AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65307

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65307.t1 MTR_5g023880 57.609 184 35 5 1 158 1 167 4.89e-58 179
MS.gene65307.t1 MTR_5g023900 54.237 177 59 3 1 157 1 175 1.47e-56 176
MS.gene65307.t1 MTR_5g023870 67.910 134 24 4 1 130 1 119 3.62e-54 167
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 69 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTCGGAAGGGTTAGGTTT+AGG 0.237072 5.2:-14769729 None:intergenic
TCTCGGAAGGGTTAGGTTTA+GGG 0.267292 5.2:-14769728 None:intergenic
TTGAGGGGACTTGTTGTTGG+TGG 0.289994 5.2:-14769760 None:intergenic
GGGCTTCTTGATCGTCCTCT+TGG 0.324765 5.2:-14770661 None:intergenic
TGCTTATCAGTTGTATCGGC+TGG 0.335441 5.2:-14770682 None:intergenic
GTCTTGAGGGGACTTGTTGT+TGG 0.343036 5.2:-14769763 None:intergenic
AGTTGGGTTGGTTTCTTTGA+GGG 0.364234 5.2:-14769805 None:intergenic
GTTGAATTCTCGGAAGGGTT+AGG 0.378551 5.2:-14769735 None:intergenic
GGCTTCTTGATCGTCCTCTT+GGG 0.380085 5.2:-14770660 None:intergenic
TAGTTGGGTTGGTTTCTTTG+AGG 0.387471 5.2:-14769806 None:intergenic
AAAGAACTCTGAAGGGTAGT+TGG 0.402173 5.2:-14769822 None:intergenic
TGAGGGGACTTGTTGTTGGT+GGG 0.402381 5.2:-14769759 None:intergenic
AGGGGACTTGTTGTTGGTGG+GGG 0.408399 5.2:-14769757 None:intergenic
TCAGAGTCCTCTATCTCTAT+TGG 0.410192 5.2:-14770567 None:intergenic
CTCTTGGGCCTTCCTTCCTC+TGG 0.410975 5.2:-14770645 None:intergenic
AAGAACTCTGAAGGGTAGTT+GGG 0.428150 5.2:-14769821 None:intergenic
CATGGTTATTCAGCACCTCC+TGG 0.431962 5.2:+14770014 MS.gene65307:CDS
TACAATGTCAAGTCAGGAAG+AGG 0.434728 5.2:+14770590 MS.gene65307:CDS
TCTTTAAGAGCTCGTGAGAA+TGG 0.434908 5.2:+14769840 MS.gene65307:CDS
CAGTGTTGTTGTTTGCGCCT+TGG 0.435389 5.2:-14770620 None:intergenic
ACCTCAACCTGATCAATATG+AGG 0.437745 5.2:+14770073 MS.gene65307:CDS
AGGTGGGGTGGCTGTTGATG+TGG 0.445640 5.2:-14770054 None:intergenic
CATCAGAGGGAGGGTCTTGA+GGG 0.445658 5.2:-14769776 None:intergenic
CCCTCATATTGATCAGGTTG+AGG 0.453934 5.2:-14770074 None:intergenic
GCAAACATGTGTTTCCCACT+TGG 0.463748 5.2:+14769943 MS.gene65307:CDS
CTTTAAGAGCTCGTGAGAAT+GGG 0.465502 5.2:+14769841 MS.gene65307:CDS
AAGTGATGGTCAAGCTATGA+AGG 0.473835 5.2:+14769890 MS.gene65307:CDS
AAGCCAGCCAATAGAGATAG+AGG 0.474391 5.2:+14770560 MS.gene65307:CDS
GCTGTTGATGTGGAAGGAAG+TGG 0.478632 5.2:-14770044 None:intergenic
CTCTGATACAATGTCAAGTC+AGG 0.478904 5.2:+14770584 MS.gene65307:CDS
CATATTGATCAGGTTGAGGT+GGG 0.500892 5.2:-14770070 None:intergenic
AGTCCTCTATCTCTATTGGC+TGG 0.503791 5.2:-14770563 None:intergenic
TCATCAGAGGGAGGGTCTTG+AGG 0.508193 5.2:-14769777 None:intergenic
ACTCTGAAGGGTAGTTGGGT+TGG 0.513668 5.2:-14769817 None:intergenic
