AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene98742

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98742.t1 MTR_7g117590 70.988 162 32 2 2 149 12 172 6.57e-78 229
MS.gene98742.t1 MTR_1g054470 52.778 144 42 4 2 145 23 140 1.51e-43 140
MS.gene98742.t1 MTR_2g012700 36.364 110 69 1 40 148 10 119 4.07e-28 100
MS.gene98742.t1 MTR_2g062330 38.793 116 66 3 34 148 27 138 1.50e-26 97.8
MS.gene98742.t1 MTR_5g071400 67.925 53 15 2 3 55 9 59 1.91e-17 72.8
MS.gene98742.t1 MTR_0010s0310 35.556 90 55 1 53 139 151 240 1.34e-15 71.6
MS.gene98742.t1 MTR_6g477950 36.275 102 61 3 48 148 46 144 5.47e-14 67.8
MS.gene98742.t1 MTR_5g078270 33.708 89 56 1 54 139 210 298 2.07e-13 66.2
MS.gene98742.t1 MTR_7g117585 36.905 84 50 2 68 149 64 146 4.03e-12 60.5
MS.gene98742.t1 MTR_3g008190 29.167 96 67 1 54 148 6 101 7.29e-12 58.5
MS.gene98742.t1 MTR_6g087720 34.940 83 53 1 55 136 216 298 9.57e-12 61.6
MS.gene98742.t1 MTR_5g071400 73.684 38 8 2 18 55 1 36 3.65e-11 55.8
MS.gene98742.t1 MTR_0010s0290 31.373 102 63 3 54 149 223 323 4.61e-11 59.7
MS.gene98742.t1 MTR_0010s0320 32.609 92 55 3 54 139 192 282 7.33e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATCAACTATTCGAATTT+TGG 0.090848 2.1:-5311791 None:intergenic
TACAGGTAATGGGTGAAAAT+TGG 0.209416 2.1:-5311503 None:intergenic
CCATCGACTTCTTCTTCATT+TGG 0.245009 2.1:-5311535 None:intergenic
GTGGATGGTTTGAGTTTGTT+AGG 0.256057 2.1:+5311881 MS.gene98742:CDS
GGCTGTTGGACGGAGTGTTC+TGG 0.356206 2.1:+5311633 MS.gene98742:CDS
CGAATAGTTGATGATGAAAC+TGG 0.373610 2.1:+5311799 MS.gene98742:CDS
GAATGTGAAGTTCGTGATAA+AGG 0.381874 2.1:+5311832 MS.gene98742:CDS
AAGTTCGTGATAAAGGAAAT+TGG 0.388847 2.1:+5311839 MS.gene98742:CDS
ACAGGTAATGGGTGAAAATT+GGG 0.407202 2.1:-5311502 None:intergenic
ATTAGTTCTGCTACGGCTGT+TGG 0.467637 2.1:+5311619 MS.gene98742:CDS
TGGATGGTTTGAGTTTGTTA+GGG 0.477462 2.1:+5311882 MS.gene98742:CDS
AAATGTCTTCTTCTAGTAGC+AGG 0.479507 2.1:+5311372 None:intergenic
CTGCAGCCATGTAATTGATC+CGG 0.509939 2.1:+5311462 MS.gene98742:intron
TTTGAAATTGTGCAGATACT+GGG 0.510532 2.1:-5311558 None:intergenic
ATGGAGAAATACGTTGGTAG+TGG 0.538951 2.1:+5311862 MS.gene98742:CDS
CCATGTAATTGATCCGGAGT+TGG 0.545499 2.1:+5311468 MS.gene98742:CDS
GATACAAATAATTTGTGTGG+AGG 0.545934 2.1:-5311952 None:intergenic
GGCATCAATTCGTCCAACTC+CGG 0.549037 2.1:-5311481 None:intergenic
CCAACTCCGGATCAATTACA+TGG 0.550497 2.1:-5311468 None:intergenic
AGAAATACGTTGGTAGTGGA+TGG 0.551017 2.1:+5311866 MS.gene98742:CDS
CTTTGAATTGCAATCTTCCG+AGG 0.557056 2.1:-5311751 None:intergenic
ATTGATACAAATAATTTGTG+TGG 0.558267 2.1:-5311955 None:intergenic
TCGTGATAAAGGAAATTGGA+TGG 0.565929 2.1:+5311843 MS.gene98742:CDS
TGAATGTGTAGCATATTCCT+CGG 0.575111 2.1:+5311734 MS.gene98742:intron
GCATAGTATTAGTTCTGCTA+CGG 0.580120 2.1:+5311612 MS.gene98742:CDS
AGGGCAAAAGAACTCAAAGA+AGG 0.584629 2.1:+5311901 MS.gene98742:CDS
GTTCTGCTACGGCTGTTGGA+CGG 0.598239 2.1:+5311623 MS.gene98742:CDS
AATTGGATGGAGAAATACGT+TGG 0.604235 2.1:+5311856 MS.gene98742:CDS
CCAAATGAAGAAGAAGTCGA+TGG 0.658231 2.1:+5311535 MS.gene98742:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAATTTCAAAAATTTCAAAA+CGG + chr2.1:5311571-5311590 MS.gene98742:CDS 15.0%
!!! AGTTTTAATTTTATTTTTGC+TGG + chr2.1:5311658-5311677 MS.gene98742:intron 15.0%
!!! TTTTTGTTTTTTTAATCTTC+TGG + chr2.1:5311416-5311435 MS.gene98742:intron 15.0%
!!! ATTGATACAAATAATTTGTG+TGG - chr2.1:5311958-5311977 None:intergenic 20.0%
