AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66475


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66475.t1 MTR_1g017780 97.516 161 4 0 1 161 1 161 5.34e-115 322
MS.gene66475.t1 MTR_8g076830 93.789 161 9 1 1 161 1 160 1.89e-98 280
MS.gene66475.t1 MTR_4g116410 93.168 161 10 1 1 161 1 160 3.69e-98 280
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66475.t1 AT5G23740 87.578 161 18 1 1 161 1 159 9.01e-93 266
MS.gene66475.t1 AT3G48930 86.335 161 21 1 1 161 1 160 3.51e-91 262
MS.gene66475.t1 AT4G30800 86.335 161 20 1 1 161 1 159 7.99e-89 256

Find 49 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGGGGATCATGTTATTAT+TGG 0.267190 1.4:-5131781 MS.gene66475:CDS
ATAATTCCTCCTAACAATAA+TGG 0.308146 1.4:+5131983 None:intergenic
AAGCGATTGCCACCCTTTCC+AGG 0.318925 1.4:+5132591 None:intergenic
TGAATAAAACCATTATTGTT+AGG 0.334061 1.4:-5131992 MS.gene66475:CDS
GACTCCTGTAAACGCCTTCT+TGG 0.362038 1.4:+5131559 None:intergenic
GGTGCCAAGAAGGCGTTTAC+AGG 0.366657 1.4:-5131563 MS.gene66475:CDS
GGGACACTTCTTGTCAATAT+AGG 0.373630 1.4:+5132076 None:intergenic
TTGCTTCAGAAAAGCCTTCT+CGG 0.396604 1.4:+5132659 None:intergenic
TTTGAGAAAGAAACCTTCAA+TGG 0.449940 1.4:+5132527 None:intergenic
CCCTAGGAGTCTTAAAACTA+AGG 0.476406 1.4:+5132553 None:intergenic
AACCTCACTGTCTTCGAAAG+TGG 0.480699 1.4:+5131629 None:intergenic
ACTCCTAGGGAAGCCATTGA+AGG 0.484194 1.4:-5132540 MS.gene66475:intron
GCTGGATCTTCTAGTGGTGC+CGG 0.487132 1.4:-5131584 MS.gene66475:CDS
ATGTTATTATTGGCCAATGC+AGG 0.499585 1.4:-5131771 MS.gene66475:intron
TACAATGATCTAACCTGCAT+TGG 0.500383 1.4:+5131758 None:intergenic
ATCCGAGGTCGTATCATATC+CGG 0.504599 1.4:-5132035 MS.gene66475:CDS
TCTGGGAAGGGGAAGAGACC+TGG 0.510724 1.4:-5132609 MS.gene66475:CDS
TAGTGGTGCCGGTGCCAAGA+AGG 0.518324 1.4:-5131573 MS.gene66475:CDS
GACAAGAAGTGTCCCTTCAC+TGG 0.524673 1.4:-5132068 MS.gene66475:CDS
ATCACCTTGTTTCCGAGTGA+AGG 0.529932 1.4:-5131803 MS.gene66475:CDS
AAGGGGAAGAGACCTGGAAA+GGG 0.530695 1.4:-5132603 MS.gene66475:CDS
CCTTGTTTCCGAGTGAAGGA+AGG 0.534218 1.4:-5131799 MS.gene66475:CDS
CCTTCCTTCACTCGGAAACA+AGG 0.542963 1.4:+5131799 None:intergenic
TGCTCGAAGATATCTGGGAA+GGG 0.550883 1.4:-5132621 MS.gene66475:CDS
CTTGTTTCCGAGTGAAGGAA+GGG 0.551830 1.4:-5131798 MS.gene66475:CDS
ATAAAACCATTATTGTTAGG+AGG 0.551945 1.4:-5131989 MS.gene66475:CDS
GTATTGAAAGTCATCCCAGC+TGG 0.559579 1.4:-5131602 MS.gene66475:CDS
GGGAAGAGACCTGGAAAGGG+TGG 0.564985 1.4:-5132600 MS.gene66475:CDS
TTTGAATTTGTAGACCGAGA+AGG 0.567346 1.4:-5132673 MS.gene66475:intron
GCACCACTAGAAGATCCAGC+TGG 0.568341 1.4:+5131587 None:intergenic
CAAACTAACTTGTTCAGCCA+TGG 0.568984 1.4:+5132772 None:intergenic
