AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380017174.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380017174.01.T01 MTR_3g102420 100.000 115 0 0 1 115 1 115 5.11e-84 240
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380017174.01.T01 AT3G25940 61.739 115 41 1 3 114 4 118 2.96e-45 142
MsG0380017174.01.T01 AT1G20065 62.069 58 22 0 3 60 4 61 1.00e-19 76.6
MsG0380017174.01.T01 AT1G20065 62.069 58 22 0 3 60 4 61 1.00e-19 76.6
MsG0380017174.01.T01 AT1G20065 62.069 58 22 0 3 60 4 61 1.00e-19 76.6
MsG0380017174.01.T01 AT1G20065 62.069 58 22 0 3 60 4 61 1.00e-19 76.6
MsG0380017174.01.T01 AT1G20065 56.000 50 22 0 3 52 4 53 9.10e-13 59.7

Find 30 sgRNAs with CRISPR-Local

Find 127 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTAATGTTTGATAGAAAA+TGG 0.164014 3:-92999059 None:intergenic
TAATACCTGTCTGGTATAAA+AGG 0.277991 3:-92998803 None:intergenic
CAAAACCAAGTGTAACATAA+AGG 0.353007 3:+92997097 MsG0380017174.01.T01:CDS
ACAGAAGGTGCAATTGTCTA+AGG 0.372837 3:+92998660 MsG0380017174.01.T01:CDS
ATTAATGTTTGATAGAAAAT+GGG 0.444016 3:-92999058 None:intergenic
CAGATGAGATCGGCGGATGA+AGG 0.477672 3:+92998909 MsG0380017174.01.T01:intron
AAAACCAAGTGTAACATAAA+GGG 0.477760 3:+92997098 MsG0380017174.01.T01:CDS
AGGCATTGTACAAGCTACAT+AGG 0.500116 3:-92999149 None:intergenic
ATGAAGTACCTTGTGGCTGC+TGG 0.500611 3:+92999224 MsG0380017174.01.T01:three_prime_UTR
GAAGTCTAGTAATACCTGTC+TGG 0.505310 3:-92998812 None:intergenic
TAGGATATCAGAAGAGAACT+TGG 0.517197 3:+92998619 MsG0380017174.01.T01:intron
AGATGAGATCGGCGGATGAA+GGG 0.551664 3:+92998910 MsG0380017174.01.T01:intron
TTGAAACTGATGACCACAGC+GGG 0.553103 3:-92998955 None:intergenic
AGTACCCTTTATGTTACACT+TGG 0.559345 3:-92997102 None:intergenic
TGATTTAATCGAGGAACAGA+AGG 0.563158 3:+92998645 MsG0380017174.01.T01:CDS
ATGGGAGCAGATTTCAGCCA+AGG 0.575855 3:-92999040 None:intergenic
CATAGTGCATAATCAGTTGA+GGG 0.577852 3:-92997065 None:intergenic
TTCCTAATTTCAGATGAGAT+CGG 0.584414 3:+92998899 MsG0380017174.01.T01:intron
GCATAGTGCATAATCAGTTG+AGG 0.598932 3:-92997066 None:intergenic
TGGGAGCAGATTTCAGCCAA+GGG 0.609973 3:-92999039 None:intergenic
AAGTTACACAATTTCTGCTG+AGG 0.612146 3:+92997953 MsG0380017174.01.T01:CDS
ACTTGGAATTGATTTAATCG+AGG 0.619946 3:+92998636 MsG0380017174.01.T01:CDS
ACGAAGAGCCAGCAGCCACA+AGG 0.628294 3:-92999232 None:intergenic
CTAATTTCAGATGAGATCGG+CGG 0.632502 3:+92998902 MsG0380017174.01.T01:intron
TTCTACACATGCACCCGCTG+TGG 0.636738 3:+92998942 MsG0380017174.01.T01:CDS
TCTCGACCACGTGAATACAT+TGG 0.647515 3:-92997002 None:intergenic
