AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580024468.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580024468.01.T01 MTR_5g011690 83.333 66 10 1 49 113 72 137 3.37e-32 110
MsG0580024468.01.T01 MTR_4g102010 71.698 53 15 0 61 113 85 137 2.88e-21 82.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580024468.01.T01 AT1G12340 39.535 129 57 4 6 113 1 129 9.03e-21 81.3
MsG0580024468.01.T01 AT1G62880 48.810 84 36 3 37 113 54 137 2.05e-20 80.5
MsG0580024468.01.T01 AT1G12390 50.000 84 35 3 37 113 54 137 6.05e-20 79.3

Find 43 sgRNAs with CRISPR-Local

Find 101 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTTATGACTTCATGTATA+TGG 0.192551 5:-5328462 MsG0580024468.01.T01:three_prime_UTR
GGTTATTTGCATAGTGTTAT+TGG 0.232406 5:-5328395 MsG0580024468.01.T01:three_prime_UTR
CAGTTGTTATGACAGAAAAT+TGG 0.279923 5:+5329359 None:intergenic
TTGTGGATCATGGCTGGTTT+GGG 0.299828 5:-5329468 MsG0580024468.01.T01:CDS
CTGGTGGCTGATGAGGGACT+TGG 0.310468 5:-5328417 MsG0580024468.01.T01:three_prime_UTR
TGACATATGACTGACTGTTT+TGG 0.360288 5:-5328565 MsG0580024468.01.T01:three_prime_UTR
TTTGTGGATCATGGCTGGTT+TGG 0.376323 5:-5329469 MsG0580024468.01.T01:CDS
ACCAAAATACAGAGAAGAAA+AGG 0.381895 5:+5328808 None:intergenic
ACACCAATTCTTCCTCTCAT+TGG 0.393963 5:+5329607 None:intergenic
CAGTAAGATATCTTTATATA+CGG 0.406836 5:-5328505 MsG0580024468.01.T01:three_prime_UTR
TCCAGTTTGTGGATCATGGC+TGG 0.430291 5:-5329474 MsG0580024468.01.T01:CDS
AGGCGATAGCGTGCAGGTAT+TGG 0.433595 5:-5329445 MsG0580024468.01.T01:CDS
ACCAGCCATGATCCACAAAC+TGG 0.451467 5:+5329473 None:intergenic
ACTTATGACTTCATGTATAT+GGG 0.453549 5:-5328461 MsG0580024468.01.T01:three_prime_UTR
CAAGTCCAGTTTGTGGATCA+TGG 0.456447 5:-5329478 MsG0580024468.01.T01:CDS
AAGGCATCAAAGGGAGGTGC+TGG 0.460614 5:-5328436 MsG0580024468.01.T01:three_prime_UTR
GGAGGTGCTGGTGGCTGATG+AGG 0.470899 5:-5328424 MsG0580024468.01.T01:three_prime_UTR
GTTCCAATGAGAGGAAGAAT+TGG 0.475347 5:-5329610 MsG0580024468.01.T01:CDS
TAATAGGCAAGTCCAGTTTG+TGG 0.491406 5:-5329485 MsG0580024468.01.T01:intron
AGATATTCAACATGCTTGCA+TGG 0.503543 5:-5328875 MsG0580024468.01.T01:CDS
GAGGTGCTGGTGGCTGATGA+GGG 0.504440 5:-5328423 MsG0580024468.01.T01:three_prime_UTR
TAGGATGATTTATACAACAT+TGG 0.510697 5:-5328706 MsG0580024468.01.T01:CDS
TGGTGGCTGATGAGGGACTT+GGG 0.523099 5:-5328416 MsG0580024468.01.T01:three_prime_UTR
