AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580025866.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580025866.01.T01 MTR_5g035830 82.143 56 10 0 17 72 1 56 1.20e-15 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 136 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTATGGCGACGGTGGTTTC+CGG 0.301036 5:+25469251 MsG0580025866.01.T01:CDS
CTGCTCTCTGCAACTGTTGT+TGG 0.326671 5:-25469220 None:intergenic
AATCCAATTGAGCAATTTCC+CGG 0.342157 5:-25469528 None:intergenic
AAACCGGGAAATTGCTCAAT+TGG 0.345610 5:+25469525 MsG0580025866.01.T01:CDS
TGCAAGTCAAATTGAACTCT+TGG 0.364328 5:+25469373 MsG0580025866.01.T01:CDS
TTAGGTCACGCTCTCAAAAC+CGG 0.385073 5:+25469509 MsG0580025866.01.T01:intron
TTGGATATCCTCATCGTAGC+TGG 0.456496 5:+25469392 MsG0580025866.01.T01:CDS
GTGAAATGTCGAGGAGCAAC+GGG 0.458005 5:-25469338 None:intergenic
TCAATTGGATTCGCAAACCC+TGG 0.504749 5:+25469540 MsG0580025866.01.T01:CDS
AGCAACGGGATCGAGGGCGG+TGG 0.505897 5:-25469324 None:intergenic
CTACAGGGTTTCAAAGGCAT+TGG 0.510960 5:+25470900 MsG0580025866.01.T01:intron
GAGAGCAGAGCATAGAGCTA+TGG 0.511153 5:+25469235 MsG0580025866.01.T01:CDS
AACCTATGCAGGCTTCAGAC+AGG 0.544641 5:+25470941 MsG0580025866.01.T01:CDS
GCCACTCAAGTATCATGCTT+AGG 0.546739 5:-25471002 None:intergenic
AGGCATTGGAGAAGCGTACA+TGG 0.549987 5:+25470914 MsG0580025866.01.T01:CDS
GAAGAATCTTCTTCGTGAGG+AGG 0.552980 5:-25469287 None:intergenic
TTTCGCCTACAGGGTTTCAA+AGG 0.561132 5:+25470894 MsG0580025866.01.T01:intron
TAGGTCACGCTCTCAAAACC+GGG 0.562221 5:+25469510 MsG0580025866.01.T01:intron
GTCGAGGAGCAACGGGATCG+AGG 0.566645 5:-25469331 None:intergenic
AGGAGCAACGGGATCGAGGG+CGG 0.570189 5:-25469327 None:intergenic
AGTGAAATGTCGAGGAGCAA+CGG 0.571296 5:-25469339 None:intergenic
TCGAGGAGCAACGGGATCGA+GGG 0.571430 5:-25469330 None:intergenic
ATCCTCATCGTAGCTGGAGT+TGG 0.575241 5:+25469398 MsG0580025866.01.T01:CDS
CAATTGGATTCGCAAACCCT+GGG 0.579078 5:+25469541 MsG0580025866.01.T01:CDS
TACATGGCAGAAACCTATGC+AGG 0.588916 5:+25470930 MsG0580025866.01.T01:CDS
GACCTGTCTGAAGCCTGCAT+AGG 0.640690 5:-25470943 None:intergenic
GAAGAAGAATCTTCTTCGTG+AGG 0.644672 5:-25469290 None:intergenic
GCATAGAGCTATGGCGACGG+TGG 0.658469 5:+25469244 MsG0580025866.01.T01:CDS
TTATTGAGAGTGAAATGTCG+AGG 0.675029 5:-25469347 None:intergenic
TACCAACTCCAGCTACGATG+AGG 0.676646 5:-25469400 None:intergenic
AGAGCATAGAGCTATGGCGA+CGG 0.699806 5:+25469241 MsG0580025866.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTACTTTAAATAAAGTTAA+GGG + Chr5:25469918-25469937 MsG0580025866.01.T01:intron 10.0%
