AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0114950

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0114950 MtrunA17_Chr1g0161491 67.005 197 50 2 34 230 9 190 7.91e-78 253
Msa0114950 MtrunA17_Chr1g0161471 65.285 193 51 2 40 230 1 179 9.11e-76 248
Msa0114950 MtrunA17_Chr1g0161511 62.887 194 54 4 40 230 1 179 1.95e-68 227
Msa0114950 MtrunA17_Chr1g0161521 62.887 194 54 4 40 230 1 179 4.49e-68 226
Msa0114950 MtrunA17_Chr1g0161451 33.871 186 108 3 44 229 3 173 2.12e-26 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0114950 AT1G14790.1 40.426 188 97 3 43 230 2 174 4.29e-41 150

Find 31 sgRNAs with CRISPR-Local

Find 135 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACGATGTTAAATTGTATTT+TGG 0.150856 1_3:+33379875 Msa0114950:CDS
AGCTTTCATATGAGAATATT+TGG 0.191630 1_3:+33380023 Msa0114950:CDS
ATGGATGCTAGTGCAGATTT+TGG 0.192772 1_3:+33379941 Msa0114950:CDS
CTATTTAAAAGTTACGAAAA+TGG 0.261211 1_3:+33379808 Msa0114950:CDS
TGCAAAGTATCTATTGATTC+AGG 0.268018 1_3:+33380078 Msa0114950:CDS
TAGAAGAATGCCGTTGGCTT+TGG 0.337561 1_3:-33379845 None:intergenic
TGCTGGAAGTTTGTAATTGA+AGG 0.450289 1_3:-33377647 None:intergenic
CTCTGTATTGTGGGGAAAGA+TGG 0.454381 1_3:+33379922 Msa0114950:CDS
AAAAGAGTTGGCATTGAAGA+TGG 0.454789 1_3:+33379514 Msa0114950:CDS
TTGGGATTGGATTGAGAAAG+TGG 0.455481 1_3:+33379960 Msa0114950:CDS
TACCTTGTCTGATCTTGTGC+TGG 0.458868 1_3:-33377664 None:intergenic
ACATTTGTAGAGCAGTATAC+TGG 0.461229 1_3:+33379599 Msa0114950:CDS
GGAAAGATTCTCTGTATTGT+GGG 0.467936 1_3:+33379913 Msa0114950:CDS
TCTACAAATGTCTTTACATC+AGG 0.480962 1_3:-33379587 None:intergenic
AGTAAAACAATTAAGTTGCA+TGG 0.485965 1_3:+33379542 Msa0114950:CDS
AGGAAAGATTCTCTGTATTG+TGG 0.507749 1_3:+33379912 Msa0114950:CDS
AGATCATGCTACATATATGA+TGG 0.530126 1_3:+33379748 Msa0114950:CDS
TATAGGAAAATCAAAAGAGT+TGG 0.542790 1_3:+33379502 Msa0114950:intron
GTTTGAACTTCTTATCGTCA+TGG 0.543349 1_3:-33379997 None:intergenic
GAGATTTGTTCAAATTCGAA+CGG 0.545671 1_3:+33379697 Msa0114950:CDS
TCAGGCACGGTGACATGATG+AGG 0.567959 1_3:-33379569 None:intergenic
AGATTGAACTGCATCAACCA+TGG 0.634369 1_3:+33380047 Msa0114950:CDS
CAGGCACGGTGACATGATGA+GGG 0.635211 1_3:-33379568 None:intergenic
AATCTGTAGAAGAATGCCGT+TGG 0.636903 1_3:-33379851 None:intergenic
AGATATTGATCCAAAGCCAA+CGG 0.640968 1_3:+33379835 Msa0114950:CDS
GAAAGATTCTCTGTATTGTG+GGG 0.645886 1_3:+33379914 Msa0114950:CDS
AAATGTCTTTACATCAGGCA+CGG 0.659012 1_3:-33379582 None:intergenic
