AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068481

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 28 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGAAACTGTCGGTGAAAT+TGG 0.283595 6.2:+75098049 MS.gene068481:CDS
GCAGATGGAGATGGTGGAAT+TGG 0.393679 6.2:-75096624 None:intergenic
GGTGAAATTGGATCAACAAT+TGG 0.412062 6.2:+75098061 MS.gene068481:CDS
ATCAACAATTGGAAAATCAA+TGG 0.438749 6.2:+75098072 MS.gene068481:CDS
TCAAGGACACACTAAATGAA+TGG 0.452007 6.2:+75097559 MS.gene068481:CDS
AATCTTCTATAGATGCATAA+AGG 0.458350 6.2:+75097700 MS.gene068481:intron
TTTCTTTCAAGGTAATCGTC+TGG 0.459069 6.2:+75096584 None:intergenic
TCAACAATTGGAAAATCAAT+GGG 0.473297 6.2:+75098073 MS.gene068481:CDS
CCTTGCTCAGTTAATTCTAG+AGG 0.485004 6.2:-75097486 None:intergenic
GGAGATGGTGGAATTGGAGC+AGG 0.489331 6.2:-75096618 None:intergenic
CAAGGACACACTAAATGAAT+GGG 0.499336 6.2:+75097560 MS.gene068481:CDS
ACCTCAACAATCTTTGCAGA+TGG 0.540270 6.2:-75096639 None:intergenic
ACAATCTTTGCAGATGGAGA+TGG 0.541131 6.2:-75096633 None:intergenic
TGCATTAGCAGCAGCTACAA+TGG 0.562915 6.2:-75097526 None:intergenic
ATCTTTGCAGATGGAGATGG+TGG 0.570345 6.2:-75096630 None:intergenic
CCTCTAGAATTAACTGAGCA+AGG 0.579469 6.2:+75097486 MS.gene068481:CDS
GTTTCTGCAGCATCATTCAG+AGG 0.586467 6.2:-75098034 None:intergenic
AATGAATGGGACAGTGAAGT+TGG 0.587826 6.2:+75097573 MS.gene068481:CDS
AAATCAATGGGAGGAACAAG+TGG 0.591320 6.2:+75098085 MS.gene068481:CDS
TAATGCACTTATAAATCTCA+AGG 0.593610 6.2:+75097542 MS.gene068481:CDS
TTTCTGCAGCATCATTCAGA+GGG 0.626507 6.2:-75098033 None:intergenic
TGGGACAGTGAAGTTGGTGA+TGG 0.631482 6.2:+75097579 MS.gene068481:CDS
ATAGATGCATAAAGGTGCAA+CGG 0.638039 6.2:+75097708 MS.gene068481:intron
TCCATCTGCAAAGATTGTTG+AGG 0.640135 6.2:+75096638 MS.gene068481:CDS
AATGATGCTGCAGAAACTGT+CGG 0.648199 6.2:+75098040 MS.gene068481:CDS
GAAGTTGGTGATGGTGACTG+TGG 0.657682 6.2:+75097588 MS.gene068481:CDS
ACAATTGGAAAATCAATGGG+AGG 0.659618 6.2:+75098076 MS.gene068481:CDS
AATCAATGGGAGGAACAAGT+GGG 0.679642 6.2:+75098086 MS.gene068481:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTACATTAGTAAATAAG+AGG - chr6.2:75097421-75097440 None:intergenic 15.0%
!! AATTACATTAGTAAATAAGA+GGG - chr6.2:75097420-75097439 None:intergenic 15.0%
!!! TAGTATAAGTTTTTCTATTA+AGG + chr6.2:75097894-75097913 MS.gene068481:intron 15.0%
!! AATAATTTATTTCACTAGCT+AGG + chr6.2:75097099-75097118 MS.gene068481:intron 20.0%
!! TATTCAATGAATCTAAAAAG+TGG - chr6.2:75096748-75096767 None:intergenic 20.0%