CCAAAATACAGAGAAGAAAA+GGG 0.534935 5:+5328809 None:intergenic
TATTGGCCGATGTGTGCCTA+TGG 0.539151 5:-5328378 MsG0580024468.01.T01:three_prime_UTR
GATGATTTATACAACATTGG+AGG 0.543797 5:-5328703 MsG0580024468.01.T01:CDS
TATATGGGTGAAGGCATCAA+AGG 0.545129 5:-5328446 MsG0580024468.01.T01:three_prime_UTR
GACTTCATGTATATGGGTGA+AGG 0.558429 5:-5328455 MsG0580024468.01.T01:three_prime_UTR
TTTGGGAGGCGATAGCGTGC+AGG 0.562149 5:-5329451 MsG0580024468.01.T01:CDS
TCACAATGAGTAATTGCAGT+TGG 0.564711 5:-5328679 MsG0580024468.01.T01:exon
TGGATCATGGCTGGTTTGGG+AGG 0.575805 5:-5329465 MsG0580024468.01.T01:CDS
GATATTCAACATGCTTGCAT+GGG 0.580279 5:-5328874 MsG0580024468.01.T01:CDS
AATCTGGAAATTTACTGCAG+TGG 0.585822 5:+5328623 None:intergenic
GCATCAAAGGGAGGTGCTGG+TGG 0.587098 5:-5328433 MsG0580024468.01.T01:three_prime_UTR
ATATGGGTGAAGGCATCAAA+GGG 0.593483 5:-5328445 MsG0580024468.01.T01:three_prime_UTR
GCAGCGACCAAACAGCATCT+CGG 0.616324 5:+5329394 None:intergenic
ATGGGCGTTGTTCCAATGAG+AGG 0.628761 5:-5329619 MsG0580024468.01.T01:CDS
GTGCAGGTATTGGTGATGCA+AGG 0.636482 5:-5329435 MsG0580024468.01.T01:CDS
TTGCATGGGAAAAGAAGCAA+CGG 0.647653 5:-5328860 MsG0580024468.01.T01:CDS
GGTGTCGCAACAATTGCCGT+AGG 0.666510 5:-5329589 MsG0580024468.01.T01:intron
TTGGTCGCTGCAATATAACA+AGG 0.667518 5:-5329382 MsG0580024468.01.T01:CDS
TGGGTGAAGGCATCAAAGGG+AGG 0.688017 5:-5328442 MsG0580024468.01.T01:three_prime_UTR
GCGACCAAACAGCATCTCGG+AGG 0.715586 5:+5329397 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTTTTAAATGTTTGTT+TGG - Chr5:5329168-5329187 MsG0580024468.01.T01:intron 10.0%
!! CAGTAAGATATCTTTATATA+CGG - Chr5:5329395-5329414 MsG0580024468.01.T01:CDS 20.0%
!! TTGAAACCTATTAAAAAGTT+CGG - Chr5:5328754-5328773 MsG0580024468.01.T01:intron 20.0%
!!! ACATTATCTTTTTTATCCAT+AGG + Chr5:5329541-5329560 None:intergenic 20.0%
!!! TTTAATTTCAATCACAAAAC+TGG + Chr5:5328374-5328393 None:intergenic 20.0%
!!! TTTACTTTGAGTTTGTTAAT+AGG - Chr5:5328399-5328418 MsG0580024468.01.T01:three_prime_UTR 20.0%
! AACTTATGACTTCATGTATA+TGG - Chr5:5329438-5329457 MsG0580024468.01.T01:CDS 25.0%
! ACTTATGACTTCATGTATAT+GGG - Chr5:5329439-5329458 MsG0580024468.01.T01:CDS 25.0%
! TAGGATGATTTATACAACAT+TGG - Chr5:5329194-5329213 MsG0580024468.01.T01:intron 25.0%
! TGAAACCTATTAAAAAGTTC+GGG - Chr5:5328755-5328774 MsG0580024468.01.T01:intron 25.0%
