AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0970250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0970250 MtrunA17_Chr6g0449111 96.154 78 3 0 4 81 2 79 1.49e-52 158
Msa0970250 MtrunA17_Chr7g0255841 75.410 61 15 0 14 74 14 74 2.74e-32 107
Msa0970250 MtrunA17_Chr3g0081631 64.865 74 25 1 4 76 2 75 9.19e-32 106
Msa0970250 MtrunA17_Chr1g0155181 57.143 70 30 0 7 76 2 71 7.62e-28 96.3
Msa0970250 MtrunA17_Chr3g0144631 56.410 78 30 1 1 74 1 78 8.81e-27 93.2
Msa0970250 MtrunA17_Chr5g0404101 56.338 71 31 0 4 74 11 81 1.10e-25 90.9
Msa0970250 MtrunA17_Chr8g0373131 57.576 66 27 1 9 74 2 66 1.92e-25 89.7
Msa0970250 MtrunA17_Chr8g0373111 57.576 66 27 1 9 74 2 66 1.93e-25 89.7
Msa0970250 MtrunA17_Chr8g0373121 57.576 66 27 1 9 74 2 66 1.93e-25 89.7
Msa0970250 MtrunA17_Chr3g0141601 54.286 70 32 0 7 76 2 71 6.61e-25 89.0
Msa0970250 MtrunA17_Chr8g0373101 51.471 68 32 1 9 76 2 68 1.60e-21 79.7
Msa0970250 MtrunA17_Chr5g0404301 53.968 63 28 1 10 72 2 63 2.40e-21 79.0
Msa0970250 MtrunA17_Chr5g0436501 51.471 68 33 0 7 74 22 89 3.92e-19 78.2
Msa0970250 MtrunA17_Chr5g0429521 47.222 72 38 0 9 80 26 97 2.58e-18 76.6
Msa0970250 MtrunA17_Chr3g0141641 47.619 63 33 0 12 74 3 65 3.73e-18 71.6
Msa0970250 MtrunA17_Chr8g0365011 56.061 66 29 0 9 74 5 70 4.18e-18 75.9
Msa0970250 MtrunA17_Chr3g0104071 46.154 78 42 0 3 80 34 111 9.67e-18 75.1
Msa0970250 MtrunA17_Chr1g0162081 48.649 74 38 0 1 74 1 74 1.73e-17 74.3
Msa0970250 MtrunA17_Chr7g0241761 46.377 69 37 0 7 75 30 98 1.92e-17 74.3
Msa0970250 MtrunA17_Chr8g0364741 50.000 68 34 0 7 74 5 72 8.87e-17 69.3
Msa0970250 MtrunA17_Chr7g0270711 49.206 63 31 1 8 69 7 69 1.14e-15 65.5
Msa0970250 MtrunA17_Chr4g0062741 45.946 74 37 1 6 76 2 75 2.32e-15 68.6
Msa0970250 MtrunA17_Chr1g0194071 48.333 60 30 1 10 68 9 68 7.75e-15 63.5
Msa0970250 MtrunA17_Chr1g0210471 43.284 67 38 0 10 76 22 88 1.41e-14 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0970250 AT1G75250.2 60.811 74 29 0 1 74 1 74 2.28e-30 103
Msa0970250 AT1G75250.1 60.811 74 29 0 1 74 1 74 8.06e-30 102
Msa0970250 AT2G21650.1 66.667 63 21 0 12 74 14 76 1.07e-29 101
Msa0970250 AT4G39250.1 68.254 63 20 0 12 74 14 76 1.19e-29 101
Msa0970250 AT1G19510.1 62.069 58 22 0 17 74 17 74 5.99e-23 84.3
Msa0970250 AT2G18328.1 59.016 61 25 0 16 76 15 75 1.08e-22 83.2
Msa0970250 AT5G08520.1 47.436 78 41 0 1 78 1 78 6.54e-19 78.6
Msa0970250 AT5G05790.2 50.000 66 33 0 9 74 28 93 1.80e-17 74.3
Msa0970250 AT5G05790.1 50.000 66 33 0 9 74 28 93 1.80e-17 74.3
Msa0970250 AT5G58900.1 46.479 71 38 0 4 74 26 96 6.59e-17 72.8
Msa0970250 AT5G23650.1 51.471 68 33 0 7 74 8 75 7.10e-17 73.2
Msa0970250 AT4G36570.1 59.091 44 18 0 12 55 12 55 7.68e-17 67.8
Msa0970250 AT3G11280.2 46.250 80 43 0 1 80 22 101 9.34e-17 72.4
Msa0970250 AT3G11280.1 46.250 80 43 0 1 80 22 101 9.34e-17 72.4
Msa0970250 AT2G38090.1 48.485 66 34 0 9 74 26 91 1.57e-16 72.0
Msa0970250 AT1G49010.1 42.667 75 40 1 7 78 3 77 4.01e-14 65.5
Msa0970250 AT5G01200.1 46.154 65 34 1 11 74 29 93 7.66e-12 58.9

