AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20929

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20929.t1 MTR_1g085590 89.630 270 23 3 1 265 1 270 2.23e-156 437
MS.gene20929.t1 MTR_1g063150 50.463 216 53 8 37 241 26 198 3.49e-45 151
MS.gene20929.t1 MTR_1g046810 37.597 258 104 8 41 266 84 316 1.13e-33 124
MS.gene20929.t1 MTR_1g063140 41.538 195 57 10 92 260 1 164 1.43e-20 86.7
MS.gene20929.t1 MTR_1g052185 35.047 214 102 11 73 266 82 278 4.69e-17 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 39 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGAAGGTGAAACTGAATT+AGG 0.203359 1.3:-60759672 MS.gene20929:CDS
AATGAAGGTGAAACTGAATT+AGG 0.203359 1.3:-60759744 MS.gene20929:CDS
GTCAAAAGTTGTGAAGAATT+TGG 0.225875 1.3:-60759649 MS.gene20929:CDS
AATGAAGGCGAAACTGAATT+AGG 0.231002 1.3:-60759600 MS.gene20929:CDS
AACTAAGATGAGGCACTAAT+TGG 0.271486 1.3:+60759515 None:intergenic
TCTATCTCGCGTGGGTTATA+AGG 0.308553 1.3:-60759901 MS.gene20929:CDS
TGAATCACCGTGGTGCTAAA+AGG 0.329449 1.3:-60759875 MS.gene20929:CDS
CCTGCACGGCTGCTGTTTCT+CGG 0.336607 1.3:+60759989 None:intergenic
CGCCATATGATCTTCTTCTC+AGG 0.345803 1.3:+60760167 None:intergenic
GAACTCGACGAAGAAGAAAA+AGG 0.396702 1.3:-60759823 MS.gene20929:CDS
GAAAGAGAAAGAAGGGTATC+TGG 0.402663 1.3:+60760229 None:intergenic
ACTTCTAACAAAGCATTGAA+TGG 0.414800 1.3:-60760062 MS.gene20929:CDS
ATGAAGGTGAAACTGAATTA+GGG 0.420619 1.3:-60759743 MS.gene20929:CDS
ATGAAGGTGAAACTGAATTA+GGG 0.430586 1.3:-60759671 MS.gene20929:CDS
ATGAAGGCGAAACTGAATTA+GGG 0.437450 1.3:-60759599 MS.gene20929:CDS
GGCTGCTGTTTCTCGGAAGA+TGG 0.453754 1.3:+60759996 None:intergenic
CCGAGAAACAGCAGCCGTGC+AGG 0.471067 1.3:-60759989 MS.gene20929:CDS
TCCTCAACAACTAATGATGC+TGG 0.472142 1.3:-60760200 MS.gene20929:CDS
TCCAGCATCATTAGTTGTTG+AGG 0.475624 1.3:+60760199 None:intergenic
GAGAAGAAGAAGATTAATGA+AGG 0.491417 1.3:-60759759 MS.gene20929:CDS
ACCCTGAGAAGAAGATCATA+TGG 0.501896 1.3:-60760169 MS.gene20929:CDS
CTCATGTGATGTTTGCAACA+AGG 0.514548 1.3:-60760090 MS.gene20929:CDS
TCTATTGCGTCTATCTCGCG+TGG 0.518757 1.3:-60759910 MS.gene20929:CDS
ATGAGATGTCACGGTCAAAA+CGG 0.520374 1.3:-60760035 MS.gene20929:CDS
TCATCTTCAAACTCATCACT+TGG 0.524025 1.3:+60759540 None:intergenic
GAAGATGGTGCTGCAACTGT+TGG 0.540873 1.3:+60760011 None:intergenic
ATATATCTTCTTCTCCTGCA+CGG 0.556539 1.3:+60759975 None:intergenic
GCCATATGATCTTCTTCTCA+GGG 0.557187 1.3:+60760168 None:intergenic
TCGCCTTCATTATCATCACT+TGG 0.560001 1.3:+60759612 None:intergenic
GACTCAACGAAAGAGAAAGA+AGG 0.560928 1.3:+60760221 None:intergenic
CAAGGTGTTCTACTAATAAG+TGG 0.561004 1.3:-60759798 MS.gene20929:CDS
TCACCTTCATTATCATCACT+TGG 0.567032 1.3:+60759684 None:intergenic
CTTCCAAGTGATGATAATGA+AGG 0.580430 1.3:-60759615 MS.gene20929:CDS
CTTCCAAGTGATGATAATGA+AGG 0.583048 1.3:-60759687 MS.gene20929:CDS
ACTCAACGAAAGAGAAAGAA+GGG 0.591599 1.3:+60760222 None:intergenic
TGGAAAGAATGATCATGAGA+AGG 0.605370 1.3:+60760290 None:intergenic
AATGGACATATGAGATGTCA+CGG 0.619984 1.3:-60760044 MS.gene20929:CDS
CTATTGCGTCTATCTCGCGT+GGG 0.626912 1.3:-60759909 MS.gene20929:CDS
TATAAGGATGTGAATCACCG+TGG 0.764003 1.3:-60759885 MS.gene20929:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTGGTTTTTGGTTTTTGA+TGG + chr1.3:60759571-60759590 None:intergenic 25.0%
!!! TTTTTGAAGAGACTGATTAT+TGG + chr1.3:60759588-60759607 None:intergenic 25.0%
