AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0349910


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0349910 MtrunA17_Chr3g0084011 93.506 77 5 0 1 77 1 77 1.20e-49 151
Msa0349910 MtrunA17_Chr3g0083921 98.630 73 1 0 1 73 1 73 5.20e-47 151
Msa0349910 MtrunA17_Chr8g0352591 76.712 73 17 0 1 73 1 73 5.46e-35 120
Msa0349910 MtrunA17_Chr3g0083901 72.603 73 20 0 1 73 1 73 3.60e-32 113
Msa0349910 MtrunA17_Chr8g0352611 69.863 73 22 0 1 73 1 73 7.68e-32 112
Msa0349910 MtrunA17_Chr8g0352621 69.863 73 21 1 1 73 1 72 2.60e-31 110
Msa0349910 MtrunA17_Chr2g0293441 56.164 73 32 0 1 73 1 73 1.26e-24 93.2
Msa0349910 MtrunA17_Chr8g0382281 55.405 74 32 1 1 73 1 74 3.80e-20 81.3
Msa0349910 MtrunA17_Chr5g0425971 52.703 74 34 1 1 73 1 74 8.24e-20 80.5
Msa0349910 MtrunA17_Chr8g0393281 54.054 74 33 1 1 73 1 74 1.90e-19 79.3
Msa0349910 MtrunA17_Chr8g0352571 54.795 73 32 1 1 72 1 73 1.23e-18 77.4
Msa0349910 MtrunA17_Chr6g0479421 53.333 75 34 1 1 74 1 75 1.67e-17 74.3
Msa0349910 MtrunA17_Chr1g0210981 49.333 75 37 1 1 74 1 75 1.09e-15 69.3
Msa0349910 MtrunA17_Chr6g0479411 50.000 74 36 1 1 73 28 101 3.29e-15 68.2
Msa0349910 MtrunA17_Chr1g0162071 44.595 74 40 1 1 73 1 74 1.26e-14 66.2
Msa0349910 MtrunA17_Chr6g0479391 52.459 61 29 0 14 74 15 75 5.93e-14 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0349910 AT5G12380.1 61.644 73 28 0 1 73 1 73 4.55e-27 100
Msa0349910 AT5G10220.1 58.108 74 30 1 1 73 1 74 1.57e-21 85.5
Msa0349910 AT5G65020.1 58.108 74 30 1 1 73 1 74 1.72e-21 85.5
Msa0349910 AT5G10230.1 58.108 74 30 1 1 73 1 74 2.00e-21 85.1
Msa0349910 AT2G38760.1 52.055 73 34 1 1 72 1 73 5.95e-21 84.0
Msa0349910 AT1G35720.1 55.405 74 32 1 1 73 1 74 3.17e-20 82.0
Msa0349910 AT5G65020.2 61.224 49 19 0 25 73 11 59 9.87e-15 67.0
Msa0349910 AT1G68090.2 50.704 71 34 1 1 70 1 71 9.38e-14 63.9
Msa0349910 AT1G68090.1 50.704 71 34 1 1 70 1 71 1.39e-13 63.9

Find 17 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCTTGAGTCTGAGCTTTC+AGG 0.157675 3_1:-14317022 Msa0349910:CDS
ATGACCTAATATTGCTATAA+TGG 0.265808 3_1:+14317114 None:intergenic
CTTGTCTGATTTGAGTCCTT+TGG 0.274325 3_1:+14317080 None:intergenic
AGTGGTTGGAAGGAGCAATA+AGG 0.292571 3_1:+14317886 None:intergenic
AAAGCCATTATAGCAATATT+AGG 0.311002 3_1:-14317118 Msa0349910:CDS
GCTCTTCAAAGGGCTGTTAA+AGG 0.314120 3_1:-14317843 Msa0349910:intron
