
AAACCAAGTAAATTCTTCAG+TGG 0.617297 8_2:+5977570 Msa1230010:CDS
AAATACATCTGATCTCATAG+TGG 0.624400 8_2:-5977708 None:intergenic
ATAACAATTTAAATTCATGG+TGG 0.674653 8_2:+5976721 Msa1230010:five_prime_UTR
AGAGGAGAAGGCTTACTCAG+TGG 0.689859 8_2:+5977642 Msa1230010:CDS
TCATCTGGCAACCAACAATG+TGG 0.701842 8_2:+5977606 Msa1230010:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAATGAATTTTTTTTATC+AGG + chr8_2:5977049-5977068 Msa1230010:intron 10.0%
!!! TTTAATGAATTTTTTTTATC+AGG + chr8_2:5977049-5977068 Msa1230010:intron 10.0%
!! TTTAGAAGACAAAAAAAAAA+AGG + chr8_2:5976826-5976845 Msa1230010:five_prime_UTR 15.0%
!!! AGTTTATATCAAAGTAATTT+TGG + chr8_2:5976910-5976929 Msa1230010:intron 15.0%
!!! GTTTATATCAAAGTAATTTT+GGG + chr8_2:5976911-5976930 Msa1230010:intron 15.0%
!! AAATAGTTTCATCAAATTTA+AGG - chr8_2:5977330-5977349 None:intergenic 15.0%
!! TTTAGAAGACAAAAAAAAAA+AGG + chr8_2:5976826-5976845 Msa1230010:five_prime_UTR 15.0%
!!! AGTTTATATCAAAGTAATTT+TGG + chr8_2:5976910-5976929 Msa1230010:intron 15.0%
!!! GTTTATATCAAAGTAATTTT+GGG + chr8_2:5976911-5976930 Msa1230010:intron 15.0%
!! AAATAGTTTCATCAAATTTA+AGG - chr8_2:5977330-5977349 None:intergenic 15.0%
!! ATAACAATTTAAATTCATGG+TGG + chr8_2:5976721-5976740 Msa1230010:five_prime_UTR 20.0%
!! TAACAATTTAAATTCATGGT+GGG + chr8_2:5976722-5976741 Msa1230010:five_prime_UTR 20.0%
!! ATATTCATATCAAAATCATG+TGG + chr8_2:5977149-5977168 Msa1230010:intron 20.0%
!! TAGTGATATATAATTTGAAG+AGG - chr8_2:5977261-5977280 None:intergenic 20.0%
!! CTTCAAATTATATATCACTA+TGG + chr8_2:5977261-5977280 Msa1230010:intron 20.0%
!! TATCTTTCCATAATAATTGA+AGG + chr8_2:5977285-5977304 Msa1230010:intron 20.0%
!!! TTTTCTTCCTTCAATTATTA+TGG - chr8_2:5977295-5977314 None:intergenic 20.0%
!!! TCTTCTTTTAAACTATTTGT+TGG + chr8_2:5977365-5977384 Msa1230010:intron 20.0%
!! ATTGCTTAAGAAAACTAATA+TGG + chr8_2:5977497-5977516 Msa1230010:intron 20.0%
!! GAAGAGAATTAATTAACATA+TGG + chr8_2:5977823-5977842 Msa1230010:three_prime_UTR 20.0%
!! GTCAAGAACAAAAATATAAA+TGG + chr8_2:5977967-5977986 Msa1230010:three_prime_UTR 20.0%
!! ATAACAATTTAAATTCATGG+TGG + chr8_2:5976721-5976740 Msa1230010:five_prime_UTR 20.0%
!! TAACAATTTAAATTCATGGT+GGG + chr8_2:5976722-5976741 Msa1230010:five_prime_UTR 20.0%
!! ATATTCATATCAAAATCATG+TGG + chr8_2:5977149-5977168 Msa1230010:intron 20.0%
!! TAGTGATATATAATTTGAAG+AGG - chr8_2:5977261-5977280 None:intergenic 20.0%
!! CTTCAAATTATATATCACTA+TGG + chr8_2:5977261-5977280 Msa1230010:intron 20.0%