!! TTAACTTATTTAATTAGTAT+TGG - Chr5:25469782-25469801 None:intergenic 10.0%
!!! ATTTTTTTTTTAACAAAGTT+TGG - Chr5:25469764-25469783 None:intergenic 10.0%
!! AAACTTCAAATTACTAATTA+GGG - Chr5:25470845-25470864 None:intergenic 15.0%
!! AATACTTTAAATAAAGTCAA+GGG - Chr5:25469696-25469715 None:intergenic 15.0%
!! ATAAACCCTAATAATAATAA+GGG - Chr5:25470021-25470040 None:intergenic 15.0%
!! ATGTTGTAATCATTATTATT+AGG + Chr5:25469565-25469584 MsG0580025866.01.T01:intron 15.0%
!! ATTTAACCCTTATTATTATT+AGG + Chr5:25470012-25470031 MsG0580025866.01.T01:intron 15.0%
!! CATTACTTTAAATAAAGTTA+AGG + Chr5:25469917-25469936 MsG0580025866.01.T01:intron 15.0%
!! TAAACTTCAAATTACTAATT+AGG - Chr5:25470846-25470865 None:intergenic 15.0%
!! TTACTTTAAATAAAGTTAAG+GGG + Chr5:25469919-25469938 MsG0580025866.01.T01:intron 15.0%
!! TTTAACCCTTATTATTATTA+GGG + Chr5:25470013-25470032 MsG0580025866.01.T01:intron 15.0%
!! TTTCTTACATTAATAATATG+TGG + Chr5:25470179-25470198 MsG0580025866.01.T01:intron 15.0%
!! TTTGAATTAAATTAACAGAA+GGG + Chr5:25469887-25469906 MsG0580025866.01.T01:intron 15.0%
!!! CTTAACTTTATTTAAAGTAA+TGG - Chr5:25469919-25469938 None:intergenic 15.0%
!!! TTATTTAATTAGTATTGGTT+TGG - Chr5:25469841-25469860 None:intergenic 15.0%
!!! TTCAAAAAAACGTTAAATTT+TGG - Chr5:25469873-25469892 None:intergenic 15.0%
!!! TTTTGAATTAAATTAACAGA+AGG + Chr5:25469886-25469905 MsG0580025866.01.T01:intron 15.0%
!! CAATACTTTAAATAAAGTCA+AGG - Chr5:25469697-25469716 None:intergenic 20.0%
!! CATAAACCCTAATAATAATA+AGG - Chr5:25470022-25470041 None:intergenic 20.0%
!! TCATTCATTATCTGTTATAT+TGG + Chr5:25470262-25470281 MsG0580025866.01.T01:intron 20.0%
!! TTAGTACCATAAGTAATAAA+AGG + Chr5:25469615-25469634 MsG0580025866.01.T01:intron 20.0%
!!! ACTTTATTTAAAGTAATGGT+TGG - Chr5:25469915-25469934 None:intergenic 20.0%
!!! AGTTTTTTTGAATTAACAGA+AGG - Chr5:25469728-25469747 None:intergenic 20.0%
!!! ATTTTATATAGAAAGAACTG+TGG + Chr5:25470479-25470498 MsG0580025866.01.T01:intron 20.0%
!!! CTTGACTTTATTTAAAGTAT+TGG + Chr5:25469695-25469714 MsG0580025866.01.T01:intron 20.0%
!!! CTTTATTTAAAGTAATGGTT+GGG - Chr5:25469914-25469933 None:intergenic 20.0%
!!! GAGATGACTTTTAAATTAAA+AGG + Chr5:25470619-25470638 MsG0580025866.01.T01:intron 20.0%
!!! GTTCTATCTTATTTTTCTAA+CGG + Chr5:25470741-25470760 MsG0580025866.01.T01:intron 20.0%
!!! GTTTTTTTGAATTAACAGAA+GGG - Chr5:25469727-25469746 None:intergenic 20.0%
!!! TTGGTCTTATAAGTAATAAA+AGG - Chr5:25469955-25469974 None:intergenic 20.0%