!! ATCATCAACTATTCGAATTT+TGG - chr2.1:5311794-5311813 None:intergenic 25.0%
AAGTTCGTGATAAAGGAAAT+TGG + chr2.1:5311839-5311858 MS.gene98742:CDS 30.0%
! AAAACGGTGATCATACTTTT+TGG + chr2.1:5311587-5311606 MS.gene98742:CDS 30.0%
! GATACAAATAATTTGTGTGG+AGG - chr2.1:5311955-5311974 None:intergenic 30.0%
! TTTGAAATTGTGCAGATACT+GGG - chr2.1:5311561-5311580 None:intergenic 30.0%
!!! TTTTGAAATTGTGCAGATAC+TGG - chr2.1:5311562-5311581 None:intergenic 30.0%
AATTGGATGGAGAAATACGT+TGG + chr2.1:5311856-5311875 MS.gene98742:CDS 35.0%
GAATGTGAAGTTCGTGATAA+AGG + chr2.1:5311832-5311851 MS.gene98742:CDS 35.0%
TCGTGATAAAGGAAATTGGA+TGG + chr2.1:5311843-5311862 MS.gene98742:CDS 35.0%
TGAATGTGTAGCATATTCCT+CGG + chr2.1:5311734-5311753 MS.gene98742:intron 35.0%
! GATTTTCGTCTACAGGTAAT+GGG - chr2.1:5311516-5311535 None:intergenic 35.0%
! TCATTTGGATTTTCGTCTAC+AGG - chr2.1:5311523-5311542 None:intergenic 35.0%
!! ACAGGTAATGGGTGAAAATT+GGG - chr2.1:5311505-5311524 None:intergenic 35.0%
!! CGAATAGTTGATGATGAAAC+TGG + chr2.1:5311799-5311818 MS.gene98742:CDS 35.0%
!! GCATAGTATTAGTTCTGCTA+CGG + chr2.1:5311612-5311631 MS.gene98742:CDS 35.0%
!! TACAGGTAATGGGTGAAAAT+TGG - chr2.1:5311506-5311525 None:intergenic 35.0%
!! TGGATGGTTTGAGTTTGTTA+GGG + chr2.1:5311882-5311901 MS.gene98742:CDS 35.0%
AGGGCAAAAGAACTCAAAGA+AGG + chr2.1:5311901-5311920 MS.gene98742:CDS 40.0%
CCAAATGAAGAAGAAGTCGA+TGG + chr2.1:5311535-5311554 MS.gene98742:CDS 40.0%
CTTTGAATTGCAATCTTCCG+AGG - chr2.1:5311754-5311773 None:intergenic 40.0%
TTGCTGGATTATTTGCGCAT+GGG + chr2.1:5311674-5311693 MS.gene98742:intron 40.0%
TTTGCTGGATTATTTGCGCA+TGG + chr2.1:5311673-5311692 MS.gene98742:intron 40.0%
! ATGGAGAAATACGTTGGTAG+TGG + chr2.1:5311862-5311881 MS.gene98742:CDS 40.0%
! GGATTTTCGTCTACAGGTAA+TGG - chr2.1:5311517-5311536 None:intergenic 40.0%
! GTGGATGGTTTGAGTTTGTT+AGG + chr2.1:5311881-5311900 MS.gene98742:CDS 40.0%
!! AGAAATACGTTGGTAGTGGA+TGG + chr2.1:5311866-5311885 MS.gene98742:CDS 40.0%
!! CCATCGACTTCTTCTTCATT+TGG - chr2.1:5311538-5311557 None:intergenic 40.0%
CCAACTCCGGATCAATTACA+TGG - chr2.1:5311471-5311490 None:intergenic 45.0%
CCATGTAATTGATCCGGAGT+TGG + chr2.1:5311468-5311487 MS.gene98742:CDS 45.0%
CTGCAGCCATGTAATTGATC+CGG + chr2.1:5311462-5311481 MS.gene98742:intron 45.0%
!! ATTAGTTCTGCTACGGCTGT+TGG + chr2.1:5311619-5311638 MS.gene98742:CDS 45.0%
CTGGATTATTTGCGCATGGG+TGG + chr2.1:5311677-5311696 MS.gene98742:intron 50.0%
GATTATTTGCGCATGGGTGG+TGG + chr2.1:5311680-5311699 MS.gene98742:intron 50.0%
GGCATCAATTCGTCCAACTC+CGG - chr2.1:5311484-5311503 None:intergenic 50.0%
GTTCTGCTACGGCTGTTGGA+CGG + chr2.1:5311623-5311642 MS.gene98742:CDS 55.0%
! GGCTGTTGGACGGAGTGTTC+TGG + chr2.1:5311633-5311652 MS.gene98742:CDS 60.0%
! GCGCATGGGTGGTGGCTTTG+TGG + chr2.1:5311688-5311707 MS.gene98742:intron 65.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 5311374 5311987 5311374 ID=MS.gene98742
chr2.1 mRNA 5311374 5311987 5311374 ID=MS.gene98742.t1;Parent=MS.gene98742
chr2.1 exon 5311374 5311393 5311374 ID=MS.gene98742.t1.exon1;Parent=MS.gene98742.t1
chr2.1 CDS 5311374 5311393 5311374 ID=cds.MS.gene98742.t1;Parent=MS.gene98742.t1
chr2.1 exon 5311468 5311654 5311468 ID=MS.gene98742.t1.exon2;Parent=MS.gene98742.t1
chr2.1 CDS 5311468 5311654 5311468 ID=cds.MS.gene98742.t1;Parent=MS.gene98742.t1
chr2.1 exon 5311745 5311987 5311745 ID=MS.gene98742.t1.exon3;Parent=MS.gene98742.t1
chr2.1 CDS 5311745 5311987 5311745 ID=cds.MS.gene98742.t1;Parent=MS.gene98742.t1
Gene Sequence