TTGTCTGATTTGAGTCCTTT+GGG 0.385685 3_1:+14317081 None:intergenic
GTGGTTGGAAGGAGCAATAA+GGG 0.389381 3_1:+14317887 None:intergenic
AGAGCTTCTGCATCTTCAAC+TGG 0.416203 3_1:+14317861 None:intergenic
CTGCATCTTCAACTGGAGAG+TGG 0.522358 3_1:+14317868 None:intergenic
AAGATGCAGAAGCTCTTCAA+AGG 0.524239 3_1:-14317854 Msa0349910:CDS
ATCTTCAACTGGAGAGTGGT+TGG 0.525012 3_1:+14317872 None:intergenic
AGGAGCAATAAGGGAAGCCA+TGG 0.568515 3_1:+14317896 None:intergenic
TCAACTGGAGAGTGGTTGGA+AGG 0.576644 3_1:+14317876 None:intergenic
AGATGCAGAAGCTCTTCAAA+GGG 0.589809 3_1:-14317853 Msa0349910:CDS
ATACTATGAACTCTATCAAG+AGG 0.590523 3_1:-14317056 Msa0349910:CDS
GTCATAGAAATGCTACCCAA+AGG 0.630775 3_1:-14317096 Msa0349910:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATTATTAATTAAAATTT+GGG + chr3_1:14317209-14317228 None:intergenic 0.0%
!! ATTAATTATTAATTAAAATT+TGG + chr3_1:14317210-14317229 None:intergenic 0.0%
!! TAATTAATAATAATTAATTA+AGG - chr3_1:14317222-14317241 Msa0349910:intron 0.0%
!! TTAATTATTAATTAAAATTT+GGG + chr3_1:14317209-14317228 None:intergenic 0.0%
!! ATTAATTATTAATTAAAATT+TGG + chr3_1:14317210-14317229 None:intergenic 0.0%
!! TAATTAATAATAATTAATTA+AGG - chr3_1:14317222-14317241 Msa0349910:intron 0.0%
!! TTGAAATTGATTAAATTACT+GGG - chr3_1:14317717-14317736 Msa0349910:intron 15.0%
!! TTGAAATTGATTAAATTACT+GGG - chr3_1:14317717-14317736 Msa0349910:intron 15.0%
!!! TGTTGTTTTTAGTTAAAAGT+TGG - chr3_1:14317298-14317317 Msa0349910:intron 20.0%
!! CTTGAAATTGATTAAATTAC+TGG - chr3_1:14317716-14317735 Msa0349910:intron 20.0%
!!! TGTTGTTTTTAGTTAAAAGT+TGG - chr3_1:14317298-14317317 Msa0349910:intron 20.0%
!! CTTGAAATTGATTAAATTAC+TGG - chr3_1:14317716-14317735 Msa0349910:intron 20.0%
! AAGAAATGAAAAGATGGATA+TGG + chr3_1:14317083-14317102 None:intergenic 25.0%
! TCAAAGAAGAAATGAAAAGA+TGG + chr3_1:14317089-14317108 None:intergenic 25.0%
! TATTCTTATGTGTGAATGAA+AGG + chr3_1:14317157-14317176 None:intergenic 25.0%
! ACAACAATACGTTAGAAAAA+TGG + chr3_1:14317508-14317527 None:intergenic 25.0%
! TTATAATCGGTGAGTTTATA+TGG - chr3_1:14317651-14317670 Msa0349910:intron 25.0%
! TATAATCGGTGAGTTTATAT+GGG - chr3_1:14317652-14317671 Msa0349910:intron 25.0%
! AAAGCCATTATAGCAATATT+AGG - chr3_1:14317773-14317792 Msa0349910:intron 25.0%
! ATGACCTAATATTGCTATAA+TGG + chr3_1:14317780-14317799 None:intergenic 25.0%
! AAGAAATGAAAAGATGGATA+TGG + chr3_1:14317083-14317102 None:intergenic 25.0%
