AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39886

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39886.t1 MTR_1g070335 92.857 70 5 0 1 70 1 70 5.27e-43 133
MS.gene39886.t1 MTR_1g070330 81.481 54 10 0 17 70 1 54 2.99e-26 90.9
MS.gene39886.t1 MTR_1g075410 60.000 70 28 0 1 70 3 72 2.72e-25 89.0
MS.gene39886.t1 MTR_5g090250 60.000 70 28 0 1 70 1 70 1.54e-23 84.3
MS.gene39886.t1 MTR_5g090250 60.000 70 28 0 1 70 1 70 1.54e-23 84.3
MS.gene39886.t1 MTR_1g075340 54.286 70 32 0 1 70 1 70 1.72e-22 82.0
MS.gene39886.t1 MTR_1g075340 54.286 70 32 0 1 70 1 70 1.72e-22 82.0
MS.gene39886.t1 MTR_5g045470 54.412 68 31 0 3 70 2 69 2.52e-20 76.3
MS.gene39886.t1 MTR_1g075380 56.061 66 29 0 5 70 6 71 1.58e-18 72.0
MS.gene39886.t1 MTR_3g020970 46.032 63 34 0 8 70 36 98 3.55e-12 56.6
MS.gene39886.t1 MTR_3g020930 41.270 63 37 0 8 70 32 94 1.60e-11 54.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39886.t1 AT2G38870 51.429 70 34 0 1 70 1 70 1.02e-18 72.4
MS.gene39886.t1 AT2G38900 49.231 65 33 0 6 70 24 88 6.48e-17 68.2
MS.gene39886.t1 AT2G38900 49.231 65 33 0 6 70 9 73 9.01e-17 67.4
MS.gene39886.t1 AT5G43580 46.875 64 34 0 7 70 36 99 1.55e-16 67.8
MS.gene39886.t1 AT3G46860 44.444 63 35 0 8 70 23 85 2.62e-11 53.9