TATATGATGGCCTTATGTAG+CGG 0.659739 1_3:+33379761 Msa0114950:CDS
TTCCAGCACAAGATCAGACA+AGG 0.664246 1_3:+33377662 Msa0114950:CDS
ATATGTAGCATGATCTGTAG+TGG 0.696738 1_3:-33379741 None:intergenic
GTATACTGGTGAAGAAAGTG+TGG 0.711055 1_3:+33379613 Msa0114950:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTCTATTTTTTTTCTT+CGG - chr1_3:33378889-33378908 None:intergenic 10.0%
!! CTTTATAATAAAGAAAAAAA+AGG + chr1_3:33379080-33379099 Msa0114950:intron 10.0%
!!! TCATTTCTTTTATTATATAT+TGG + chr1_3:33379276-33379295 Msa0114950:intron 10.0%
!! AAATAATTCAAAAAAGAAAA+TGG - chr1_3:33379467-33379486 None:intergenic 10.0%
!!! TTTAATTTAACCATAATTCA+AGG - chr1_3:33377997-33378016 None:intergenic 15.0%
!!! ATATGTCATTTTTTTTTTGA+AGG - chr1_3:33378693-33378712 None:intergenic 15.0%
!! AAATGACATATTTACATAAA+TGG + chr1_3:33378702-33378721 Msa0114950:intron 15.0%
!!! ATTTGAGTTTTTATTTTCCT+CGG + chr1_3:33377820-33377839 Msa0114950:intron 20.0%
!!! GTCAACTTTTTCTTATAATA+AGG - chr1_3:33378036-33378055 None:intergenic 20.0%
!!! TAAGAAAAAGTTGACTTTTT+AGG + chr1_3:33378041-33378060 Msa0114950:intron 20.0%
!!! GTCAATTGTTTCTTATAATA+AGG + chr1_3:33378135-33378154 Msa0114950:intron 20.0%
!!! TCATTACTCTATTGAATTTT+AGG - chr1_3:33378254-33378273 None:intergenic 20.0%
!! TTCTTATTGGTCAAAAATAA+TGG + chr1_3:33378326-33378345 Msa0114950:intron 20.0%
!!! TCAAATTTTGAAAACTTCAT+TGG - chr1_3:33378471-33378490 None:intergenic 20.0%
!!! AATATGTCATTTTGAAACTT+TGG - chr1_3:33378665-33378684 None:intergenic 20.0%
!!! CATTTTCGTAACTTTTAAAT+AGG - chr1_3:33379810-33379829 None:intergenic 20.0%
!! CTATTTAAAAGTTACGAAAA+TGG + chr1_3:33379808-33379827 Msa0114950:CDS 20.0%
!! ACTAAAATTGCGTATGTTTT+TGG + chr1_3:33377601-33377620 Msa0114950:CDS 25.0%
! GAAAATTGACAAGTAAAACA+AGG + chr1_3:33377782-33377801 Msa0114950:intron 25.0%
! TTTAACCATAATTCAAGGTT+TGG - chr1_3:33377992-33378011 None:intergenic 25.0%
! AAATTAAAAAATACTCCCTC+CGG + chr1_3:33378009-33378028 Msa0114950:intron 25.0%
!! CTTTTTCTTATAATAAGGAC+CGG - chr1_3:33378031-33378050 None:intergenic 25.0%
! ACGTTAGTAATTTATACAAG+TGG - chr1_3:33378193-33378212 None:intergenic 25.0%
! AAGCACACAATATTAATACA+AGG + chr1_3:33378227-33378246 Msa0114950:intron 25.0%
! AATAAGAAGTGAGAAAAACA+AGG - chr1_3:33378314-33378333 None:intergenic 25.0%
!!! TTGTTTTTCTCACTTCTTAT+TGG + chr1_3:33378313-33378332 Msa0114950:intron 25.0%
!! TATTTGTCATTTGTCTAGTT+TGG - chr1_3:33378579-33378598 None:intergenic 25.0%
! AGCATTTACAGAAAAAGTAA+AGG + chr1_3:33378780-33378799 Msa0114950:intron 25.0%