ATCCCAGCTGGATCTTCTAG+TGG 0.570183 1.4:-5131590 MS.gene66475:CDS
GAAGGGGAAGAGACCTGGAA+AGG 0.571357 1.4:-5132604 MS.gene66475:CDS
CGTGTGCAGGAATATTAGAA+TGG 0.572181 1.4:+5131827 None:intergenic
CTTAGCACTATGGCAAGTAC+CGG 0.576116 1.4:+5132016 None:intergenic
CATGATCCCCTTCCTTCACT+CGG 0.580378 1.4:+5131791 None:intergenic
GTGCTCGAAGATATCTGGGA+AGG 0.582495 1.4:-5132622 MS.gene66475:CDS
AAACCTTCAATGGCTTCCCT+AGG 0.582868 1.4:+5132537 None:intergenic
AAACAAGGTGATACGTGTGC+AGG 0.596227 1.4:+5131814 None:intergenic
GCTCGAAGATATCTGGGAAG+GGG 0.598893 1.4:-5132620 MS.gene66475:CDS
GATTGAGACATTACCAGTGA+AGG 0.618985 1.4:+5132055 None:intergenic
TTGTTTCCGAGTGAAGGAAG+GGG 0.622320 1.4:-5131797 MS.gene66475:CDS
ATTGAGACATTACCAGTGAA+GGG 0.624989 1.4:+5132056 None:intergenic
CACCACTAGAAGATCCAGCT+GGG 0.629304 1.4:+5131588 None:intergenic
ACTGGTAATGTCTCAATCCG+AGG 0.640857 1.4:-5132050 MS.gene66475:CDS
TGTAAACGCCTTCTTGGCAC+CGG 0.648607 1.4:+5131565 None:intergenic
ATTTCATTAAGAAATATCAG+AGG 0.666848 1.4:-5131956 MS.gene66475:intron
GGCCACTTTCGAAGACAGTG+AGG 0.699031 1.4:-5131631 MS.gene66475:CDS
TACCGGATATGATACGACCT+CGG 0.712271 1.4:+5132033 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTACCAATTTATTTATATA+AGG - chr1.4:5132181-5132200 MS.gene66475:intron 15.0%
!!! TTTTTTGTTTTGATAAATCT+TGG - chr1.4:5131605-5131624 MS.gene66475:CDS 15.0%
!! AGGACCTTATATAAATAAAT+TGG + chr1.4:5132188-5132207 None:intergenic 20.0%
!! ATTTCATTAAGAAATATCAG+AGG - chr1.4:5132370-5132389 MS.gene66475:intron 20.0%
!! CAAATTATAGATTAATGTGA+AGG + chr1.4:5131583-5131602 None:intergenic 20.0%
!! GTATTAGATTACAAAAACAA+AGG + chr1.4:5132208-5132227 None:intergenic 20.0%
!! TGAATAAAACCATTATTGTT+AGG - chr1.4:5132334-5132353 MS.gene66475:intron 20.0%
!! TTCCTATAAGATTAAGAAAA+AGG + chr1.4:5132230-5132249 None:intergenic 20.0%
!!! TACCTTTTTCTTAATCTTAT+AGG - chr1.4:5132225-5132244 MS.gene66475:intron 20.0%
!!! TAGATTGGTTTATTATTGAT+AGG - chr1.4:5131914-5131933 MS.gene66475:intron 20.0%
! AGGACTTATTAAAACAGTTT+AGG + chr1.4:5132092-5132111 None:intergenic 25.0%
! ATAAAACCATTATTGTTAGG+AGG - chr1.4:5132337-5132356 MS.gene66475:intron 25.0%
! ATAATTCCTCCTAACAATAA+TGG + chr1.4:5132346-5132365 None:intergenic 25.0%
! TAAACCACGAATATGAAAAT+TGG + chr1.4:5131831-5131850 None:intergenic 25.0%
! TAGCTTATGAAAATAGCTTA+TGG + chr1.4:5132022-5132041 None:intergenic 25.0%
! TCTTGGATTTACTAACTAAT+TGG - chr1.4:5131622-5131641 MS.gene66475:CDS 25.0%
! TTTAAGAATCATAGGTAGAT+TGG - chr1.4:5131899-5131918 MS.gene66475:intron 25.0%
!! TTTTATTCATCTTAGCACTA+TGG + chr1.4:5132323-5132342 None:intergenic 25.0%
!! TTTTCATATTCGTGGTTTAA+TGG - chr1.4:5131832-5131851 MS.gene66475:CDS 25.0%
