AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene030918

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030918.t1 MTR_8g089170 92.308 156 12 0 1 156 1 156 2.25e-99 283
MS.gene030918.t1 MTR_8g089130 84.177 158 23 2 1 156 1 158 1.08e-90 261
MS.gene030918.t1 MTR_8g089145 87.671 73 9 0 1 73 1 73 1.81e-42 136
MS.gene030918.t1 MTR_1g089830 36.842 152 67 4 4 155 3 125 4.61e-22 86.3
MS.gene030918.t1 MTR_4g028990 54.545 77 33 1 81 155 20 96 2.62e-20 80.5
MS.gene030918.t1 MTR_1g045040 39.333 150 65 4 7 155 6 130 1.97e-19 79.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATACCTTCAAATGAAAT+TGG 0.214941 4.3:-11228090 MS.gene030918:CDS
CATAAAACTGGCTTGTCTTT+TGG 0.254968 4.3:+11228584 None:intergenic
CTTTGAGGTTTCCCCAGTTT+TGG 0.256311 4.3:+11228540 None:intergenic
ATTCTCAAACTACGTCTCTT+TGG 0.299791 4.3:+11228237 None:intergenic
TCAAACAATAAGGCCTCTTC+TGG 0.301830 4.3:+11228126 None:intergenic
TGGCGCCATGCTGGAGTTGC+TGG 0.314815 4.3:+11228611 None:intergenic
GATGTTTCTGATTCAGATAA+TGG 0.318368 4.3:-11228425 MS.gene030918:intron
CTGTTCGTAACAAGTTCTTT+TGG 0.340372 4.3:+11228494 None:intergenic
TTTGGTCCCTGGCGCCATGC+TGG 0.374123 4.3:+11228602 None:intergenic
GAAAACAACGTTTGAGAGAA+TGG 0.387976 4.3:+11228516 None:intergenic
GTGGACTAAGATACCAAAAC+TGG 0.405891 4.3:-11228553 MS.gene030918:CDS
CCACATGCATTGCATAAAAC+TGG 0.410323 4.3:+11228572 None:intergenic
CCTTCAAATGAAATTGGCCT+TGG 0.419265 4.3:-11228084 MS.gene030918:CDS
CCAAGGCCAATTTCATTTGA+AGG 0.421742 4.3:+11228084 None:intergenic
AGCAACTCCAGCATGGCGCC+AGG 0.436034 4.3:-11228609 MS.gene030918:CDS
GTTTGAGAGAATGGTCTTTG+AGG 0.475222 4.3:+11228525 None:intergenic
TCTTCTGGAGATGACTCATC+TGG 0.489997 4.3:+11228141 None:intergenic
TCTTGTTGAAACTTCTCCAT+CGG 0.530728 4.3:+11228195 None:intergenic
ATCTGAATCAGAAACATCAA+TGG 0.539843 4.3:+11228430 None:intergenic
TTCTACATAGAAGAACCGTC+TGG 0.563851 4.3:+11228045 None:intergenic
GCAACTCCAGCATGGCGCCA+GGG 0.585142 4.3:-11228608 MS.gene030918:CDS
AGATGAGTCATCTCCAGAAG+AGG 0.604525 4.3:-11228139 MS.gene030918:CDS
GCGGTTCTTCTTAAACCAGA+CGG 0.605404 4.3:-11228060 MS.gene030918:CDS
AAATGAAATTGGCCTTGGAG+CGG 0.608265 4.3:-11228079 MS.gene030918:CDS
CAATCAGAAGATGACACCGA+TGG 0.614119 4.3:-11228211 MS.gene030918:CDS
TGGACTAAGATACCAAAACT+GGG 0.618651 4.3:-11228552 MS.gene030918:CDS
GTTTAAGAAGAACCGCTCCA+AGG 0.637380 4.3:+11228067 None:intergenic
AAAGAACTTGTTACGAACAG+TGG 0.644687 4.3:-11228491 MS.gene030918:CDS
CATCACCAGCAACTCCAGCA+TGG 0.651498 4.3:-11228616 MS.gene030918:CDS
GGACTAAGATACCAAAACTG+GGG 0.731002 4.3:-11228551 MS.gene030918:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGTAAAGAAAAGAGTGAAAA+TGG + chr4.3:11228293-11228312 None:intergenic 25.0%
! TTCATACCTTCAAATGAAAT+TGG - chr4.3:11228580-11228599 MS.gene030918:CDS 25.0%
!! GTTCACATTTTCAAACAATA+AGG + chr4.3:11228557-11228576 None:intergenic 25.0%
!!! GATATATACTACTTTTGTGA+GGG - chr4.3:11228315-11228334 MS.gene030918:intron 25.0%
!!! TGATATATACTACTTTTGTG+AGG - chr4.3:11228314-11228333 MS.gene030918:intron 25.0%
ATCTGAATCAGAAACATCAA+TGG + chr4.3:11228243-11228262 None:intergenic 30.0%
! GATGTTTCTGATTCAGATAA+TGG - chr4.3:11228245-11228264 MS.gene030918:CDS 30.0%
ATTCTCAAACTACGTCTCTT+TGG + chr4.3:11228436-11228455 None:intergenic 35.0%
GAAAACAACGTTTGAGAGAA+TGG + chr4.3:11228157-11228176 None:intergenic 35.0%
TCTTGTTGAAACTTCTCCAT+CGG + chr4.3:11228478-11228497 None:intergenic 35.0%
TGGACTAAGATACCAAAACT+GGG - chr4.3:11228118-11228137 MS.gene030918:CDS 35.0%
! CTGTTCGTAACAAGTTCTTT+TGG + chr4.3:11228179-11228198 None:intergenic 35.0%
!! AAAGAACTTGTTACGAACAG+TGG - chr4.3:11228179-11228198 MS.gene030918:CDS 35.0%
!! ATATACTACTTTTGTGAGGG+TGG - chr4.3:11228318-11228337 MS.gene030918:intron 35.0%
!! TATACTACTTTTGTGAGGGT+GGG - chr4.3:11228319-11228338 MS.gene030918:intron 35.0%
!!! CATAAAACTGGCTTGTCTTT+TGG + chr4.3:11228089-11228108 None:intergenic 35.0%
CCAAGGCCAATTTCATTTGA+AGG + chr4.3:11228589-11228608 None:intergenic 40.0%
CCACATGCATTGCATAAAAC+TGG + chr4.3:11228101-11228120 None:intergenic 40.0%
GGACTAAGATACCAAAACTG+GGG - chr4.3:11228119-11228138 MS.gene030918:CDS 40.0%
GTTTGAGAGAATGGTCTTTG+AGG + chr4.3:11228148-11228167 None:intergenic 40.0%
TCAAACAATAAGGCCTCTTC+TGG + chr4.3:11228547-11228566 None:intergenic 40.0%
! CCTTCAAATGAAATTGGCCT+TGG - chr4.3:11228586-11228605 MS.gene030918:CDS 40.0%
! GTGGACTAAGATACCAAAAC+TGG - chr4.3:11228117-11228136 MS.gene030918:CDS 40.0%
!! AAATGAAATTGGCCTTGGAG+CGG - chr4.3:11228591-11228610 MS.gene030918:CDS 40.0%
!! CCAGTTTTATGCAATGCATG+TGG - chr4.3:11228098-11228117 MS.gene030918:CDS 40.0%
AGATGAGTCATCTCCAGAAG+AGG - chr4.3:11228531-11228550 MS.gene030918:CDS 45.0%
CAATCAGAAGATGACACCGA+TGG - chr4.3:11228459-11228478 MS.gene030918:CDS 45.0%
GCGGTTCTTCTTAAACCAGA+CGG - chr4.3:11228610-11228629 MS.gene030918:CDS 45.0%
GTTTAAGAAGAACCGCTCCA+AGG + chr4.3:11228606-11228625 None:intergenic 45.0%
! TCTTCTGGAGATGACTCATC+TGG + chr4.3:11228532-11228551 None:intergenic 45.0%
!!! CTTTGAGGTTTCCCCAGTTT+TGG + chr4.3:11228133-11228152 None:intergenic 45.0%
CATCACCAGCAACTCCAGCA+TGG - chr4.3:11228054-11228073 MS.gene030918:CDS 55.0%
!! CTGGCTTGTCTTTTGGTCCC+TGG + chr4.3:11228082-11228101 None:intergenic 55.0%
AGCAACTCCAGCATGGCGCC+AGG - chr4.3:11228061-11228080 MS.gene030918:CDS 65.0%
GCAACTCCAGCATGGCGCCA+GGG - chr4.3:11228062-11228081 MS.gene030918:CDS 65.0%
TGGCGCCATGCTGGAGTTGC+TGG + chr4.3:11228062-11228081 None:intergenic 65.0%
TTTGGTCCCTGGCGCCATGC+TGG + chr4.3:11228071-11228090 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 11228047 11228645 11228047 ID=MS.gene030918
chr4.3 mRNA 11228047 11228645 11228047 ID=MS.gene030918.t1;Parent=MS.gene030918
chr4.3 exon 11228426 11228645 11228426 ID=MS.gene030918.t1.exon1;Parent=MS.gene030918.t1
chr4.3 CDS 11228426 11228645 11228426 ID=cds.MS.gene030918.t1;Parent=MS.gene030918.t1
chr4.3 exon 11228047 11228297 11228047 ID=MS.gene030918.t1.exon2;Parent=MS.gene030918.t1
chr4.3 CDS 11228047 11228297 11228047 ID=cds.MS.gene030918.t1;Parent=MS.gene030918.t1
Gene Sequence