!!! TTTCTCTTTTATTTTGTGGT+GGG - chr1_3:33378948-33378967 None:intergenic 25.0%
! ACTTAATTACTCATGTTCAT+GGG - chr1_3:33378973-33378992 None:intergenic 25.0%
! AACTTAATTACTCATGTTCA+TGG - chr1_3:33378974-33378993 None:intergenic 25.0%
! ATGAAAGTAACTAGTGATAA+AGG + chr1_3:33379128-33379147 Msa0114950:intron 25.0%
!!! GCATTCTATTATTTTTACAG+TGG + chr1_3:33379219-33379238 Msa0114950:intron 25.0%
! AATGGTATATCTAAGAAAGA+AGG - chr1_3:33379449-33379468 None:intergenic 25.0%
!! TTGATTTTCCTATATAGGAT+TGG - chr1_3:33379496-33379515 None:intergenic 25.0%
!!! CTCTTTTGATTTTCCTATAT+AGG - chr1_3:33379501-33379520 None:intergenic 25.0%
! TATAGGAAAATCAAAAGAGT+TGG + chr1_3:33379502-33379521 Msa0114950:intron 25.0%
!! AGTAAAACAATTAAGTTGCA+TGG + chr1_3:33379542-33379561 Msa0114950:CDS 25.0%
!! GACGATGTTAAATTGTATTT+TGG + chr1_3:33379875-33379894 Msa0114950:CDS 25.0%
! AGCTTTCATATGAGAATATT+TGG + chr1_3:33380023-33380042 Msa0114950:CDS 25.0%
!!! TTGTTTTTAGCACAGGATAA+TGG + chr1_3:33377716-33377735 Msa0114950:intron 30.0%
TTTCTTATAATAAGGACCGA+AGG + chr1_3:33378143-33378162 Msa0114950:intron 30.0%
TTCTTATAATAAGGACCGAA+GGG + chr1_3:33378144-33378163 Msa0114950:intron 30.0%
TACTAACGTGAACTTATTCT+TGG + chr1_3:33378204-33378223 Msa0114950:intron 30.0%
TCAACAAAGTTGTCATCAAA+TGG - chr1_3:33378288-33378307 None:intergenic 30.0%
!!! AACCACTTTTTGACAACTTT+TGG - chr1_3:33378411-33378430 None:intergenic 30.0%
!!! TCATTTTGAAACTTTGGATG+AGG - chr1_3:33378659-33378678 None:intergenic 30.0%
!!! GTTTCTCTTTTATTTTGTGG+TGG - chr1_3:33378949-33378968 None:intergenic 30.0%
!!! GGTGTTTCTCTTTTATTTTG+TGG - chr1_3:33378952-33378971 None:intergenic 30.0%
TAGTGATAAAGGACATATGT+GGG + chr1_3:33379139-33379158 Msa0114950:intron 30.0%
GGTGATATATCAACAATCAT+TGG + chr1_3:33379240-33379259 Msa0114950:intron 30.0%
TTTCTTCTCCAATCCTATAT+AGG + chr1_3:33379485-33379504 Msa0114950:intron 30.0%
TCTACAAATGTCTTTACATC+AGG - chr1_3:33379590-33379609 None:intergenic 30.0%
GTGTGGTTGCTATAAAAATA+AGG + chr1_3:33379630-33379649 Msa0114950:CDS 30.0%
! GAGATTTGTTCAAATTCGAA+CGG + chr1_3:33379697-33379716 Msa0114950:CDS 30.0%
AGATCATGCTACATATATGA+TGG + chr1_3:33379748-33379767 Msa0114950:CDS 30.0%
!!! CAATTTTTTTCCGCTACATA+AGG - chr1_3:33379774-33379793 None:intergenic 30.0%
!!! TACTTTGCAGTTTTAAACCA+TGG - chr1_3:33380067-33380086 None:intergenic 30.0%
!! TGCAAAGTATCTATTGATTC+AGG + chr1_3:33380078-33380097 Msa0114950:CDS 30.0%
TGCTGGAAGTTTGTAATTGA+AGG - chr1_3:33377650-33377669 None:intergenic 35.0%