AGCTCGTGAGAATGGGAAGC+TGG 0.517710 5.2:+14769848 MS.gene65307:CDS
CAAACATGTGTTTCCCACTT+GGG 0.531651 5.2:+14769944 MS.gene65307:CDS
GCTTATCAGTTGTATCGGCT+GGG 0.531837 5.2:-14770681 None:intergenic
TATATTTGTTGTCATCCTCA+TGG 0.532111 5.2:+14769996 MS.gene65307:CDS
TTGATCAGGTTGAGGTGGGG+TGG 0.544768 5.2:-14770066 None:intergenic
GAGGGGACTTGTTGTTGGTG+GGG 0.544991 5.2:-14769758 None:intergenic
TCATATTGATCAGGTTGAGG+TGG 0.558741 5.2:-14770071 None:intergenic
ACACTGGACCAGAGGAAGGA+AGG 0.561168 5.2:+14770637 MS.gene65307:CDS
TTTGAGGGATTCATCATCAG+AGG 0.561409 5.2:-14769790 None:intergenic
GAGCTGCTTATCAGTTGTAT+CGG 0.563493 5.2:-14770686 None:intergenic
GAGCTCTTAAAGAACTCTGA+AGG 0.564348 5.2:-14769830 None:intergenic
TTGAGGGATTCATCATCAGA+GGG 0.579951 5.2:-14769789 None:intergenic
CAAGGCGCAAACAACAACAC+TGG 0.583137 5.2:+14770621 MS.gene65307:CDS
AAACAACAACACTGGACCAG+AGG 0.583233 5.2:+14770629 MS.gene65307:CDS
CAGGAAGAGGGAAGGAACCA+AGG 0.586582 5.2:+14770603 MS.gene65307:CDS
GGGGTGGCTGTTGATGTGGA+AGG 0.586960 5.2:-14770050 None:intergenic
ATATTGATCAGGTTGAGGTG+GGG 0.595131 5.2:-14770069 None:intergenic
AACAACACTGGACCAGAGGA+AGG 0.595528 5.2:+14770633 MS.gene65307:CDS
CAGAGGAAGGAAGGCCCAAG+AGG 0.596615 5.2:+14770646 MS.gene65307:CDS
AGTGATGGTCAAGCTATGAA+GGG 0.603559 5.2:+14769891 MS.gene65307:CDS
AATGGGAAGCTGGCAGCTGA+TGG 0.610197 5.2:+14769858 MS.gene65307:CDS
AAGCTGGCAGCTGATGGCGA+AGG 0.613924 5.2:+14769864 MS.gene65307:CDS
AGCTCTTAAAGAACTCTGAA+GGG 0.626255 5.2:-14769829 None:intergenic
AGGGATTCATCATCAGAGGG+AGG 0.627786 5.2:-14769786 None:intergenic
CTTCATCAAAGTAGCCCAAG+TGG 0.635469 5.2:-14769958 None:intergenic
ATGGTCAAGCTATGAAGGGG+AGG 0.636182 5.2:+14769895 MS.gene65307:CDS
ACAATGTCAAGTCAGGAAGA+GGG 0.642713 5.2:+14770591 MS.gene65307:CDS
GGGATTCATCATCAGAGGGA+GGG 0.650027 5.2:-14769785 None:intergenic
CCTCAACCTGATCAATATGA+GGG 0.650750 5.2:+14770074 MS.gene65307:CDS
ATCAGAGGGAGGGTCTTGAG+GGG 0.650850 5.2:-14769775 None:intergenic
TTCATCAAAGTAGCCCAAGT+GGG 0.657037 5.2:-14769957 None:intergenic
TGTCAAGTCAGGAAGAGGGA+AGG 0.657401 5.2:+14770595 MS.gene65307:CDS
GATGGCGAAGGAGTAAGTGA+TGG 0.658846 5.2:+14769876 MS.gene65307:CDS
GTGATGGTCAAGCTATGAAG+GGG 0.659294 5.2:+14769892 MS.gene65307:CDS
GGAGGTGCTGAATAACCATG+AGG 0.763451 5.2:-14770011 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATTAAATAATTGAATCT+TGG - chr5.2:14770220-14770239 None:intergenic 15.0%
!!! TTTTTCACACTATAATTTTT+AGG + chr5.2:14770150-14770169 MS.gene65307:intron 15.0%
!!! AATGTTTTTCTTTTGTTACT+AGG + chr5.2:14770528-14770547 MS.gene65307:intron 20.0%
!!! ACAATAAATAGTTTTGAGAT+AGG - chr5.2:14770119-14770138 None:intergenic 20.0%