!!! TACTTGTTTTGATATAATCA+TGG + chr6.2:75097800-75097819 MS.gene068481:intron 20.0%
! AATCTTCTATAGATGCATAA+AGG + chr6.2:75097700-75097719 MS.gene068481:intron 25.0%
! AGATTCATTGAATATGTATC+TGG + chr6.2:75096754-75096773 MS.gene068481:intron 25.0%
! AGCTATACAATGAATCTAAA+AGG + chr6.2:75096791-75096810 MS.gene068481:intron 25.0%
! ATAATGCCCTAATTTGATTA+AGG - chr6.2:75096913-75096932 None:intergenic 25.0%
! ATCAACAATTGGAAAATCAA+TGG + chr6.2:75098072-75098091 MS.gene068481:CDS 25.0%
! TAACCCATGAATATATCTTA+AGG - chr6.2:75097782-75097801 None:intergenic 25.0%
! TAACTGGAAATAAGATTTGT+TGG - chr6.2:75097199-75097218 None:intergenic 25.0%
! TAATGCACTTATAAATCTCA+AGG + chr6.2:75097542-75097561 MS.gene068481:CDS 25.0%
! TCAACAATTGGAAAATCAAT+GGG + chr6.2:75098073-75098092 MS.gene068481:CDS 25.0%
! TGTAAAAATAACAGTACTTC+AGG - chr6.2:75098009-75098028 None:intergenic 25.0%
! TTGATATAATCATGGATGAT+TGG + chr6.2:75097808-75097827 MS.gene068481:intron 25.0%
! TTGCCTTAAGATATATTCAT+GGG + chr6.2:75097776-75097795 MS.gene068481:intron 25.0%
! TTTGCCTTAAGATATATTCA+TGG + chr6.2:75097775-75097794 MS.gene068481:intron 25.0%
!! AACTGGAAATAAGATTTGTT+GGG - chr6.2:75097198-75097217 None:intergenic 25.0%
!! CTAATGTAATTTGTGAAATC+TGG + chr6.2:75097429-75097448 MS.gene068481:intron 25.0%
!! TAAATAAGCAGACAATTTTG+AGG - chr6.2:75097632-75097651 None:intergenic 25.0%
!! TTTTTGGATATAATAGTGAC+CGG - chr6.2:75096724-75096743 None:intergenic 25.0%
!!! GAATCTAAAAAGTGGTTTTT+TGG - chr6.2:75096740-75096759 None:intergenic 25.0%
!!! GACATATTTTTTTGTTGTTG+AGG + chr6.2:75097045-75097064 MS.gene068481:intron 25.0%
!!! TGTAATTTTGAGATCTTCAT+TGG + chr6.2:75097073-75097092 MS.gene068481:intron 25.0%
ACATTAGTAAATAAGAGGGA+GGG - chr6.2:75097416-75097435 None:intergenic 30.0%
TACATTAGTAAATAAGAGGG+AGG - chr6.2:75097417-75097436 None:intergenic 30.0%
TGCTTACAATAGTTACTGAA+GGG + chr6.2:75096822-75096841 MS.gene068481:intron 30.0%
TTCCATATTTGCTTCATGTA+AGG + chr6.2:75097452-75097471 MS.gene068481:intron 30.0%
TTGCTTACAATAGTTACTGA+AGG + chr6.2:75096821-75096840 MS.gene068481:intron 30.0%
! TATTTTCTGTTAACCGATAG+AGG - chr6.2:75097230-75097249 None:intergenic 30.0%
!! TAATATGTCAAGTTGACACA+TGG + chr6.2:75097834-75097853 MS.gene068481:intron 30.0%
AACTAAAACAGAAAAACCGC+TGG - chr6.2:75096957-75096976 None:intergenic 35.0%
AATTTATGTACCTTGCGTGA+TGG + chr6.2:75097341-75097360 MS.gene068481:intron 35.0%
ACAATTGGAAAATCAATGGG+AGG + chr6.2:75098076-75098095 MS.gene068481:CDS 35.0%
