AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene015645

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015645.t1 MTR_6g016850 88.636 88 10 0 1 88 1 88 9.54e-53 162
MS.gene015645.t1 MTR_8g105600 87.500 88 11 0 1 88 1 88 1.14e-47 159
MS.gene015645.t1 MTR_4g021790 53.750 80 37 0 9 88 10 89 7.29e-26 96.7
MS.gene015645.t1 MTR_4g021845 48.837 86 44 0 3 88 4 89 2.30e-24 91.7
MS.gene015645.t1 MTR_5g055260 50.617 81 40 0 9 89 10 90 5.98e-24 91.3
MS.gene015645.t1 MTR_4g021760 50.000 80 40 0 9 88 11 90 2.40e-23 90.9
MS.gene015645.t1 MTR_8g093040 52.326 86 40 1 4 88 9 94 1.73e-22 87.8
MS.gene015645.t1 MTR_4g021855 48.750 80 41 0 9 88 10 89 1.76e-22 88.2
MS.gene015645.t1 MTR_6g045327 48.780 82 41 1 8 88 13 94 1.41e-17 75.9
MS.gene015645.t1 MTR_1g032570 43.373 83 46 1 7 88 9 91 3.27e-17 75.1
MS.gene015645.t1 MTR_3g086100 41.463 82 47 1 8 88 12 93 4.92e-16 71.6
MS.gene015645.t1 MTR_4g121020 40.964 83 48 1 7 88 29 111 5.79e-15 68.6
MS.gene015645.t1 MTR_4g121020 40.964 83 48 1 7 88 29 111 5.79e-15 68.6
MS.gene015645.t1 MTR_1g013170 39.759 83 49 1 7 88 3 85 2.80e-14 66.6
MS.gene015645.t1 MTR_8g079940 40.741 81 47 1 9 88 25 105 3.89e-14 66.2
MS.gene015645.t1 MTR_4g131600 40.000 85 50 1 5 88 16 100 5.40e-14 65.9
MS.gene015645.t1 MTR_7g117705 38.095 84 50 1 7 88 3 86 6.11e-14 65.9
MS.gene015645.t1 MTR_1g013180 38.554 83 50 1 7 88 154 236 6.31e-14 65.9
MS.gene015645.t1 MTR_2g034960 40.964 83 48 1 7 88 27 109 7.25e-14 65.5
MS.gene015645.t1 MTR_3g106220 38.095 84 51 1 6 88 5 88 1.58e-12 61.6
MS.gene015645.t1 MTR_4g131570 37.647 85 52 1 5 88 13 97 8.68e-12 59.7
MS.gene015645.t1 MTR_2g450070 33.735 83 54 1 7 88 16 98 1.97e-11 58.5
MS.gene015645.t1 MTR_2g450070 33.735 83 54 1 7 88 16 98 2.06e-11 58.5
MS.gene015645.t1 MTR_4g131580 35.802 81 51 1 9 88 17 97 6.11e-11 57.4
MS.gene015645.t1 MTR_3g102600 36.471 85 53 1 5 88 4 88 6.67e-11 55.8
MS.gene015645.t1 MTR_3g102600 36.471 85 53 1 5 88 4 88 8.56e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015645.t1 AT3G16857 38.272 81 49 1 9 88 33 113 5.70e-14 65.9
MS.gene015645.t1 AT3G16857 38.272 81 49 1 9 88 33 113 7.58e-14 65.5
MS.gene015645.t1 AT1G67710 38.750 80 48 1 10 88 8 87 1.82e-13 64.3
MS.gene015645.t1 AT2G01760 38.095 84 50 2 7 88 5 88 3.42e-13 63.5
MS.gene015645.t1 AT2G25180 37.349 83 51 1 7 88 11 93 3.90e-13 63.5
MS.gene015645.t1 AT4G31920 36.585 82 51 1 8 88 12 93 4.52e-12 60.5
MS.gene015645.t1 AT5G49240 35.294 85 54 1 5 88 34 118 7.27e-12 59.7

