AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41724

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41724.t1 MTR_7g085610 88.636 88 9 1 1 88 1 87 4.68e-53 160
MS.gene41724.t1 MTR_6g029390 61.111 90 31 2 1 88 1 88 7.11e-34 112
MS.gene41724.t1 MTR_5g098200 59.302 86 31 2 1 84 1 84 3.64e-31 105
MS.gene41724.t1 MTR_5g098280 40.000 80 45 2 1 80 1 77 3.16e-13 59.3
MS.gene41724.t1 MTR_5g075070 35.955 89 40 2 1 76 1 85 3.66e-12 57.0
MS.gene41724.t1 MTR_3g466420 40.244 82 43 2 1 76 1 82 3.73e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41724.t1 AT5G18150 57.143 84 28 3 1 84 1 76 6.23e-27 94.0
MS.gene41724.t1 AT5G14602 45.238 84 42 1 1 84 1 80 1.93e-22 82.8
MS.gene41724.t1 AT5G58375 46.988 83 35 3 1 78 1 79 1.17e-17 70.9

Find 22 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGATGATTAAGAATGGATTT+TGG 0.215303 7.2:+22171772 MS.gene41724:intron
TCATCCAACAAGGATCATTT+TGG 0.237826 7.2:+22171638 MS.gene41724:CDS
TGGAAGAAATGTGTCCTCTT+AGG 0.322863 7.2:+22171501 None:intergenic
TGGCCAGTGGGAGATATCTT+TGG 0.389035 7.2:+22171808 MS.gene41724:CDS
AAAACCAAAATGATCCTTGT+TGG 0.442824 7.2:-22171642 None:intergenic
TAGTTGGACATGATTATTTG+TGG 0.484852 7.2:-22171844 None:intergenic
TGGTTTCAGATGATTAAGAA+TGG 0.487583 7.2:+22171765 MS.gene41724:intron
AAAATGATCCTTGTTGGATG+AGG 0.493557 7.2:-22171636 None:intergenic
GTCAAACTCCTGTGTGGTGG+AGG 0.501263 7.2:-22171585 None:intergenic
ACTCTTAAGAGTTCTGTAGT+TGG 0.518236 7.2:-22171860 None:intergenic
CTGTGTGGTGGAGGAGCTCA+CGG 0.518529 7.2:-22171576 None:intergenic
AAGATCAAGAGGAACCTAAG+AGG 0.559496 7.2:-22171515 None:intergenic
CGATAAATCCTCATCCAACA+AGG 0.594299 7.2:+22171628 MS.gene41724:CDS
TTTCCAAAGATATCTCCCAC+TGG 0.618699 7.2:-22171811 None:intergenic
GTATTAGTTGACATGGCCAG+TGG 0.636543 7.2:+22171795 MS.gene41724:CDS
CGTGAGCTCCTCCACCACAC+AGG 0.640612 7.2:+22171577 MS.gene41724:CDS
TATTAGTTGACATGGCCAGT+GGG 0.647697 7.2:+22171796 MS.gene41724:CDS
GGTGGTCCACGCAAAATAAG+CGG 0.650418 7.2:-22171555 None:intergenic
AAAGTCAAACTCCTGTGTGG+TGG 0.659212 7.2:-22171588 None:intergenic
TGGATGAGGATTTATCGTTG+TGG 0.666330 7.2:-22171622 None:intergenic
TGCAAAGTCAAACTCCTGTG+TGG 0.706129 7.2:-22171591 None:intergenic
TGTGGTGGAGGAGCTCACGG+TGG 0.767016 7.2:-22171573 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGAATTGCATAAAGAAAATG+TGG - chr7.2:22171686-22171705 None:intergenic 25.0%
!! GATATCTTTGGAAAAATTTG+AGG + chr7.2:22171820-22171839 MS.gene41724:CDS 25.0%
!!! AGATGATTAAGAATGGATTT+TGG + chr7.2:22171772-22171791 MS.gene41724:intron 25.0%
!!! ATTGACTTGAAATGTTACTT+TGG + chr7.2:22171745-22171764 MS.gene41724:intron 25.0%
!!! GATGATTAAGAATGGATTTT+GGG + chr7.2:22171773-22171792 MS.gene41724:intron 25.0%
AAAACCAAAATGATCCTTGT+TGG - chr7.2:22171645-22171664 None:intergenic 30.0%
AATACAAGCACGAAAAAGAT+AGG - chr7.2:22171728-22171747 None:intergenic 30.0%
TAGTTGGACATGATTATTTG+TGG - chr7.2:22171847-22171866 None:intergenic 30.0%