GTTAAATATGAAGTACCTTG+TGG 0.695271 3:+92999217 MsG0380017174.01.T01:three_prime_UTR
GGGAGCAGATTTCAGCCAAG+GGG 0.708240 3:-92999038 None:intergenic
ACAGTGCCAATGTATTCACG+TGG 0.744012 3:+92996996 None:intergenic
CTTGAAACTGATGACCACAG+CGG 0.759797 3:-92998956 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTAATATATTTATTGATTAT+TGG + Chr3:92998567-92998586 MsG0380017174.01.T01:intron 10.0%
!! AAATAAGCTTCAAATTAAAT+TGG - Chr3:92998852-92998871 None:intergenic 15.0%
!! AAATTATATCTAAATATGCA+AGG - Chr3:92997817-92997836 None:intergenic 15.0%
!! AATTAATGTTTGATAGAAAA+TGG - Chr3:92999062-92999081 None:intergenic 15.0%
!! ATATAATCATATCATATGTT+AGG - Chr3:92998029-92998048 None:intergenic 15.0%
!! ATCCTACAATATATATTTAA+TGG + Chr3:92998689-92998708 MsG0380017174.01.T01:intron 15.0%
!! ATTAATGTTTGATAGAAAAT+GGG - Chr3:92999061-92999080 None:intergenic 15.0%
!! TTTAATATCTGAAAATTACA+AGG - Chr3:92997922-92997941 None:intergenic 15.0%
!!! TTGTAATTTTCAGATATTAA+AGG + Chr3:92997921-92997940 MsG0380017174.01.T01:intron 15.0%
!!! TTTTCTATCAAACATTAATT+TGG + Chr3:92999062-92999081 MsG0380017174.01.T01:three_prime_UTR 15.0%
!! AAAAAAATTAGGTGACTTTA+TGG + Chr3:92997565-92997584 MsG0380017174.01.T01:intron 20.0%
!! AAAATTAGAAGAAAGAAGTT+TGG - Chr3:92998182-92998201 None:intergenic 20.0%
!! AACTAATATATTGTGTGTTT+AGG + Chr3:92997868-92997887 MsG0380017174.01.T01:intron 20.0%
!! ACATATATGGAAATAACATT+AGG + Chr3:92997411-92997430 MsG0380017174.01.T01:intron 20.0%
!! ACATTTATTACAACTTAACA+GGG - Chr3:92997645-92997664 None:intergenic 20.0%
!! CTTAAATGGTTTACTAATTT+GGG + Chr3:92997214-92997233 MsG0380017174.01.T01:intron 20.0%
!! TATTAAGATCATTGCTTAAA+TGG + Chr3:92997200-92997219 MsG0380017174.01.T01:intron 20.0%
!! TGCCATTAAATATATATTGT+AGG - Chr3:92998694-92998713 None:intergenic 20.0%
!!! AAACTTCTTTCTTCTAATTT+TGG + Chr3:92998181-92998200 MsG0380017174.01.T01:intron 20.0%
!!! ATTTTCAGATATTAAAGGAA+AGG + Chr3:92997926-92997945 MsG0380017174.01.T01:intron 20.0%
!!! GATTTCAGTATAAAATTTTC+AGG - Chr3:92999172-92999191 None:intergenic 20.0%
!!! TACATAGGATCTTTTTTTTA+AGG - Chr3:92999137-92999156 None:intergenic 20.0%
! AAAACCAAGTGTAACATAAA+GGG + Chr3:92997098-92997117 MsG0380017174.01.T01:CDS 25.0%
! AACAAAACATGTGAAAAATG+TGG + Chr3:92998766-92998785 MsG0380017174.01.T01:CDS 25.0%
! ATAGATGATATATGATACGA+GGG - Chr3:92998259-92998278 None:intergenic 25.0%
! CATTTATTACAACTTAACAG+GGG - Chr3:92997644-92997663 None:intergenic 25.0%