ACCAATTGTAATATACCCTC+CGG + chr6.2:75096702-75096721 MS.gene068481:intron 35.0%
AGGGAGTAAGAATTTAGTCA+AGG + chr6.2:75096841-75096860 MS.gene068481:intron 35.0%
ATAGCTCATGTACTGGATTA+CGG + chr6.2:75097864-75097883 MS.gene068481:intron 35.0%
ATCACGCAAGGTACATAAAT+TGG - chr6.2:75097342-75097361 None:intergenic 35.0%
CAAGGACACACTAAATGAAT+GGG + chr6.2:75097560-75097579 MS.gene068481:CDS 35.0%
CATTAGTAAATAAGAGGGAG+GGG - chr6.2:75097415-75097434 None:intergenic 35.0%
CATTGTATAGCTGATGTATC+TGG - chr6.2:75096783-75096802 None:intergenic 35.0%
GCGGATCCTTAATCAAATTA+GGG + chr6.2:75096904-75096923 MS.gene068481:intron 35.0%
GGTGAAATTGGATCAACAAT+TGG + chr6.2:75098061-75098080 MS.gene068481:CDS 35.0%
TCAAGGACACACTAAATGAA+TGG + chr6.2:75097559-75097578 MS.gene068481:CDS 35.0%
TGCCTTACATGAAGCAAATA+TGG - chr6.2:75097457-75097476 None:intergenic 35.0%
TGCGGATCCTTAATCAAATT+AGG + chr6.2:75096903-75096922 MS.gene068481:intron 35.0%
! AAGGTACATAAATTGGTGGT+AGG - chr6.2:75097335-75097354 None:intergenic 35.0%
! ATAGATGCATAAAGGTGCAA+CGG + chr6.2:75097708-75097727 MS.gene068481:intron 35.0%
! TACATAAATTGGTGGTAGGA+GGG - chr6.2:75097331-75097350 None:intergenic 35.0%
!! ACTAAGCTTTGTTATCTCTG+TGG + chr6.2:75097008-75097027 MS.gene068481:intron 35.0%
AAATCAATGGGAGGAACAAG+TGG + chr6.2:75098085-75098104 MS.gene068481:CDS 40.0%
AATCAATGGGAGGAACAAGT+GGG + chr6.2:75098086-75098105 MS.gene068481:CDS 40.0%
AATGAATGGGACAGTGAAGT+TGG + chr6.2:75097573-75097592 MS.gene068481:CDS 40.0%
AATGATGCTGCAGAAACTGT+CGG + chr6.2:75098040-75098059 MS.gene068481:CDS 40.0%
ACAATCTTTGCAGATGGAGA+TGG - chr6.2:75096636-75096655 None:intergenic 40.0%
ACCTCAACAATCTTTGCAGA+TGG - chr6.2:75096642-75096661 None:intergenic 40.0%
ACGCAAGGTACATAAATTGG+TGG - chr6.2:75097339-75097358 None:intergenic 40.0%
AGTTACCTTGAAGCCTCTAT+CGG + chr6.2:75097214-75097233 MS.gene068481:intron 40.0%
ATGCCCTTGAGAAAATGTGA+AGG + chr6.2:75097936-75097955 MS.gene068481:intron 40.0%
CATTATCTGAGTCTCTGACT+GGG + chr6.2:75096927-75096946 MS.gene068481:intron 40.0%
CCAGTACATGAGCTATTAAC+TGG - chr6.2:75097860-75097879 None:intergenic 40.0%
CCAGTTAATAGCTCATGTAC+TGG + chr6.2:75097857-75097876 MS.gene068481:intron 40.0%
CCTTGCTCAGTTAATTCTAG+AGG - chr6.2:75097489-75097508 None:intergenic 40.0%
TAGCTCATGTACTGGATTAC+GGG + chr6.2:75097865-75097884 MS.gene068481:intron 40.0%
TCCATCTGCAAAGATTGTTG+AGG + chr6.2:75096638-75096657 MS.gene068481:CDS 40.0%
TGGATATAATAGTGACCGGA+GGG - chr6.2:75096720-75096739 None:intergenic 40.0%
