AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014576.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014576.01.T02 MTR_3g060670 91.919 99 3 2 1 95 1 98 2.62e-57 180
MsG0380014576.01.T02 MTR_4g133440 55.000 100 41 1 1 96 1 100 9.34e-34 114
MsG0380014576.01.T02 MTR_4g134120 55.000 100 41 1 1 96 1 100 9.34e-34 114
MsG0380014576.01.T02 MTR_2g027140 55.556 99 40 1 2 96 7 105 2.52e-31 112
MsG0380014576.01.T02 MTR_2g027140 64.000 50 18 0 47 96 1 50 7.24e-17 73.2
MsG0380014576.01.T01 MTR_3g060670 91.919 99 3 2 1 95 1 98 2.62e-57 180
MsG0380014576.01.T01 MTR_4g133440 55.000 100 41 1 1 96 1 100 9.34e-34 114
MsG0380014576.01.T01 MTR_4g134120 55.000 100 41 1 1 96 1 100 9.34e-34 114
MsG0380014576.01.T01 MTR_2g027140 55.556 99 40 1 2 96 7 105 2.52e-31 112
MsG0380014576.01.T01 MTR_2g027140 64.000 50 18 0 47 96 1 50 7.24e-17 73.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014576.01.T02 AT1G55840 55.556 99 40 1 2 96 7 105 2.03e-35 123
MsG0380014576.01.T02 AT5G47730 55.556 99 40 1 2 96 7 105 1.12e-31 113
MsG0380014576.01.T02 AT5G47730 55.556 99 40 1 2 96 7 105 1.12e-31 113
MsG0380014576.01.T02 AT1G55840 64.789 71 25 0 23 93 5 75 7.49e-30 107
MsG0380014576.01.T02 AT5G47730 64.000 50 18 0 47 96 1 50 5.25e-18 76.6
MsG0380014576.01.T02 AT5G47730 64.000 50 18 0 47 96 1 50 5.25e-18 76.6
MsG0380014576.01.T01 AT1G55840 55.556 99 40 1 2 96 7 105 2.03e-35 123
MsG0380014576.01.T01 AT5G47730 55.556 99 40 1 2 96 7 105 1.12e-31 113
MsG0380014576.01.T01 AT5G47730 55.556 99 40 1 2 96 7 105 1.12e-31 113
MsG0380014576.01.T01 AT1G55840 64.789 71 25 0 23 93 5 75 7.49e-30 107
MsG0380014576.01.T01 AT5G47730 64.000 50 18 0 47 96 1 50 5.25e-18 76.6
MsG0380014576.01.T01 AT5G47730 64.000 50 18 0 47 96 1 50 5.25e-18 76.6