TGGTTTCAGATGATTAAGAA+TGG + chr7.2:22171765-22171784 MS.gene41724:intron 30.0%
!! ATTTTGGGTATTAGTTGACA+TGG + chr7.2:22171788-22171807 MS.gene41724:CDS 30.0%
!!! GGATCATTTTGGTTTTATCA+AGG + chr7.2:22171649-22171668 MS.gene41724:CDS 30.0%
AAAATGATCCTTGTTGGATG+AGG - chr7.2:22171639-22171658 None:intergenic 35.0%
CATAAAGAAAATGTGGAACC+GGG - chr7.2:22171679-22171698 None:intergenic 35.0%
GCATAAAGAAAATGTGGAAC+CGG - chr7.2:22171680-22171699 None:intergenic 35.0%
! TCATCCAACAAGGATCATTT+TGG + chr7.2:22171638-22171657 MS.gene41724:CDS 35.0%
!!! TGGTTTTATCAAGGTATTCC+CGG + chr7.2:22171658-22171677 MS.gene41724:intron 35.0%
AAGATCAAGAGGAACCTAAG+AGG - chr7.2:22171518-22171537 None:intergenic 40.0%
CAGCTGAGAAAAAGATCAAG+AGG - chr7.2:22171529-22171548 None:intergenic 40.0%
CGATAAATCCTCATCCAACA+AGG + chr7.2:22171628-22171647 MS.gene41724:CDS 40.0%
TATTAGTTGACATGGCCAGT+GGG + chr7.2:22171796-22171815 MS.gene41724:CDS 40.0%
TGGATGAGGATTTATCGTTG+TGG - chr7.2:22171625-22171644 None:intergenic 40.0%
TTTCCAAAGATATCTCCCAC+TGG - chr7.2:22171814-22171833 None:intergenic 40.0%
! GATCTTTTTCTCAGCTGTGT+TGG + chr7.2:22171532-22171551 MS.gene41724:CDS 40.0%
AAAGTCAAACTCCTGTGTGG+TGG - chr7.2:22171591-22171610 None:intergenic 45.0%
GTATTAGTTGACATGGCCAG+TGG + chr7.2:22171795-22171814 MS.gene41724:CDS 45.0%
TGCAAAGTCAAACTCCTGTG+TGG - chr7.2:22171594-22171613 None:intergenic 45.0%
GGTGGTCCACGCAAAATAAG+CGG - chr7.2:22171558-22171577 None:intergenic 50.0%
TGGCCAGTGGGAGATATCTT+TGG + chr7.2:22171808-22171827 MS.gene41724:CDS 50.0%
!!! TGTTGGCCGCTTATTTTGCG+TGG + chr7.2:22171549-22171568 MS.gene41724:CDS 50.0%
GTCAAACTCCTGTGTGGTGG+AGG - chr7.2:22171588-22171607 None:intergenic 55.0%
! CTGTGTGGTGGAGGAGCTCA+CGG - chr7.2:22171579-22171598 None:intergenic 60.0%
CGTGAGCTCCTCCACCACAC+AGG + chr7.2:22171577-22171596 MS.gene41724:CDS 65.0%
! TGTGGTGGAGGAGCTCACGG+TGG - chr7.2:22171576-22171595 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 22171509 22171878 22171509 ID=MS.gene41724
chr7.2 mRNA 22171509 22171878 22171509 ID=MS.gene41724.t1;Parent=MS.gene41724
chr7.2 exon 22171509 22171670 22171509 ID=MS.gene41724.t1.exon1;Parent=MS.gene41724.t1
chr7.2 CDS 22171509 22171670 22171509 ID=cds.MS.gene41724.t1;Parent=MS.gene41724.t1
chr7.2 exon 22171774 22171878 22171774 ID=MS.gene41724.t1.exon2;Parent=MS.gene41724.t1
chr7.2 CDS 22171774 22171878 22171774 ID=cds.MS.gene41724.t1;Parent=MS.gene41724.t1
Gene Sequence

>MS.gene41724

ATGTGTCCTCTTAGGTTCCTCTTGATCTTTTTCTCAGCTGTGTTGGCCGCTTATTTTGCGTGGACCACCGTGAGCTCCTCCACCACACAGGAGTTTGACTTTGCAGCTCACGACCACAACGATAAATCCTCATCCAACAAGGATCATTTTGGTTTTATCAAGGTATTCCCGGTTCCACATTTTCTTTATGCAATTCAACATCATATTTTGTATTTTCCTATCTTTTTCGTGCTTGTATTGACTTGAAATGTTACTTTGGTTTCAGATGATTAAGAATGGATTTTGGGTATTAGTTGACATGGCCAGTGGGAGATATCTTTGGAAAAATTTGAGGTCCACAAATAATCATGTCCAACTACAGAACTCTTAA
Protein sequence

>MS.gene41724.t1

MCPLRFLLIFFSAVLAAYFAWTTVSSSTTQEFDFAAHDHNDKSSSNKDHFGFIKMIKNGFWVLVDMASGRYLWKNLRSTNNHVQLQNS