!!! AATCGCTTTTATAAATCTGT+TGG - chr1.4:5131750-5131769 MS.gene66475:intron 25.0%
!!! CATTGTGTTTTAAGAATCAT+AGG - chr1.4:5131891-5131910 MS.gene66475:intron 25.0%
!!! TTGTTTTGTTTATCCAAGTA+AGG - chr1.4:5132619-5132638 MS.gene66475:CDS 25.0%
AGAAGAAGTAAAGGTAATCA+AGG + chr1.4:5132667-5132686 None:intergenic 30.0%
CTATGAACAAGAAGAAGTAA+AGG + chr1.4:5132676-5132695 None:intergenic 30.0%
CTCTGTTTGGTAAAAAATAG+TGG + chr1.4:5131999-5132018 None:intergenic 30.0%
CTTTACTTCTTCTTGTTCAT+AGG - chr1.4:5132674-5132693 MS.gene66475:intron 30.0%
GAAGAAGTAAAGGTAATCAA+GGG + chr1.4:5132666-5132685 None:intergenic 30.0%
TGTGTATGCTTGTTCTTATT+AGG - chr1.4:5132465-5132484 MS.gene66475:intron 30.0%
TTTGAGAAAGAAACCTTCAA+TGG + chr1.4:5131802-5131821 None:intergenic 30.0%
! GTTTCCAATTTTCATATTCG+TGG - chr1.4:5131824-5131843 MS.gene66475:CDS 30.0%
! TTGGTAACATAAACAAGACA+TGG + chr1.4:5132169-5132188 None:intergenic 30.0%
AAGCTATCATGAAGAGCTTA+TGG - chr1.4:5132036-5132055 MS.gene66475:CDS 35.0%
ACAAATAGTTAACACACCTG+TGG + chr1.4:5132445-5132464 None:intergenic 35.0%
ATGTTATTATTGGCCAATGC+AGG - chr1.4:5132555-5132574 MS.gene66475:CDS 35.0%
ATTGAGACATTACCAGTGAA+GGG + chr1.4:5132273-5132292 None:intergenic 35.0%
CACAAAAACAGTTCCTTACT+TGG + chr1.4:5132635-5132654 None:intergenic 35.0%
CATGAAGAGCTTATGGAAAT+AGG - chr1.4:5132043-5132062 MS.gene66475:CDS 35.0%
GAAGGGGATCATGTTATTAT+TGG - chr1.4:5132545-5132564 MS.gene66475:CDS 35.0%
TACAATGATCTAACCTGCAT+TGG + chr1.4:5132571-5132590 None:intergenic 35.0%
TTACTGTATTTGTATGCCAC+AGG - chr1.4:5132426-5132445 MS.gene66475:intron 35.0%
TTTGAATTTGTAGACCGAGA+AGG - chr1.4:5131653-5131672 MS.gene66475:intron 35.0%
! AAATAGCTTATGGCTCTGTT+TGG + chr1.4:5132012-5132031 None:intergenic 35.0%
! TTTTGTGCTCGAAGATATCT+GGG - chr1.4:5131700-5131719 MS.gene66475:intron 35.0%
! TTTTTGTGCTCGAAGATATC+TGG - chr1.4:5131699-5131718 MS.gene66475:intron 35.0%
!!! CCTTAGTTTTAAGACTCCTA+GGG - chr1.4:5131773-5131792 MS.gene66475:CDS 35.0%
ATTCATTCCCCTTTCTTACC+AGG - chr1.4:5132394-5132413 MS.gene66475:intron 40.0%
CCCTAGGAGTCTTAAAACTA+AGG + chr1.4:5131776-5131795 None:intergenic 40.0%
CGTGTGCAGGAATATTAGAA+TGG + chr1.4:5132502-5132521 None:intergenic 40.0%
GATTGAGACATTACCAGTGA+AGG + chr1.4:5132274-5132293 None:intergenic 40.0%
GGGACACTTCTTGTCAATAT+AGG + chr1.4:5132253-5132272 None:intergenic 40.0%
TTCATTCCCCTTTCTTACCA+GGG - chr1.4:5132395-5132414 MS.gene66475:intron 40.0%
TTGCTTCAGAAAAGCCTTCT+CGG + chr1.4:5131670-5131689 None:intergenic 40.0%
!!! GCCTTAGTTTTAAGACTCCT+AGG - chr1.4:5131772-5131791 MS.gene66475:CDS 40.0%
AAACAAGGTGATACGTGTGC+AGG + chr1.4:5132515-5132534 None:intergenic 45.0%
