AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1109440


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 136 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAATACATCTATACATTTC+AGG 0.192407 7_3:+53048837 None:intergenic
CGAGGTACTGGTTCATATTT+TGG 0.199965 7_3:+53048306 None:intergenic
GTTTCGTTCCATCGTGATTT+AGG 0.209765 7_3:+53048900 None:intergenic
CTGAAGAAGTTTATGTTTCA+TGG 0.232107 7_3:-53048364 Msa1109440:CDS
TCCTCATCGATATCAAAATT+TGG 0.244038 7_3:+53048943 None:intergenic
CATGGATAGGGATGCTCTTT+TGG 0.277125 7_3:-53049045 Msa1109440:intron
TGGTACAATCAAACAATTAA+AGG 0.314366 7_3:-53048344 Msa1109440:CDS
CATGAAACATAAACTTCTTC+AGG 0.363412 7_3:+53048365 None:intergenic
TTCTCATGGAATGGGAGAAT+TGG 0.365757 7_3:-53048439 Msa1109440:CDS
AAATACATCTATACATTTCA+GGG 0.407480 7_3:+53048838 None:intergenic
GGTTCGTGTTCTCATGGAAT+GGG 0.501771 7_3:-53048447 Msa1109440:CDS
GAGCACTTATTAGAAACAAA+TGG 0.507222 7_3:-53048468 Msa1109440:CDS
ACAAATGGTTCGTGTTCTCA+TGG 0.511558 7_3:-53048453 Msa1109440:CDS
GAGGAGATTGATTCCAACAT+TGG 0.512903 7_3:-53048925 Msa1109440:CDS
TATACCTGTGTGAGAAAAGC+AGG 0.520086 7_3:-53049022 Msa1109440:CDS
ACATTTCAGGGAACTTTGCA+AGG 0.520718 7_3:+53048850 None:intergenic
TGGTTCGTGTTCTCATGGAA+TGG 0.528047 7_3:-53048448 Msa1109440:CDS
CGTGATTTAGGATCCAATGT+TGG 0.568225 7_3:+53048912 None:intergenic
TTAAACTACTCGCAGAAGTG+TGG 0.590321 7_3:-53048491 Msa1109440:intron
TAAACTACTCGCAGAAGTGT+GGG 0.599255 7_3:-53048490 Msa1109440:intron
ATCACGATGGAACGAAACAA+AGG 0.615663 7_3:-53048895 Msa1109440:CDS
CATTGGATCCTAAATCACGA+TGG 0.674545 7_3:-53048908 Msa1109440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAATAAAGTTAAAGA+GGG - chr7_3:53048464-53048483 Msa1109440:CDS 10.0%
!! AAAAAAAATAAAGTTAAAGA+GGG - chr7_3:53048464-53048483 Msa1109440:CDS 10.0%
!! GAAAAAAAATAAAGTTAAAG+AGG - chr7_3:53048463-53048482 Msa1109440:CDS 15.0%
!! GAAAAAAAATAAAGTTAAAG+AGG - chr7_3:53048463-53048482 Msa1109440:CDS 15.0%
!!! AATCTCTTTAATTTTGATGT+CGG + chr7_3:53048496-53048515 None:intergenic 20.0%
!!! ACATCTCTAAAAGAATAATT+CGG + chr7_3:53048716-53048735 None:intergenic 20.0%
!! AAATACATCTATACATTTCA+GGG + chr7_3:53048946-53048965 None:intergenic 20.0%
!! AAAATACATCTATACATTTC+AGG + chr7_3:53048947-53048966 None:intergenic 20.0%
!!! AATCTCTTTAATTTTGATGT+CGG + chr7_3:53048496-53048515 None:intergenic 20.0%
!!! ACATCTCTAAAAGAATAATT+CGG + chr7_3:53048716-53048735 None:intergenic 20.0%
!! AAATACATCTATACATTTCA+GGG + chr7_3:53048946-53048965 None:intergenic 20.0%
!! AAAATACATCTATACATTTC+AGG + chr7_3:53048947-53048966 None:intergenic 20.0%
! ACATTACTATGAAAAGAATC+TGG - chr7_3:53048408-53048427 Msa1109440:CDS 25.0%
!!! TATTAGCTTTTACAAACCAT+AGG - chr7_3:53048515-53048534 Msa1109440:intron 25.0%