! TCAAAGAAGAAATGAAAAGA+TGG + chr3_1:14317089-14317108 None:intergenic 25.0%
! TATTCTTATGTGTGAATGAA+AGG + chr3_1:14317157-14317176 None:intergenic 25.0%
! ACAACAATACGTTAGAAAAA+TGG + chr3_1:14317508-14317527 None:intergenic 25.0%
! TTATAATCGGTGAGTTTATA+TGG - chr3_1:14317651-14317670 Msa0349910:intron 25.0%
! TATAATCGGTGAGTTTATAT+GGG - chr3_1:14317652-14317671 Msa0349910:intron 25.0%
! AAAGCCATTATAGCAATATT+AGG - chr3_1:14317773-14317792 Msa0349910:intron 25.0%
! ATGACCTAATATTGCTATAA+TGG + chr3_1:14317780-14317799 None:intergenic 25.0%
!! GGTTTGATGAATTTTCAAGA+TGG + chr3_1:14317136-14317155 None:intergenic 30.0%
ACGATTCCATGTGTTATAAT+CGG - chr3_1:14317638-14317657 Msa0349910:intron 30.0%
ATACTATGAACTCTATCAAG+AGG - chr3_1:14317835-14317854 Msa0349910:intron 30.0%
!! GGTTTGATGAATTTTCAAGA+TGG + chr3_1:14317136-14317155 None:intergenic 30.0%
ACGATTCCATGTGTTATAAT+CGG - chr3_1:14317638-14317657 Msa0349910:intron 30.0%
ATACTATGAACTCTATCAAG+AGG - chr3_1:14317835-14317854 Msa0349910:intron 30.0%
TTTAGTCCTTTACCTTCGAT+GGG + chr3_1:14317417-14317436 None:intergenic 35.0%
ATCGAAGGTAAAGGACTAAA+GGG - chr3_1:14317417-14317436 Msa0349910:intron 35.0%
AATATTGGCACCAGGAAAAA+GGG + chr3_1:14317472-14317491 None:intergenic 35.0%
GGTGTAACATGTCAGAATAT+TGG + chr3_1:14317487-14317506 None:intergenic 35.0%
! AACTCACCGATTATAACACA+TGG + chr3_1:14317647-14317666 None:intergenic 35.0%
! GCTTCGAAATTTTGTAGGTT+GGG - chr3_1:14317739-14317758 Msa0349910:intron 35.0%
! CTTCGAAATTTTGTAGGTTG+GGG - chr3_1:14317740-14317759 Msa0349910:intron 35.0%
! TTGTCTGATTTGAGTCCTTT+GGG + chr3_1:14317813-14317832 None:intergenic 35.0%
TTTAGTCCTTTACCTTCGAT+GGG + chr3_1:14317417-14317436 None:intergenic 35.0%
ATCGAAGGTAAAGGACTAAA+GGG - chr3_1:14317417-14317436 Msa0349910:intron 35.0%
AATATTGGCACCAGGAAAAA+GGG + chr3_1:14317472-14317491 None:intergenic 35.0%
GGTGTAACATGTCAGAATAT+TGG + chr3_1:14317487-14317506 None:intergenic 35.0%
! AACTCACCGATTATAACACA+TGG + chr3_1:14317647-14317666 None:intergenic 35.0%
! GCTTCGAAATTTTGTAGGTT+GGG - chr3_1:14317739-14317758 Msa0349910:intron 35.0%
! CTTCGAAATTTTGTAGGTTG+GGG - chr3_1:14317740-14317759 Msa0349910:intron 35.0%
! TTGTCTGATTTGAGTCCTTT+GGG + chr3_1:14317813-14317832 None:intergenic 35.0%
AAGATGCAGAAGCTCTTCAA+AGG - chr3_1:14317037-14317056 Msa0349910:CDS 40.0%