! CATATATATGTTTGTGTCTA+TGG - chr5.2:14770345-14770364 None:intergenic 25.0%
! TTATGAGATCTAATTCATGT+AGG + chr5.2:14770388-14770407 MS.gene65307:intron 25.0%
!!! TAGTTTTGAGATAGGAAATT+AGG - chr5.2:14770111-14770130 None:intergenic 25.0%
GAATCTTGGACATGATATAT+AGG - chr5.2:14770206-14770225 None:intergenic 30.0%
TATATAGGCAATAAAACCCT+AGG - chr5.2:14770191-14770210 None:intergenic 30.0%
!! TATATTTGTTGTCATCCTCA+TGG + chr5.2:14769996-14770015 MS.gene65307:CDS 30.0%
AGCTCTTAAAGAACTCTGAA+GGG - chr5.2:14769832-14769851 None:intergenic 35.0%
! GTTTTACCCTCATATTGATC+AGG - chr5.2:14770083-14770102 None:intergenic 35.0%
AAGTGATGGTCAAGCTATGA+AGG + chr5.2:14769890-14769909 MS.gene65307:CDS 40.0%
ACAATGTCAAGTCAGGAAGA+GGG + chr5.2:14770591-14770610 MS.gene65307:CDS 40.0%
ACCTCAACCTGATCAATATG+AGG + chr5.2:14770073-14770092 MS.gene65307:CDS 40.0%
AGTGATGGTCAAGCTATGAA+GGG + chr5.2:14769891-14769910 MS.gene65307:CDS 40.0%
CAAACATGTGTTTCCCACTT+GGG + chr5.2:14769944-14769963 MS.gene65307:CDS 40.0%
CCTCAACCTGATCAATATGA+GGG + chr5.2:14770074-14770093 MS.gene65307:CDS 40.0%
CTCTGATACAATGTCAAGTC+AGG + chr5.2:14770584-14770603 MS.gene65307:CDS 40.0%
GAGCTCTTAAAGAACTCTGA+AGG - chr5.2:14769833-14769852 None:intergenic 40.0%
TACAATGTCAAGTCAGGAAG+AGG + chr5.2:14770590-14770609 MS.gene65307:CDS 40.0%
TCAGAGTCCTCTATCTCTAT+TGG - chr5.2:14770570-14770589 None:intergenic 40.0%
TTCATCAAAGTAGCCCAAGT+GGG - chr5.2:14769960-14769979 None:intergenic 40.0%
TTGAGGGATTCATCATCAGA+GGG - chr5.2:14769792-14769811 None:intergenic 40.0%
TTTGAGGGATTCATCATCAG+AGG - chr5.2:14769793-14769812 None:intergenic 40.0%
! AAAGAACTCTGAAGGGTAGT+TGG - chr5.2:14769825-14769844 None:intergenic 40.0%
! AAGAACTCTGAAGGGTAGTT+GGG - chr5.2:14769824-14769843 None:intergenic 40.0%
! CTTTAAGAGCTCGTGAGAAT+GGG + chr5.2:14769841-14769860 MS.gene65307:CDS 40.0%
! TCTTTAAGAGCTCGTGAGAA+TGG + chr5.2:14769840-14769859 MS.gene65307:CDS 40.0%
!! AGTTGGGTTGGTTTCTTTGA+GGG - chr5.2:14769808-14769827 None:intergenic 40.0%
!! ATATTGATCAGGTTGAGGTG+GGG - chr5.2:14770072-14770091 None:intergenic 40.0%
!! CATATTGATCAGGTTGAGGT+GGG - chr5.2:14770073-14770092 None:intergenic 40.0%
!! TAGTTGGGTTGGTTTCTTTG+AGG - chr5.2:14769809-14769828 None:intergenic 40.0%
!! TCATATTGATCAGGTTGAGG+TGG - chr5.2:14770074-14770093 None:intergenic 40.0%
AAACAACAACACTGGACCAG+AGG + chr5.2:14770629-14770648 MS.gene65307:CDS 45.0%
AAGCCAGCCAATAGAGATAG+AGG + chr5.2:14770560-14770579 MS.gene65307:CDS 45.0%
AGTCCTCTATCTCTATTGGC+TGG - chr5.2:14770566-14770585 None:intergenic 45.0%
CTTCATCAAAGTAGCCCAAG+TGG - chr5.2:14769961-14769980 None:intergenic 45.0%
GAAGGAAGTGGAGAAAAACC+AGG - chr5.2:14770035-14770054 None:intergenic 45.0%