! TTAAATGTTTGTTTGGTTGT+AGG - Chr5:5329175-5329194 MsG0580024468.01.T01:intron 25.0%
!! AGTAAATTTCCAGATTTTTG+TGG - Chr5:5329284-5329303 MsG0580024468.01.T01:intron 25.0%
ACCAAAATACAGAGAAGAAA+AGG + Chr5:5329095-5329114 None:intergenic 30.0%
ATGCTTGACATCTTATGTAA+GGG - Chr5:5328918-5328937 MsG0580024468.01.T01:intron 30.0%
CAGTTGTTATGACAGAAAAT+TGG + Chr5:5328544-5328563 None:intergenic 30.0%
CATAACATTGACAGATAATC+AGG + Chr5:5329127-5329146 None:intergenic 30.0%
CCAAAATACAGAGAAGAAAA+GGG + Chr5:5329094-5329113 None:intergenic 30.0%
CTGTCATAACAACTGAAATT+GGG - Chr5:5328549-5328568 MsG0580024468.01.T01:three_prime_UTR 30.0%
GATGATTTATACAACATTGG+AGG - Chr5:5329197-5329216 MsG0580024468.01.T01:intron 30.0%
GGTTATTTGCATAGTGTTAT+TGG - Chr5:5329505-5329524 MsG0580024468.01.T01:intron 30.0%
TCTGTCATAACAACTGAAAT+TGG - Chr5:5328548-5328567 MsG0580024468.01.T01:three_prime_UTR 30.0%
TTCTATACTCAAACGATCTT+AGG + Chr5:5328665-5328684 None:intergenic 30.0%
! CATATTTTATTCCTGTGATC+AGG - Chr5:5328968-5328987 MsG0580024468.01.T01:intron 30.0%
! CTAATCCCGAACTTTTTAAT+AGG + Chr5:5328763-5328782 None:intergenic 30.0%
! TGGGTAATAGTTATGTTTTC+TGG - Chr5:5328568-5328587 MsG0580024468.01.T01:three_prime_UTR 30.0%
AATCTGGAAATTTACTGCAG+TGG + Chr5:5329280-5329299 None:intergenic 35.0%
ACAAGCATGGTTGTTAAACT+CGG - Chr5:5328621-5328640 MsG0580024468.01.T01:three_prime_UTR 35.0%
AGATATTCAACATGCTTGCA+TGG - Chr5:5329025-5329044 MsG0580024468.01.T01:intron 35.0%
ATACTCAAACGATCTTAGGT+AGG + Chr5:5328661-5328680 None:intergenic 35.0%
GATATTCAACATGCTTGCAT+GGG - Chr5:5329026-5329045 MsG0580024468.01.T01:intron 35.0%
GATGCTTGACATCTTATGTA+AGG - Chr5:5328917-5328936 MsG0580024468.01.T01:intron 35.0%
TAACTGGAACACCTATCATA+GGG + Chr5:5328835-5328854 None:intergenic 35.0%
TCACAATGAGTAATTGCAGT+TGG - Chr5:5329221-5329240 MsG0580024468.01.T01:intron 35.0%
TGTAAGGGAATGTGCTTAAA+TGG - Chr5:5328933-5328952 MsG0580024468.01.T01:intron 35.0%
! ACATATGACTGACTGTTTTG+GGG - Chr5:5329337-5329356 MsG0580024468.01.T01:intron 35.0%
! CCCTTTTCTTCTCTGTATTT+TGG - Chr5:5329091-5329110 MsG0580024468.01.T01:intron 35.0%
! GACATATGACTGACTGTTTT+GGG - Chr5:5329336-5329355 MsG0580024468.01.T01:intron 35.0%
! TGACATATGACTGACTGTTT+TGG - Chr5:5329335-5329354 MsG0580024468.01.T01:intron 35.0%
! TTTTATCCATAGGCACACAT+CGG + Chr5:5329531-5329550 None:intergenic 35.0%
