AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99821


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99821.t1 MTR_2g082990 93.636 220 11 1 1 220 1 217 6.59e-150 415
MS.gene99821.t1 MTR_4g081200 48.276 203 99 4 8 207 11 210 1.44e-58 184
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99821.t1 AT3G20600 42.381 210 113 5 8 213 13 218 1.47e-46 153
MS.gene99821.t1 AT3G20590 41.206 199 102 5 9 202 14 202 3.87e-35 125
MS.gene99821.t1 AT3G20610 34.483 203 119 7 22 217 26 221 1.31e-27 105
MS.gene99821.t1 AT4G05220 22.159 176 122 4 13 180 47 215 9.99e-12 62.8

Find 61 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAATACCTTTATCTTTATT+AGG 0.156001 2.3:-14635440 None:intergenic
TGCGGTTAAGTATAAGATTT+TGG 0.193625 2.3:+14635670 MS.gene99821:CDS
TGGAGATTCTGGGGAGAAAA+TGG 0.196345 2.3:+14635742 MS.gene99821:CDS
CTTGTTAATGCTACTGTAAA+TGG 0.211165 2.3:+14635521 MS.gene99821:CDS
CATCATAACCATAGGCTTAA+TGG 0.228595 2.3:+14635277 MS.gene99821:CDS
TGGGTCTTGTTTATTGGTCT+TGG 0.228865 2.3:+14635860 MS.gene99821:CDS
TGATCTTGCTGTTGTGTTTA+GGG 0.236469 2.3:-14635381 None:intergenic
AATGTGGAAATTGGAGATTC+TGG 0.246829 2.3:+14635731 MS.gene99821:CDS
GAATACCTTTATCTTTATTA+GGG 0.259706 2.3:-14635439 None:intergenic
TTGATCTTGCTGTTGTGTTT+AGG 0.268959 2.3:-14635382 None:intergenic
ATCGTGCGCTTCTTGTGTTT+TGG 0.270001 2.3:+14635840 MS.gene99821:CDS
TTGATGGTAAAGTTTATCTA+AGG 0.284290 2.3:+14635633 MS.gene99821:CDS
GGAGGGGCAAATGTGGAAAT+TGG 0.299189 2.3:+14635722 MS.gene99821:CDS
AAGGTGAAGTTAAGATGAAT+AGG 0.325470 2.3:-14635470 None:intergenic
GGGTCTTGTTTATTGGTCTT+GGG 0.348639 2.3:+14635861 MS.gene99821:CDS
AGCTGTTGTTCATGCTGTTC+AGG 0.351132 2.3:+14635251 MS.gene99821:CDS
AATTTAACTGCGAGTGTTAA+GGG 0.363654 2.3:+14635605 MS.gene99821:CDS
GTATGCTTAGCCATATGAAT+AGG 0.380130 2.3:-14635301 None:intergenic
GTTAACCCTAATAAAGATAA+AGG 0.389560 2.3:+14635434 MS.gene99821:CDS
GAATTTAACTGCGAGTGTTA+AGG 0.395995 2.3:+14635604 MS.gene99821:CDS
AGTGTTGAGAGTATTGTAAA+AGG 0.426836 2.3:-14635489 None:intergenic
ACTGTAAATGGATTCTATCA+AGG 0.430123 2.3:+14635533 MS.gene99821:CDS
GGAGATTCTGGGGAGAAAAT+GGG 0.447531 2.3:+14635743 MS.gene99821:CDS
AAAGAGATCGGGTATGGGGA+GGG 0.451284 2.3:+14635705 MS.gene99821:CDS
AGTGTTAAGGGTGTTGTTGA+TGG 0.454047 2.3:+14635617 MS.gene99821:CDS
GCTTAATGGCCCTATTCATA+TGG 0.461217 2.3:+14635291 MS.gene99821:CDS
