AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0780040186.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0780040186.01.T01 MTR_7g062720 64.646 99 35 0 1 99 1 99 4.42e-43 143
MsG0780040186.01.T01 MTR_5g061150 65.000 80 28 0 20 99 10 89 3.60e-29 107
MsG0780040186.01.T01 MTR_1g036690 58.537 82 27 3 153 233 5 80 1.28e-23 90.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 42 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGAGGCTCTTAATATTTC+TGG 0.080746 7:-74093013 MsG0780040186.01.T01:CDS
TTCGGCATTTAAATGAATTT+TGG 0.166319 7:+74092961 None:intergenic
CACTTCAAAATAAGGATAAA+AGG 0.234592 7:-74092126 MsG0780040186.01.T01:CDS
CCAACAATCACTTCAAAATA+AGG 0.244294 7:-74092134 MsG0780040186.01.T01:CDS
AAATTGTCCCAAAGATCTTT+TGG 0.267031 7:+74092815 None:intergenic
TAAAGATCAACAAGATGTTT+TGG 0.271287 7:+74092157 None:intergenic
TATTTCTGGAAATAATTATC+TGG 0.282933 7:-74092999 MsG0780040186.01.T01:CDS
TAGAAGATCCAAAAGATCTT+TGG 0.283634 7:-74092823 MsG0780040186.01.T01:CDS
TATAGGTGGGGTTCTATTCC+TGG 0.331534 7:+74091972 None:intergenic
TGAAGATGATTATGGTAATA+TGG 0.338642 7:-74092074 MsG0780040186.01.T01:CDS
CTGGAAATAATTATCTGGCT+TGG 0.347827 7:-74092994 MsG0780040186.01.T01:CDS
TGGAAATAATTATCTGGCTT+GGG 0.353242 7:-74092993 MsG0780040186.01.T01:CDS
GAAAATGATGAAGATGATTA+TGG 0.391347 7:-74092082 MsG0780040186.01.T01:CDS
TACCATTCATTACGAGCATT+AGG 0.392976 7:+74092755 None:intergenic
TTTGGGACAATTTAAAAGAA+AGG 0.395342 7:-74092805 MsG0780040186.01.T01:CDS
AGAAGATCCAAAAGATCTTT+GGG 0.400056 7:-74092822 MsG0780040186.01.T01:CDS
TGCTATCGTTGTGGAGGAAA+AGG 0.414829 7:-74092205 MsG0780040186.01.T01:CDS
CCTTCGTCACCACCTTCATA+AGG 0.433246 7:-74092870 MsG0780040186.01.T01:CDS
CAAAACAACTGAACAACAAA+AGG 0.454927 7:-74092909 MsG0780040186.01.T01:CDS
AATTGTATCTCCATGCCCTT+CGG 0.460742 7:+74092943 None:intergenic
AGAAATCAGCAGCATCTAAG+TGG 0.464577 7:+74092044 None:intergenic
TTTCACGGTATTGTTGCTGC+AGG 0.465441 7:+74092582 None:intergenic
GCAGCAACAATACCGTGAAA+AGG 0.474876 7:-74092579 MsG0780040186.01.T01:CDS
ACTTCAAAATAAGGATAAAA+GGG 0.487291 7:-74092125 MsG0780040186.01.T01:CDS
CATTTAAATGCCGAAGGGCA+TGG 0.494088 7:-74092953 MsG0780040186.01.T01:CDS
CAGCAACAATACCGTGAAAA+GGG 0.498612 7:-74092578 MsG0780040186.01.T01:CDS
GTTGTGGAGGAAAAGGTCAT+TGG 0.504176 7:-74092198 MsG0780040186.01.T01:CDS
TACATTAGATGCATGAAAAG+TGG 0.516304 7:+74092607 None:intergenic
CATTAGAGATGAAAATATCC+AGG 0.532865 7:-74091990 MsG0780040186.01.T01:CDS