Find 25 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAATTAAGTGGGTTGTTT+AGG 0.221417 6_4:-1679689 None:intergenic
TAATGGCTCTTGACTTGTTC+AGG 0.298811 6_4:-1679599 None:intergenic
TGAATTAAGTGGGTTGTTTA+GGG 0.374249 6_4:-1679688 None:intergenic
GCAATATTGTACCAACGTTC+AGG 0.389152 6_4:-1679554 None:intergenic
TACAATATTGCTAAGGTTGT+TGG 0.405177 6_4:+1679566 Msa0970250:CDS
GACATTCACCTCATTGAATC+AGG 0.413822 6_4:+1679638 Msa0970250:CDS
ATTCCATGTAGTACTGGAAC+TGG 0.418503 6_4:-1679477 None:intergenic
CTTGGAGAAGGAGTTGATAA+TGG 0.437914 6_4:-1679616 None:intergenic
TGTTTAGGGTTGGTGTAGGA+AGG 0.444513 6_4:-1679674 None:intergenic
TGTAGGAAGGAAAGGGAACT+TGG 0.465307 6_4:-1679661 None:intergenic
TTCAACATTCCATGTAGTAC+TGG 0.497227 6_4:-1679483 None:intergenic
AGGGTTGGTGTAGGAAGGAA+AGG 0.512474 6_4:-1679669 None:intergenic
TGTAGTACTGGAACTGGATG+AGG 0.512918 6_4:-1679471 None:intergenic
AATATTGCTAAGGTTGTTGG+TGG 0.514753 6_4:+1679569 Msa0970250:CDS
CATCCAGTTCCAGTACTACA+TGG 0.515242 6_4:+1679474 Msa0970250:CDS
TTAAGTGGGTTGTTTAGGGT+TGG 0.518885 6_4:-1679684 None:intergenic
GGGTTGTTTAGGGTTGGTGT+AGG 0.549344 6_4:-1679678 None:intergenic
ATTCAATGAGGTGAATGTCT+TGG 0.553073 6_4:-1679634 None:intergenic
GATATTTGAATGAATTAAGT+GGG 0.559629 6_4:-1679698 None:intergenic
GGATATTTGAATGAATTAAG+TGG 0.567687 6_4:-1679699 None:intergenic
GGGTTGGTGTAGGAAGGAAA+GGG 0.579312 6_4:-1679668 None:intergenic
TGAGGTGAATGTCTTGGAGA+AGG 0.588190 6_4:-1679628 None:intergenic
ACGTTGGTACAATATTGCTA+AGG 0.612999 6_4:+1679559 Msa0970250:CDS
ACAAAGACACACCTGAACGT+TGG 0.679810 6_4:+1679543 Msa0970250:CDS
GAACTTGGCCTGATTCAATG+AGG 0.697485 6_4:-1679646 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TACAATATTGCTAAGGTTGT+TGG + chr6_4:1679566-1679585 Msa0970250:CDS 30.0%
TTCAACATTCCATGTAGTAC+TGG - chr6_4:1679486-1679505 None:intergenic 35.0%
ACGTTGGTACAATATTGCTA+AGG + chr6_4:1679559-1679578 Msa0970250:CDS 35.0%
AATATTGCTAAGGTTGTTGG+TGG + chr6_4:1679569-1679588 Msa0970250:CDS 35.0%
ATTCAATGAGGTGAATGTCT+TGG - chr6_4:1679637-1679656 None:intergenic 35.0%