Find 5 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCAGTCTTTGATGGAAAA+TGG 0.286433 3:-56657543 MsG0380014576.01.T01:intron
TAAGCAGTTGCAGTCTTTGA+TGG 0.306038 3:-56657550 MsG0380014576.01.T01:CDS
ATGAATAAATAGAGTAATAT+AGG 0.332323 3:+56657860 None:intergenic
GCTTCCTATGTTGAAACTAT+AGG 0.401617 3:+56657776 None:intergenic
ACATCCTATAGTTTCAACAT+AGG 0.611986 3:-56657780 MsG0380014576.01.T01:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTAAATTTCTTTATGA+AGG - Chr3:56656806-56656825 MsG0380014576.01.T01:intron 10.0%
!! AAAAAATTGAAATTTGCAAA+TGG + Chr3:56656526-56656545 None:intergenic 15.0%
!! AAAAATTGAAATTTGCAAAT+GGG + Chr3:56656525-56656544 None:intergenic 15.0%
!! ATGAATAAATAGAGTAATAT+AGG + Chr3:56656265-56656284 None:intergenic 15.0%
!!! AAGTTGTTAAGAATTTTTTT+AGG - Chr3:56656887-56656906 MsG0380014576.01.T01:intron 15.0%
!!! AGTTGTTAAGAATTTTTTTA+GGG - Chr3:56656888-56656907 MsG0380014576.01.T01:intron 15.0%
!!! ATTCTGAAATATAAAATGAA+AGG + Chr3:56657408-56657427 None:intergenic 15.0%
!!! GAAAAAGATTAAATTTTTAC+AGG + Chr3:56656477-56656496 None:intergenic 15.0%
!! AGTTAATTGATTGTTTACAT+TGG - Chr3:56657612-56657631 MsG0380014576.01.T01:intron 20.0%
!! GTAAAATTGATCTTGATTTA+TGG - Chr3:56656857-56656876 MsG0380014576.01.T01:intron 20.0%
!! GTAAAGAAAGAAAAATTAGT+GGG + Chr3:56656305-56656324 None:intergenic 20.0%
!! TGTAAAGAAAGAAAAATTAG+TGG + Chr3:56656306-56656325 None:intergenic 20.0%
!!! TTAAGTTTTTTATTCGAACA+TGG - Chr3:56657308-56657327 MsG0380014576.01.T01:intron 20.0%
!!! TTTGTTTTGTTTTTCACATA+TGG + Chr3:56656399-56656418 None:intergenic 20.0%
!!! TTTTCATATATGCTATAACT+TGG + Chr3:56657216-56657235 None:intergenic 20.0%
! AAGAAAAAACTGTGAAATGA+GGG + Chr3:56657678-56657697 None:intergenic 25.0%
! AATATAAAATGAAAGGCTTC+AGG + Chr3:56657401-56657420 None:intergenic 25.0%
! ACATACTATTTACTTAACTG+AGG + Chr3:56657334-56657353 None:intergenic 25.0%
! TACCAAAACAAAAATTGTAG+AGG + Chr3:56657035-56657054 None:intergenic 25.0%
! TTGTTGATCATTGACAAATT+TGG - Chr3:56656653-56656672 MsG0380014576.01.T01:CDS 25.0%
!! ACATTGAAAGATCCTTATTT+AGG + Chr3:56656986-56657005 None:intergenic 25.0%
!!! GTTAAGAATTTTTTTAGGGA+TGG - Chr3:56656892-56656911 MsG0380014576.01.T01:intron 25.0%
!!! TTTGGTAATTCATTTTTGAC+CGG - Chr3:56657048-56657067 MsG0380014576.01.T01:intron 25.0%
!!! TTTTTCAGTATAGAAGAAGA+TGG - Chr3:56656542-56656561 MsG0380014576.01.T01:intron 25.0%
ACATCCTATAGTTTCAACAT+AGG - Chr3:56656342-56656361 MsG0380014576.01.T01:intron 30.0%
GAAGAAAAAACTGTGAAATG+AGG + Chr3:56657679-56657698 None:intergenic 30.0%
GCGAATAATATTAGTAAGAC+GGG + Chr3:56657358-56657377 None:intergenic 30.0%
GGCGAATAATATTAGTAAGA+CGG + Chr3:56657359-56657378 None:intergenic 30.0%
TACAGGATTAAGACAGAAAA+AGG + Chr3:56656460-56656479 None:intergenic 30.0%
TAGAAAAACAGAAGAATGCA+AGG + Chr3:56656625-56656644 None:intergenic 30.0%
TCTTAGATGGAATTTCAGAT+AGG - Chr3:56657537-56657556 MsG0380014576.01.T01:intron 30.0%
TTGGTTTCTGCTATACAAAA+AGG + Chr3:56657863-56657882 None:intergenic 30.0%
! TTACGCATCTGAATCTATTT+TGG - Chr3:56657763-56657782 MsG0380014576.01.T01:five_prime_UTR 30.0%