GCAAACATGTGTTTCCCACT+TGG + chr5.2:14769943-14769962 MS.gene65307:CDS 45.0%
GCAATAAAACCCTAGGTCAC+TGG - chr5.2:14770184-14770203 None:intergenic 45.0%
GTGATGGTCAAGCTATGAAG+GGG + chr5.2:14769892-14769911 MS.gene65307:CDS 45.0%
GTTGAATTCTCGGAAGGGTT+AGG - chr5.2:14769738-14769757 None:intergenic 45.0%
TCTCGGAAGGGTTAGGTTTA+GGG - chr5.2:14769731-14769750 None:intergenic 45.0%
TTCTCGGAAGGGTTAGGTTT+AGG - chr5.2:14769732-14769751 None:intergenic 45.0%
! CCCTCATATTGATCAGGTTG+AGG - chr5.2:14770077-14770096 None:intergenic 45.0%
!!! TAATTTTTTTTATAACTTAT+TGG + chr5.2:14770429-14770448 MS.gene65307:intron 5.0%
AACAACACTGGACCAGAGGA+AGG + chr5.2:14770633-14770652 MS.gene65307:CDS 50.0%
AGGGATTCATCATCAGAGGG+AGG - chr5.2:14769789-14769808 None:intergenic 50.0%
ATGGTCAAGCTATGAAGGGG+AGG + chr5.2:14769895-14769914 MS.gene65307:CDS 50.0%
CAAGGCGCAAACAACAACAC+TGG + chr5.2:14770621-14770640 MS.gene65307:CDS 50.0%
CATGGTTATTCAGCACCTCC+TGG + chr5.2:14770014-14770033 MS.gene65307:CDS 50.0%
GATGGCGAAGGAGTAAGTGA+TGG + chr5.2:14769876-14769895 MS.gene65307:CDS 50.0%
GCTGTTGATGTGGAAGGAAG+TGG - chr5.2:14770047-14770066 None:intergenic 50.0%
GGAAGTGGAGAAAAACCAGG+AGG - chr5.2:14770032-14770051 None:intergenic 50.0%
GGCTTCTTGATCGTCCTCTT+GGG - chr5.2:14770663-14770682 None:intergenic 50.0%
GGGATTCATCATCAGAGGGA+GGG - chr5.2:14769788-14769807 None:intergenic 50.0%
GTCAACACTCCAGTGACCTA+GGG + chr5.2:14770172-14770191 MS.gene65307:intron 50.0%
TGGGGGTTGAATTCTCGGAA+GGG - chr5.2:14769743-14769762 None:intergenic 50.0%
TGTCAAGTCAGGAAGAGGGA+AGG + chr5.2:14770595-14770614 MS.gene65307:CDS 50.0%
! ACTCTGAAGGGTAGTTGGGT+TGG - chr5.2:14769820-14769839 None:intergenic 50.0%
! GTTGGTGGGGGTTGAATTCT+CGG - chr5.2:14769748-14769767 None:intergenic 50.0%
!! CAGTGTTGTTGTTTGCGCCT+TGG - chr5.2:14770623-14770642 None:intergenic 50.0%
!! GGAGGTGCTGAATAACCATG+AGG - chr5.2:14770014-14770033 None:intergenic 50.0%
!! GTCTTGAGGGGACTTGTTGT+TGG - chr5.2:14769766-14769785 None:intergenic 50.0%
!! TGAGGGGACTTGTTGTTGGT+GGG - chr5.2:14769762-14769781 None:intergenic 50.0%
!! TTGAGGGGACTTGTTGTTGG+TGG - chr5.2:14769763-14769782 None:intergenic 50.0%
AATGGGAAGCTGGCAGCTGA+TGG + chr5.2:14769858-14769877 MS.gene65307:CDS 55.0%
ACACTGGACCAGAGGAAGGA+AGG + chr5.2:14770637-14770656 MS.gene65307:CDS 55.0%
AGCTCGTGAGAATGGGAAGC+TGG + chr5.2:14769848-14769867 MS.gene65307:CDS 55.0%
ATCAGAGGGAGGGTCTTGAG+GGG - chr5.2:14769778-14769797 None:intergenic 55.0%
CAGGAAGAGGGAAGGAACCA+AGG + chr5.2:14770603-14770622 MS.gene65307:CDS 55.0%
CATCAGAGGGAGGGTCTTGA+GGG - chr5.2:14769779-14769798 None:intergenic 55.0%