! CTAATGTTATGTTTCTTTAC+AGG + Chr3:92998741-92998760 MsG0380017174.01.T01:intron 25.0%
! CTTAGAGTGAAAAGAAAATT+TGG + Chr3:92997272-92997291 MsG0380017174.01.T01:intron 25.0%
! GACATTTATTACAACTTAAC+AGG - Chr3:92997646-92997665 None:intergenic 25.0%
! GCTTAAATGGTTTACTAATT+TGG + Chr3:92997213-92997232 MsG0380017174.01.T01:intron 25.0%
! TCAATTTCATCTAAATACAC+TGG - Chr3:92998290-92998309 None:intergenic 25.0%
! TGATATCAAATCTTAAACCT+AGG - Chr3:92998499-92998518 None:intergenic 25.0%
AATTACAAGGACATTCAGTT+AGG - Chr3:92997909-92997928 None:intergenic 30.0%
AATTATCCTCATCTACTTTG+TGG + Chr3:92998592-92998611 MsG0380017174.01.T01:intron 30.0%
CAAAACCAAGTGTAACATAA+AGG + Chr3:92997097-92997116 MsG0380017174.01.T01:CDS 30.0%
CATAGATGATATATGATACG+AGG - Chr3:92998260-92998279 None:intergenic 30.0%
CTATGATAAACTGTGTTTGT+TGG + Chr3:92998355-92998374 MsG0380017174.01.T01:intron 30.0%
GGAATCTTCATGATTCTTTA+AGG + Chr3:92997593-92997612 MsG0380017174.01.T01:intron 30.0%
GTAGGTGATCAAATAACTAA+TGG + Chr3:92997298-92997317 MsG0380017174.01.T01:intron 30.0%
GTTTAGGCTGCATAATATAT+AGG + Chr3:92997371-92997390 MsG0380017174.01.T01:intron 30.0%
TAATACCTGTCTGGTATAAA+AGG - Chr3:92998806-92998825 None:intergenic 30.0%
TAGATGATATATGATACGAG+GGG - Chr3:92998258-92998277 None:intergenic 30.0%
TATATCACTATGTTATGCTG+CGG + Chr3:92998044-92998063 MsG0380017174.01.T01:intron 30.0%
TCATATCATATGTTAGGAGA+TGG - Chr3:92998023-92998042 None:intergenic 30.0%
TCTCATCTTGTTAATGCTTA+TGG + Chr3:92997664-92997683 MsG0380017174.01.T01:intron 30.0%
TTCCTAATTTCAGATGAGAT+CGG + Chr3:92998899-92998918 MsG0380017174.01.T01:intron 30.0%
! ACTTGGAATTGATTTAATCG+AGG + Chr3:92998636-92998655 MsG0380017174.01.T01:CDS 30.0%
! GTTAAATATGAAGTACCTTG+TGG + Chr3:92999217-92999236 MsG0380017174.01.T01:three_prime_UTR 30.0%
! TATTGTGACTTTGTTCTAGA+AGG - Chr3:92998235-92998254 None:intergenic 30.0%
!! ATTCTGATTTTGAAAGAGCA+AGG + Chr3:92997338-92997357 MsG0380017174.01.T01:intron 30.0%
!! ATTGTGACTTTGTTCTAGAA+GGG - Chr3:92998234-92998253 None:intergenic 30.0%
!! GAAAAGAAAATTTGGTGTGT+AGG + Chr3:92997280-92997299 MsG0380017174.01.T01:intron 30.0%
!!! GCTGATAGATTATTTTGAAG+AGG - Chr3:92997142-92997161 None:intergenic 30.0%
!!! GCTTTTTGAAATATCAACCT+AGG + Chr3:92998479-92998498 MsG0380017174.01.T01:intron 30.0%
AAGTTACACAATTTCTGCTG+AGG + Chr3:92997953-92997972 MsG0380017174.01.T01:CDS 35.0%
ACATGTGAAAAATGTGGTCA+TGG + Chr3:92998772-92998791 MsG0380017174.01.T01:CDS 35.0%
AGTACCCTTTATGTTACACT+TGG - Chr3:92997105-92997124 None:intergenic 35.0%