AAACCTTCAATGGCTTCCCT+AGG + chr1.4:5131792-5131811 None:intergenic 45.0%
AACCTCACTGTCTTCGAAAG+TGG + chr1.4:5132700-5132719 None:intergenic 45.0%
ATCCGAGGTCGTATCATATC+CGG - chr1.4:5132291-5132310 MS.gene66475:intron 45.0%
CTTAGCACTATGGCAAGTAC+CGG + chr1.4:5132313-5132332 None:intergenic 45.0%
CTTGTTTCCGAGTGAAGGAA+GGG - chr1.4:5132528-5132547 MS.gene66475:intron 45.0%
GTATTGAAAGTCATCCCAGC+TGG - chr1.4:5132724-5132743 MS.gene66475:intron 45.0%
TACCGGATATGATACGACCT+CGG + chr1.4:5132296-5132315 None:intergenic 45.0%
TGCTCGAAGATATCTGGGAA+GGG - chr1.4:5131705-5131724 MS.gene66475:intron 45.0%
TTGTTTCCGAGTGAAGGAAG+GGG - chr1.4:5132529-5132548 MS.gene66475:intron 45.0%
! ACTGGTAATGTCTCAATCCG+AGG - chr1.4:5132276-5132295 MS.gene66475:intron 45.0%
! ATCACCTTGTTTCCGAGTGA+AGG - chr1.4:5132523-5132542 MS.gene66475:intron 45.0%
AAGGGGAAGAGACCTGGAAA+GGG - chr1.4:5131723-5131742 MS.gene66475:intron 50.0%
ACTCCTAGGGAAGCCATTGA+AGG - chr1.4:5131786-5131805 MS.gene66475:CDS 50.0%
ATACAGTAAACTGCGCACCC+TGG + chr1.4:5132415-5132434 None:intergenic 50.0%
ATCCCAGCTGGATCTTCTAG+TGG - chr1.4:5132736-5132755 MS.gene66475:intron 50.0%
CACCACTAGAAGATCCAGCT+GGG + chr1.4:5132741-5132760 None:intergenic 50.0%
CATGATCCCCTTCCTTCACT+CGG + chr1.4:5132538-5132557 None:intergenic 50.0%
CCTTCCTTCACTCGGAAACA+AGG + chr1.4:5132530-5132549 None:intergenic 50.0%
GACTCCTGTAAACGCCTTCT+TGG + chr1.4:5132770-5132789 None:intergenic 50.0%
GCTCGAAGATATCTGGGAAG+GGG - chr1.4:5131706-5131725 MS.gene66475:intron 50.0%
GTGACATCATTTGCGTTGCG+AGG + chr1.4:5132112-5132131 None:intergenic 50.0%
GTGCTCGAAGATATCTGGGA+AGG - chr1.4:5131704-5131723 MS.gene66475:intron 50.0%
TGTAAACGCCTTCTTGGCAC+CGG + chr1.4:5132764-5132783 None:intergenic 50.0%
! CCTTGTTTCCGAGTGAAGGA+AGG - chr1.4:5132527-5132546 MS.gene66475:intron 50.0%
!! GACAAGAAGTGTCCCTTCAC+TGG - chr1.4:5132258-5132277 MS.gene66475:intron 50.0%
AAGCGATTGCCACCCTTTCC+AGG + chr1.4:5131738-5131757 None:intergenic 55.0%
ACTGCGCACCCTGGTAAGAA+AGG + chr1.4:5132406-5132425 None:intergenic 55.0%
CTGCGCACCCTGGTAAGAAA+GGG + chr1.4:5132405-5132424 None:intergenic 55.0%
GAAGGGGAAGAGACCTGGAA+AGG - chr1.4:5131722-5131741 MS.gene66475:intron 55.0%
GCACCACTAGAAGATCCAGC+TGG + chr1.4:5132742-5132761 None:intergenic 55.0%
GCTGGATCTTCTAGTGGTGC+CGG - chr1.4:5132742-5132761 MS.gene66475:intron 55.0%
TGCGCACCCTGGTAAGAAAG+GGG + chr1.4:5132404-5132423 None:intergenic 55.0%
! GGCCACTTTCGAAGACAGTG+AGG - chr1.4:5132695-5132714 MS.gene66475:intron 55.0%
!! GGTGCCAAGAAGGCGTTTAC+AGG - chr1.4:5132763-5132782 MS.gene66475:intron 55.0%
GGGAAGAGACCTGGAAAGGG+TGG - chr1.4:5131726-5131745 MS.gene66475:intron 60.0%