! TTGTTTTCATTAGCAACCAA+AGG + Chr3:56657129-56657148 None:intergenic 30.0%
!! AGCCTCTACAATTTTTGTTT+TGG - Chr3:56657030-56657049 MsG0380014576.01.T01:intron 30.0%
!! TGAGATTGACAAAGTTTTAG+CGG - Chr3:56657646-56657665 MsG0380014576.01.T01:intron 30.0%
!!! ACTAACCATTTTTTGAGCTT+TGG + Chr3:56657495-56657514 None:intergenic 30.0%
AGAAGATTGCATTCAAGGTT+TGG - Chr3:56656707-56656726 MsG0380014576.01.T01:intron 35.0%
AGATGGAATTTCAGATAGGT+TGG - Chr3:56657541-56657560 MsG0380014576.01.T01:intron 35.0%
AGTGATTCTGCACCTAAATA+AGG - Chr3:56656971-56656990 MsG0380014576.01.T01:intron 35.0%
ATATTTCAGAATCTGCACCA+GGG - Chr3:56657416-56657435 MsG0380014576.01.T01:intron 35.0%
ATGTCTAGTGAAGTCTTAGA+TGG - Chr3:56657524-56657543 MsG0380014576.01.T01:intron 35.0%
CTTGGTTTCATAAGCTATCT+TGG + Chr3:56657198-56657217 None:intergenic 35.0%
GCTTCCTATGTTGAAACTAT+AGG + Chr3:56656349-56656368 None:intergenic 35.0%
GGATTAAGACAGAAAAAGGA+AGG + Chr3:56656456-56656475 None:intergenic 35.0%
GTTTCATAAGCTATCTTGGA+AGG + Chr3:56657194-56657213 None:intergenic 35.0%
TAGGGATGGTTGATTGTAAA+GGG - Chr3:56656906-56656925 MsG0380014576.01.T01:intron 35.0%
TATATTTCAGAATCTGCACC+AGG - Chr3:56657415-56657434 MsG0380014576.01.T01:intron 35.0%
TGATTGTTTACATTGGAGAG+TGG - Chr3:56657619-56657638 MsG0380014576.01.T01:intron 35.0%
TGTTGCCAAAGCTCAAAAAA+TGG - Chr3:56657487-56657506 MsG0380014576.01.T01:intron 35.0%
TTAGGGATGGTTGATTGTAA+AGG - Chr3:56656905-56656924 MsG0380014576.01.T01:intron 35.0%
TTCAGGACCAAAAAAAACTC+AGG + Chr3:56657384-56657403 None:intergenic 35.0%
TTGCAGTCTTTGATGGAAAA+TGG - Chr3:56656579-56656598 MsG0380014576.01.T01:intron 35.0%
! AGCTAGAATCTTTTCACACA+AGG - Chr3:56656418-56656437 MsG0380014576.01.T01:intron 35.0%
! ATCTAAGACTTCACTAGACA+TGG + Chr3:56657525-56657544 None:intergenic 35.0%
! GCTAGAATCTTTTCACACAA+GGG - Chr3:56656419-56656438 MsG0380014576.01.T01:intron 35.0%
! TAGTACCTCTTTTGTGTAAC+CGG + Chr3:56657937-56657956 None:intergenic 35.0%
!!! GTTTGGTTTTTGCTTGATCT+TGG - Chr3:56656724-56656743 MsG0380014576.01.T01:intron 35.0%
AATCGTGCCAACATTTCAGT+AGG + Chr3:56657446-56657465 None:intergenic 40.0%
AATGTCCGGTTACACAAAAG+AGG - Chr3:56657929-56657948 MsG0380014576.01.T01:five_prime_UTR 40.0%
ACAACTTGCACATCTTCCTT+TGG - Chr3:56657110-56657129 MsG0380014576.01.T01:intron 40.0%
ATAGCAGAAACCAATTCCTG+CGG - Chr3:56657869-56657888 MsG0380014576.01.T01:five_prime_UTR 40.0%
ATCGTGCCAACATTTCAGTA+GGG + Chr3:56657445-56657464 None:intergenic 40.0%
GCAACAGAAGATTGCATTCA+AGG - Chr3:56656702-56656721 MsG0380014576.01.T01:intron 40.0%
GGACCAAAAAAAACTCAGGA+CGG + Chr3:56657380-56657399 None:intergenic 40.0%
TAAGCAGTTGCAGTCTTTGA+TGG - Chr3:56656572-56656591 MsG0380014576.01.T01:intron 40.0%
TCTCAACTCATAGGAATGTC+CGG - Chr3:56657915-56657934 MsG0380014576.01.T01:five_prime_UTR 40.0%
TTGTACAAATCCGCAGGAAT+TGG + Chr3:56657882-56657901 None:intergenic 40.0%
! AGACTCTTTGAGAGAGCTAA+TGG - Chr3:56657085-56657104 MsG0380014576.01.T01:intron 40.0%
! CATATGGCTCTCTCTGTTTT+TGG + Chr3:56656383-56656402 None:intergenic 40.0%