TTGGATATAATAGTGACCGG+AGG - chr6.2:75096721-75096740 None:intergenic 40.0%
TTTCTGCAGCATCATTCAGA+GGG - chr6.2:75098036-75098055 None:intergenic 40.0%
! ACCACCTTCACATTTTCTCA+AGG - chr6.2:75097943-75097962 None:intergenic 40.0%
! ACCGGAGGGTATATTACAAT+TGG - chr6.2:75096706-75096725 None:intergenic 40.0%
! CCACCTTCACATTTTCTCAA+GGG - chr6.2:75097942-75097961 None:intergenic 40.0%
! GTACATAAATTGGTGGTAGG+AGG - chr6.2:75097332-75097351 None:intergenic 40.0%
!! CCTCTAGAATTAACTGAGCA+AGG + chr6.2:75097486-75097505 MS.gene068481:CDS 40.0%
!!! CTGTTTTAGTTCATGTCTGC+TGG + chr6.2:75096966-75096985 MS.gene068481:intron 40.0%
ACCCTGTGAAGATGTTCATG+CGG + chr6.2:75096885-75096904 MS.gene068481:intron 45.0%
AGTAAATAAGAGGGAGGGGT+AGG - chr6.2:75097411-75097430 None:intergenic 45.0%
ATCCGCATGAACATCTTCAC+AGG - chr6.2:75096890-75096909 None:intergenic 45.0%
ATCTTTGCAGATGGAGATGG+TGG - chr6.2:75096633-75096652 None:intergenic 45.0%
CCCTTGAGAAAATGTGAAGG+TGG + chr6.2:75097939-75097958 MS.gene068481:intron 45.0%
GATAGAGGCTTCAAGGTAAC+TGG - chr6.2:75097215-75097234 None:intergenic 45.0%
GCAGAAACTGTCGGTGAAAT+TGG + chr6.2:75098049-75098068 MS.gene068481:CDS 45.0%
GCATTATCTGAGTCTCTGAC+TGG + chr6.2:75096926-75096945 MS.gene068481:intron 45.0%
GTAAATAAGAGGGAGGGGTA+GGG - chr6.2:75097410-75097429 None:intergenic 45.0%
GTTAACCGATAGAGGCTTCA+AGG - chr6.2:75097222-75097241 None:intergenic 45.0%
GTTTCTGCAGCATCATTCAG+AGG - chr6.2:75098037-75098056 None:intergenic 45.0%
TCCGCATGAACATCTTCACA+GGG - chr6.2:75096889-75096908 None:intergenic 45.0%
TGCATTAGCAGCAGCTACAA+TGG - chr6.2:75097529-75097548 None:intergenic 45.0%
! AAATTGGTGGTAGGAGGGAA+AGG - chr6.2:75097326-75097345 None:intergenic 45.0%
CTAGATCTGACCATCACGCA+AGG - chr6.2:75097354-75097373 None:intergenic 50.0%
GCGTGATGGTCAGATCTAGA+GGG + chr6.2:75097355-75097374 MS.gene068481:intron 50.0%
TCTCTGACTGGGTTATCCAG+CGG + chr6.2:75096938-75096957 MS.gene068481:intron 50.0%
TGCGTGATGGTCAGATCTAG+AGG + chr6.2:75097354-75097373 MS.gene068481:intron 50.0%
!! GAAGTTGGTGATGGTGACTG+TGG + chr6.2:75097588-75097607 MS.gene068481:CDS 50.0%
!! GCAGATGGAGATGGTGGAAT+TGG - chr6.2:75096627-75096646 None:intergenic 50.0%
!! TGGGACAGTGAAGTTGGTGA+TGG + chr6.2:75097579-75097598 MS.gene068481:CDS 50.0%
!! GGAGATGGTGGAATTGGAGC+AGG - chr6.2:75096621-75096640 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 75096595 75098113 75096595 ID=MS.gene068481
chr6.2 mRNA 75096595 75098113 75096595 ID=MS.gene068481.t1;Parent=MS.gene068481