Find 23 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCACTAGGGTTTGGGTTT+GGG 0.263801 1.4:-57576725 MS.gene39886:CDS
AATGCACTAGGGTTTGGGTT+TGG 0.268397 1.4:-57576726 MS.gene39886:CDS
ATTTCAAATGCACTAGGGTT+TGG 0.318537 1.4:-57576732 MS.gene39886:CDS
TTTCAAATGCACTAGGGTTT+GGG 0.339535 1.4:-57576731 MS.gene39886:CDS
AAAATGGAAGGTCGATGTTT+AGG 0.365392 1.4:-57577021 MS.gene39886:intron
GAATAAGTGGCCAGAGGTTG+TGG 0.391845 1.4:-57576848 MS.gene39886:CDS
CCGTCCACTCCCACAACCTC+TGG 0.453884 1.4:+57576838 None:intergenic
CAATGGATTTCAAATGCACT+AGG 0.456321 1.4:-57576738 MS.gene39886:CDS
TTACTTTAGGGAAGAATAAG+TGG 0.467450 1.4:-57576861 MS.gene39886:intron
GTGGCCAGAGGTTGTGGGAG+TGG 0.469941 1.4:-57576842 MS.gene39886:CDS
TGGGTTTGGGTCGACAAACA+TGG 0.500413 1.4:-57576712 MS.gene39886:CDS
ATTGTCACAACATGCCCTTC+CGG 0.508925 1.4:+57576757 None:intergenic
CCAGAGGTTGTGGGAGTGGA+CGG 0.522662 1.4:-57576838 MS.gene39886:CDS
AGTGAATGCAATAGTGGTGC+CGG 0.530167 1.4:-57576776 MS.gene39886:CDS
AATAAGTGGCCAGAGGTTGT+GGG 0.533246 1.4:-57576847 MS.gene39886:CDS
GGGTTTGGGTCGACAAACAT+GGG 0.568932 1.4:-57576711 MS.gene39886:CDS
ATGCAATAGTGGTGCCGGAA+GGG 0.587071 1.4:-57576771 MS.gene39886:CDS
TGAGAGAGTGAATGCAATAG+TGG 0.591365 1.4:-57576782 MS.gene39886:CDS
AATGGATTTCAAATGCACTA+GGG 0.595211 1.4:-57576737 MS.gene39886:CDS
AAGCAGAAAAGCAAAATGGA+AGG 0.626986 1.4:-57577033 None:intergenic
AATGCAATAGTGGTGCCGGA+AGG 0.641397 1.4:-57576772 MS.gene39886:CDS
GGAAGGGCATGTTGTGACAA+TGG 0.645412 1.4:-57576755 MS.gene39886:CDS
AGGGAAGAATAAGTGGCCAG+AGG 0.676552 1.4:-57576854 MS.gene39886:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTAATGATTTACTTTA+GGG - chr1.4:57576826-57576845 MS.gene39886:CDS 10.0%
!!! GAATTTTAATGATTTACTTT+AGG - chr1.4:57576825-57576844 MS.gene39886:CDS 15.0%
! GATTGAATGAAAATACTCTA+GGG - chr1.4:57576741-57576760 MS.gene39886:CDS 25.0%
! TGATTGAATGAAAATACTCT+AGG - chr1.4:57576740-57576759 MS.gene39886:CDS 25.0%
! AATGGATTTCAAATGCACTA+GGG - chr1.4:57576962-57576981 MS.gene39886:intron 30.0%
! TTACTTTAGGGAAGAATAAG+TGG - chr1.4:57576838-57576857 MS.gene39886:CDS 30.0%
ATTTCAAATGCACTAGGGTT+TGG - chr1.4:57576967-57576986 MS.gene39886:intron 35.0%
GTTATTCGTGTGCCAAAAAT+AGG - chr1.4:57577014-57577033 MS.gene39886:intron 35.0%
TTTCAAATGCACTAGGGTTT+GGG - chr1.4:57576968-57576987 MS.gene39886:intron 35.0%
! CAATGGATTTCAAATGCACT+AGG - chr1.4:57576961-57576980 MS.gene39886:intron 35.0%
TGAGAGAGTGAATGCAATAG+TGG - chr1.4:57576917-57576936 MS.gene39886:intron 40.0%
AATAAGTGGCCAGAGGTTGT+GGG - chr1.4:57576852-57576871 MS.gene39886:CDS 45.0%
AGTGAATGCAATAGTGGTGC+CGG - chr1.4:57576923-57576942 MS.gene39886:intron 45.0%
ATTGTCACAACATGCCCTTC+CGG + chr1.4:57576945-57576964 None:intergenic 45.0%
! AATGCACTAGGGTTTGGGTT+TGG - chr1.4:57576973-57576992 MS.gene39886:intron 45.0%
! ATGCACTAGGGTTTGGGTTT+GGG - chr1.4:57576974-57576993 MS.gene39886:intron 45.0%
AGGGAAGAATAAGTGGCCAG+AGG - chr1.4:57576845-57576864 MS.gene39886:CDS 50.0%
GAATAAGTGGCCAGAGGTTG+TGG - chr1.4:57576851-57576870 MS.gene39886:CDS 50.0%
GGGTTTGGGTCGACAAACAT+GGG - chr1.4:57576988-57577007 MS.gene39886:intron 50.0%
TGGGTTTGGGTCGACAAACA+TGG - chr1.4:57576987-57577006 MS.gene39886:intron 50.0%
! AATGCAATAGTGGTGCCGGA+AGG - chr1.4:57576927-57576946 MS.gene39886:intron 50.0%
! ATGCAATAGTGGTGCCGGAA+GGG - chr1.4:57576928-57576947 MS.gene39886:intron 50.0%
! GGAAGGGCATGTTGTGACAA+TGG - chr1.4:57576944-57576963 MS.gene39886:intron 50.0%
CCAGAGGTTGTGGGAGTGGA+CGG - chr1.4:57576861-57576880 MS.gene39886:intron 60.0%
CCGTCCACTCCCACAACCTC+TGG + chr1.4:57576864-57576883 None:intergenic 65.0%
GTGGCCAGAGGTTGTGGGAG+TGG - chr1.4:57576857-57576876 MS.gene39886:intron 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 57576681 57577040 57576681 ID=MS.gene39886
chr1.4 mRNA 57576681 57577040 57576681 ID=MS.gene39886.t1;Parent=MS.gene39886
chr1.4 exon 57577022 57577040 57577022 ID=MS.gene39886.t1.exon1;Parent=MS.gene39886.t1
chr1.4 CDS 57577022 57577040 57577022 ID=cds.MS.gene39886.t1;Parent=MS.gene39886.t1
chr1.4 exon 57576681 57576874 57576681 ID=MS.gene39886.t1.exon2;Parent=MS.gene39886.t1
chr1.4 CDS 57576681 57576874 57576681 ID=cds.MS.gene39886.t1;Parent=MS.gene39886.t1
Gene Sequence

>MS.gene39886

ATGGAAGGTCGATGTTTAGGTGATCATACATATAATATGCTATATTTTTTAATTTAATTTGATTGAATGAAAATACTCTAGGGATCAAGTTCTATAATCTATAGTTATGATTGTATTATTTCTACATGCATGCTTACTAATATTGAATTTTAATGATTTACTTTAGGGAAGAATAAGTGGCCAGAGGTTGTGGGAGTGGACGGTGATGAAGCAGCAGAGAAGATTGAAAGAGAGAATGAGAGAGTGAATGCAATAGTGGTGCCGGAAGGGCATGTTGTGACAATGGATTTCAAATGCACTAGGGTTTGGGTTTGGGTCGACAAACATGGGAGAGTTATTCGTGTGCCAAAAATAGGATAA
Protein sequence

>MS.gene39886.t1

MEGRCLGKNKWPEVVGVDGDEAAEKIERENERVNAIVVPEGHVVTMDFKCTRVWVWVDKHGRVIRVPKIG