CATGGAGATACAATTAAAGA+AGG 0.533844 7:-74092935 MsG0780040186.01.T01:CDS
AAAATTCATTTAAATGCCGA+AGG 0.537172 7:-74092959 MsG0780040186.01.T01:CDS
TAACACTGTGTGGAGGAGAA+AGG 0.541108 7:-74092663 MsG0780040186.01.T01:CDS
AACTGAACAACAAAAGGCTA+AGG 0.582581 7:-74092903 MsG0780040186.01.T01:CDS
GAGAGTATTTGCTATCGTTG+TGG 0.583351 7:-74092214 MsG0780040186.01.T01:CDS
ATTCATTACGAGCATTAGGA+AGG 0.589984 7:+74092759 None:intergenic
CCTTATGAAGGTGGTGACGA+AGG 0.598722 7:+74092870 None:intergenic
AGTATTTGCTATCGTTGTGG+AGG 0.599695 7:-74092211 MsG0780040186.01.T01:CDS
GAAATCAGCAGCATCTAAGT+GGG 0.621669 7:+74092045 None:intergenic
AAATTCATTTAAATGCCGAA+GGG 0.631745 7:-74092958 MsG0780040186.01.T01:CDS
GTGGTGACGAAGGAATATCA+TGG 0.663314 7:+74092880 None:intergenic
ACTTCTCTATTAACACTGTG+TGG 0.668278 7:-74092673 MsG0780040186.01.T01:CDS
TCTCTATTAACACTGTGTGG+AGG 0.693331 7:-74092670 MsG0780040186.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATGTTGTAAGAATGAT+TGG - Chr7:74092766-74092785 MsG0780040186.01.T01:intron 20.0%
!! ACTTCAAAATAAGGATAAAA+GGG - Chr7:74092897-74092916 MsG0780040186.01.T01:CDS 20.0%
!!! TATTTCTGGAAATAATTATC+TGG - Chr7:74092023-74092042 MsG0780040186.01.T01:CDS 20.0%
! AAAATTCATTTAAATGCCGA+AGG - Chr7:74092063-74092082 MsG0780040186.01.T01:CDS 25.0%
! AAATTCATTTAAATGCCGAA+GGG - Chr7:74092064-74092083 MsG0780040186.01.T01:CDS 25.0%
! CACTTCAAAATAAGGATAAA+AGG - Chr7:74092896-74092915 MsG0780040186.01.T01:CDS 25.0%
! GAAAATGATGAAGATGATTA+TGG - Chr7:74092940-74092959 MsG0780040186.01.T01:CDS 25.0%
! TGAAGATGATTATGGTAATA+TGG - Chr7:74092948-74092967 MsG0780040186.01.T01:CDS 25.0%
!! AAAGATCAACAAGATGTTTT+GGG + Chr7:74092867-74092886 None:intergenic 25.0%
!! TAAAGATCAACAAGATGTTT+TGG + Chr7:74092868-74092887 None:intergenic 25.0%
!! TATTTTCATCTCTAATGAGA+TGG + Chr7:74093029-74093048 None:intergenic 25.0%
!! TTACAACATTTTTCATCTTC+TGG + Chr7:74092759-74092778 None:intergenic 25.0%
!! TTCGGCATTTAAATGAATTT+TGG + Chr7:74092064-74092083 None:intergenic 25.0%
!! TTTGGGACAATTTAAAAGAA+AGG - Chr7:74092217-74092236 MsG0780040186.01.T01:CDS 25.0%
!!! CATTTTTTAGATCCTTATGA+AGG + Chr7:74092167-74092186 None:intergenic 25.0%
!!! GAGAAAATGTGTTTTTGTTT+TGG + Chr7:74092735-74092754 None:intergenic 25.0%
AATGGTATATTTGCGTTTAC+AGG - Chr7:74092283-74092302 MsG0780040186.01.T01:intron 30.0%
AGAAGATCCAAAAGATCTTT+GGG - Chr7:74092200-74092219 MsG0780040186.01.T01:CDS 30.0%
CAAAACAACTGAACAACAAA+AGG - Chr7:74092113-74092132 MsG0780040186.01.T01:CDS 30.0%