chr6.2 exon 75096595 75096659 75096595 ID=MS.gene068481.t1.exon1;Parent=MS.gene068481.t1
chr6.2 CDS 75096595 75096659 75096595 ID=cds.MS.gene068481.t1;Parent=MS.gene068481.t1
chr6.2 exon 75097474 75097617 75097474 ID=MS.gene068481.t1.exon2;Parent=MS.gene068481.t1
chr6.2 CDS 75097474 75097617 75097474 ID=cds.MS.gene068481.t1;Parent=MS.gene068481.t1
chr6.2 exon 75097712 75097752 75097712 ID=MS.gene068481.t1.exon3;Parent=MS.gene068481.t1
chr6.2 CDS 75097712 75097752 75097712 ID=cds.MS.gene068481.t1;Parent=MS.gene068481.t1
chr6.2 exon 75098030 75098113 75098030 ID=MS.gene068481.t1.exon4;Parent=MS.gene068481.t1
chr6.2 CDS 75098030 75098113 75098030 ID=cds.MS.gene068481.t1;Parent=MS.gene068481.t1
Gene Sequence

>MS.gene068481

GTAATCGTCTGGCTGCAAAGATTCCTGCTCCAATTCCACCATCTCCATCTGCAAAGATTGTTGAGGTATTTTCATTAAAATTGTGTCATTTCTCTTCTATGACACGAACCAATTGTAATATACCCTCCGGTCACTATTATATCCAAAAAACCACTTTTTAGATTCATTGAATATGTATCTGGTGACCAGATACATCAGCTATACAATGAATCTAAAAGGTGTTTTCTTGCTTACAATAGTTACTGAAGGGAGTAAGAATTTAGTCAAGGACAAATCATGTTTACTTAATAACCCTGTGAAGATGTTCATGCGGATCCTTAATCAAATTAGGGCATTATCTGAGTCTCTGACTGGGTTATCCAGCGGTTTTTCTGTTTTAGTTCATGTCTGCTGGCTAGCATTTGATTTATTTTACTAAGCTTTGTTATCTCTGTGGTTAGCTGTAATTTTGACATATTTTTTTGTTGTTGAGGAAAGCTGTAATTTTGAGATCTTCATTGGTTTAATAATTTATTTCACTAGCTAGGACATCTCTAGCTCAAACATGTGAATAATTAAGATGATAATCATATTTTATCTGTATGTAATATCGTTATTATGCCCAACAAATCTTATTTCCAGTTACCTTGAAGCCTCTATCGGTTAACAGAAAATAGTATTTGCAACAAATTTCATGTTCAACTTTTATTGATATTTGATGCAACAGTTCAACTTCAACAATTTAAAGTCCTTTCCCTCCTACCACCAATTTATGTACCTTGCGTGATGGTCAGATCTAGAGGGAAATAAATCTTTTTTTTTGTCAGAAGCTTCCCTACCCCTCCCTCTTATTTACTAATGTAATTTGTGAAATCTGGTTCCATATTTGCTTCATGTAAGGCACAGAGTCAGCCTCTAGAATTAACTGAGCAAGGACAACTTCTTGAGCTAGCCATTGTAGCTGCTGCTAATGCACTTATAAATCTCAAGGACACACTAAATGAATGGGACAGTGAAGTTGGTGATGGTGACTGTGGTTCAACTGTGAGTCTTATCCTCAAAATTGTCTGCTTATTTACTATATGATTTGATATGTACTACATCATTCACGTTACTTTTTTTGATAAATCTTCTATAGATGCATAAAGGTGCAACGGCAGTTCTTGAAGACATGAAAAAGTAAGTTTGTTCTACATGCTGCTTTGCCTTAAGATATATTCATGGGTTACTTGTTTTGATATAATCATGGATGATTGGTGCTAATATGTCAAGTTGACACATGGCCAGTTAATAGCTCATGTACTGGATTACGGGATATATTAGTATAAGTTTTTCTATTAAGGCTTTTATAAATAACTCTTTATGCCCTTGAGAAAATGTGAAGGTGGTTGCTGCAACAGCATTGTTAATTTGAATTTGTTATGCTGTCTGACCTGAAGTACTGTTATTTTTACAGTTACCCTCTGAATGATGCTGCAGAAACTGTCGGTGAAATTGGATCAACAATTGGAAAATCAATGGGAGGAACAAGTGGGATCAT
Protein sequence

>MS.gene068481.t1

VIVWLQRFLLQFHHLHLQRLLRHRVSLUNULSKDNFLSUPLULLLMHLUISRTHUMNGTVKLVMVTVVQLCIKVQRQFLKTUKITLUMMLQKLSVKLDQQLENQWEEQVGS