ATGTGGAAATTGGAGATTCT+GGG 0.462099 2.3:+14635732 MS.gene99821:CDS
AGGTGAAGTTAAGATGAATA+GGG 0.473108 2.3:-14635469 None:intergenic
GGTATGGGGAGGGGCAAATG+TGG 0.473413 2.3:+14635715 MS.gene99821:CDS
TATGCTTAGCCATATGAATA+GGG 0.474917 2.3:-14635300 None:intergenic
AAGAAAAGTGTGAGGCTTGG+AGG 0.475890 2.3:+14635767 MS.gene99821:CDS
CAGCATGAACAACAGCTGTT+GGG 0.497130 2.3:-14635245 None:intergenic
GAATAGGGCCATTAAGCCTA+TGG 0.501191 2.3:-14635285 None:intergenic
ATACGAAAAGAGATCGGGTA+TGG 0.508627 2.3:+14635699 MS.gene99821:CDS
AAGAATGGAGTGGTGGAAGC+TGG 0.512376 2.3:+14635575 MS.gene99821:CDS
TCCGGCGCATGGAAAGTGTA+TGG 0.512912 2.3:+14635812 MS.gene99821:CDS
GAACCAAGGGTGATAGTGTC+CGG 0.513905 2.3:+14635794 MS.gene99821:CDS
AAGAGATCGGGTATGGGGAG+GGG 0.523912 2.3:+14635706 MS.gene99821:CDS
AGAAAAGTGTGAGGCTTGGA+GGG 0.526565 2.3:+14635768 MS.gene99821:CDS
TCAGGTTTCATCATAACCAT+AGG 0.529456 2.3:+14635269 MS.gene99821:CDS
GGGTGATAGTGTCCGGCGCA+TGG 0.534538 2.3:+14635801 MS.gene99821:CDS
TACGAAAAGAGATCGGGTAT+GGG 0.536489 2.3:+14635700 MS.gene99821:CDS
ACAGCATGAACAACAGCTGT+TGG 0.541536 2.3:-14635246 None:intergenic
TCCATACACTTTCCATGCGC+CGG 0.542433 2.3:-14635813 None:intergenic
GGAAAGAAAAGTGTGAGGCT+TGG 0.543228 2.3:+14635764 MS.gene99821:CDS
TTGGTATACGAAAAGAGATC+GGG 0.544628 2.3:+14635694 MS.gene99821:CDS
AGCTAAGAAGAATGGAGTGG+TGG 0.547361 2.3:+14635568 MS.gene99821:CDS
AAAAGAGATCGGGTATGGGG+AGG 0.556071 2.3:+14635704 MS.gene99821:CDS
GCGCCGGACACTATCACCCT+TGG 0.558967 2.3:-14635797 None:intergenic
CTGTAAATGGATTCTATCAA+GGG 0.559809 2.3:+14635534 MS.gene99821:CDS
TTTGGTATACGAAAAGAGAT+CGG 0.560749 2.3:+14635693 MS.gene99821:CDS
TGGTAAAGTTTATCTAAGGG+TGG 0.560905 2.3:+14635637 MS.gene99821:CDS
TGATGGTAAAGTTTATCTAA+GGG 0.567329 2.3:+14635634 MS.gene99821:CDS
TTTACAGTAGCATTAACAAG+TGG 0.593952 2.3:-14635518 None:intergenic
ACGAAAAGAGATCGGGTATG+GGG 0.597221 2.3:+14635701 MS.gene99821:CDS
GGCTTGGAGGGAATGAACCA+AGG 0.634018 2.3:+14635780 MS.gene99821:CDS
GCTTGGAGGGAATGAACCAA+GGG 0.643282 2.3:+14635781 MS.gene99821:CDS
TGTGGAAATTGGAGATTCTG+GGG 0.648415 2.3:+14635733 MS.gene99821:CDS
AAAAGCTAAGAAGAATGGAG+TGG 0.661701 2.3:+14635565 MS.gene99821:CDS
AAATGGGAAAGAAAAGTGTG+AGG 0.693699 2.3:+14635759 MS.gene99821:CDS
GGCGCATGGAAAGTGTATGG+AGG 0.700562 2.3:+14635815 MS.gene99821:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAATACCTTTATCTTTATTA+GGG - chr2.3:14635442-14635461 None:intergenic 20.0%
!! TGAATACCTTTATCTTTATT+AGG - chr2.3:14635443-14635462 None:intergenic 20.0%
!!! TTAAGTATAAGATTTTGGTT+TGG + chr2.3:14635675-14635694 MS.gene99821:CDS 20.0%
! GTTAACCCTAATAAAGATAA+AGG + chr2.3:14635434-14635453 MS.gene99821:CDS 25.0%
! TGATGGTAAAGTTTATCTAA+GGG + chr2.3:14635634-14635653 MS.gene99821:CDS 25.0%
!! ATTTTGTCTATGTAAAGCTT+TGG - chr2.3:14635338-14635357 None:intergenic 25.0%
!! TTGATGGTAAAGTTTATCTA+AGG + chr2.3:14635633-14635652 MS.gene99821:CDS 25.0%
AAGGTGAAGTTAAGATGAAT+AGG - chr2.3:14635473-14635492 None:intergenic 30.0%
AATTTAACTGCGAGTGTTAA+GGG + chr2.3:14635605-14635624 MS.gene99821:CDS 30.0%
AGGTGAAGTTAAGATGAATA+GGG - chr2.3:14635472-14635491 None:intergenic 30.0%
CTTGTTAATGCTACTGTAAA+TGG + chr2.3:14635521-14635540 MS.gene99821:CDS 30.0%
GAGAAAAAAGCTAAGAAGAA+TGG + chr2.3:14635560-14635579 MS.gene99821:CDS 30.0%
TATGCTTAGCCATATGAATA+GGG - chr2.3:14635303-14635322 None:intergenic 30.0%
TTTACAGTAGCATTAACAAG+TGG - chr2.3:14635521-14635540 None:intergenic 30.0%
TTTGGTATACGAAAAGAGAT+CGG + chr2.3:14635693-14635712 MS.gene99821:CDS 30.0%
! ACTGTAAATGGATTCTATCA+AGG + chr2.3:14635533-14635552 MS.gene99821:CDS 30.0%
! CTGTAAATGGATTCTATCAA+GGG + chr2.3:14635534-14635553 MS.gene99821:CDS 30.0%
! TGCGGTTAAGTATAAGATTT+TGG + chr2.3:14635670-14635689 MS.gene99821:CDS 30.0%
!! AGTGTTGAGAGTATTGTAAA+AGG - chr2.3:14635492-14635511 None:intergenic 30.0%
!! GTTAACAAGTTTTAACGTGA+AGG - chr2.3:14635420-14635439 None:intergenic 30.0%
AAAAGCTAAGAAGAATGGAG+TGG + chr2.3:14635565-14635584 MS.gene99821:CDS 35.0%
AATGTGGAAATTGGAGATTC+TGG + chr2.3:14635731-14635750 MS.gene99821:CDS 35.0%
ATGTGGAAATTGGAGATTCT+GGG + chr2.3:14635732-14635751 MS.gene99821:CDS 35.0%
CATCATAACCATAGGCTTAA+TGG + chr2.3:14635277-14635296 MS.gene99821:CDS 35.0%
GAATTTAACTGCGAGTGTTA+AGG + chr2.3:14635604-14635623 MS.gene99821:CDS 35.0%
GTATGCTTAGCCATATGAAT+AGG - chr2.3:14635304-14635323 None:intergenic 35.0%
TCAGGTTTCATCATAACCAT+AGG + chr2.3:14635269-14635288 MS.gene99821:CDS 35.0%
TGGTAAAGTTTATCTAAGGG+TGG + chr2.3:14635637-14635656 MS.gene99821:CDS 35.0%
TTGGTATACGAAAAGAGATC+GGG + chr2.3:14635694-14635713 MS.gene99821:CDS 35.0%
! AAATGGGAAAGAAAAGTGTG+AGG + chr2.3:14635759-14635778 MS.gene99821:CDS 35.0%
! TTTTAACGTGAAGGTGATAG+TGG - chr2.3:14635411-14635430 None:intergenic 35.0%
!! TGATCTTGCTGTTGTGTTTA+GGG - chr2.3:14635384-14635403 None:intergenic 35.0%
!! TTGATCTTGCTGTTGTGTTT+AGG - chr2.3:14635385-14635404 None:intergenic 35.0%
!!! AAGGGTGGATTATTTTACTG+CGG + chr2.3:14635652-14635671 MS.gene99821:CDS 35.0%
!!! GTGTTTTGGGTCTTGTTTAT+TGG + chr2.3:14635854-14635873 MS.gene99821:CDS 35.0%
!!! TGTGTTTAGGGTTTTGTTGA+GGG - chr2.3:14635372-14635391 None:intergenic 35.0%
!!! TTGTGTTTAGGGTTTTGTTG+AGG - chr2.3:14635373-14635392 None:intergenic 35.0%
ATACGAAAAGAGATCGGGTA+TGG + chr2.3:14635699-14635718 MS.gene99821:CDS 40.0%
GCTTAATGGCCCTATTCATA+TGG + chr2.3:14635291-14635310 MS.gene99821:CDS 40.0%
TACGAAAAGAGATCGGGTAT+GGG + chr2.3:14635700-14635719 MS.gene99821:CDS 40.0%
TGTGGAAATTGGAGATTCTG+GGG + chr2.3:14635733-14635752 MS.gene99821:CDS 40.0%
!! AGTGTTAAGGGTGTTGTTGA+TGG + chr2.3:14635617-14635636 MS.gene99821:CDS 40.0%
!! GGGTCTTGTTTATTGGTCTT+GGG + chr2.3:14635861-14635880 MS.gene99821:CDS 40.0%
!! TGGGTCTTGTTTATTGGTCT+TGG + chr2.3:14635860-14635879 MS.gene99821:CDS 40.0%
ACAGCATGAACAACAGCTGT+TGG - chr2.3:14635249-14635268 None:intergenic 45.0%
ACGAAAAGAGATCGGGTATG+GGG + chr2.3:14635701-14635720 MS.gene99821:CDS 45.0%
AGCTAAGAAGAATGGAGTGG+TGG + chr2.3:14635568-14635587 MS.gene99821:CDS 45.0%
AGCTGTTGTTCATGCTGTTC+AGG + chr2.3:14635251-14635270 MS.gene99821:CDS 45.0%
CAGCATGAACAACAGCTGTT+GGG - chr2.3:14635248-14635267 None:intergenic 45.0%
GAATAGGGCCATTAAGCCTA+TGG - chr2.3:14635288-14635307 None:intergenic 45.0%
! AAGAAAAGTGTGAGGCTTGG+AGG + chr2.3:14635767-14635786 MS.gene99821:CDS 45.0%
! AGAAAAGTGTGAGGCTTGGA+GGG + chr2.3:14635768-14635787 MS.gene99821:CDS 45.0%
! ATCGTGCGCTTCTTGTGTTT+TGG + chr2.3:14635840-14635859 MS.gene99821:CDS 45.0%
! GGAAAGAAAAGTGTGAGGCT+TGG + chr2.3:14635764-14635783 MS.gene99821:CDS 45.0%
! GGAGATTCTGGGGAGAAAAT+GGG + chr2.3:14635743-14635762 MS.gene99821:CDS 45.0%
! TCGTGCGCTTCTTGTGTTTT+GGG + chr2.3:14635841-14635860 MS.gene99821:CDS 45.0%
! TGGAGATTCTGGGGAGAAAA+TGG + chr2.3:14635742-14635761 MS.gene99821:CDS 45.0%
!!! TTTAGGGTTTTGTTGAGGGC+AGG - chr2.3:14635368-14635387 None:intergenic 45.0%
AAAAGAGATCGGGTATGGGG+AGG + chr2.3:14635704-14635723 MS.gene99821:CDS 50.0%
AAAGAGATCGGGTATGGGGA+GGG + chr2.3:14635705-14635724 MS.gene99821:CDS 50.0%
GCTTGGAGGGAATGAACCAA+GGG + chr2.3:14635781-14635800 MS.gene99821:CDS 50.0%
GGAGGGGCAAATGTGGAAAT+TGG + chr2.3:14635722-14635741 MS.gene99821:CDS 50.0%
TCCATACACTTTCCATGCGC+CGG - chr2.3:14635816-14635835 None:intergenic 50.0%
! AAGAATGGAGTGGTGGAAGC+TGG + chr2.3:14635575-14635594 MS.gene99821:CDS 50.0%
! GAACCAAGGGTGATAGTGTC+CGG + chr2.3:14635794-14635813 MS.gene99821:CDS 50.0%
AAGAGATCGGGTATGGGGAG+GGG + chr2.3:14635706-14635725 MS.gene99821:CDS 55.0%
GGCTTGGAGGGAATGAACCA+AGG + chr2.3:14635780-14635799 MS.gene99821:CDS 55.0%
! GGCGCATGGAAAGTGTATGG+AGG + chr2.3:14635815-14635834 MS.gene99821:CDS 55.0%
! TCCGGCGCATGGAAAGTGTA+TGG + chr2.3:14635812-14635831 MS.gene99821:CDS 55.0%
!!! GGGTTTTGTTGAGGGCAGGA+AGG - chr2.3:14635364-14635383 None:intergenic 55.0%
GGTATGGGGAGGGGCAAATG+TGG + chr2.3:14635715-14635734 MS.gene99821:CDS 60.0%
GCGCCGGACACTATCACCCT+TGG - chr2.3:14635800-14635819 None:intergenic 65.0%
! GGGTGATAGTGTCCGGCGCA+TGG + chr2.3:14635801-14635820 MS.gene99821:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 14635230 14635892 14635230 ID=MS.gene99821
chr2.3 mRNA 14635230 14635892 14635230 ID=MS.gene99821.t1;Parent=MS.gene99821
chr2.3 exon 14635230 14635892 14635230 ID=MS.gene99821.t1.exon1;Parent=MS.gene99821.t1
chr2.3 CDS 14635230 14635892 14635230 ID=cds.MS.gene99821.t1;Parent=MS.gene99821.t1
Gene Sequence

>MS.gene99821

ATGGCATCATCAAAACCCAACAGCTGTTGTTCATGCTGTTCAGGTTTCATCATAACCATAGGCTTAATGGCCCTATTCATATGGCTAAGCATACGTGTCGATGAACCAAAGCTTTACATAGACAAAATTTACCTTCCTGCCCTCAACAAAACCCTAAACACAACAGCAAGATCAAACACCACTATCACCTTCACGTTAAAACTTGTTAACCCTAATAAAGATAAAGGTATTCAATATGACCCTATTCATCTTAACTTCACCTTTTACAATACTCTCAACACTACTCTTCCACTTGTTAATGCTACTGTAAATGGATTCTATCAAGGGCATGAGAAAAAAGCTAAGAAGAATGGAGTGGTGGAAGCTGGTGTTAAGAATTTAACTGCGAGTGTTAAGGGTGTTGTTGATGGTAAAGTTTATCTAAGGGTGGATTATTTTACTGCGGTTAAGTATAAGATTTTGGTTTGGTATACGAAAAGAGATCGGGTATGGGGAGGGGCAAATGTGGAAATTGGAGATTCTGGGGAGAAAATGGGAAAGAAAAGTGTGAGGCTTGGAGGGAATGAACCAAGGGTGATAGTGTCCGGCGCATGGAAAGTGTATGGAGGCTATCGTGCGCTTCTTGTGTTTTGGGTCTTGTTTATTGGTCTTGGGTTTACTTGA

Protein sequence

>MS.gene99821.t1

MASSKPNSCCSCCSGFIITIGLMALFIWLSIRVDEPKLYIDKIYLPALNKTLNTTARSNTTITFTLKLVNPNKDKGIQYDPIHLNFTFYNTLNTTLPLVNATVNGFYQGHEKKAKKNGVVEAGVKNLTASVKGVVDGKVYLRVDYFTAVKYKILVWYTKRDRVWGGANVEIGDSGEKMGKKSVRLGGNEPRVIVSGAWKVYGGYRALLVFWVLFIGLGFT