ATTCAGTTAGGACGCATAAT+GGG - Chr3:92997897-92997916 None:intergenic 35.0%
CATAGTGCATAATCAGTTGA+GGG - Chr3:92997068-92997087 None:intergenic 35.0%
GCAAGGTGCAAAAATTGTTT+AGG + Chr3:92997355-92997374 MsG0380017174.01.T01:intron 35.0%
GCAGACAGATTTAATATGCA+GGG + Chr3:92997458-92997477 MsG0380017174.01.T01:intron 35.0%
TAGGATATCAGAAGAGAACT+TGG + Chr3:92998619-92998638 MsG0380017174.01.T01:intron 35.0%
TAGTCTCCAGAAAATAGAGA+AGG - Chr3:92998210-92998229 None:intergenic 35.0%
TATATGTGCCTATGTCATAG+TGG - Chr3:92998325-92998344 None:intergenic 35.0%
TGATTTAATCGAGGAACAGA+AGG + Chr3:92998645-92998664 MsG0380017174.01.T01:CDS 35.0%
TGCAGACAGATTTAATATGC+AGG + Chr3:92997457-92997476 MsG0380017174.01.T01:intron 35.0%
TTTCCATATATGTGTGTAGC+TGG - Chr3:92997404-92997423 None:intergenic 35.0%
! GATCTCATCTGAAATTAGGA+AGG - Chr3:92998900-92998919 None:intergenic 35.0%
! TTAGGTGACTTTATGGATTG+AGG + Chr3:92997572-92997591 MsG0380017174.01.T01:intron 35.0%
!! ACCTTGATTTGCTTTGTCTT+GGG + Chr3:92998396-92998415 MsG0380017174.01.T01:intron 35.0%
!! TACCTTGATTTGCTTTGTCT+TGG + Chr3:92998395-92998414 MsG0380017174.01.T01:intron 35.0%
!! TTTTGTTCTGTCACTTGTGT+GGG + Chr3:92997027-92997046 MsG0380017174.01.T01:CDS 35.0%
!! TTTTTGTTCTGTCACTTGTG+TGG + Chr3:92997026-92997045 MsG0380017174.01.T01:CDS 35.0%
!!! TTACACTTGGTTTTGCACAA+GGG - Chr3:92997092-92997111 None:intergenic 35.0%
ACATTAGGTGACATCTCTGA+TGG + Chr3:92997426-92997445 MsG0380017174.01.T01:intron 40.0%
AGATTTAATATGCAGGGACG+CGG + Chr3:92997464-92997483 MsG0380017174.01.T01:intron 40.0%
ATCCTCATCTACTTTGTGGT+TGG + Chr3:92998596-92998615 MsG0380017174.01.T01:intron 40.0%
ATGCCAGCTACACACATATA+TGG + Chr3:92997398-92997417 MsG0380017174.01.T01:intron 40.0%
ATGTTATGCTGCGGCTTATA+GGG + Chr3:92998053-92998072 MsG0380017174.01.T01:intron 40.0%
CATTCAGTTAGGACGCATAA+TGG - Chr3:92997898-92997917 None:intergenic 40.0%
CTAATTTCAGATGAGATCGG+CGG + Chr3:92998902-92998921 MsG0380017174.01.T01:intron 40.0%
GAAGTCTAGTAATACCTGTC+TGG - Chr3:92998815-92998834 None:intergenic 40.0%
GCATAGTGCATAATCAGTTG+AGG - Chr3:92997069-92997088 None:intergenic 40.0%
GGTCTACTGATATGTGCATT+GGG + Chr3:92998074-92998093 MsG0380017174.01.T01:intron 40.0%
GTGACATCTCTGATGGTAAA+AGG + Chr3:92997433-92997452 MsG0380017174.01.T01:intron 40.0%
TACCAACCACAAAGTAGATG+AGG - Chr3:92998601-92998620 None:intergenic 40.0%
TATGTTATGCTGCGGCTTAT+AGG + Chr3:92998052-92998071 MsG0380017174.01.T01:intron 40.0%
TCATCTACTTTGTGGTTGGT+AGG + Chr3:92998600-92998619 MsG0380017174.01.T01:intron 40.0%