! ATTCCATGTAGTACTGGAAC+TGG - chr6_4:1679480-1679499 None:intergenic 40.0%
GCAATATTGTACCAACGTTC+AGG - chr6_4:1679557-1679576 None:intergenic 40.0%
!! TAATGGCTCTTGACTTGTTC+AGG - chr6_4:1679602-1679621 None:intergenic 40.0%
!! CTTGGAGAAGGAGTTGATAA+TGG - chr6_4:1679619-1679638 None:intergenic 40.0%
GACATTCACCTCATTGAATC+AGG + chr6_4:1679638-1679657 Msa0970250:CDS 40.0%
!! TTAAGTGGGTTGTTTAGGGT+TGG - chr6_4:1679687-1679706 None:intergenic 40.0%
! TGTAGTACTGGAACTGGATG+AGG - chr6_4:1679474-1679493 None:intergenic 45.0%
CATCCAGTTCCAGTACTACA+TGG + chr6_4:1679474-1679493 Msa0970250:CDS 45.0%
ACAAAGACACACCTGAACGT+TGG + chr6_4:1679543-1679562 Msa0970250:CDS 45.0%
TGAGGTGAATGTCTTGGAGA+AGG - chr6_4:1679631-1679650 None:intergenic 45.0%
GAACTTGGCCTGATTCAATG+AGG - chr6_4:1679649-1679668 None:intergenic 45.0%
TGTAGGAAGGAAAGGGAACT+TGG - chr6_4:1679664-1679683 None:intergenic 45.0%
!! TGTTTAGGGTTGGTGTAGGA+AGG - chr6_4:1679677-1679696 None:intergenic 45.0%
!! GGGTTGGTGTAGGAAGGAAA+GGG - chr6_4:1679671-1679690 None:intergenic 50.0%
!! AGGGTTGGTGTAGGAAGGAA+AGG - chr6_4:1679672-1679691 None:intergenic 50.0%
!! GGGTTGTTTAGGGTTGGTGT+AGG - chr6_4:1679681-1679700 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 1679461 1679706 1679461 ID=Msa0970250;Name=Msa0970250
chr6_4 mRNA 1679461 1679706 1679461 ID=Msa0970250-mRNA-1;Parent=Msa0970250;Name=Msa0970250-mRNA-1;_AED=0.41;_eAED=0.43;_QI=0|-1|0|1|-1|1|1|0|81
chr6_4 exon 1679461 1679706 1679461 ID=Msa0970250-mRNA-1:exon:820;Parent=Msa0970250-mRNA-1
chr6_4 CDS 1679461 1679706 1679461 ID=Msa0970250-mRNA-1:cds;Parent=Msa0970250-mRNA-1
Gene Sequence

>Msa0970250

ATGTCTTCTTCCTCATCCAGTTCCAGTACTACATGGAATGTTGAAGACAATAAAGCTTTTGAAAGAGCTCTAGCAGTTTATGACAAAGACACACCTGAACGTTGGTACAATATTGCTAAGGTTGTTGGTGGAAAAACTCCTGAACAAGTCAAGAGCCATTATCAACTCCTTCTCCAAGACATTCACCTCATTGAATCAGGCCAAGTTCCCTTTCCTTCCTACACCAACCCTAAACAACCCACTTAA
Protein sequence

>Msa0970250

MSSSSSSSSTTWNVEDNKAFERALAVYDKDTPERWYNIAKVVGGKTPEQVKSHYQLLLQDIHLIESGQVPFPSYTNPKQPT*