!! ATAGTTATGTTTTCTGGCAG+AGG - Chr5:5328574-5328593 MsG0580024468.01.T01:three_prime_UTR 35.0%
!! TAGTTATGTTTTCTGGCAGA+GGG - Chr5:5328575-5328594 MsG0580024468.01.T01:three_prime_UTR 35.0%
!!! CTCTGTATTTTGGTATGAGA+AGG - Chr5:5329101-5329120 MsG0580024468.01.T01:intron 35.0%
!!! TGCAAGCTTGTTTTGATAGT+TGG - Chr5:5329371-5329390 MsG0580024468.01.T01:intron 35.0%
AAAACTACCCTCTCTACCTA+CGG + Chr5:5328330-5328349 None:intergenic 40.0%
ACACCAATTCTTCCTCTCAT+TGG + Chr5:5328296-5328315 None:intergenic 40.0%
ATGATAGGTGTTCCAGTTAG+AGG - Chr5:5328836-5328855 MsG0580024468.01.T01:CDS 40.0%
CAAGCATGGTTGTTAAACTC+GGG - Chr5:5328622-5328641 MsG0580024468.01.T01:three_prime_UTR 40.0%
CTAACTGGAACACCTATCAT+AGG + Chr5:5328836-5328855 None:intergenic 40.0%
GACTTCATGTATATGGGTGA+AGG - Chr5:5329445-5329464 MsG0580024468.01.T01:CDS 40.0%
GTGTTCCAGTTAGAGGATTT+GGG - Chr5:5328843-5328862 MsG0580024468.01.T01:CDS 40.0%
GTTCCAATGAGAGGAAGAAT+TGG - Chr5:5328290-5328309 MsG0580024468.01.T01:three_prime_UTR 40.0%
TAATAGGCAAGTCCAGTTTG+TGG - Chr5:5328415-5328434 MsG0580024468.01.T01:three_prime_UTR 40.0%
TCAAACGATCTTAGGTAGGT+GGG + Chr5:5328657-5328676 None:intergenic 40.0%
TCTTGAAACCACCCTATGAT+AGG - Chr5:5328821-5328840 MsG0580024468.01.T01:CDS 40.0%
TGCTCTCTACCACAAAAATC+TGG + Chr5:5329296-5329315 None:intergenic 40.0%
TGTTCCAGTTAGAGGATTTG+GGG - Chr5:5328844-5328863 MsG0580024468.01.T01:CDS 40.0%
TTGCATGGGAAAAGAAGCAA+CGG - Chr5:5329040-5329059 MsG0580024468.01.T01:intron 40.0%
TTGGTCGCTGCAATATAACA+AGG - Chr5:5328518-5328537 MsG0580024468.01.T01:three_prime_UTR 40.0%
! TAGAGAGGGTAGTTTTCTAG+TGG - Chr5:5328334-5328353 MsG0580024468.01.T01:three_prime_UTR 40.0%
! TTTTGTCTGTACCTGATCAC+AGG + Chr5:5328982-5329001 None:intergenic 40.0%
!! AGAGAGGGTAGTTTTCTAGT+GGG - Chr5:5328335-5328354 MsG0580024468.01.T01:three_prime_UTR 40.0%
!! ATATGGGTGAAGGCATCAAA+GGG - Chr5:5329455-5329474 MsG0580024468.01.T01:CDS 40.0%
!! TATATGGGTGAAGGCATCAA+AGG - Chr5:5329454-5329473 MsG0580024468.01.T01:CDS 40.0%
!!! GCAGTTGGTTACTTGTTTTG+TGG - Chr5:5329236-5329255 MsG0580024468.01.T01:intron 40.0%
AACAATTGCCGTAGGTAGAG+AGG - Chr5:5328319-5328338 MsG0580024468.01.T01:three_prime_UTR 45.0%
ACAATTGCCGTAGGTAGAGA+GGG - Chr5:5328320-5328339 MsG0580024468.01.T01:three_prime_UTR 45.0%
ATCTCCCCAAATCCTCTAAC+TGG + Chr5:5328851-5328870 None:intergenic 45.0%