!! TATCTTTCCATAATAATTGA+AGG + chr8_2:5977285-5977304 Msa1230010:intron 20.0%
!!! TTTTCTTCCTTCAATTATTA+TGG - chr8_2:5977295-5977314 None:intergenic 20.0%
!!! TCTTCTTTTAAACTATTTGT+TGG + chr8_2:5977365-5977384 Msa1230010:intron 20.0%
!! ATTGCTTAAGAAAACTAATA+TGG + chr8_2:5977497-5977516 Msa1230010:intron 20.0%
!! GAAGAGAATTAATTAACATA+TGG + chr8_2:5977823-5977842 Msa1230010:three_prime_UTR 20.0%
!! GTCAAGAACAAAAATATAAA+TGG + chr8_2:5977967-5977986 Msa1230010:three_prime_UTR 20.0%
! ATTAGTGACTAAATGTAGTT+CGG + chr8_2:5976698-5976717 Msa1230010:five_prime_UTR 25.0%
! CGGATAACAATTTAAATTCA+TGG + chr8_2:5976718-5976737 Msa1230010:five_prime_UTR 25.0%
!!! GTCTTCTAAAATAATGTAAG+TGG - chr8_2:5976816-5976835 None:intergenic 25.0%
! GAAGACAAAAAAAAAAAGGA+TGG + chr8_2:5976830-5976849 Msa1230010:exon 25.0%
!! GTTTCATCAAATTTAAGGTT+TGG - chr8_2:5977325-5977344 None:intergenic 25.0%
!! GAAAACTAATATGGTTCTTT+TGG + chr8_2:5977506-5977525 Msa1230010:intron 25.0%
! TTAATTCTCTTCTCACTAAA+GGG - chr8_2:5977815-5977834 None:intergenic 25.0%
! ATTAATTCTCTTCTCACTAA+AGG - chr8_2:5977816-5977835 None:intergenic 25.0%
! ATTAGTGACTAAATGTAGTT+CGG + chr8_2:5976698-5976717 Msa1230010:five_prime_UTR 25.0%
! CGGATAACAATTTAAATTCA+TGG + chr8_2:5976718-5976737 Msa1230010:five_prime_UTR 25.0%
!!! GTCTTCTAAAATAATGTAAG+TGG - chr8_2:5976816-5976835 None:intergenic 25.0%
! GAAGACAAAAAAAAAAAGGA+TGG + chr8_2:5976830-5976849 Msa1230010:exon 25.0%
!! GTTTCATCAAATTTAAGGTT+TGG - chr8_2:5977325-5977344 None:intergenic 25.0%
!! GAAAACTAATATGGTTCTTT+TGG + chr8_2:5977506-5977525 Msa1230010:intron 25.0%
! TTAATTCTCTTCTCACTAAA+GGG - chr8_2:5977815-5977834 None:intergenic 25.0%
! ATTAATTCTCTTCTCACTAA+AGG - chr8_2:5977816-5977835 None:intergenic 25.0%
ATTTATAGAATCCCAGAAGT+TGG - chr8_2:5976757-5976776 None:intergenic 30.0%
!! ACTTCTGGGATTCTATAAAT+TGG + chr8_2:5976757-5976776 Msa1230010:five_prime_UTR 30.0%
CAAAAAAAAAAAGGATGGAG+AGG + chr8_2:5976835-5976854 Msa1230010:exon 30.0%
AAACCAAGTAAATTCTTCAG+TGG + chr8_2:5977570-5977589 Msa1230010:CDS 30.0%
AAATACATCTGATCTCATAG+TGG - chr8_2:5977711-5977730 None:intergenic 30.0%
TCATAGCTAGATTATGTTCA+TGG + chr8_2:5977765-5977784 Msa1230010:three_prime_UTR 30.0%
!! TTAGTTCTGTTACACTATGT+TGG - chr8_2:5977945-5977964 None:intergenic 30.0%
ATTTATAGAATCCCAGAAGT+TGG - chr8_2:5976757-5976776 None:intergenic 30.0%
!! ACTTCTGGGATTCTATAAAT+TGG + chr8_2:5976757-5976776 Msa1230010:five_prime_UTR 30.0%