! ATAAGTGAGAAATAACAGTT+AGG + chr7_3:53048668-53048687 None:intergenic 25.0%
!!! TTATTCTTTTAGAGATGTCA+TGG - chr7_3:53048718-53048737 Msa1109440:intron 25.0%
!! CTTTTACAGCAACAAAATTT+CGG - chr7_3:53048994-53049013 Msa1109440:intron 25.0%
! TAACATTGCATATATGATAC+AGG - chr7_3:53049046-53049065 Msa1109440:intron 25.0%
! AACATTGCATATATGATACA+GGG - chr7_3:53049047-53049066 Msa1109440:intron 25.0%
!!! AGTTATTTGGTGTCTATATT+TGG - chr7_3:53049075-53049094 Msa1109440:intron 25.0%
! TGGTACAATCAAACAATTAA+AGG - chr7_3:53049437-53049456 Msa1109440:intron 25.0%
! AATTAAAGGCAGAAAAATTG+AGG - chr7_3:53049451-53049470 Msa1109440:intron 25.0%
! ACATTACTATGAAAAGAATC+TGG - chr7_3:53048408-53048427 Msa1109440:CDS 25.0%
!!! TATTAGCTTTTACAAACCAT+AGG - chr7_3:53048515-53048534 Msa1109440:intron 25.0%
! ATAAGTGAGAAATAACAGTT+AGG + chr7_3:53048668-53048687 None:intergenic 25.0%
!!! TTATTCTTTTAGAGATGTCA+TGG - chr7_3:53048718-53048737 Msa1109440:intron 25.0%
!! CTTTTACAGCAACAAAATTT+CGG - chr7_3:53048994-53049013 Msa1109440:intron 25.0%
! TAACATTGCATATATGATAC+AGG - chr7_3:53049046-53049065 Msa1109440:intron 25.0%
! AACATTGCATATATGATACA+GGG - chr7_3:53049047-53049066 Msa1109440:intron 25.0%
!!! AGTTATTTGGTGTCTATATT+TGG - chr7_3:53049075-53049094 Msa1109440:intron 25.0%
! TGGTACAATCAAACAATTAA+AGG - chr7_3:53049437-53049456 Msa1109440:intron 25.0%
! AATTAAAGGCAGAAAAATTG+AGG - chr7_3:53049451-53049470 Msa1109440:intron 25.0%
AATAATTTCCATACCACCTA+TGG + chr7_3:53048534-53048553 None:intergenic 30.0%
ATAGGTGGTATGGAAATTAT+TGG - chr7_3:53048533-53048552 Msa1109440:intron 30.0%
! TTTCGTTCGACATATGTTTT+TGG - chr7_3:53048576-53048595 Msa1109440:intron 30.0%
!! TTTTAGAGATGTCATGGATA+GGG - chr7_3:53048724-53048743 Msa1109440:intron 30.0%
!! TCCAAATTTTGATATCGATG+AGG - chr7_3:53048837-53048856 Msa1109440:intron 30.0%
TCCTCATCGATATCAAAATT+TGG + chr7_3:53048841-53048860 None:intergenic 30.0%
! CTGTAAAAGCATATATTCGT+GGG + chr7_3:53048983-53049002 None:intergenic 30.0%
! ATACAGGGATTCTAGTTATT+TGG - chr7_3:53049062-53049081 Msa1109440:intron 30.0%
!! ATTTGGTGTCTATATTTGGT+TGG - chr7_3:53049079-53049098 Msa1109440:intron 30.0%
GAGCACTTATTAGAAACAAA+TGG - chr7_3:53049313-53049332 Msa1109440:intron 30.0%
CATGAAACATAAACTTCTTC+AGG + chr7_3:53049419-53049438 None:intergenic 30.0%
CTGAAGAAGTTTATGTTTCA+TGG - chr7_3:53049417-53049436 Msa1109440:intron 30.0%
AATAATTTCCATACCACCTA+TGG + chr7_3:53048534-53048553 None:intergenic 30.0%
ATAGGTGGTATGGAAATTAT+TGG - chr7_3:53048533-53048552 Msa1109440:intron 30.0%
! TTTCGTTCGACATATGTTTT+TGG - chr7_3:53048576-53048595 Msa1109440:intron 30.0%
!! TTTTAGAGATGTCATGGATA+GGG - chr7_3:53048724-53048743 Msa1109440:intron 30.0%
!! TCCAAATTTTGATATCGATG+AGG - chr7_3:53048837-53048856 Msa1109440:intron 30.0%