! AAGTAATAAAAGGTCTGTTT+AGG - Chr5:25469945-25469964 None:intergenic 25.0%
! ACTTTGATTATTGCATTTCT+AGG + Chr5:25470077-25470096 MsG0580025866.01.T01:intron 25.0%
! AGGTTAGAAAATAGTTATAC+CGG + Chr5:25470114-25470133 MsG0580025866.01.T01:intron 25.0%
! CTGAATATGCTAATTCTATT+TGG + Chr5:25470230-25470249 MsG0580025866.01.T01:intron 25.0%
! TATAAAATCAGTGTAGAAAG+TGG - Chr5:25470467-25470486 None:intergenic 25.0%
! TATGCTAATTCTATTTGGTT+TGG + Chr5:25470235-25470254 MsG0580025866.01.T01:intron 25.0%
! TCTAAATATAAGTGTGTGTT+TGG - Chr5:25470601-25470620 None:intergenic 25.0%
! TCTCTTAAATTGCTTAAAGA+AGG - Chr5:25470337-25470356 None:intergenic 25.0%
!! AAATGCTCAATTTCAAGTAT+CGG + Chr5:25469591-25469610 MsG0580025866.01.T01:intron 25.0%
!!! AATACCACCTTATTTTCATT+TGG - Chr5:25470527-25470546 None:intergenic 25.0%
AGGGAAACCAAATGAAAATA+AGG + Chr5:25470517-25470536 MsG0580025866.01.T01:intron 30.0%
ATAATGATTACAACATACCC+AGG - Chr5:25469561-25469580 None:intergenic 30.0%
GAAACCAAATGAAAATAAGG+TGG + Chr5:25470520-25470539 MsG0580025866.01.T01:intron 30.0%
GATACTTGAAACCAAGTTAA+GGG + Chr5:25469978-25469997 MsG0580025866.01.T01:intron 30.0%
GCAATAATCAAAGTTGTGAA+AGG - Chr5:25470071-25470090 None:intergenic 30.0%
GCTGTCATTATCTGTTAATA+TGG + Chr5:25470775-25470794 MsG0580025866.01.T01:intron 30.0%
TAATGATTACAACATACCCA+GGG - Chr5:25469560-25469579 None:intergenic 30.0%
! CCTTTTTCCTTCGAAAATTA+CGG - Chr5:25469642-25469661 None:intergenic 30.0%
! CTTAACTTGGTTTCAAGTAT+CGG - Chr5:25469979-25469998 None:intergenic 30.0%
! TACGGACCTTTTATTACTTA+TGG - Chr5:25469624-25469643 None:intergenic 30.0%
! TCTAGGATTTGTTCAAAAGA+AGG + Chr5:25470094-25470113 MsG0580025866.01.T01:intron 30.0%
! TTGTGAAAGGTATAATGAGA+TGG - Chr5:25470058-25470077 None:intergenic 30.0%
! TTTTCTAACGGTAACAAGTT+TGG + Chr5:25470753-25470772 MsG0580025866.01.T01:intron 30.0%
AATCCAATTGAGCAATTTCC+CGG - Chr5:25469531-25469550 None:intergenic 35.0%
ATAAAGTCAAGGGACCTAAA+CGG - Chr5:25469686-25469705 None:intergenic 35.0%
CGATACTTGAAACCAAGTTA+AGG + Chr5:25469977-25469996 MsG0580025866.01.T01:intron 35.0%
GAGAAGAACATAACAAAGCA+TGG - Chr5:25469469-25469488 None:intergenic 35.0%
TAGAACAACACCTTCAAATC+TGG - Chr5:25470727-25470746 None:intergenic 35.0%
TGCAAGTCAAATTGAACTCT+TGG + Chr5:25469373-25469392 MsG0580025866.01.T01:CDS 35.0%
TGTAGAAAGTGGAAACAAGA+TGG - Chr5:25470456-25470475 None:intergenic 35.0%
TTATTGAGAGTGAAATGTCG+AGG - Chr5:25469350-25469369 None:intergenic 35.0%