TCCCAAGACAAAGCAAATCA+AGG - Chr3:92998400-92998419 None:intergenic 40.0%
TCTACTGCTTGATACTCCTT+AGG + Chr3:92997758-92997777 MsG0380017174.01.T01:intron 40.0%
TTGATACTCCTTAGGTGTAG+TGG + Chr3:92997766-92997785 MsG0380017174.01.T01:intron 40.0%
! ACAGAAGGTGCAATTGTCTA+AGG + Chr3:92998660-92998679 MsG0380017174.01.T01:CDS 40.0%
! AGGCATTGTACAAGCTACAT+AGG - Chr3:92999152-92999171 None:intergenic 40.0%
! ATGGTTTCGCAAAGTATCTG+TGG + Chr3:92997683-92997702 MsG0380017174.01.T01:intron 40.0%
! TGGCTTCCTTCTCTATTTTC+TGG + Chr3:92998201-92998220 MsG0380017174.01.T01:intron 40.0%
! TGGTTTCGCAAAGTATCTGT+GGG + Chr3:92997684-92997703 MsG0380017174.01.T01:intron 40.0%
!!! GTTACACTTGGTTTTGCACA+AGG - Chr3:92997093-92997112 None:intergenic 40.0%
!!! TACACTTGGTTTTGCACAAG+GGG - Chr3:92997091-92997110 None:intergenic 40.0%
!!! TCCTTTCTTTTTTGTCCCCT+TGG + Chr3:92999023-92999042 MsG0380017174.01.T01:three_prime_UTR 40.0%
ATCCACCTCCACTATGACAT+AGG + Chr3:92998314-92998333 MsG0380017174.01.T01:intron 45.0%
ATGTGCCTATGTCATAGTGG+AGG - Chr3:92998322-92998341 None:intergenic 45.0%
CTTGAAACTGATGACCACAG+CGG - Chr3:92998959-92998978 None:intergenic 45.0%
GCCAAGGGGACAAAAAAGAA+AGG - Chr3:92999027-92999046 None:intergenic 45.0%
GGGTCTACTGATATGTGCAT+TGG + Chr3:92998073-92998092 MsG0380017174.01.T01:intron 45.0%
TTGAAACTGATGACCACAGC+GGG - Chr3:92998958-92998977 None:intergenic 45.0%
TTGCTTTGTCTTGGGACTCT+TGG + Chr3:92998404-92998423 MsG0380017174.01.T01:intron 45.0%
TTTGTCTTGGGACTCTTGGT+GGG + Chr3:92998408-92998427 MsG0380017174.01.T01:intron 45.0%
! AGCTGCCTTTTATACCAGAC+AGG + Chr3:92998798-92998817 MsG0380017174.01.T01:CDS 45.0%
! CGCCGATCTCATCTGAAATT+AGG - Chr3:92998904-92998923 None:intergenic 45.0%
! TGTGTCTGAGTTTTGCTGCT+AGG + Chr3:92997523-92997542 MsG0380017174.01.T01:intron 45.0%
!! ACACACTAAGTGCTGAGAAG+TGG - Chr3:92997508-92997527 None:intergenic 45.0%
!! ACACTAAGTGCTGAGAAGTG+GGG - Chr3:92997506-92997525 None:intergenic 45.0%
!! CACACTAAGTGCTGAGAAGT+GGG - Chr3:92997507-92997526 None:intergenic 45.0%
!! AACAAAAAAAAAAAAAAATT+AGG + Chr3:92997554-92997573 MsG0380017174.01.T01:intron 5.0%
AGATGAGATCGGCGGATGAA+GGG + Chr3:92998910-92998929 MsG0380017174.01.T01:intron 50.0%
ATGGGAGCAGATTTCAGCCA+AGG - Chr3:92999043-92999062 None:intergenic 50.0%
CTTTGTCTTGGGACTCTTGG+TGG + Chr3:92998407-92998426 MsG0380017174.01.T01:intron 50.0%
GACGTGTACCACTACACCTA+AGG - Chr3:92997777-92997796 None:intergenic 50.0%
TGCTGAGAAGTGGGGAATTG+CGG - Chr3:92997498-92997517 None:intergenic 50.0%