TCCTCATCGATATCAAAATT+TGG + chr7_3:53048841-53048860 None:intergenic 30.0%
! CTGTAAAAGCATATATTCGT+GGG + chr7_3:53048983-53049002 None:intergenic 30.0%
! ATACAGGGATTCTAGTTATT+TGG - chr7_3:53049062-53049081 Msa1109440:intron 30.0%
!! ATTTGGTGTCTATATTTGGT+TGG - chr7_3:53049079-53049098 Msa1109440:intron 30.0%
GAGCACTTATTAGAAACAAA+TGG - chr7_3:53049313-53049332 Msa1109440:intron 30.0%
CATGAAACATAAACTTCTTC+AGG + chr7_3:53049419-53049438 None:intergenic 30.0%
CTGAAGAAGTTTATGTTTCA+TGG - chr7_3:53049417-53049436 Msa1109440:intron 30.0%
GTAACAGACGAAAATTCAGA+AGG + chr7_3:53048390-53048409 None:intergenic 35.0%
! TAGCTTTTACAAACCATAGG+TGG - chr7_3:53048518-53048537 Msa1109440:intron 35.0%
TTTACAAACCATAGGTGGTA+TGG - chr7_3:53048523-53048542 Msa1109440:intron 35.0%
AACATATGTCGAACGAAATG+AGG + chr7_3:53048574-53048593 None:intergenic 35.0%
CAGTTAGGAACTGCTAAAAA+AGG + chr7_3:53048653-53048672 None:intergenic 35.0%
!! CTTTTAGAGATGTCATGGAT+AGG - chr7_3:53048723-53048742 Msa1109440:intron 35.0%
! TAACAGTTGCCTTTAGTTCA+AGG - chr7_3:53048808-53048827 Msa1109440:intron 35.0%
! GCTGTAAAAGCATATATTCG+TGG + chr7_3:53048984-53049003 None:intergenic 35.0%
ATTAAGATCATCACGGGAAA+AGG + chr7_3:53049211-53049230 None:intergenic 35.0%
!!! AAGGAGGAATTTTGACTCTT+TGG - chr7_3:53049245-53049264 Msa1109440:intron 35.0%
CTGCGAGTAGTTTAATTATC+CGG + chr7_3:53049285-53049304 None:intergenic 35.0%
GTAACAGACGAAAATTCAGA+AGG + chr7_3:53048390-53048409 None:intergenic 35.0%
! TAGCTTTTACAAACCATAGG+TGG - chr7_3:53048518-53048537 Msa1109440:intron 35.0%
TTTACAAACCATAGGTGGTA+TGG - chr7_3:53048523-53048542 Msa1109440:intron 35.0%
AACATATGTCGAACGAAATG+AGG + chr7_3:53048574-53048593 None:intergenic 35.0%
CAGTTAGGAACTGCTAAAAA+AGG + chr7_3:53048653-53048672 None:intergenic 35.0%
!! CTTTTAGAGATGTCATGGAT+AGG - chr7_3:53048723-53048742 Msa1109440:intron 35.0%
! TAACAGTTGCCTTTAGTTCA+AGG - chr7_3:53048808-53048827 Msa1109440:intron 35.0%
! GCTGTAAAAGCATATATTCG+TGG + chr7_3:53048984-53049003 None:intergenic 35.0%
ATTAAGATCATCACGGGAAA+AGG + chr7_3:53049211-53049230 None:intergenic 35.0%
!!! AAGGAGGAATTTTGACTCTT+TGG - chr7_3:53049245-53049264 Msa1109440:intron 35.0%
CTGCGAGTAGTTTAATTATC+CGG + chr7_3:53049285-53049304 None:intergenic 35.0%
ACAAACTGCTTCTGCATCAA+GGG + chr7_3:53048341-53048360 None:intergenic 40.0%
AACAAACTGCTTCTGCATCA+AGG + chr7_3:53048342-53048361 None:intergenic 40.0%
CGAACGAAATGAGGAACAAA+GGG + chr7_3:53048565-53048584 None:intergenic 40.0%
TCGAACGAAATGAGGAACAA+AGG + chr7_3:53048566-53048585 None:intergenic 40.0%
TATACCTGTGTGAGAAAAGC+AGG - chr7_3:53048759-53048778 Msa1109440:intron 40.0%
! GGAGTATCTCCTTGAACTAA+AGG + chr7_3:53048820-53048839 None:intergenic 40.0%
! GAGGAGATTGATTCCAACAT+TGG - chr7_3:53048856-53048875 Msa1109440:CDS 40.0%