AATGAAGGTGAAACTGAATT+AGG - chr1.3:60760094-60760113 MS.gene20929:CDS 30.0%
ATGAAGGTGAAACTGAATTA+GGG - chr1.3:60760095-60760114 MS.gene20929:CDS 30.0%
GAGAAGAAGAAGATTAATGA+AGG - chr1.3:60760079-60760098 MS.gene20929:CDS 30.0%
GTCAAAAGTTGTGAAGAATT+TGG - chr1.3:60760189-60760208 MS.gene20929:CDS 30.0%
!! ACTTCTAACAAAGCATTGAA+TGG - chr1.3:60759776-60759795 MS.gene20929:CDS 30.0%
!!! AGAGACTGATTATTGGTTTT+TGG + chr1.3:60759581-60759600 None:intergenic 30.0%
AATGAAGGCGAAACTGAATT+AGG - chr1.3:60760238-60760257 MS.gene20929:CDS 35.0%
AATGGACATATGAGATGTCA+CGG - chr1.3:60759794-60759813 MS.gene20929:CDS 35.0%
ACGAAGAAGAAAAAGGAACA+AGG - chr1.3:60760022-60760041 MS.gene20929:CDS 35.0%
ACTCAACGAAAGAGAAAGAA+GGG + chr1.3:60759619-60759638 None:intergenic 35.0%
ATATATCTTCTTCTCCTGCA+CGG + chr1.3:60759866-60759885 None:intergenic 35.0%
ATGAAGGCGAAACTGAATTA+GGG - chr1.3:60760239-60760258 MS.gene20929:CDS 35.0%
TCACCTTCATTATCATCACT+TGG + chr1.3:60760157-60760176 None:intergenic 35.0%
TCATCTTCAAACTCATCACT+TGG + chr1.3:60760301-60760320 None:intergenic 35.0%
TGGAAAGAATGATCATGAGA+AGG + chr1.3:60759551-60759570 None:intergenic 35.0%
! CAAGGTGTTCTACTAATAAG+TGG - chr1.3:60760040-60760059 MS.gene20929:CDS 35.0%
! CTTCCAAGTGATGATAATGA+AGG - chr1.3:60760151-60760170 MS.gene20929:CDS 35.0%
ACCCTGAGAAGAAGATCATA+TGG - chr1.3:60759669-60759688 MS.gene20929:CDS 40.0%
ATGAGATGTCACGGTCAAAA+CGG - chr1.3:60759803-60759822 MS.gene20929:CDS 40.0%
CTCATGTGATGTTTGCAACA+AGG - chr1.3:60759748-60759767 MS.gene20929:CDS 40.0%
GAACTCGACGAAGAAGAAAA+AGG - chr1.3:60760015-60760034 MS.gene20929:CDS 40.0%
GACTCAACGAAAGAGAAAGA+AGG + chr1.3:60759620-60759639 None:intergenic 40.0%
GCCATATGATCTTCTTCTCA+GGG + chr1.3:60759673-60759692 None:intergenic 40.0%
TATAAGGATGTGAATCACCG+TGG - chr1.3:60759953-60759972 MS.gene20929:CDS 40.0%
TCCAGCATCATTAGTTGTTG+AGG + chr1.3:60759642-60759661 None:intergenic 40.0%
TCCTCAACAACTAATGATGC+TGG - chr1.3:60759638-60759657 MS.gene20929:CDS 40.0%
TCGCCTTCATTATCATCACT+TGG + chr1.3:60760229-60760248 None:intergenic 40.0%
!! GAAAGAGAAAGAAGGGTATC+TGG + chr1.3:60759612-60759631 None:intergenic 40.0%
CGCCATATGATCTTCTTCTC+AGG + chr1.3:60759674-60759693 None:intergenic 45.0%
! GCTTTTGCCTTTTAGCACCA+CGG + chr1.3:60759973-60759992 None:intergenic 45.0%
! TCTATCTCGCGTGGGTTATA+AGG - chr1.3:60759937-60759956 MS.gene20929:CDS 45.0%
! TGAATCACCGTGGTGCTAAA+AGG - chr1.3:60759963-60759982 MS.gene20929:CDS 45.0%
CTATTGCGTCTATCTCGCGT+GGG - chr1.3:60759929-60759948 MS.gene20929:CDS 50.0%
TCTATTGCGTCTATCTCGCG+TGG - chr1.3:60759928-60759947 MS.gene20929:CDS 50.0%
!! GAAGATGGTGCTGCAACTGT+TGG + chr1.3:60759830-60759849 None:intergenic 50.0%
!! GGCTGCTGTTTCTCGGAAGA+TGG + chr1.3:60759845-60759864 None:intergenic 55.0%
!! CCTGCACGGCTGCTGTTTCT+CGG + chr1.3:60759852-60759871 None:intergenic 60.0%
CCGAGAAACAGCAGCCGTGC+AGG - chr1.3:60759849-60759868 MS.gene20929:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 60759530 60760330 60759530 ID=MS.gene20929
chr1.3 mRNA 60759530 60760330 60759530 ID=MS.gene20929.t1;Parent=MS.gene20929
chr1.3 exon 60759530 60760330 60759530 ID=MS.gene20929.t1.exon1;Parent=MS.gene20929.t1
chr1.3 CDS 60759530 60760330 60759530 ID=cds.MS.gene20929.t1;Parent=MS.gene20929.t1
Gene Sequence