AGATGCAGAAGCTCTTCAAA+GGG - chr3_1:14317038-14317057 Msa0349910:CDS 40.0%
CGATGGGGCTATTAGTATTT+CGG + chr3_1:14317401-14317420 None:intergenic 40.0%
AATACTAATAGCCCCATCGA+AGG - chr3_1:14317402-14317421 Msa0349910:intron 40.0%
TTAGTCCTTTACCTTCGATG+GGG + chr3_1:14317416-14317435 None:intergenic 40.0%
CTTTAGTCCTTTACCTTCGA+TGG + chr3_1:14317418-14317437 None:intergenic 40.0%
CATCGAAGGTAAAGGACTAA+AGG - chr3_1:14317416-14317435 Msa0349910:intron 40.0%
! ATAGCTTAGACCCTTTTTCC+TGG - chr3_1:14317459-14317478 Msa0349910:intron 40.0%
GAATATTGGCACCAGGAAAA+AGG + chr3_1:14317473-14317492 None:intergenic 40.0%
! ACTGGGCTTCGAAATTTTGT+AGG - chr3_1:14317734-14317753 Msa0349910:intron 40.0%
! GGCTTCGAAATTTTGTAGGT+TGG - chr3_1:14317738-14317757 Msa0349910:intron 40.0%
GTCATAGAAATGCTACCCAA+AGG - chr3_1:14317795-14317814 Msa0349910:intron 40.0%
! CTTGTCTGATTTGAGTCCTT+TGG + chr3_1:14317814-14317833 None:intergenic 40.0%
!! TGAGCTTTCAGGTGATTTTG+AGG - chr3_1:14317880-14317899 Msa0349910:CDS 40.0%
!!! GTGATTTTGAGGTACATCCA+CGG - chr3_1:14317891-14317910 Msa0349910:CDS 40.0%
AAGATGCAGAAGCTCTTCAA+AGG - chr3_1:14317037-14317056 Msa0349910:CDS 40.0%
AGATGCAGAAGCTCTTCAAA+GGG - chr3_1:14317038-14317057 Msa0349910:CDS 40.0%
CGATGGGGCTATTAGTATTT+CGG + chr3_1:14317401-14317420 None:intergenic 40.0%
AATACTAATAGCCCCATCGA+AGG - chr3_1:14317402-14317421 Msa0349910:intron 40.0%
TTAGTCCTTTACCTTCGATG+GGG + chr3_1:14317416-14317435 None:intergenic 40.0%
CTTTAGTCCTTTACCTTCGA+TGG + chr3_1:14317418-14317437 None:intergenic 40.0%
CATCGAAGGTAAAGGACTAA+AGG - chr3_1:14317416-14317435 Msa0349910:intron 40.0%
! ATAGCTTAGACCCTTTTTCC+TGG - chr3_1:14317459-14317478 Msa0349910:intron 40.0%
GAATATTGGCACCAGGAAAA+AGG + chr3_1:14317473-14317492 None:intergenic 40.0%
! ACTGGGCTTCGAAATTTTGT+AGG - chr3_1:14317734-14317753 Msa0349910:intron 40.0%
! GGCTTCGAAATTTTGTAGGT+TGG - chr3_1:14317738-14317757 Msa0349910:intron 40.0%
GTCATAGAAATGCTACCCAA+AGG - chr3_1:14317795-14317814 Msa0349910:intron 40.0%
! CTTGTCTGATTTGAGTCCTT+TGG + chr3_1:14317814-14317833 None:intergenic 40.0%
!! TGAGCTTTCAGGTGATTTTG+AGG - chr3_1:14317880-14317899 Msa0349910:CDS 40.0%
!!! GTGATTTTGAGGTACATCCA+CGG - chr3_1:14317891-14317910 Msa0349910:CDS 40.0%
GTGGTTGGAAGGAGCAATAA+GGG + chr3_1:14317007-14317026 None:intergenic 45.0%
AGTGGTTGGAAGGAGCAATA+AGG + chr3_1:14317008-14317027 None:intergenic 45.0%