! AAAAGGTCCGTAATTTTCGA+AGG + Chr5:25469632-25469651 MsG0580025866.01.T01:intron 35.0%
! AGAATGATCCTCCTCATTTT+CGG - Chr5:25470142-25470161 None:intergenic 35.0%
! CCGTAATTTTCGAAGGAAAA+AGG + Chr5:25469639-25469658 MsG0580025866.01.T01:intron 35.0%
! TTCACTCCGTTTGTTTCTTT+AGG + Chr5:25469491-25469510 MsG0580025866.01.T01:intron 35.0%
AAACCGGGAAATTGCTCAAT+TGG + Chr5:25469525-25469544 MsG0580025866.01.T01:CDS 40.0%
ACACTTATAGCAGACGTACA+AGG + Chr5:25470310-25470329 MsG0580025866.01.T01:intron 40.0%
AGGTCCGTTTAGGTGATAAA+AGG + Chr5:25469659-25469678 MsG0580025866.01.T01:intron 40.0%
AGGTGATAAAAGGTCCGTTT+AGG + Chr5:25469669-25469688 MsG0580025866.01.T01:intron 40.0%
ATCTTCATGCTCACTCACTT+GGG - Chr5:25470364-25470383 None:intergenic 40.0%
CACTTATAGCAGACGTACAA+GGG + Chr5:25470311-25470330 MsG0580025866.01.T01:intron 40.0%
CCTGAATATCTGTGTGAACT+GGG - Chr5:25470700-25470719 None:intergenic 40.0%
CTGAATATCTGTGTGAACTG+GGG - Chr5:25470699-25470718 None:intergenic 40.0%
GAAGAAGAATCTTCTTCGTG+AGG - Chr5:25469293-25469312 None:intergenic 40.0%
GCGTGACCTAAAGAAACAAA+CGG - Chr5:25469500-25469519 None:intergenic 40.0%
GCTCAATTAGTCCCTTAACT+TGG - Chr5:25469992-25470011 None:intergenic 40.0%
GTGGAAACAATGCTGTATCA+GGG + Chr5:25470498-25470517 MsG0580025866.01.T01:intron 40.0%
TATCTTCATGCTCACTCACT+TGG - Chr5:25470365-25470384 None:intergenic 40.0%
TCCTGAATATCTGTGTGAAC+TGG - Chr5:25470701-25470720 None:intergenic 40.0%
TGTGGAAACAATGCTGTATC+AGG + Chr5:25470497-25470516 MsG0580025866.01.T01:intron 40.0%
TTCAGGAACTCCAGATTTGA+AGG + Chr5:25470714-25470733 MsG0580025866.01.T01:intron 40.0%
! ATGATACTGTTTTCGCCTAC+AGG + Chr5:25470884-25470903 MsG0580025866.01.T01:intron 40.0%
! CGGACCTTTTATCACCTAAA+CGG - Chr5:25469666-25469685 None:intergenic 40.0%
! GAATGATCCTCCTCATTTTC+GGG - Chr5:25470141-25470160 None:intergenic 40.0%
! TGAAGAAAGAGGAAAGGTGT+CGG - Chr5:25470646-25470665 None:intergenic 40.0%
! TGATACTGTTTTCGCCTACA+GGG + Chr5:25470885-25470904 MsG0580025866.01.T01:intron 40.0%
!! CTTGGTTTCAAGTATCGGTT+TGG - Chr5:25469974-25469993 None:intergenic 40.0%
ACCTTTCCTCTTTCTTCAGC+TGG + Chr5:25470648-25470667 MsG0580025866.01.T01:intron 45.0%
AGAGAGAGAGAGAGAAAGAG+AGG - Chr5:25469435-25469454 None:intergenic 45.0%
AGGATCATTCTGTACAGGTG+GGG + Chr5:25470151-25470170 MsG0580025866.01.T01:intron 45.0%
AGTGAAATGTCGAGGAGCAA+CGG - Chr5:25469342-25469361 None:intergenic 45.0%
CAATTGGATTCGCAAACCCT+GGG + Chr5:25469541-25469560 MsG0580025866.01.T01:CDS 45.0%
