AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53534

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53534.t1 MTR_1g045040 85.821 134 19 0 1 134 1 134 1.09e-76 223
MS.gene53534.t1 MTR_1g089830 76.336 131 24 2 1 130 1 125 8.44e-68 201
MS.gene53534.t1 MTR_8g089170 38.776 147 64 3 6 127 7 152 2.02e-22 86.7
MS.gene53534.t1 MTR_8g089130 36.424 151 70 3 6 130 7 157 5.61e-22 85.9
MS.gene53534.t1 MTR_8g039350 73.171 41 11 0 4 44 15 55 4.10e-17 70.9
MS.gene53534.t1 MTR_4g028990 40.625 96 47 4 43 130 3 96 2.73e-12 59.3
MS.gene53534.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 2.70e-11 60.1
MS.gene53534.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 4.22e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAAAGCTTCAAAGTCTA+TGG 0.184389 1.2:+27947087 MS.gene53534:CDS
CCACAAGCATTACATAGTAT+TGG 0.433061 1.2:-27946478 None:intergenic
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.2:-27946605 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.2:+27946442 MS.gene53534:CDS
TGCTTGTGGACTACATTTCA+AGG 0.461822 1.2:+27946492 MS.gene53534:CDS
GGACTACATTTCAAGGCTAA+AGG 0.474721 1.2:+27946499 MS.gene53534:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.2:-27946525 None:intergenic
TGTATACCAAGCAATGAGAT+AGG 0.478624 1.2:+27947176 MS.gene53534:CDS
ATCAGACCTTGACATTGAAA+AGG 0.486095 1.2:+27946567 MS.gene53534:CDS
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.2:+27947055 MS.gene53534:CDS
CATAGTATTGGCTTCTCATA+CGG 0.492997 1.2:-27946466 None:intergenic
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.2:-27946604 None:intergenic
CCAAGCAATGAGATAGGCAT+TGG 0.496933 1.2:+27947182 MS.gene53534:CDS
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.2:-27947053 None:intergenic
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.2:+27947088 MS.gene53534:CDS
CCAATGCCTATCTCATTGCT+TGG 0.566560 1.2:-27947182 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.2:+27946607 MS.gene53534:CDS
CCAATACTATGTAATGCTTG+TGG 0.579274 1.2:+27946478 MS.gene53534:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.2:-27946524 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.2:+27947058 MS.gene53534:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.2:27946668-27946687 None:intergenic 15.0%
!!! CTTTTAATTTTTTTGTAGAA+AGG + chr1.2:27947027-27947046 MS.gene53534:intron 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.2:27946667-27946686 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.2:27946773-27946792 MS.gene53534:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.2:27947006-27947025 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.2:27946722-27946741 MS.gene53534:intron 20.0%
!!! GCTTTATATTTGTTGAAAAA+TGG - chr1.2:27946669-27946688 None:intergenic 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.2:27946628-27946647 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.2:27946866-27946885 MS.gene53534:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.2:27946865-27946884 MS.gene53534:intron 20.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.2:27946812-27946831 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.2:27946915-27946934 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.2:27946813-27946832 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.2:27946867-27946886 MS.gene53534:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.2:27946733-27946752 MS.gene53534:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.2:27946434-27946453 MS.gene53534:CDS 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.2:27946621-27946640 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.2:27947087-27947106 MS.gene53534:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.2:27947088-27947107 MS.gene53534:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.2:27946909-27946928 MS.gene53534:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.2:27947055-27947074 MS.gene53534:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.2:27946820-27946839 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.2:27947056-27947075 None:intergenic 30.0%
AGCATTCATTTGAGTAGACA+CGG + chr1.2:27946835-27946854 MS.gene53534:intron 35.0%
ATCAGACCTTGACATTGAAA+AGG + chr1.2:27946567-27946586 MS.gene53534:CDS 35.0%
ATTTGAGTAGACACGGTATT+AGG + chr1.2:27946842-27946861 MS.gene53534:intron 35.0%
CCAATACTATGTAATGCTTG+TGG + chr1.2:27946478-27946497 MS.gene53534:CDS 35.0%
CCACAAGCATTACATAGTAT+TGG - chr1.2:27946481-27946500 None:intergenic 35.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.2:27946527-27946546 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.2:27946442-27946461 MS.gene53534:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.2:27947058-27947077 MS.gene53534:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.2:27946993-27947012 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.2:27946528-27946547 None:intergenic 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.2:27947176-27947195 MS.gene53534:CDS 35.0%
! CAGATTCCTTTTCAATGTCA+AGG - chr1.2:27946576-27946595 None:intergenic 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.2:27946873-27946892 MS.gene53534:intron 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.2:27946469-27946488 None:intergenic 35.0%
!! GTCTGATAACTGATTTTGCT+GGG - chr1.2:27946554-27946573 None:intergenic 35.0%
GGACTACATTTCAAGGCTAA+AGG + chr1.2:27946499-27946518 MS.gene53534:CDS 40.0%
! TGATTTTGCTGGGATGTCTT+CGG - chr1.2:27946544-27946563 None:intergenic 40.0%
! TGCTTGTGGACTACATTTCA+AGG + chr1.2:27946492-27946511 MS.gene53534:CDS 40.0%
!! GGTCTGATAACTGATTTTGC+TGG - chr1.2:27946555-27946574 None:intergenic 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.2:27946608-27946627 None:intergenic 40.0%
CCAAGCAATGAGATAGGCAT+TGG + chr1.2:27947182-27947201 MS.gene53534:CDS 45.0%
CCAATGCCTATCTCATTGCT+TGG - chr1.2:27947185-27947204 None:intergenic 45.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.2:27946607-27946626 MS.gene53534:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.2:27946607-27946626 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27946430 27947250 27946430 ID=MS.gene53534
chr1.2 mRNA 27946430 27947250 27946430 ID=MS.gene53534.t1;Parent=MS.gene53534
chr1.2 exon 27946430 27946628 27946430 ID=MS.gene53534.t1.exon1;Parent=MS.gene53534.t1
chr1.2 CDS 27946430 27946628 27946430 ID=cds.MS.gene53534.t1;Parent=MS.gene53534.t1
chr1.2 exon 27947045 27947250 27947045 ID=MS.gene53534.t1.exon2;Parent=MS.gene53534.t1
chr1.2 CDS 27947045 27947250 27947045 ID=cds.MS.gene53534.t1;Parent=MS.gene53534.t1
Gene Sequence

>MS.gene53534

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAATGCTTGTGGACTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAGCAAAATCAGTTATCAGACCTTGACATTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGCACAATTTATACAAGAAGAGTGATCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACACGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATAAATGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGAAGACAATATTTTGTTGTTTGATAATATCAACAACTGTATACCAAGCAATGAGATAGGCATTGGATGCACTCTACTAAAGACAGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene53534.t1

MVLTETKLWRKGPYEKPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDIEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSLWESEKESNESSEDNILLFDNINNCIPSNEIGIGCTLLKTDVTSKKSA