!! TCAGATAGGTTGGTTACTCT+TGG - Chr3:56657551-56657570 MsG0380014576.01.T01:CDS 40.0%
ACAGGTTTGTACAAATCCGC+AGG + Chr3:56657888-56657907 None:intergenic 45.0%
CGATTTCTCAAAGCTAGGGA+CGG - Chr3:56657461-56657480 MsG0380014576.01.T01:intron 45.0%
GATTTCTCAAAGCTAGGGAC+GGG - Chr3:56657462-56657481 MsG0380014576.01.T01:intron 45.0%
GGCACGATTTCTCAAAGCTA+GGG - Chr3:56657457-56657476 MsG0380014576.01.T01:intron 45.0%
GGGATACCCTACTGAAATGT+TGG - Chr3:56657436-56657455 MsG0380014576.01.T01:intron 45.0%
GTGCGAGATTCTCAACTCAT+AGG - Chr3:56657906-56657925 MsG0380014576.01.T01:five_prime_UTR 45.0%
TGGCACGATTTCTCAAAGCT+AGG - Chr3:56657456-56657475 MsG0380014576.01.T01:intron 45.0%
! ACATTTCAGTAGGGTATCCC+TGG + Chr3:56657436-56657455 None:intergenic 45.0%
! ATGAGTTGAGAATCTCGCAC+AGG + Chr3:56657906-56657925 None:intergenic 45.0%
!!! TCGCCGTCCTGAGTTTTTTT+TGG - Chr3:56657374-56657393 MsG0380014576.01.T01:intron 45.0%
CTCTCAAAGAGTCTCACACG+TGG + Chr3:56657079-56657098 None:intergenic 50.0%
AGTCTCACACGTGGTTACGC+CGG + Chr3:56657070-56657089 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
Chr3 gene 56656176 56657968 56656176 ID=MsG0380014576.01;Name=MsG0380014576.01
Chr3 mRNA 56656176 56657968 56656176 ID=MsG0380014576.01.T01;Parent=MsG0380014576.01;Name=MsG0380014576.01.T01;_AED=0.45;_eAED=0.46;_QI=276|0.6|0.66|1|0|0|6|0|96
Chr3 exon 56657544 56657594 56657544 ID=MsG0380014576.01.T01:exon:23900;Parent=MsG0380014576.01.T01
Chr3 exon 56657704 56657968 56657704 ID=MsG0380014576.01.T01:exon:23899;Parent=MsG0380014576.01.T01
Chr3 five_prime_UTR 56657704 56657968 56657704 ID=MsG0380014576.01.T01:five_prime_utr;Parent=MsG0380014576.01.T01
Chr3 five_prime_UTR 56657584 56657594 56657584 ID=MsG0380014576.01.T01:five_prime_utr;Parent=MsG0380014576.01.T01
Chr3 CDS 56657544 56657583 56657544 ID=MsG0380014576.01.T01:cds;Parent=MsG0380014576.01.T01
Chr3 CDS 56657421 56657449 56657421 ID=MsG0380014576.01.T01:cds;Parent=MsG0380014576.01.T01
Chr3 CDS 56656636 56656707 56656636 ID=MsG0380014576.01.T01:cds;Parent=MsG0380014576.01.T01
Chr3 CDS 56656477 56656530 56656477 ID=MsG0380014576.01.T01:cds;Parent=MsG0380014576.01.T01
Chr3 CDS 56656176 56656271 56656176 ID=MsG0380014576.01.T01:cds;Parent=MsG0380014576.01.T01
Chr3 mRNA 56656176 56657614 56656176 ID=MsG0380014576.01.T02;Parent=MsG0380014576.01;Name=MsG0380014576.01.T02;_AED=0.47;_eAED=0.49;_QI=31|0.5|0.6|1|0|0|5|0|96
Chr3 exon 56657544 56657614 56657544 ID=MsG0380014576.01.T02:exon:23905;Parent=MsG0380014576.01.T02
Chr3 five_prime_UTR 56657584 56657614 56657584 ID=MsG0380014576.01.T02:five_prime_utr;Parent=MsG0380014576.01.T02
Chr3 CDS 56657544 56657583 56657544 ID=MsG0380014576.01.T02:cds;Parent=MsG0380014576.01.T02
Chr3 CDS 56657421 56657449 56657421 ID=MsG0380014576.01.T02:cds;Parent=MsG0380014576.01.T02
Chr3 CDS 56656636 56656707 56656636 ID=MsG0380014576.01.T02:cds;Parent=MsG0380014576.01.T02
Chr3 CDS 56656477 56656530 56656477 ID=MsG0380014576.01.T02:cds;Parent=MsG0380014576.01.T02
Chr3 CDS 56656176 56656271 56656176 ID=MsG0380014576.01.T02:cds;Parent=MsG0380014576.01.T02
Gene Sequence