Find 10 sgRNAs with CRISPR-Local

Find 15 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGAATTTGATAGCACAAA+AGG 0.421977 4.2:-1311707 MS.gene015645:CDS
ACAAGAACTTTAACATTGGC+TGG 0.429953 4.2:+1311926 None:intergenic
TATATTTACTTACTAATGAC+AGG 0.483959 4.2:+1311595 None:intergenic
TGAAGCTGAAATGCCGGACA+TGG 0.511513 4.2:-1311662 MS.gene015645:CDS
AATCACAAGAACTTTAACAT+TGG 0.529369 4.2:+1311922 None:intergenic
AAATCAAATGAATCCATGTC+CGG 0.545425 4.2:+1311649 None:intergenic
ACTACTTGAAGCTGAAATGC+CGG 0.587583 4.2:-1311668 MS.gene015645:CDS
TGGTCTCAATTCAATTACCA+AGG 0.596923 4.2:-1311860 MS.gene015645:intron
GGCTGGAAACTCATTCCCAA+AGG 0.633277 4.2:+1311943 None:intergenic
TCAATGCTATTGAGAAAACA+TGG 0.646799 4.2:-1311880 MS.gene015645:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGGTTTGTAAATTAATATA+TGG - chr4.2:1311712-1311731 MS.gene015645:CDS 15.0%
!! ATATATTAATTTACAAACCT+TGG + chr4.2:1311713-1311732 None:intergenic 15.0%
!! ATTCAATAAACAATCAAAGA+AGG + chr4.2:1311740-1311759 None:intergenic 20.0%
! AAAAAGATTGAGACTTTCAT+AGG + chr4.2:1311771-1311790 None:intergenic 25.0%
! AATCACAAGAACTTTAACAT+TGG + chr4.2:1311634-1311653 None:intergenic 25.0%
AAATCAAATGAATCCATGTC+CGG + chr4.2:1311907-1311926 None:intergenic 30.0%
TCAATGCTATTGAGAAAACA+TGG - chr4.2:1311673-1311692 MS.gene015645:CDS 30.0%
! CTTGAATTTGATAGCACAAA+AGG - chr4.2:1311846-1311865 MS.gene015645:intron 30.0%
! CTTTTGTGCTATCAAATTCA+AGG + chr4.2:1311848-1311867 None:intergenic 30.0%
!!! ACAAAAGGTGCATTTTGATT+TGG - chr4.2:1311861-1311880 MS.gene015645:CDS 30.0%
ACAAGAACTTTAACATTGGC+TGG + chr4.2:1311630-1311649 None:intergenic 35.0%
TGGTCTCAATTCAATTACCA+AGG - chr4.2:1311693-1311712 MS.gene015645:CDS 35.0%
ACTACTTGAAGCTGAAATGC+CGG - chr4.2:1311885-1311904 MS.gene015645:CDS 40.0%
GGCTGGAAACTCATTCCCAA+AGG + chr4.2:1311613-1311632 None:intergenic 50.0%
TGAAGCTGAAATGCCGGACA+TGG - chr4.2:1311891-1311910 MS.gene015645:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 1311600 1311975 1311600 ID=MS.gene015645
chr4.2 mRNA 1311600 1311975 1311600 ID=MS.gene015645.t1;Parent=MS.gene015645
chr4.2 exon 1311861 1311975 1311861 ID=MS.gene015645.t1.exon1;Parent=MS.gene015645.t1
chr4.2 CDS 1311861 1311975 1311861 ID=cds.MS.gene015645.t1;Parent=MS.gene015645.t1
chr4.2 exon 1311600 1311757 1311600 ID=MS.gene015645.t1.exon2;Parent=MS.gene015645.t1
chr4.2 CDS 1311600 1311757 1311600 ID=cds.MS.gene015645.t1;Parent=MS.gene015645.t1
Gene Sequence

>MS.gene015645

ATGGATTTTTCCTTTGGGAATGAGTTTCCAGCCAATGTTAAAGTTCTTGTGATTGATCATGATATCGATCTTCTCAATGCTATTGAGAAAACATGGTCTCAATTCAATTACCAAGGTTTGTAAATTAATATATGGTACCTTCTTTGATTGTTTATTGAATTATGTTAACCTATGAAAGTCTCAATCTTTTTGTTACAATTCTTGTTTCATTGTTTCAGTTACTACATGTTCGACAGTTTCTTCAGCCTTGAATTTGATAGCACAAAAGGTGCATTTTGATTTGGTACTACTTGAAGCTGAAATGCCGGACATGGATTCATTTGATTTCTTGCAAAAAATTACACAACAAATCGATATTCCTGTCATTAGTAAGTAA
Protein sequence

>MS.gene015645.t1

MDFSFGNEFPANVKVLVIDHDIDLLNAIEKTWSQFNYQVTTCSTVSSALNLIAQKVHFDLVLLEAEMPDMDSFDFLQKITQQIDIPVISK