CAAGTCCAGTTTGTGGATCA+TGG - Chr5:5328422-5328441 MsG0580024468.01.T01:three_prime_UTR 45.0%
CTCAAACGATCTTAGGTAGG+TGG + Chr5:5328658-5328677 None:intergenic 45.0%
GGTGTTCCAGTTAGAGGATT+TGG - Chr5:5328842-5328861 MsG0580024468.01.T01:CDS 45.0%
TGGTTGTTAAACTCGGGAGT+CGG - Chr5:5328628-5328647 MsG0580024468.01.T01:three_prime_UTR 45.0%
! TTTGTGGATCATGGCTGGTT+TGG - Chr5:5328431-5328450 MsG0580024468.01.T01:three_prime_UTR 45.0%
! TTTTCCTCCGAGATGCTGTT+TGG - Chr5:5328499-5328518 MsG0580024468.01.T01:three_prime_UTR 45.0%
!! AGAGGGTAGTTTTCTAGTGG+GGG - Chr5:5328337-5328356 MsG0580024468.01.T01:three_prime_UTR 45.0%
!! GAGAGGGTAGTTTTCTAGTG+GGG - Chr5:5328336-5328355 MsG0580024468.01.T01:three_prime_UTR 45.0%
!! TTATGTTTTCTGGCAGAGGG+TGG - Chr5:5328578-5328597 MsG0580024468.01.T01:three_prime_UTR 45.0%
!! TTGTGGATCATGGCTGGTTT+GGG - Chr5:5328432-5328451 MsG0580024468.01.T01:three_prime_UTR 45.0%
AAGGCTGCGACAAACAAGCA+TGG - Chr5:5328608-5328627 MsG0580024468.01.T01:three_prime_UTR 50.0%
ACCAGCCATGATCCACAAAC+TGG + Chr5:5328430-5328449 None:intergenic 50.0%
CTGGAACACCTATCATAGGG+TGG + Chr5:5328832-5328851 None:intergenic 50.0%
GGGTGGTTTCAAGAGATCGA+AGG + Chr5:5328815-5328834 None:intergenic 50.0%
GGTTGTTAAACTCGGGAGTC+GGG - Chr5:5328629-5328648 MsG0580024468.01.T01:three_prime_UTR 50.0%
TATTGGCCGATGTGTGCCTA+TGG - Chr5:5329522-5329541 MsG0580024468.01.T01:intron 50.0%
TCCAGTTTGTGGATCATGGC+TGG - Chr5:5328426-5328445 MsG0580024468.01.T01:three_prime_UTR 50.0%
TTCTGGCAGAGGGTGGTTTA+AGG - Chr5:5328585-5328604 MsG0580024468.01.T01:three_prime_UTR 50.0%
! ATGGGCGTTGTTCCAATGAG+AGG - Chr5:5328281-5328300 MsG0580024468.01.T01:three_prime_UTR 50.0%
!! GTGCAGGTATTGGTGATGCA+AGG - Chr5:5328465-5328484 MsG0580024468.01.T01:three_prime_UTR 50.0%
AGGCGATAGCGTGCAGGTAT+TGG - Chr5:5328455-5328474 MsG0580024468.01.T01:three_prime_UTR 55.0%
GCAGCGACCAAACAGCATCT+CGG + Chr5:5328509-5328528 None:intergenic 55.0%
GGCAGAGGGTGGTTTAAGGA+AGG - Chr5:5328589-5328608 MsG0580024468.01.T01:three_prime_UTR 55.0%
TGGTGGCTGATGAGGGACTT+GGG - Chr5:5329484-5329503 MsG0580024468.01.T01:intron 55.0%
! AAGGCATCAAAGGGAGGTGC+TGG - Chr5:5329464-5329483 MsG0580024468.01.T01:CDS 55.0%
! GGTGTCGCAACAATTGCCGT+AGG - Chr5:5328311-5328330 MsG0580024468.01.T01:three_prime_UTR 55.0%