! CGTGATTTAGGATCCAATGT+TGG + chr7_3:53048872-53048891 None:intergenic 40.0%
CATTGGATCCTAAATCACGA+TGG - chr7_3:53048873-53048892 Msa1109440:CDS 40.0%
GTTTCGTTCCATCGTGATTT+AGG + chr7_3:53048884-53048903 None:intergenic 40.0%
ATCACGATGGAACGAAACAA+AGG - chr7_3:53048886-53048905 Msa1109440:CDS 40.0%
ACATTTCAGGGAACTTTGCA+AGG + chr7_3:53048934-53048953 None:intergenic 40.0%
TGTCCTGCAAGCTTATAAAC+TGG - chr7_3:53049120-53049139 Msa1109440:intron 40.0%
CAACCAGTTTATAAGCTTGC+AGG + chr7_3:53049126-53049145 None:intergenic 40.0%
CGCATCATTAAGATCATCAC+GGG + chr7_3:53049217-53049236 None:intergenic 40.0%
CCGCATCATTAAGATCATCA+CGG + chr7_3:53049218-53049237 None:intergenic 40.0%
CCGTGATGATCTTAATGATG+CGG - chr7_3:53049215-53049234 Msa1109440:intron 40.0%
CGTGATGATCTTAATGATGC+GGG - chr7_3:53049216-53049235 Msa1109440:intron 40.0%
TTAATGATGCGGGTGTTTGA+AGG - chr7_3:53049226-53049245 Msa1109440:intron 40.0%
TTTGGAGATCACTGTATCTC+CGG - chr7_3:53049263-53049282 Msa1109440:intron 40.0%
TTAAACTACTCGCAGAAGTG+TGG - chr7_3:53049290-53049309 Msa1109440:intron 40.0%
! TAAACTACTCGCAGAAGTGT+GGG - chr7_3:53049291-53049310 Msa1109440:intron 40.0%
ACAAATGGTTCGTGTTCTCA+TGG - chr7_3:53049328-53049347 Msa1109440:intron 40.0%
TTCTCATGGAATGGGAGAAT+TGG - chr7_3:53049342-53049361 Msa1109440:intron 40.0%
ACAAACTGCTTCTGCATCAA+GGG + chr7_3:53048341-53048360 None:intergenic 40.0%
AACAAACTGCTTCTGCATCA+AGG + chr7_3:53048342-53048361 None:intergenic 40.0%
CGAACGAAATGAGGAACAAA+GGG + chr7_3:53048565-53048584 None:intergenic 40.0%
TCGAACGAAATGAGGAACAA+AGG + chr7_3:53048566-53048585 None:intergenic 40.0%
TATACCTGTGTGAGAAAAGC+AGG - chr7_3:53048759-53048778 Msa1109440:intron 40.0%
! GGAGTATCTCCTTGAACTAA+AGG + chr7_3:53048820-53048839 None:intergenic 40.0%
! GAGGAGATTGATTCCAACAT+TGG - chr7_3:53048856-53048875 Msa1109440:CDS 40.0%
! CGTGATTTAGGATCCAATGT+TGG + chr7_3:53048872-53048891 None:intergenic 40.0%
CATTGGATCCTAAATCACGA+TGG - chr7_3:53048873-53048892 Msa1109440:CDS 40.0%
GTTTCGTTCCATCGTGATTT+AGG + chr7_3:53048884-53048903 None:intergenic 40.0%
ATCACGATGGAACGAAACAA+AGG - chr7_3:53048886-53048905 Msa1109440:CDS 40.0%
ACATTTCAGGGAACTTTGCA+AGG + chr7_3:53048934-53048953 None:intergenic 40.0%
TGTCCTGCAAGCTTATAAAC+TGG - chr7_3:53049120-53049139 Msa1109440:intron 40.0%
CAACCAGTTTATAAGCTTGC+AGG + chr7_3:53049126-53049145 None:intergenic 40.0%
CGCATCATTAAGATCATCAC+GGG + chr7_3:53049217-53049236 None:intergenic 40.0%
CCGCATCATTAAGATCATCA+CGG + chr7_3:53049218-53049237 None:intergenic 40.0%
CCGTGATGATCTTAATGATG+CGG - chr7_3:53049215-53049234 Msa1109440:intron 40.0%
CGTGATGATCTTAATGATGC+GGG - chr7_3:53049216-53049235 Msa1109440:intron 40.0%
TTAATGATGCGGGTGTTTGA+AGG - chr7_3:53049226-53049245 Msa1109440:intron 40.0%