CATGGAGATACAATTAAAGA+AGG - Chr7:74092087-74092106 MsG0780040186.01.T01:CDS 30.0%
CATTAGAGATGAAAATATCC+AGG - Chr7:74093032-74093051 MsG0780040186.01.T01:CDS 30.0%
CCAACAATCACTTCAAAATA+AGG - Chr7:74092888-74092907 MsG0780040186.01.T01:CDS 30.0%
GTCTGTAATCGAATATAACT+CGG - Chr7:74092313-74092332 MsG0780040186.01.T01:intron 30.0%
TACATTAGATGCATGAAAAG+TGG + Chr7:74092418-74092437 None:intergenic 30.0%
TAGAAGATCCAAAAGATCTT+TGG - Chr7:74092199-74092218 MsG0780040186.01.T01:CDS 30.0%
! AAATTGTCCCAAAGATCTTT+TGG + Chr7:74092210-74092229 None:intergenic 30.0%
! AAGATCAACAAGATGTTTTG+GGG + Chr7:74092866-74092885 None:intergenic 30.0%
! AAGATCTTTTGGATCTTCTA+TGG + Chr7:74092199-74092218 None:intergenic 30.0%
! AGCTTTGATGAAAAATCACT+CGG - Chr7:74092522-74092541 MsG0780040186.01.T01:intron 30.0%
! TGGAAATAATTATCTGGCTT+GGG - Chr7:74092029-74092048 MsG0780040186.01.T01:CDS 30.0%
! TTTGAGGCTCTTAATATTTC+TGG - Chr7:74092009-74092028 MsG0780040186.01.T01:CDS 30.0%
! TTTTTAGATCCTTATGAAGG+TGG + Chr7:74092164-74092183 None:intergenic 30.0%
!! GGTTTTAATCGTAATCACAA+TGG - Chr7:74092686-74092705 MsG0780040186.01.T01:intron 30.0%
!!! ACCTTTTAAAACCCTTTTCA+CGG + Chr7:74092458-74092477 None:intergenic 30.0%
!!! CCTTATTTTGAAGTGATTGT+TGG + Chr7:74092891-74092910 None:intergenic 30.0%
AACTGAACAACAAAAGGCTA+AGG - Chr7:74092119-74092138 MsG0780040186.01.T01:CDS 35.0%
ACTTCTCTATTAACACTGTG+TGG - Chr7:74092349-74092368 MsG0780040186.01.T01:intron 35.0%
ATTCATTACGAGCATTAGGA+AGG + Chr7:74092266-74092285 None:intergenic 35.0%
CTGGAAATAATTATCTGGCT+TGG - Chr7:74092028-74092047 MsG0780040186.01.T01:CDS 35.0%
TACCATTCATTACGAGCATT+AGG + Chr7:74092270-74092289 None:intergenic 35.0%
TTCCTAATGCTCGTAATGAA+TGG - Chr7:74092265-74092284 MsG0780040186.01.T01:intron 35.0%
! AGATGGTCAATCTTTTCATC+AGG + Chr7:74093012-74093031 None:intergenic 35.0%
! CCTCAAAATCAAGTTTTGCA+AGG + Chr7:74091996-74092015 None:intergenic 35.0%
! CCTTGCAAAACTTGATTTTG+AGG - Chr7:74091993-74092012 MsG0780040186.01.T01:CDS 35.0%
! CTTTTGGATCTTCTATGGTA+AGG + Chr7:74092194-74092213 None:intergenic 35.0%
!!! ACCGTGAAAAGGGTTTTAAA+AGG - Chr7:74092454-74092473 MsG0780040186.01.T01:intron 35.0%
AATTGTATCTCCATGCCCTT+CGG + Chr7:74092082-74092101 None:intergenic 40.0%
AGAAATCAGCAGCATCTAAG+TGG + Chr7:74092981-74093000 None:intergenic 40.0%
CAGCAACAATACCGTGAAAA+GGG - Chr7:74092444-74092463 MsG0780040186.01.T01:intron 40.0%
CTTAATATCATGCCTGCTTG+TGG - Chr7:74092485-74092504 MsG0780040186.01.T01:intron 40.0%