CCCAGTTCACACAGATATTC+AGG + Chr5:25470697-25470716 MsG0580025866.01.T01:intron 45.0%
CGAAGGAAAAAGGTCCGTTT+AGG + Chr5:25469649-25469668 MsG0580025866.01.T01:intron 45.0%
CGCAAAAAAAGCCTTCAAGG+TGG + Chr5:25470671-25470690 MsG0580025866.01.T01:intron 45.0%
GAAGAATCTTCTTCGTGAGG+AGG - Chr5:25469290-25469309 None:intergenic 45.0%
GAGAGAGAGAGAGAAAGAGA+GGG - Chr5:25469434-25469453 None:intergenic 45.0%
GAGGATCATTCTGTACAGGT+GGG + Chr5:25470150-25470169 MsG0580025866.01.T01:intron 45.0%
TACATGGCAGAAACCTATGC+AGG + Chr5:25470930-25470949 MsG0580025866.01.T01:CDS 45.0%
TCAATTGGATTCGCAAACCC+TGG + Chr5:25469540-25469559 MsG0580025866.01.T01:CDS 45.0%
TGAGGAGGATCATTCTGTAC+AGG + Chr5:25470146-25470165 MsG0580025866.01.T01:intron 45.0%
TGGCGCAAAAAAAGCCTTCA+AGG + Chr5:25470668-25470687 MsG0580025866.01.T01:intron 45.0%
TTAGGTCACGCTCTCAAAAC+CGG + Chr5:25469509-25469528 MsG0580025866.01.T01:intron 45.0%
TTATACCGGTCCCGAAAATG+AGG + Chr5:25470128-25470147 MsG0580025866.01.T01:intron 45.0%
TTGGATATCCTCATCGTAGC+TGG + Chr5:25469392-25469411 MsG0580025866.01.T01:CDS 45.0%
TTTCGCCTACAGGGTTTCAA+AGG + Chr5:25470894-25470913 MsG0580025866.01.T01:intron 45.0%
! CTACAGGGTTTCAAAGGCAT+TGG + Chr5:25470900-25470919 MsG0580025866.01.T01:intron 45.0%
!! CAATGCCTTTGAAACCCTGT+AGG - Chr5:25470902-25470921 None:intergenic 45.0%
!! GAAGAAAGAGGAAAGGTGTC+GGG - Chr5:25470645-25470664 None:intergenic 45.0%
!! AATAATAATTAAATAAGTTA+AGG + Chr5:25469813-25469832 MsG0580025866.01.T01:intron 5.0%
!! ATAATAATTAAATAAGTTAA+GGG + Chr5:25469814-25469833 MsG0580025866.01.T01:intron 5.0%
!! TTATTTAATTATTATTAGTT+TGG - Chr5:25469809-25469828 None:intergenic 5.0%
AACCTATGCAGGCTTCAGAC+AGG + Chr5:25470941-25470960 MsG0580025866.01.T01:CDS 50.0%
AGAGCATAGAGCTATGGCGA+CGG + Chr5:25469241-25469260 MsG0580025866.01.T01:CDS 50.0%
ATCCTCATCGTAGCTGGAGT+TGG + Chr5:25469398-25469417 MsG0580025866.01.T01:CDS 50.0%
CTGCTCTCTGCAACTGTTGT+TGG - Chr5:25469223-25469242 None:intergenic 50.0%
GAGAGCAGAGCATAGAGCTA+TGG + Chr5:25469235-25469254 MsG0580025866.01.T01:CDS 50.0%
GCCAGCTGAAGAAAGAGGAA+AGG - Chr5:25470652-25470671 None:intergenic 50.0%
GGAGGATCATTCTGTACAGG+TGG + Chr5:25470149-25470168 MsG0580025866.01.T01:intron 50.0%
GTGAAATGTCGAGGAGCAAC+GGG - Chr5:25469341-25469360 None:intergenic 50.0%
TACCAACTCCAGCTACGATG+AGG - Chr5:25469403-25469422 None:intergenic 50.0%
TAGGTCACGCTCTCAAAACC+GGG + Chr5:25469510-25469529 MsG0580025866.01.T01:intron 50.0%
TTTGCGCCAGCTGAAGAAAG+AGG - Chr5:25470657-25470676 None:intergenic 50.0%