>MsG0380014576.01.T02

ATGGATGCAATTAAGCAGTTGCAGTCTTTGATGGAAAATGTTGATGAGCAACAGAAGATTGCATTCAAGGGATACCCTACTGAAATGTTGGCACGATTTCTCAAAGCTAGGGACGGGAATGTTGCCAAAGCTCAAAAAATGTTAATTGATTGTTTACATTGGAGAGTGGAAAATGAGATTGACAAAGTTTTAGCGCAGAAACCAATTCCTGCGGATTTGTACAAACCTGTGCGAGATTCTCAACTCATAGGAATGTCCGGTTACACAAAAGAGGTACTACTCATATTTTAG

>MsG0380014576.01.T01

ATGGATGCAATTAAGCAGTTGCAGTCTTTGATGGAAAATGTTGATGAGCAACAGAAGATTGCATTCAAGGGATACCCTACTGAAATGTTGGCACGATTTCTCAAAGCTAGGGACGGGAATGTTGCCAAAGCTCAAAAAATGTTAATTGATTGTTTACATTGGAGAGTGGAAAATGAGATTGACAAAGTTTTAGCGCAGAAACCAATTCCTGCGGATTTGTACAAACCTGTGCGAGATTCTCAACTCATAGGAATGTCCGGTTACACAAAAGAGGTACTACTCATATTTTAG

Protein sequence

>MsG0380014576.01.T02

MDAIKQLQSLMENVDEQQKIAFKGYPTEMLARFLKARDGNVAKAQKMLIDCLHWRVENEIDKVLAQKPIPADLYKPVRDSQLIGMSGYTKEVLLIF*

>MsG0380014576.01.T01

MDAIKQLQSLMENVDEQQKIAFKGYPTEMLARFLKARDGNVAKAQKMLIDCLHWRVENEIDKVLAQKPIPADLYKPVRDSQLIGMSGYTKEVLLIF*