ATCTTCAACTGGAGAGTGGT+TGG + chr3_1:14317022-14317041 None:intergenic 45.0%
AGAGCTTCTGCATCTTCAAC+TGG + chr3_1:14317033-14317052 None:intergenic 45.0%
GCTCTTCAAAGGGCTGTTAA+AGG - chr3_1:14317048-14317067 Msa0349910:CDS 45.0%
AATAGCCCCATCGAAGGTAA+AGG - chr3_1:14317408-14317427 Msa0349910:intron 45.0%
CATGTCAGAATATTGGCACC+AGG + chr3_1:14317480-14317499 None:intergenic 45.0%
GTGGTTGGAAGGAGCAATAA+GGG + chr3_1:14317007-14317026 None:intergenic 45.0%
AGTGGTTGGAAGGAGCAATA+AGG + chr3_1:14317008-14317027 None:intergenic 45.0%
ATCTTCAACTGGAGAGTGGT+TGG + chr3_1:14317022-14317041 None:intergenic 45.0%
AGAGCTTCTGCATCTTCAAC+TGG + chr3_1:14317033-14317052 None:intergenic 45.0%
GCTCTTCAAAGGGCTGTTAA+AGG - chr3_1:14317048-14317067 Msa0349910:CDS 45.0%
AATAGCCCCATCGAAGGTAA+AGG - chr3_1:14317408-14317427 Msa0349910:intron 45.0%
CATGTCAGAATATTGGCACC+AGG + chr3_1:14317480-14317499 None:intergenic 45.0%
TCAACTGGAGAGTGGTTGGA+AGG + chr3_1:14317018-14317037 None:intergenic 50.0%
CTGCATCTTCAACTGGAGAG+TGG + chr3_1:14317026-14317045 None:intergenic 50.0%
CGTCTTGAGTCTGAGCTTTC+AGG - chr3_1:14317869-14317888 Msa0349910:CDS 50.0%
TCAACTGGAGAGTGGTTGGA+AGG + chr3_1:14317018-14317037 None:intergenic 50.0%
CTGCATCTTCAACTGGAGAG+TGG + chr3_1:14317026-14317045 None:intergenic 50.0%
CGTCTTGAGTCTGAGCTTTC+AGG - chr3_1:14317869-14317888 Msa0349910:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 14316997 14317916 14316997 ID=Msa0349910;Name=Msa0349910
chr3_1 mRNA 14316997 14317916 14316997 ID=Msa0349910-mRNA-1;Parent=Msa0349910;Name=Msa0349910-mRNA-1;_AED=0.48;_eAED=0.48;_QI=0|0|0|1|1|1|2|0|77
chr3_1 exon 14317844 14317916 14317844 ID=Msa0349910-mRNA-1:exon:3571;Parent=Msa0349910-mRNA-1
chr3_1 exon 14316997 14317157 14316997 ID=Msa0349910-mRNA-1:exon:3570;Parent=Msa0349910-mRNA-1
chr3_1 CDS 14317844 14317916 14317844 ID=Msa0349910-mRNA-1:cds;Parent=Msa0349910-mRNA-1
chr3_1 CDS 14316997 14317157 14316997 ID=Msa0349910-mRNA-1:cds;Parent=Msa0349910-mRNA-1
Gene Sequence

>Msa0349910

ATGGCTTCCCTTATTGCTCCTTCCAACCACTCTCCAGTTGAAGATGCAGAAGCTCTTCAAAGGGCTGTTAAAGGTTGGGGAGCTGATGAAAAAGCCATTATAGCAATATTAGGTCATAGAAATGCTACCCAAAGGACTCAAATCAGACAAGCATACTATGAACTCTATCAAGAGGATCTCATCAAACGTCTTGAGTCTGAGCTTTCAGGTGATTTTGAGGTACATCCACGGTAA

Protein sequence

>Msa0349910

MASLIAPSNHSPVEDAEALQRAVKGWGADEKAIIAILGHRNATQRTQIRQAYYELYQEDLIKRLESELSGDFEVHPR*