! AGGAGGTTTTCTAACGTCGC+CGG - Chr5:25469273-25469292 None:intergenic 50.0%
!! AGGCATTGGAGAAGCGTACA+TGG + Chr5:25470914-25470933 MsG0580025866.01.T01:CDS 50.0%
!! ATCCTCCTCATTTTCGGGAC+CGG - Chr5:25470136-25470155 None:intergenic 50.0%
TACCGGTCCCGAAAATGAGG+AGG + Chr5:25470131-25470150 MsG0580025866.01.T01:intron 55.0%
! GACCTGTCTGAAGCCTGCAT+AGG - Chr5:25470946-25470965 None:intergenic 55.0%
GCATAGAGCTATGGCGACGG+TGG + Chr5:25469244-25469263 MsG0580025866.01.T01:CDS 60.0%
GCTATGGCGACGGTGGTTTC+CGG + Chr5:25469251-25469270 MsG0580025866.01.T01:CDS 60.0%
TCGAGGAGCAACGGGATCGA+GGG - Chr5:25469333-25469352 None:intergenic 60.0%
! GAACTGGGGCACCACCTTGA+AGG - Chr5:25470685-25470704 None:intergenic 60.0%
AGGAGCAACGGGATCGAGGG+CGG - Chr5:25469330-25469349 None:intergenic 65.0%
GTCGAGGAGCAACGGGATCG+AGG - Chr5:25469334-25469353 None:intergenic 65.0%
AGCAACGGGATCGAGGGCGG+TGG - Chr5:25469327-25469346 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr5 gene 25469195 25471019 25469195 ID=MsG0580025866.01;Name=MsG0580025866.01
Chr5 mRNA 25469195 25471019 25469195 ID=MsG0580025866.01.T01;Parent=MsG0580025866.01;Name=MsG0580025866.01.T01;_AED=0.47;_eAED=0.54;_QI=11|0.5|0.66|1|1|1|3|0|125
Chr5 exon 25469195 25469419 25469195 ID=MsG0580025866.01.T01:exon:4163;Parent=MsG0580025866.01.T01
Chr5 exon 25469513 25469562 25469513 ID=MsG0580025866.01.T01:exon:4164;Parent=MsG0580025866.01.T01
Chr5 exon 25470906 25471019 25470906 ID=MsG0580025866.01.T01:exon:4165;Parent=MsG0580025866.01.T01
Chr5 five_prime_UTR 25469195 25469205 25469195 ID=MsG0580025866.01.T01:five_prime_utr;Parent=MsG0580025866.01.T01
Chr5 CDS 25469206 25469419 25469206 ID=MsG0580025866.01.T01:cds;Parent=MsG0580025866.01.T01
Chr5 CDS 25469513 25469562 25469513 ID=MsG0580025866.01.T01:cds;Parent=MsG0580025866.01.T01
Chr5 CDS 25470906 25471019 25470906 ID=MsG0580025866.01.T01:cds;Parent=MsG0580025866.01.T01
Gene Sequence

>MsG0580025866.01.T01

ATGAGAAACGATAACCAACAACAGTTGCAGAGAGCAGAGCATAGAGCTATGGCGACGGTGGTTTCCGGCGACGTTAGAAAACCTCCTCACGAAGAAGATTCTTCTTCTGACTCAGTTTCCACCGCCCTCGATCCCGTTGCTCCTCGACATTTCACTCTCAATAACATTGCAAGTCAAATTGAACTCTTGGATATCCTCATCGTAGCTGGAGTTGGTCACGCTCTCAAAACCGGGAAATTGCTCAATTGGATTCGCAAACCCTGGGGTTTCAAAGGCATTGGAGAAGCGTACATGGCAGAAACCTATGCAGGCTTCAGACAGGTCAGCTTCAGATTCTATCATAATGATTTTCATATAGCACCTAAGCATGATACTTGA
Protein sequence

>MsG0580025866.01.T01

MRNDNQQQLQRAEHRAMATVVSGDVRKPPHEEDSSSDSVSTALDPVAPRHFTLNNIASQIELLDILIVAGVGHALKTGKLLNWIRKPWGFKGIGEAYMAETYAGFRQVSFRFYHNDFHIAPKHDT*