CAAAAAAAAAAAGGATGGAG+AGG + chr8_2:5976835-5976854 Msa1230010:exon 30.0%
AAACCAAGTAAATTCTTCAG+TGG + chr8_2:5977570-5977589 Msa1230010:CDS 30.0%
AAATACATCTGATCTCATAG+TGG - chr8_2:5977711-5977730 None:intergenic 30.0%
TCATAGCTAGATTATGTTCA+TGG + chr8_2:5977765-5977784 Msa1230010:three_prime_UTR 30.0%
!! TTAGTTCTGTTACACTATGT+TGG - chr8_2:5977945-5977964 None:intergenic 30.0%
!! TGGTCTTATCACTTTGACTA+AGG + chr8_2:5976603-5976622 Msa1230010:five_prime_UTR 35.0%
TGACTAAGGAGTAACATTCA+TGG + chr8_2:5976617-5976636 Msa1230010:five_prime_UTR 35.0%
! GGAATACTTTTCCAACTTCT+GGG + chr8_2:5976743-5976762 Msa1230010:five_prime_UTR 35.0%
TGCAAAGATAACCACATTGT+TGG - chr8_2:5977620-5977639 None:intergenic 35.0%
AACAATGTGGTTATCTTTGC+AGG + chr8_2:5977619-5977638 Msa1230010:CDS 35.0%
!! TGGTCTTATCACTTTGACTA+AGG + chr8_2:5976603-5976622 Msa1230010:five_prime_UTR 35.0%
TGACTAAGGAGTAACATTCA+TGG + chr8_2:5976617-5976636 Msa1230010:five_prime_UTR 35.0%
! GGAATACTTTTCCAACTTCT+GGG + chr8_2:5976743-5976762 Msa1230010:five_prime_UTR 35.0%
TGCAAAGATAACCACATTGT+TGG - chr8_2:5977620-5977639 None:intergenic 35.0%
AACAATGTGGTTATCTTTGC+AGG + chr8_2:5977619-5977638 Msa1230010:CDS 35.0%
! GGGAATACTTTTCCAACTTC+TGG + chr8_2:5976742-5976761 Msa1230010:five_prime_UTR 40.0%
GGAAATTTCAGAAGAAGCAG+TGG + chr8_2:5977527-5977546 Msa1230010:intron 40.0%
GCACCACTGAAGAATTTACT+TGG - chr8_2:5977576-5977595 None:intergenic 40.0%
TTCTTCAGTGGTGCATGTAT+TGG + chr8_2:5977582-5977601 Msa1230010:CDS 40.0%
! TCATAGTGGAGATGTTCAAC+AGG - chr8_2:5977697-5977716 None:intergenic 40.0%
TCTCTTCTCACTAAAGGGAA+GGG - chr8_2:5977810-5977829 None:intergenic 40.0%
TTCTCTTCTCACTAAAGGGA+AGG - chr8_2:5977811-5977830 None:intergenic 40.0%
! GGGAATACTTTTCCAACTTC+TGG + chr8_2:5976742-5976761 Msa1230010:five_prime_UTR 40.0%
GGAAATTTCAGAAGAAGCAG+TGG + chr8_2:5977527-5977546 Msa1230010:intron 40.0%
GCACCACTGAAGAATTTACT+TGG - chr8_2:5977576-5977595 None:intergenic 40.0%
TTCTTCAGTGGTGCATGTAT+TGG + chr8_2:5977582-5977601 Msa1230010:CDS 40.0%
! TCATAGTGGAGATGTTCAAC+AGG - chr8_2:5977697-5977716 None:intergenic 40.0%
TCTCTTCTCACTAAAGGGAA+GGG - chr8_2:5977810-5977829 None:intergenic 40.0%
TTCTCTTCTCACTAAAGGGA+AGG - chr8_2:5977811-5977830 None:intergenic 40.0%
TGCTAGCATGTGCTTCTTTG+TGG + chr8_2:5976656-5976675 Msa1230010:five_prime_UTR 45.0%
GCTAGCATGTGCTTCTTTGT+GGG + chr8_2:5976657-5976676 Msa1230010:five_prime_UTR 45.0%
CTAGCATGTGCTTCTTTGTG+GGG + chr8_2:5976658-5976677 Msa1230010:five_prime_UTR 45.0%