>MS.gene98742

ATGTCTTCTTCTAGTAGCAGGTAACTTCAATGTTTGAGTTGTTTTTTGTTTTTTTAATCTTCTGGTTATTTATTAGATTTTGTTGAAACTGCAGCCATGTAATTGATCCGGAGTTGGACGAATTGATGCCCAATTTTCACCCATTACCTGTAGACGAAAATCCAAATGAAGAAGAAGTCGATGGCCCAGTATCTGCACAATTTCAAAAATTTCAAAACGGTGATCATACTTTTTGGATGCATAGTATTAGTTCTGCTACGGCTGTTGGACGGAGTGTTCTGGTTAGTTTTAATTTTATTTTTGCTGGATTATTTGCGCATGGGTGGTGGCTTTGTGGTTGAAAAGTAATATTATTTGTTTTGAATGTGTAGCATATTCCTCGGAAGATTGCAATTCAAAGTATGTATGTGAATCAATCCAAAATTCGAATAGTTGATGATGAAACTGGAGAAGAATATGAATGTGAAGTTCGTGATAAAGGAAATTGGATGGAGAAATACGTTGGTAGTGGATGGTTTGAGTTTGTTAGGGCAAAAGAACTCAAAGAAGGAGATTCGTTGTTCTTCACTATTGATAATCCTCCACACAAATTATTTGTATCAATGATTAGATAG
Protein sequence

>MS.gene98742.t1

MSSSSSSHVIDPELDELMPNFHPLPVDENPNEEEVDGPVSAQFQKFQNGDHTFWMHSISSATAVGRSVLHIPRKIAIQSMYVNQSKIRIVDDETGEEYECEVRDKGNWMEKYVGSGWFEFVRAKELKEGDSLFFTIDNPPHKLFVSMIR