TTTGGAGATCACTGTATCTC+CGG - chr7_3:53049263-53049282 Msa1109440:intron 40.0%
TTAAACTACTCGCAGAAGTG+TGG - chr7_3:53049290-53049309 Msa1109440:intron 40.0%
! TAAACTACTCGCAGAAGTGT+GGG - chr7_3:53049291-53049310 Msa1109440:intron 40.0%
ACAAATGGTTCGTGTTCTCA+TGG - chr7_3:53049328-53049347 Msa1109440:intron 40.0%
TTCTCATGGAATGGGAGAAT+TGG - chr7_3:53049342-53049361 Msa1109440:intron 40.0%
! CATGGATAGGGATGCTCTTT+TGG - chr7_3:53048736-53048755 Msa1109440:intron 45.0%
!! TAGACCTGCTTTTCTCACAC+AGG + chr7_3:53048766-53048785 None:intergenic 45.0%
TGGTTCGTGTTCTCATGGAA+TGG - chr7_3:53049333-53049352 Msa1109440:intron 45.0%
GGTTCGTGTTCTCATGGAAT+GGG - chr7_3:53049334-53049353 Msa1109440:intron 45.0%
! CATGGATAGGGATGCTCTTT+TGG - chr7_3:53048736-53048755 Msa1109440:intron 45.0%
!! TAGACCTGCTTTTCTCACAC+AGG + chr7_3:53048766-53048785 None:intergenic 45.0%
TGGTTCGTGTTCTCATGGAA+TGG - chr7_3:53049333-53049352 Msa1109440:intron 45.0%
GGTTCGTGTTCTCATGGAAT+GGG - chr7_3:53049334-53049353 Msa1109440:intron 45.0%
ATGATGCGGGTGTTTGAAGG+AGG - chr7_3:53049229-53049248 Msa1109440:intron 50.0%
ATGATGCGGGTGTTTGAAGG+AGG - chr7_3:53049229-53049248 Msa1109440:intron 50.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 53048318 53049485 53048318 ID=Msa1109440;Name=Msa1109440
chr7_3 mRNA 53048318 53049485 53048318 ID=Msa1109440-mRNA-1;Parent=Msa1109440;Name=Msa1109440-mRNA-1;_AED=0.51;_eAED=0.61;_QI=0|0|0|0.75|0|0|4|0|124
chr7_3 exon 53049481 53049485 53049481 ID=Msa1109440-mRNA-1:exon:11206;Parent=Msa1109440-mRNA-1
chr7_3 exon 53048998 53049058 53048998 ID=Msa1109440-mRNA-1:exon:11205;Parent=Msa1109440-mRNA-1
chr7_3 exon 53048852 53048979 53048852 ID=Msa1109440-mRNA-1:exon:11204;Parent=Msa1109440-mRNA-1
chr7_3 exon 53048318 53048498 53048318 ID=Msa1109440-mRNA-1:exon:11203;Parent=Msa1109440-mRNA-1
chr7_3 CDS 53049481 53049485 53049481 ID=Msa1109440-mRNA-1:cds;Parent=Msa1109440-mRNA-1
chr7_3 CDS 53048998 53049058 53048998 ID=Msa1109440-mRNA-1:cds;Parent=Msa1109440-mRNA-1
chr7_3 CDS 53048852 53048979 53048852 ID=Msa1109440-mRNA-1:cds;Parent=Msa1109440-mRNA-1
chr7_3 CDS 53048318 53048498 53048318 ID=Msa1109440-mRNA-1:cds;Parent=Msa1109440-mRNA-1
Gene Sequence

>Msa1109440

ATGTGGGATGCTCTTTTGGTATACCTGTGTGAGAAAAGCAGGTCTACAAGTGACTCTGCTTCAAATTTCAAGGAGATACTCCAAATTTTGATATCGATGAGGAGATTGATTCCAACATTGGATCCTAAATCACGATGGAACGAAACAAAGGATTATGAAGTTACAAACTACATCCTTGCAAAGTTCCCTGAAATAAGTGTGGGAGCACTTATTAGAAACAAATGGTTCGTGTTCTCATGGAATGGGAGAATTGGAATTCAAACTGAGAAAGCTCTTCAGTTTGATAGATGTCTCAAGCTCTTCTTCCTGAAGAAGTTTATGTTTCATGGTACAATCAAACAATTAAAGGCAGAAAAATTGAGGACCAAAATATGA

Protein sequence

>Msa1109440

MWDALLVYLCEKSRSTSDSASNFKEILQILISMRRLIPTLDPKSRWNETKDYEVTNYILAKFPEISVGALIRNKWFVFSWNGRIGIQTEKALQFDRCLKLFFLKKFMFHGTIKQLKAEKLRTKI*