!! TTTTTAGCACAGGATAATGG+CGG + chr1_3:33377719-33377738 Msa0114950:intron 35.0%
!!! GGGGTATTTTGGTATTTTAC+TGG + chr1_3:33377891-33377910 Msa0114950:intron 35.0%
TGCTGTTCACACATGTTAAA+GGG - chr1_3:33377928-33377947 None:intergenic 35.0%
! TTGCTGTTCACACATGTTAA+AGG - chr1_3:33377929-33377948 None:intergenic 35.0%
CAAGTCCAAACCTTGAATTA+TGG + chr1_3:33377984-33378003 Msa0114950:intron 35.0%
TTCTTATAATAAGGACCGGA+GGG - chr1_3:33378027-33378046 None:intergenic 35.0%
TTTCTTATAATAAGGACCGG+AGG - chr1_3:33378028-33378047 None:intergenic 35.0%
GTGGTTTAGATGAGATGATA+TGG - chr1_3:33378174-33378193 None:intergenic 35.0%
AGAGAGAAAAAGAAAGAGAG+AGG + chr1_3:33378349-33378368 Msa0114950:intron 35.0%
GTCCAAAAGTTGTCAAAAAG+TGG + chr1_3:33378406-33378425 Msa0114950:intron 35.0%
ACTAGATGCATATGTTTGTG+CGG - chr1_3:33378540-33378559 None:intergenic 35.0%
! ATTTGTCTAGTTTGGTCGTT+AGG - chr1_3:33378571-33378590 None:intergenic 35.0%
AAAAGTAAAGGCAACCATCA+AGG + chr1_3:33378792-33378811 Msa0114950:intron 35.0%
CTAGTGATAAAGGACATATG+TGG + chr1_3:33379138-33379157 Msa0114950:intron 35.0%
!! CACTGACTTCAAATAGTTTG+AGG + chr1_3:33379320-33379339 Msa0114950:intron 35.0%
! AAAAGAGTTGGCATTGAAGA+TGG + chr1_3:33379514-33379533 Msa0114950:CDS 35.0%
AAATGTCTTTACATCAGGCA+CGG - chr1_3:33379585-33379604 None:intergenic 35.0%
ACATTTGTAGAGCAGTATAC+TGG + chr1_3:33379599-33379618 Msa0114950:CDS 35.0%
ATATGTAGCATGATCTGTAG+TGG - chr1_3:33379744-33379763 None:intergenic 35.0%
!! TATATGATGGCCTTATGTAG+CGG + chr1_3:33379761-33379780 Msa0114950:CDS 35.0%
AGATATTGATCCAAAGCCAA+CGG + chr1_3:33379835-33379854 Msa0114950:CDS 35.0%
AGGAAAGATTCTCTGTATTG+TGG + chr1_3:33379912-33379931 Msa0114950:CDS 35.0%
GGAAAGATTCTCTGTATTGT+GGG + chr1_3:33379913-33379932 Msa0114950:CDS 35.0%
GAAAGATTCTCTGTATTGTG+GGG + chr1_3:33379914-33379933 Msa0114950:CDS 35.0%
GTTTGAACTTCTTATCGTCA+TGG - chr1_3:33380000-33380019 None:intergenic 35.0%
CACAAGATCAGACAAGGTAA+TGG + chr1_3:33377668-33377687 Msa0114950:intron 40.0%
CTAAAAACAACAACGCGAAC+AGG - chr1_3:33377706-33377725 None:intergenic 40.0%
! TAATGGCGGAAATAGATCAG+AGG + chr1_3:33377733-33377752 Msa0114950:intron 40.0%
AGATGATATGGTACTCCCTT+CGG - chr1_3:33378162-33378181 None:intergenic 40.0%
AGTCAAGTCCTTACTTGTCA+CGG + chr1_3:33378491-33378510 Msa0114950:intron 40.0%
! GTGGTCACGATTTGTTTGTT+TGG - chr1_3:33378518-33378537 None:intergenic 40.0%
!!! AACGGTGTCATTCTTTTGGT+AGG - chr1_3:33378821-33378840 None:intergenic 40.0%