>MS.gene20929

ATGTATTCTTCTTCATCTCCTTCTCATGATCATTCTTTCCATCAAAAACCAAAAACCAATAATCAGTCTCTTCAAAAAACCAGATACCCTTCTTTCTCTTTCGTTGAGTCCTCAACAACTAATGATGCTGGAAAAGAGAACCCTGAGAAGAAGATCATATGGCGTTTTTCTTATTCTGTTGCTTATAATCATAATGATGTAGTAAAACAGAAGAAACACTCATGTGATGTTTGCAACAAGGTTTTTACTTCTAACAAAGCATTGAATGGACATATGAGATGTCACGGTCAAAACGGTCCAACAGTTGCAGCACCATCTTCCGAGAAACAGCAGCCGTGCAGGAGAAGAAGATATATGAATATTGACGACGACGATGTTATTGAAACAGTTGCAGAAATTCTATTGCGTCTATCTCGCGTGGGTTATAAGGATGTGAATCACCGTGGTGCTAAAAGGCAAAAGCTTTCTTGCAATATGATCGATGAGAACTCGACGAAGAAGAAAAAGGAACAAGGTGTTCTACTAATAAGTGGTTGTCATGATATTGAAGAGAAGAAGAAGATTAATGAAGGTGAAACTGAATTAGGGTCAAAAGTTGTGAAGAATGTTGATTTGAACGAGCTTCCAAGTGATGATAATGAAGGTGAAACTGAATTAGGGTCAAAAGTTGTGAAGAATTTGGATTTGAACGAGCTTCCAAGTGATGATAATGAAGGCGAAACTGAATTAGGGTCAAAAGTTGTGAAGAATTTTGATTTGAACGAGCTTCCAAGTGATGAGTTTGAAGATGAAACCAATTAG
Protein sequence

>MS.gene20929.t1

MYSSSSPSHDHSFHQKPKTNNQSLQKTRYPSFSFVESSTTNDAGKENPEKKIIWRFSYSVAYNHNDVVKQKKHSCDVCNKVFTSNKALNGHMRCHGQNGPTVAAPSSEKQQPCRRRRYMNIDDDDVIETVAEILLRLSRVGYKDVNHRGAKRQKLSCNMIDENSTKKKKEQGVLLISGCHDIEEKKKINEGETELGSKVVKNVDLNELPSDDNEGETELGSKVVKNLDLNELPSDDNEGETELGSKVVKNFDLNELPSDEFEDETN