AGAAGCAGTGGTGCAAATTG+AGG + chr8_2:5977539-5977558 Msa1230010:CDS 45.0%
!! GGTGCATGTATTGGTTCATC+TGG + chr8_2:5977591-5977610 Msa1230010:CDS 45.0%
TCATCTGGCAACCAACAATG+TGG + chr8_2:5977606-5977625 Msa1230010:CDS 45.0%
TGTGGTTATCTTTGCAGGAG+AGG + chr8_2:5977624-5977643 Msa1230010:CDS 45.0%
TATCTTTGCAGGAGAGGAGA+AGG + chr8_2:5977630-5977649 Msa1230010:CDS 45.0%
TGCTAGCATGTGCTTCTTTG+TGG + chr8_2:5976656-5976675 Msa1230010:five_prime_UTR 45.0%
GCTAGCATGTGCTTCTTTGT+GGG + chr8_2:5976657-5976676 Msa1230010:five_prime_UTR 45.0%
CTAGCATGTGCTTCTTTGTG+GGG + chr8_2:5976658-5976677 Msa1230010:five_prime_UTR 45.0%
AGAAGCAGTGGTGCAAATTG+AGG + chr8_2:5977539-5977558 Msa1230010:CDS 45.0%
!! GGTGCATGTATTGGTTCATC+TGG + chr8_2:5977591-5977610 Msa1230010:CDS 45.0%
TCATCTGGCAACCAACAATG+TGG + chr8_2:5977606-5977625 Msa1230010:CDS 45.0%
TGTGGTTATCTTTGCAGGAG+AGG + chr8_2:5977624-5977643 Msa1230010:CDS 45.0%
TATCTTTGCAGGAGAGGAGA+AGG + chr8_2:5977630-5977649 Msa1230010:CDS 45.0%
!!! TTTATATTTTGTAATAAAAA+AGG - chr8_2:5976980-5976999 None:intergenic 5.0%
!!! TTTATATTTTGTAATAAAAA+AGG - chr8_2:5976980-5976999 None:intergenic 5.0%
AGAGGAGAAGGCTTACTCAG+TGG + chr8_2:5977642-5977661 Msa1230010:CDS 50.0%
AGAGGAGAAGGCTTACTCAG+TGG + chr8_2:5977642-5977661 Msa1230010:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 5976584 5978025 5976584 ID=Msa1230010;Name=Msa1230010
chr8_2 mRNA 5976584 5978025 5976584 ID=Msa1230010-mRNA-1;Parent=Msa1230010;Name=Msa1230010-mRNA-1;_AED=0.01;_eAED=0.01;_QI=265|1|1|1|1|1|2|324|73
chr8_2 exon 5976584 5976906 5976584 ID=Msa1230010-mRNA-1:exon:2102;Parent=Msa1230010-mRNA-1
chr8_2 exon 5977538 5978025 5977538 ID=Msa1230010-mRNA-1:exon:2103;Parent=Msa1230010-mRNA-1
chr8_2 five_prime_UTR 5976584 5976848 5976584 ID=Msa1230010-mRNA-1:five_prime_utr;Parent=Msa1230010-mRNA-1
chr8_2 CDS 5976849 5976906 5976849 ID=Msa1230010-mRNA-1:cds;Parent=Msa1230010-mRNA-1
chr8_2 CDS 5977538 5977701 5977538 ID=Msa1230010-mRNA-1:cds;Parent=Msa1230010-mRNA-1
chr8_2 three_prime_UTR 5977702 5978025 5977702 ID=Msa1230010-mRNA-1:three_prime_utr;Parent=Msa1230010-mRNA-1
Gene Sequence

>Msa1230010

ATGGAGAGGAAAACACTTGCTAGCTTGTGCTTCTTTCTTATTGTTCTCTTAGCTGCTCAAGAAGCAGTGGTGCAAATTGAGGCTTGTGAGAAACCAAGTAAATTCTTCAGTGGTGCATGTATTGGTTCATCTGGCAACCAACAATGTGGTTATCTTTGCAGGAGAGGAGAAGGCTTACTCAGTGGTTCTTGCAAAAATCTGAAATGTGTTTGTGCCTGTTGA
Protein sequence

>Msa1230010

MERKTLASLCFFLIVLLAAQEAVVQIEACEKPSKFFSGACIGSSGNQQCGYLCRRGEGLLSGSCKNLKCVCAC*