TGGGAGCAGATTTCAGCCAA+GGG - Chr3:92999042-92999061 None:intergenic 50.0%
! ATGAAGTACCTTGTGGCTGC+TGG + Chr3:92999224-92999243 MsG0380017174.01.T01:three_prime_UTR 50.0%
! TGCCTATGTCATAGTGGAGG+TGG - Chr3:92998319-92998338 None:intergenic 50.0%
CAGATGAGATCGGCGGATGA+AGG + Chr3:92998909-92998928 MsG0380017174.01.T01:intron 55.0%
GCTGAGAAGTGGGGAATTGC+GGG - Chr3:92997497-92997516 None:intergenic 55.0%
GGGAGCAGATTTCAGCCAAG+GGG - Chr3:92999041-92999060 None:intergenic 55.0%
TTCTACACATGCACCCGCTG+TGG + Chr3:92998942-92998961 MsG0380017174.01.T01:CDS 55.0%
ACGAAGAGCCAGCAGCCACA+AGG - Chr3:92999235-92999254 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr3 gene 92997005 92999256 92997005 ID=MsG0380017174.01;Name=MsG0380017174.01
Chr3 mRNA 92997005 92999256 92997005 ID=MsG0380017174.01.T01;Parent=MsG0380017174.01;Name=MsG0380017174.01.T01;_AED=0.43;_eAED=0.43;_QI=0|1|1|1|0.6|0.66|6|270|115
Chr3 exon 92997005 92997119 92997005 ID=MsG0380017174.01.T01:exon:25422;Parent=MsG0380017174.01.T01
Chr3 exon 92997934 92997974 92997934 ID=MsG0380017174.01.T01:exon:25423;Parent=MsG0380017174.01.T01
Chr3 exon 92998622 92998681 92998622 ID=MsG0380017174.01.T01:exon:25424;Parent=MsG0380017174.01.T01
Chr3 exon 92998763 92998819 92998763 ID=MsG0380017174.01.T01:exon:25425;Parent=MsG0380017174.01.T01
Chr3 exon 92998912 92999256 92998912 ID=MsG0380017174.01.T01:exon:25426;Parent=MsG0380017174.01.T01
Chr3 CDS 92997005 92997119 92997005 ID=MsG0380017174.01.T01:cds;Parent=MsG0380017174.01.T01
Chr3 CDS 92997934 92997974 92997934 ID=MsG0380017174.01.T01:cds;Parent=MsG0380017174.01.T01
Chr3 CDS 92998622 92998681 92998622 ID=MsG0380017174.01.T01:cds;Parent=MsG0380017174.01.T01
Chr3 CDS 92998763 92998819 92998763 ID=MsG0380017174.01.T01:cds;Parent=MsG0380017174.01.T01
Chr3 CDS 92998912 92998986 92998912 ID=MsG0380017174.01.T01:cds;Parent=MsG0380017174.01.T01
Chr3 three_prime_UTR 92998987 92999256 92998987 ID=MsG0380017174.01.T01:three_prime_utr;Parent=MsG0380017174.01.T01
Gene Sequence

>MsG0380017174.01.T01

ATGTATTCACGTGGTCGAGATTTTTTGTTCTGTCACTTGTGTGGGACAATGCTCACAGTTCCCTCAACTGATTATGCACTATGCCCCTTGTGCAAAACCAAGTGTAACATAAAGGATATTAAAGGAAAGGAAATAAGTTACACAATTTCTGCTGAGGATATCAGAAGAGAACTTGGAATTGATTTAATCGAGGAACAGAAGGTGCAATTGTCTAAGGTCAACAAAACATGTGAAAAATGTGGTCATGGTGAAGCTGCCTTTTATACCAGACAGATGAGATCGGCGGATGAAGGGCAAACTACTTTCTACACATGCACCCGCTGTGGTCATCAGTTTCAAGAGAATTAA
Protein sequence

>MsG0380017174.01.T01

MYSRGRDFLFCHLCGTMLTVPSTDYALCPLCKTKCNIKDIKGKEISYTISAEDIRRELGIDLIEEQKVQLSKVNKTCEKCGHGEAAFYTRQMRSADEGQTTFYTCTRCGHQFQEN*