GAAATCAGCAGCATCTAAGT+GGG + Chr7:74092980-74092999 None:intergenic 40.0%
GATCACTATGGACAAAATCG+TGG - Chr7:74092594-74092613 MsG0780040186.01.T01:CDS 40.0%
GTAGCAACACATGATCACTA+TGG - Chr7:74092582-74092601 MsG0780040186.01.T01:CDS 40.0%
TCTCTATTAACACTGTGTGG+AGG - Chr7:74092352-74092371 MsG0780040186.01.T01:intron 40.0%
TTATTTGTTCTGCCACAAGC+AGG + Chr7:74092500-74092519 None:intergenic 40.0%
! ATGTGTTGCTACATCACTTC+TGG + Chr7:74092574-74092593 None:intergenic 40.0%
! GAAGGATGACAGTTTTCTGA+TGG + Chr7:74092248-74092267 None:intergenic 40.0%
! TGTGTTGCTACATCACTTCT+GGG + Chr7:74092573-74092592 None:intergenic 40.0%
!! AGTATTTGCTATCGTTGTGG+AGG - Chr7:74092811-74092830 MsG0780040186.01.T01:CDS 40.0%
!! GAGAGTATTTGCTATCGTTG+TGG - Chr7:74092808-74092827 MsG0780040186.01.T01:CDS 40.0%
CATTTAAATGCCGAAGGGCA+TGG - Chr7:74092069-74092088 MsG0780040186.01.T01:CDS 45.0%
GCAGCAACAATACCGTGAAA+AGG - Chr7:74092443-74092462 MsG0780040186.01.T01:intron 45.0%
GTTGTGGAGGAAAAGGTCAT+TGG - Chr7:74092824-74092843 MsG0780040186.01.T01:CDS 45.0%
TAACACTGTGTGGAGGAGAA+AGG - Chr7:74092359-74092378 MsG0780040186.01.T01:intron 45.0%
TATGGACAAAATCGTGGTCG+TGG - Chr7:74092600-74092619 MsG0780040186.01.T01:CDS 45.0%
TGCTATCGTTGTGGAGGAAA+AGG - Chr7:74092817-74092836 MsG0780040186.01.T01:CDS 45.0%
TTTCACGGTATTGTTGCTGC+AGG + Chr7:74092443-74092462 None:intergenic 45.0%
! GTGGTGACGAAGGAATATCA+TGG + Chr7:74092145-74092164 None:intergenic 45.0%
! TGCTACATCACTTCTGGGAA+TGG + Chr7:74092568-74092587 None:intergenic 45.0%
! TTATGGAAGGGACGTGGTTT+TGG - Chr7:74092665-74092684 MsG0780040186.01.T01:CDS 45.0%
!!! AAGATGTTTTGGGGTACGAC+AGG + Chr7:74092857-74092876 None:intergenic 45.0%
ACGTGGTCGTGGTTATGGAA+GGG - Chr7:74092653-74092672 MsG0780040186.01.T01:CDS 50.0%
CCTTCGTCACCACCTTCATA+AGG - Chr7:74092152-74092171 MsG0780040186.01.T01:CDS 50.0%
! CCTTATGAAGGTGGTGACGA+AGG + Chr7:74092155-74092174 None:intergenic 50.0%
GACGTGGTCGTGGTTATGGA+AGG - Chr7:74092652-74092671 MsG0780040186.01.T01:CDS 55.0%
TCGTGGTTATGGAAGGGACG+TGG - Chr7:74092659-74092678 MsG0780040186.01.T01:CDS 55.0%
! GGGAATGGAGCACTACCAGT+GGG + Chr7:74092553-74092572 None:intergenic 55.0%
! TGGGAATGGAGCACTACCAG+TGG + Chr7:74092554-74092573 None:intergenic 55.0%
CAAAATCGTGGTCGTGGCCG+TGG - Chr7:74092606-74092625 MsG0780040186.01.T01:CDS 60.0%
CACGTCCACGACCATGACCA+CGG + Chr7:74092626-74092645 None:intergenic 60.0%
CGTGGACGTGGTCGTGGTTA+TGG - Chr7:74092648-74092667 MsG0780040186.01.T01:CDS 60.0%