!!! GTTCAACGGTGTCATTCTTT+TGG - chr1_3:33378825-33378844 None:intergenic 40.0%
CTAGTAGATTCGACGTTCAA+CGG - chr1_3:33378839-33378858 None:intergenic 40.0%
! TCGAATTGATTCACATGCGA+CGG + chr1_3:33379103-33379122 Msa0114950:intron 40.0%
AAGCAAGAAGAAGTTGTCGT+GGG - chr1_3:33379197-33379216 None:intergenic 40.0%
TAAGCAAGAAGAAGTTGTCG+TGG - chr1_3:33379198-33379217 None:intergenic 40.0%
GTATACTGGTGAAGAAAGTG+TGG + chr1_3:33379613-33379632 Msa0114950:CDS 40.0%
GCGGAAAAAAATTGCAGTTC+TGG + chr1_3:33379780-33379799 Msa0114950:CDS 40.0%
AATCTGTAGAAGAATGCCGT+TGG - chr1_3:33379854-33379873 None:intergenic 40.0%
!! TTTTGGCTGTCAGATCTCAA+AGG + chr1_3:33379892-33379911 Msa0114950:CDS 40.0%
! ATGGATGCTAGTGCAGATTT+TGG + chr1_3:33379941-33379960 Msa0114950:CDS 40.0%
! TGGATGCTAGTGCAGATTTT+GGG + chr1_3:33379942-33379961 Msa0114950:CDS 40.0%
TTGGGATTGGATTGAGAAAG+TGG + chr1_3:33379960-33379979 Msa0114950:CDS 40.0%
AGATTGAACTGCATCAACCA+TGG + chr1_3:33380047-33380066 Msa0114950:CDS 40.0%
TTCCAGCACAAGATCAGACA+AGG + chr1_3:33377662-33377681 Msa0114950:CDS 45.0%
TACCTTGTCTGATCTTGTGC+TGG - chr1_3:33377667-33377686 None:intergenic 45.0%
!!! CGCGTTGTTGTTTTTAGCAC+AGG + chr1_3:33377709-33377728 Msa0114950:intron 45.0%
!! CAGCCGGGTTTATTTTTCCT+CGG + chr1_3:33377853-33377872 Msa0114950:intron 45.0%
CTGCCGAGGAAAAATAAACC+CGG - chr1_3:33377859-33377878 None:intergenic 45.0%
!!! TAACTGCAGAGGGGGTATTT+TGG + chr1_3:33377880-33377899 Msa0114950:intron 45.0%
TGTTTGGTCCGTGACAAGTA+AGG - chr1_3:33378502-33378521 None:intergenic 45.0%
AGATGCATATGTTTGTGCGG+TGG - chr1_3:33378537-33378556 None:intergenic 45.0%
AGTTTGGTCGTTAGGCTTGT+CGG - chr1_3:33378563-33378582 None:intergenic 45.0%
! CTTTTGGTAGGCTTCCTTGA+TGG - chr1_3:33378809-33378828 None:intergenic 45.0%
! CGAATTGATTCACATGCGAC+GGG + chr1_3:33379104-33379123 Msa0114950:intron 45.0%
AAGAAGAAGTTGTCGTGGGT+TGG - chr1_3:33379193-33379212 None:intergenic 45.0%
TTGTCGTCAATGTCAACGTC+AGG - chr1_3:33379361-33379380 None:intergenic 45.0%
GACATTCTTGCTCTCTTTCC+AGG + chr1_3:33379383-33379402 Msa0114950:intron 45.0%
TCTCTTTCCAGGATTCCTCA+AGG + chr1_3:33379394-33379413 Msa0114950:intron 45.0%
!! TAGAAGAATGCCGTTGGCTT+TGG - chr1_3:33379848-33379867 None:intergenic 45.0%
CTCTGTATTGTGGGGAAAGA+TGG + chr1_3:33379922-33379941 Msa0114950:CDS 45.0%
!!! GCTAGTGCAGATTTTGGGAT+TGG + chr1_3:33379947-33379966 Msa0114950:CDS 45.0%
!! ATCAGCATCGACAGACCTTG+AGG - chr1_3:33379412-33379431 None:intergenic 50.0%