>MS.gene030918

ATGGATTCATCACCAGCAACTCCAGCATGGCGCCAGGGACCAAAAGACAAGCCAGTTTTATGCAATGCATGTGGACTAAGATACCAAAACTGGGGAAACCTCAAAGACCATTCTCTCAAACGTTGTTTTCCAAAAGAACTTGTTACGAACAGTGGCAACAGTAGCAACAACAGTCTCAAAGAAAGTTCATCAACCATTGATGTTTCTGATTCAGATAATGGTATGTGTTTATACTAGTACTAGCCATTTTCACTCTTTTCTTTACAATGATATATACTACTTTTGTGAGGGTGGGCGTGCGTGAATACTTCTTTTAAATTGTCAATAAATAAGAGAATTTTTACTCAGATGAAAAAGATTCAGATTCATGCAAGTCTGCAGTCTCTCCAAAGAGACGTAGTTTGAGAATTATCAATCAGAAGATGACACCGATGGAGAAGTTTCAACAAGAACTTCTCGATGAGTTGAAAAATCACGAGATACCAGATGAGTCATCTCCAGAAGAGGCCTTATTGTTTGAAAATGTGAACAACTTCATACCTTCAAATGAAATTGGCCTTGGAGCGGTTCTTCTTAAACCAGACGGTTCTTCTATGTAG
Protein sequence

>MS.gene030918.t1

MDSSPATPAWRQGPKDKPVLCNACGLRYQNWGNLKDHSLKRCFPKELVTNSGNSSNNSLKESSSTIDVSDSDNDEKDSDSCKSAVSPKRRSLRIINQKMTPMEKFQQELLDELKNHEIPDESSPEEALLFENVNNFIPSNEIGLGAVLLKPDGSSM