TCTGGGAAGGGGAAGAGACC+TGG - chr1.4:5131717-5131736 MS.gene66475:intron 60.0%
!! TAGTGGTGCCGGTGCCAAGA+AGG - chr1.4:5132753-5132772 MS.gene66475:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 5131556 5132792 5131556 ID=MS.gene66475
chr1.4 mRNA 5131556 5132792 5131556 ID=MS.gene66475.t1;Parent=MS.gene66475
chr1.4 exon 5132781 5132792 5132781 ID=MS.gene66475.t1.exon1;Parent=MS.gene66475.t1
chr1.4 CDS 5132781 5132792 5132781 ID=cds.MS.gene66475.t1;Parent=MS.gene66475.t1
chr1.4 exon 5132541 5132682 5132541 ID=MS.gene66475.t1.exon2;Parent=MS.gene66475.t1
chr1.4 CDS 5132541 5132682 5132541 ID=cds.MS.gene66475.t1;Parent=MS.gene66475.t1
chr1.4 exon 5131957 5132101 5131957 ID=MS.gene66475.t1.exon3;Parent=MS.gene66475.t1
chr1.4 CDS 5131957 5132101 5131957 ID=cds.MS.gene66475.t1;Parent=MS.gene66475.t1
chr1.4 exon 5131772 5131861 5131772 ID=MS.gene66475.t1.exon4;Parent=MS.gene66475.t1
chr1.4 CDS 5131772 5131861 5131772 ID=cds.MS.gene66475.t1;Parent=MS.gene66475.t1
chr1.4 exon 5131556 5131652 5131556 ID=MS.gene66475.t1.exon5;Parent=MS.gene66475.t1
chr1.4 CDS 5131556 5131652 5131556 ID=cds.MS.gene66475.t1;Parent=MS.gene66475.t1
Gene Sequence

>MS.gene66475

ATGGCTGAACAAGTTAGTTTGTTACCTTCACATTAATCTATAATTTGAATTTTTTGTTTTGATAAATCTTGGATTTACTAACTAATTGGTTTGTGATTTTGAATTTGTAGACCGAGAAGGCTTTTCTGAAGCAAAATAAAGTGTTTTTGTGCTCGAAGATATCTGGGAAGGGGAAGAGACCTGGAAAGGGTGGCAATCGCTTTTATAAATCTGTTGGCCTTAGTTTTAAGACTCCTAGGGAAGCCATTGAAGGTTTCTTTCTCAAATTGTTTCCAATTTTCATATTCGTGGTTTAATGGAGTAATTATATACTCATAAACTCACTTTTTAATTCACATTGTGTTTTAAGAATCATAGGTAGATTGGTTTATTATTGATAGGTTTGTATATATGAAACTGTAGTTACTCAGATTGTATGACATTCAATTGTTTTAAGCTATCCACTATTTTTTACCAAACAGAGCCATAAGCTATTTTCATAAGCTATCATGAAGAGCTTATGGAAATAGGCTGAAAACAGCGTATGAATATGTCCTAAACTGTTTTAATAAGTCCTCGCAACGCAAATGATGTCACAAGTGCTTATGTCAAATAGATAAGCTCAAATAAGCCATGTCTTGTTTATGTTACCAATTTATTTATATAAGGTCCTTTGTTTTTGTAATCTAATACCTTTTTCTTAATCTTATAGGAACCTATATTGACAAGAAGTGTCCCTTCACTGGTAATGTCTCAATCCGAGGTCGTATCATATCCGGTACTTGCCATAGTGCTAAGATGAATAAAACCATTATTGTTAGGAGGAATTATCTTCATTTCATTAAGAAATATCAGAGGTATTCATTCCCCTTTCTTACCAGGGTGCGCAGTTTACTGTATTTGTATGCCACAGGTGTGTTAACTATTTGTTGTGTATGCTTGTTCTTATTAGGTATGAGAAGCGCCATTCTAATATTCCTGCACACGTATCACCTTGTTTCCGAGTGAAGGAAGGGGATCATGTTATTATTGGCCAATGCAGGTTAGATCATTGTAGAATTGTAGAATAATAACGCTTTTTTATTTGTTTTGTTTATCCAAGTAAGGAACTGTTTTTGTGTGTTTTAGCCCTTGATTACCTTTACTTCTTCTTGTTCATAGGCCACTTTCGAAGACAGTGAGGTTCAATGTATTGAAAGTCATCCCAGCTGGATCTTCTAGTGGTGCCGGTGCCAAGAAGGCGTTTACAGGAGTCTGA

Protein sequence

>MS.gene66475.t1

MAEQTEKAFLKQNKVFLCSKISGKGKRPGKGGNRFYKSVGLSFKTPREAIEGTYIDKKCPFTGNVSIRGRIISGTCHSAKMNKTIIVRRNYLHFIKKYQRYEKRHSNIPAHVSPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGSSSGAGAKKAFTGV