AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1440500

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1440500 MtrunA17_Chr2g0292521 82.474 97 17 0 5 101 873 969 7.73e-52 174
Msa1440500 MtrunA17_Chr2g0316131 72.277 101 11 1 1 101 2 85 9.98e-45 141
Msa1440500 MtrunA17_Chr2g0316171 72.277 101 11 1 1 101 2 85 9.98e-45 141
Msa1440500 MtrunA17_Chr5g0440581 53.571 84 39 0 9 92 803 886 2.29e-26 102
Msa1440500 MtrunA17_Chr3g0129081 52.809 89 41 1 13 101 849 936 3.25e-24 95.9
Msa1440500 MtrunA17_Chr5g0437741 47.619 84 42 2 16 99 592 673 4.80e-16 72.4
Msa1440500 MtrunA17_Chr4g0005201 42.857 77 43 1 16 92 600 675 1.05e-13 65.9
Msa1440500 MtrunA17_Chr3g0134221 43.590 78 40 3 13 90 485 558 2.76e-12 61.6
Msa1440500 MtrunA17_Chr4g0053221 39.773 88 48 3 13 100 457 539 1.77e-11 59.3
Msa1440500 MtrunA17_Chr5g0439801 40.244 82 43 4 13 90 352 431 2.17e-11 59.3
Msa1440500 MtrunA17_Chr7g0237801 41.463 82 45 2 12 91 475 555 2.25e-11 59.3
Msa1440500 MtrunA17_Chr4g0061201 39.744 78 44 2 15 90 904 980 3.98e-11 58.5
Msa1440500 MtrunA17_Chr4g0054521 41.860 86 46 3 8 90 778 862 4.12e-11 58.5
Msa1440500 MtrunA17_Chr4g0005411 43.662 71 34 3 8 73 501 570 4.47e-11 58.5
Msa1440500 MtrunA17_Chr2g0315151 42.857 77 41 2 16 90 763 838 9.87e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1440500 AT4G20940.1 74.227 97 25 0 5 101 843 939 1.87e-47 162
Msa1440500 AT5G10020.2 53.086 81 37 1 13 93 817 896 5.87e-24 95.5
Msa1440500 AT5G10020.1 53.086 81 37 1 13 93 865 944 5.88e-24 95.5
Msa1440500 AT2G27060.3 52.000 75 36 0 19 93 741 815 9.82e-20 83.6
Msa1440500 AT2G27060.1 52.000 75 36 0 19 93 834 908 9.88e-20 83.6
Msa1440500 AT3G51740.1 45.238 84 43 2 11 92 627 709 3.09e-15 70.5
Msa1440500 AT2G26730.1 32.710 107 56 3 8 114 440 530 6.37e-13 63.9
Msa1440500 AT3G24660.1 42.683 82 44 2 12 91 467 547 2.26e-12 62.4
Msa1440500 AT1G29720.1 43.529 85 45 2 8 90 760 843 3.21e-11 59.3
Msa1440500 AT1G15530.1 38.554 83 48 2 13 93 453 534 5.71e-11 58.5
Msa1440500 AT3G50230.1 41.772 79 42 3 13 91 480 554 8.68e-11 57.8
Msa1440500 AT3G50230.2 41.772 79 42 3 13 91 492 566 8.70e-11 57.8

Find 28 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAACACATTTGTAGCTTTA+AGG 0.084448 tig0029087:-47620 None:intergenic
ATTCTTGATGCTGGTGTCTT+AGG 0.234146 tig0029087:+47723 Msa1440500:CDS
GAAGGAAGGCATTGGCTTCT+TGG 0.275803 tig0029087:-47776 None:intergenic
AACATAGACATCTGACTTGA+AGG 0.416250 tig0029087:-47794 None:intergenic
GAGGAACAGCTCGGTCGAAA+TGG 0.424838 tig0029087:-47590 None:intergenic
TGTCTTAGGTTATCACGTTC+CGG 0.427126 tig0029087:+47737 Msa1440500:CDS
GGTCGAAATGGAGATAGTTC+AGG 0.434244 tig0029087:-47578 None:intergenic
GGCATTGGCTTCTTGGAAGC+AGG 0.455212 tig0029087:-47769 None:intergenic
ATCCTTTGAGCCCATGTTGA+CGG 0.477954 tig0029087:-47528 None:intergenic
TTCGACCGAGCTGTTCCTCA+TGG 0.501348 tig0029087:+47594 Msa1440500:CDS
TGGAAGCAGGCAGTTAACTC+CGG 0.528125 tig0029087:-47756 None:intergenic
CACCGTCAACATGGGCTCAA+AGG 0.529373 tig0029087:+47526 Msa1440500:CDS
ATTGAAATTCTCAGATCGAC+CGG 0.538455 tig0029087:+47491 None:intergenic
AAAACGGTCCACCGTCAACA+TGG 0.545651 tig0029087:+47517 Msa1440500:CDS
ATTGAACAGATTCTTGATGC+TGG 0.555236 tig0029087:+47714 Msa1440500:CDS
TCTGACTTGAAGGAAGGCAT+TGG 0.560617 tig0029087:-47784 None:intergenic
CTTTGAGCCCATGTTGACGG+TGG 0.591853 tig0029087:-47525 None:intergenic
AAACGGTCCACCGTCAACAT+GGG 0.596418 tig0029087:+47518 Msa1440500:CDS
TTGAAATTCTCAGATCGACC+GGG 0.604402 tig0029087:+47492 Msa1440500:CDS
CATCGACTTATGACTCAGGC+TGG 0.607968 tig0029087:+47687 Msa1440500:CDS
TCTTCATCGACTTATGACTC+AGG 0.614088 tig0029087:+47683 Msa1440500:CDS
TAGACATCTGACTTGAAGGA+AGG 0.620556 tig0029087:-47790 None:intergenic
AACACATGCATTCATACCGA+CGG 0.626540 tig0029087:-47649 None:intergenic
GGTTTCCATGAGGAACAGCT+CGG 0.634183 tig0029087:-47599 None:intergenic
TGAAATTCTCAGATCGACCG+GGG 0.683170 tig0029087:+47493 Msa1440500:CDS
AATGTGTTGTTAGATACCGT+CGG 0.697479 tig0029087:+47633 Msa1440500:CDS
ATAGCAGTCGATGTAGCACG+TGG 0.726604 tig0029087:+47555 Msa1440500:CDS
GTAGCTTTAAGGTTTCCATG+AGG 0.732655 tig0029087:-47609 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACAACACATTTGTAGCTTTA+AGG - tig0029087:47623-47642 None:intergenic 30.0%
! AAGTCAGATGTCTATGTTTT+CGG + tig0029087:47799-47818 Msa1440500:CDS 30.0%
! AATGTGTTGTTAGATACCGT+CGG + tig0029087:47633-47652 Msa1440500:CDS 35.0%
ATTGAACAGATTCTTGATGC+TGG + tig0029087:47714-47733 Msa1440500:CDS 35.0%
! AACATAGACATCTGACTTGA+AGG - tig0029087:47797-47816 None:intergenic 35.0%
TTGAAATTCTCAGATCGACC+GGG + tig0029087:47492-47511 Msa1440500:CDS 40.0%
!! GTAGCTTTAAGGTTTCCATG+AGG - tig0029087:47612-47631 None:intergenic 40.0%
AACACATGCATTCATACCGA+CGG - tig0029087:47652-47671 None:intergenic 40.0%
!! TCTTCATCGACTTATGACTC+AGG + tig0029087:47683-47702 Msa1440500:CDS 40.0%
ATTCTTGATGCTGGTGTCTT+AGG + tig0029087:47723-47742 Msa1440500:CDS 40.0%
TGTCTTAGGTTATCACGTTC+CGG + tig0029087:47737-47756 Msa1440500:CDS 40.0%
! TAGACATCTGACTTGAAGGA+AGG - tig0029087:47793-47812 None:intergenic 40.0%
TGAAATTCTCAGATCGACCG+GGG + tig0029087:47493-47512 Msa1440500:CDS 45.0%
ATCCTTTGAGCCCATGTTGA+CGG - tig0029087:47531-47550 None:intergenic 45.0%
GGTCGAAATGGAGATAGTTC+AGG - tig0029087:47581-47600 None:intergenic 45.0%
! TCTGACTTGAAGGAAGGCAT+TGG - tig0029087:47787-47806 None:intergenic 45.0%
TCAGATCGACCGGGGAAAAA+CGG + tig0029087:47501-47520 Msa1440500:CDS 50.0%
AAAACGGTCCACCGTCAACA+TGG + tig0029087:47517-47536 Msa1440500:CDS 50.0%
AAACGGTCCACCGTCAACAT+GGG + tig0029087:47518-47537 Msa1440500:CDS 50.0%
ATAGCAGTCGATGTAGCACG+TGG + tig0029087:47555-47574 Msa1440500:CDS 50.0%
GGTTTCCATGAGGAACAGCT+CGG - tig0029087:47602-47621 None:intergenic 50.0%
!! CATCGACTTATGACTCAGGC+TGG + tig0029087:47687-47706 Msa1440500:CDS 50.0%
TGGAAGCAGGCAGTTAACTC+CGG - tig0029087:47759-47778 None:intergenic 50.0%
!! GAAGGAAGGCATTGGCTTCT+TGG - tig0029087:47779-47798 None:intergenic 50.0%
CTTTGAGCCCATGTTGACGG+TGG - tig0029087:47528-47547 None:intergenic 55.0%
CACCGTCAACATGGGCTCAA+AGG + tig0029087:47526-47545 Msa1440500:CDS 55.0%
GAGGAACAGCTCGGTCGAAA+TGG - tig0029087:47593-47612 None:intergenic 55.0%
TTCGACCGAGCTGTTCCTCA+TGG + tig0029087:47594-47613 Msa1440500:CDS 55.0%
!! GGCATTGGCTTCTTGGAAGC+AGG - tig0029087:47772-47791 None:intergenic 55.0%
!! GACGGTGGACCGTTTTTCCC+CGG - tig0029087:47513-47532 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0029087 gene 47492 47836 47492 ID=Msa1440500;Name=Msa1440500
tig0029087 mRNA 47492 47836 47492 ID=Msa1440500-mRNA-1;Parent=Msa1440500;Name=Msa1440500-mRNA-1;_AED=0.09;_eAED=0.32;_QI=0|-1|0|1|-1|1|1|0|114
tig0029087 exon 47492 47836 47492 ID=Msa1440500-mRNA-1:exon:12260;Parent=Msa1440500-mRNA-1
tig0029087 CDS 47492 47836 47492 ID=Msa1440500-mRNA-1:cds;Parent=Msa1440500-mRNA-1
Gene Sequence

>Msa1440500

TTGAAATTCTCAGATCGACCGGGGAAAAACGGTCCACCGTCAACATGGGCTCAAAGGATCAAAATAGCAGTCGATGTAGCACGTGGCCTGAACTATCTCCATTTCGACCGAGCTGTTCCTCATGGAAACCTTAAAGCTACAAATGTGTTGTTAGATACCGTCGGTATGAATGCATGTGTTATTGATTATTGTCTTCATCGACTTATGACTCAGGCTGGTACTATTGAACAGATTCTTGATGCTGGTGTCTTAGGTTATCACGTTCCGGAGTTAACTGCCTGCTTCCAAGAAGCCAATGCCTTCCTTCAAGTCAGATGTCTATGTTTTCGGTGTGATGCTTTTTGA
Protein sequence

>Msa1440500

LKFSDRPGKNGPPSTWAQRIKIAVDVARGLNYLHFDRAVPHGNLKATNVLLDTVGMNACVIDYCLHRLMTQAGTIEQILDAGVLGYHVPELTACFQEANAFLQVRCLCFRCDAF*