! AATCACTCGGCTCGTCCCAC+TGG - Chr7:74092535-74092554 MsG0780040186.01.T01:intron 60.0%
CATGGTCGTGGACGTGGACG+TGG - Chr7:74092630-74092649 MsG0780040186.01.T01:CDS 65.0%
CGTGGTCATGGTCGTGGACG+TGG - Chr7:74092624-74092643 MsG0780040186.01.T01:CDS 65.0%
CGTGGACGTGGACGTGGACG+TGG - Chr7:74092636-74092655 MsG0780040186.01.T01:CDS 70.0%
CGTGGACGTGGACGTGGTCG+TGG - Chr7:74092642-74092661 MsG0780040186.01.T01:CDS 70.0%
CGTGGCCGTGGTCATGGTCG+TGG - Chr7:74092618-74092637 MsG0780040186.01.T01:CDS 70.0%
CGTGGTCGTGGCCGTGGTCA+TGG - Chr7:74092612-74092631 MsG0780040186.01.T01:CDS 70.0%
Chromosome Type Strat End Strand Name
Chr7 gene 74091985 74093059 74091985 ID=MsG0780040186.01;Name=MsG0780040186.01
Chr7 mRNA 74091985 74093059 74091985 ID=MsG0780040186.01.T01;Parent=MsG0780040186.01;Name=MsG0780040186.01.T01;_AED=0.47;_eAED=0.61;_QI=0|0|0|1|1|1|3|0|233
Chr7 exon 74092768 74093059 74092768 ID=MsG0780040186.01.T01:exon:525;Parent=MsG0780040186.01.T01
Chr7 exon 74092569 74092698 74092569 ID=MsG0780040186.01.T01:exon:524;Parent=MsG0780040186.01.T01
Chr7 exon 74091985 74092264 74091985 ID=MsG0780040186.01.T01:exon:523;Parent=MsG0780040186.01.T01
Chr7 CDS 74092768 74093059 74092768 ID=MsG0780040186.01.T01:cds;Parent=MsG0780040186.01.T01
Chr7 CDS 74092569 74092698 74092569 ID=MsG0780040186.01.T01:cds;Parent=MsG0780040186.01.T01
Chr7 CDS 74091985 74092264 74091985 ID=MsG0780040186.01.T01:cds;Parent=MsG0780040186.01.T01
Gene Sequence

>MsG0780040186.01.T01

ATGTCGAACCTTGCAAAACTTGATTTTGAGGCTCTTAATATTTCTGGAAATAATTATCTGGCTTGGGCTCTAGATGCCAAAATTCATTTAAATGCCGAAGGGCATGGAGATACAATTAAAGAAGGAAACAAAACAACTGAACAACAAAAGGCTAAGGCCATGATATTCCTTCGTCACCACCTTCATAAGGATCTAAAAAATGAATACCTTACCATAGAAGATCCAAAAGATCTTTGGGACAATTTAAAAGAAAGGTTTGACCATCAGAAAACTGTCATCCTTCCTAATGCTCATTACTTCTCTATTAACACTGTGTGGAGGAGAAAGGTGACTGATGCGCAGATGTTAGAAAAAACATTCTCCACTTTTCATGCATCTAATGTAATCCTGCAGCAACAATACCGTGAAAAGGGTTTTAAAAGAATGATTGGTCAAAGCAGCAAAAGTAATGAGAGTATTTGCTATCGTTGTGGAGGAAAAGGTCATTGGAGTCGTACCTGTCGTACCCCAAAACATCTTGTTGATCTTTACCAACAATCACTTCAAAATAAGGATAAAAGGGCTGAAACGCACTTTGCATGCGAAAATGATGAAGATGATTATGGTAATATGGAAAGTACCCACTTAGATGCTGCTGATTTCTTTGTTGATCCTGATGAAAAGATTGACCATCTCATTAGAGATGAAAATATCCAGGAATAG
Protein sequence

>MsG0780040186.01.T01

MSNLAKLDFEALNISGNNYLAWALDAKIHLNAEGHGDTIKEGNKTTEQQKAKAMIFLRHHLHKDLKNEYLTIEDPKDLWDNLKERFDHQKTVILPNAHYFSINTVWRRKVTDAQMLEKTFSTFHASNVILQQQYREKGFKRMIGQSSKSNESICYRCGGKGHWSRTCRTPKHLVDLYQQSLQNKDKRAETHFACENDEDDYGNMESTHLDAADFFVDPDEKIDHLIRDENIQE*