GGGCTTCTTGATCGTCCTCT+TGG - chr5.2:14770664-14770683 None:intergenic 55.0%
GGTCAACACTCCAGTGACCT+AGG + chr5.2:14770171-14770190 MS.gene65307:intron 55.0%
GTGGGGGTTGAATTCTCGGA+AGG - chr5.2:14769744-14769763 None:intergenic 55.0%
TCATCAGAGGGAGGGTCTTG+AGG - chr5.2:14769780-14769799 None:intergenic 55.0%
!! AGGGGACTTGTTGTTGGTGG+GGG - chr5.2:14769760-14769779 None:intergenic 55.0%
!! GAGGGGACTTGTTGTTGGTG+GGG - chr5.2:14769761-14769780 None:intergenic 55.0%
!! TTGATCAGGTTGAGGTGGGG+TGG - chr5.2:14770069-14770088 None:intergenic 55.0%
AGGTGGGGTGGCTGTTGATG+TGG - chr5.2:14770057-14770076 None:intergenic 60.0%
CAGAGGAAGGAAGGCCCAAG+AGG + chr5.2:14770646-14770665 MS.gene65307:CDS 60.0%
CTCTTGGGCCTTCCTTCCTC+TGG - chr5.2:14770648-14770667 None:intergenic 60.0%
GGGGTGGCTGTTGATGTGGA+AGG - chr5.2:14770053-14770072 None:intergenic 60.0%
! AAGCTGGCAGCTGATGGCGA+AGG + chr5.2:14769864-14769883 MS.gene65307:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 14769720 14770698 14769720 ID=MS.gene65307
chr5.2 mRNA 14769720 14770698 14769720 ID=MS.gene65307.t1;Parent=MS.gene65307
chr5.2 exon 14769720 14770095 14769720 ID=MS.gene65307.t1.exon1;Parent=MS.gene65307.t1
chr5.2 CDS 14769720 14770095 14769720 ID=cds.MS.gene65307.t1;Parent=MS.gene65307.t1
chr5.2 exon 14770550 14770698 14770550 ID=MS.gene65307.t1.exon2;Parent=MS.gene65307.t1
chr5.2 CDS 14770550 14770698 14770550 ID=cds.MS.gene65307.t1;Parent=MS.gene65307.t1
Gene Sequence

>MS.gene65307

ATGCAGAACCCTAAACCTAACCCTTCCGAGAATTCAACCCCCACCAACAACAAGTCCCCTCAAGACCCTCCCTCTGATGATGAATCCCTCAAAGAAACCAACCCAACTACCCTTCAGAGTTCTTTAAGAGCTCGTGAGAATGGGAAGCTGGCAGCTGATGGCGAAGGAGTAAGTGATGGTCAAGCTATGAAGGGGAGGAAGAGTAATATTTGTTGTCATAGATGCAAACATGTGTTTCCCACTTGGGCTACTTTGATGAAGCATTATCAAGAACACTATATTTGTTGTCATCCTCATGGTTATTCAGCACCTCCTGGTTTTTCTCCACTTCCTTCCACATCAACAGCCACCCCACCTCAACCTGATCAATATGAGGGTAAAACTAAAACCTAATTTCCTATCTCAAAACTATTTATTGTCATGTCTTTTTTTTTTCACACTATAATTTTTAGGTCAACACTCCAGTGACCTAGGGTTTTATTGCCTATATATCATGTCCAAGATTCAATTATTTAATGTTATATAATTATTATTTTTTTCATTTAATTATTTTGATTTCAAAGTACTTGTGTATAGATCATTCATAAAATACTTGTGTATAGATCATTCATAAAAGATTGCACCATAGACACAAACATATATATGTTCACTTTGAGTGTTGCTTAATTTTATGAGATCTAATTCATGTAGGCATCTATATATATATCTTTAATTTTTTTTATAACTTATTGGTTTTTAATTTAACAATTTGTTTTTTTTTCTTTCAAACTAATGATTTTACAATGAAGCAATTATAATTATAATTTTGAATGTTTTTCTTTTGTTACTAGGTGATGATCAAAGCCAGCCAATAGAGATAGAGGACTCTGATACAATGTCAAGTCAGGAAGAGGGAAGGAACCAAGGCGCAAACAACAACACTGGACCAGAGGAAGGAAGGCCCAAGAGGACGATCAAGAAGCCCAGCCGATACAACTGA
Protein sequence

>MS.gene65307.t1

MQNPKPNPSENSTPTNNKSPQDPPSDDESLKETNPTTLQSSLRARENGKLAADGEGVSDGQAMKGRKSNICCHRCKHVFPTWATLMKHYQEHYICCHPHGYSAPPGFSPLPSTSTATPPQPDQYEGDDQSQPIEIEDSDTMSSQEEGRNQGANNNTGPEEGRPKRTIKKPSRYN