!! TGGATCATGGCTGGTTTGGG+AGG - Chr5:5328435-5328454 MsG0580024468.01.T01:three_prime_UTR 55.0%
!! TGGGTGAAGGCATCAAAGGG+AGG - Chr5:5329458-5329477 MsG0580024468.01.T01:CDS 55.0%
CTGGTGGCTGATGAGGGACT+TGG - Chr5:5329483-5329502 MsG0580024468.01.T01:intron 60.0%
GCGACCAAACAGCATCTCGG+AGG + Chr5:5328506-5328525 None:intergenic 60.0%
TTTGGGAGGCGATAGCGTGC+AGG - Chr5:5328449-5328468 MsG0580024468.01.T01:three_prime_UTR 60.0%
!! GAGGTGCTGGTGGCTGATGA+GGG - Chr5:5329477-5329496 MsG0580024468.01.T01:CDS 60.0%
!! GCATCAAAGGGAGGTGCTGG+TGG - Chr5:5329467-5329486 MsG0580024468.01.T01:CDS 60.0%
!! GGAGGTGCTGGTGGCTGATG+AGG - Chr5:5329476-5329495 MsG0580024468.01.T01:CDS 65.0%
Chromosome Type Strat End Strand Name
Chr5 gene 5328281 5329641 5328281 ID=MsG0580024468.01;Name=MsG0580024468.01
Chr5 mRNA 5328281 5329641 5328281 ID=MsG0580024468.01.T01;Parent=MsG0580024468.01;Name=MsG0580024468.01.T01;_AED=0.36;_eAED=0.52;_QI=0|0.33|0.5|1|1|0.75|4|408|113
Chr5 exon 5328281 5328725 5328281 ID=MsG0580024468.01.T01:exon:19053;Parent=MsG0580024468.01.T01
Chr5 exon 5328810 5328932 5328810 ID=MsG0580024468.01.T01:exon:19052;Parent=MsG0580024468.01.T01
Chr5 exon 5329372 5329501 5329372 ID=MsG0580024468.01.T01:exon:19051;Parent=MsG0580024468.01.T01
Chr5 exon 5329590 5329641 5329590 ID=MsG0580024468.01.T01:exon:19050;Parent=MsG0580024468.01.T01
Chr5 CDS 5329590 5329641 5329590 ID=MsG0580024468.01.T01:cds;Parent=MsG0580024468.01.T01
Chr5 CDS 5329372 5329501 5329372 ID=MsG0580024468.01.T01:cds;Parent=MsG0580024468.01.T01
Chr5 CDS 5328810 5328932 5328810 ID=MsG0580024468.01.T01:cds;Parent=MsG0580024468.01.T01
Chr5 CDS 5328689 5328725 5328689 ID=MsG0580024468.01.T01:cds;Parent=MsG0580024468.01.T01
Chr5 three_prime_UTR 5328281 5328688 5328281 ID=MsG0580024468.01.T01:three_prime_utr;Parent=MsG0580024468.01.T01
Gene Sequence

>MsG0580024468.01.T01

ATGGGCGTTGTTCCAATGAGAGGAAGAATTGGTGTCGCAACAATTGCCGTAGGCAAGTCCAGTTTGTGGATCATGGCTGGTTTGGGAGGCGATAGCGTGCAGGTATTGGTGATGCAAGGCGAATGTAGTGTTTTCCTCCGAGATGCTGTTTGGTCGCTGCAATATAACAAGGCCAATTTTCTGTACAGACAAAAAAAGCATTTAGTCGATGTTACTGAGATATTCAACATGCTTGCATGGGAAAAGAAGCAACGGCTCGTCAAACTTTTCTATCTTGTTTTAACCCTTTTCTTCTCTGTATTTTGGATGATTTATACAACATTGGAGGATCACAATGAGTAA
Protein sequence

>MsG0580024468.01.T01

MGVVPMRGRIGVATIAVGKSSLWIMAGLGGDSVQVLVMQGECSVFLRDAVWSLQYNKANFLYRQKKHLVDVTEIFNMLAWEKKQRLVKLFYLVLTLFFSVFWMIYTTLEDHNE*