CCTCGGTAGTTAACTGCAGC+CGG + chr1_3:33377837-33377856 Msa0114950:intron 55.0%
CTCGGTAGTTAACTGCAGCC+GGG + chr1_3:33377838-33377857 Msa0114950:intron 55.0%
TCCTCGGCAGTTAACTGCAG+AGG + chr1_3:33377869-33377888 Msa0114950:intron 55.0%
CCTCGGCAGTTAACTGCAGA+GGG + chr1_3:33377870-33377889 Msa0114950:intron 55.0%
CTCGGCAGTTAACTGCAGAG+GGG + chr1_3:33377871-33377890 Msa0114950:intron 55.0%
TCGGCAGTTAACTGCAGAGG+GGG + chr1_3:33377872-33377891 Msa0114950:intron 55.0%
CGACAGACCTTGAGGAATCC+TGG - chr1_3:33379404-33379423 None:intergenic 55.0%
CAGGCACGGTGACATGATGA+GGG - chr1_3:33379571-33379590 None:intergenic 55.0%
TCAGGCACGGTGACATGATG+AGG - chr1_3:33379572-33379591 None:intergenic 55.0%
CCGGCTGCAGTTAACTACCG+AGG - chr1_3:33377840-33377859 None:intergenic 60.0%
CCCTCTGCAGTTAACTGCCG+AGG - chr1_3:33377873-33377892 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 33377593 33380129 33377593 ID=Msa0114950;Name=Msa0114950
chr1_3 mRNA 33377593 33380129 33377593 ID=Msa0114950-mRNA-1;Parent=Msa0114950;Name=Msa0114950-mRNA-1;_AED=0.17;_eAED=0.17;_QI=0|0|0|0.5|0|0.5|2|0|237
chr1_3 exon 33377593 33377683 33377593 ID=Msa0114950-mRNA-1:exon:10474;Parent=Msa0114950-mRNA-1
chr1_3 exon 33379507 33380129 33379507 ID=Msa0114950-mRNA-1:exon:10475;Parent=Msa0114950-mRNA-1
chr1_3 CDS 33377593 33377683 33377593 ID=Msa0114950-mRNA-1:cds;Parent=Msa0114950-mRNA-1
chr1_3 CDS 33379507 33380129 33379507 ID=Msa0114950-mRNA-1:cds;Parent=Msa0114950-mRNA-1
Gene Sequence

>Msa0114950

ATGTTCAAACTAAAATTGCGTATGTTTTTGGAATTACAAAATGAAGCTGTGTCACCTTCAATTACAAACTTCCAGCACAAGATCAGACAAGGAAAATCAAAAGAGTTGGCATTGAAGATGGTTAAAAGTAAAACAATTAAGTTGCATGGATTCCCTCATCATGTCACCGTGCCTGATGTAAAGACATTTGTAGAGCAGTATACTGGTGAAGAAAGTGTGGTTGCTATAAAAATAAGGAAGTGTAGTTGCTATAAAAATAAGTGTTGTTGCTATAAAAAGAAGAGATTTGTTCAAATTCGAACGGCATTTGCAATTATTCAATTCACCACTACAGATCATGCTACATATATGATGGCCTTATGTAGCGGAAAAAAATTGCAGTTCTGGAAATCCTATTTAAAAGTTACGAAAATGGAAAGAGATATTGATCCAAAGCCAACGGCATTCTTCTACAGATTAGACGATGTTAAATTGTATTTTGGCTGTCAGATCTCAAAGGAAAGATTCTCTGTATTGTGGGGAAAGATGGATGCTAGTGCAGATTTTGGGATTGGATTGAGAAAGTGGCGATTCTCTATGTGCCATGACGATAAGAAGTTCAAACTTGAGCTTTCATATGAGAATATTTGGAAGATTGAACTGCATCAACCATGGTTTAAAACTGCAAAGTATCTATTGATTCAGGTTGTTAAATTCAACTTTTCATTATTTTAA
Protein sequence

>Msa0114950

MFKLKLRMFLELQNEAVSPSITNFQHKIRQGKSKELALKMVKSKTIKLHGFPHHVTVPDVKTFVEQYTGEESVVAIKIRKCSCYKNKCCCYKKKRFVQIRTAFAIIQFTTTDHATYMMALCSGKKLQFWKSYLKVTKMERDIDPKPTAFFYRLDDVKLYFGCQISKERFSVLWGKMDASADFGIGLRKWRFSMCHDDKKFKLELSYENIWKIELHQPWFKTAKYLLIQVVKFNFSLF*