AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene058268


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 67 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTACCCAGTTTGGCCATTT+TGG 0.134807 2.2:+55249003 None:intergenic
CAGCTAGTTGCAGGCCTTCT+AGG 0.184241 2.2:-55248234 MS.gene058268:CDS
AAGGATATTATCTTGCAATT+TGG 0.237243 2.2:-55248974 MS.gene058268:CDS
CAAACTGGGTACATTTATTA+AGG 0.242603 2.2:-55248993 MS.gene058268:CDS
CCCACCTATTGGGGCCAAAA+TGG 0.283148 2.2:-55249017 MS.gene058268:CDS
TGGGGCCAAAATGGCCAAAC+TGG 0.309884 2.2:-55249008 MS.gene058268:CDS
TCAGCGCTTAGGAATGAATT+AGG 0.319413 2.2:-55248105 MS.gene058268:CDS
CTTAATAAATGTACCCAGTT+TGG 0.325391 2.2:+55248994 None:intergenic
ATTCCTTATGTCGGTCTTAC+CGG 0.330047 2.2:-55248626 MS.gene058268:CDS
GAAATATTGAGAATTGTATA+TGG 0.347955 2.2:-55247997 MS.gene058268:CDS
ACAATTCTCAATATTTCAAT+TGG 0.353451 2.2:+55248003 None:intergenic
ATCTCAGGAAATATCCTTGC+TGG 0.373800 2.2:-55248057 MS.gene058268:CDS
CAATTTGGTTTGCAAGAAGT+TGG 0.389960 2.2:-55248959 MS.gene058268:CDS
GCATGGAAGGTGTATCCTTA+TGG 0.391268 2.2:-55248159 MS.gene058268:CDS
TGGATTGGATGTAGTTGATT+CGG 0.408733 2.2:-55249059 MS.gene058268:CDS
CTTAGATCCATACATGGCCT+TGG 0.431043 2.2:+55248755 None:intergenic
AAGTTGACATCATTTGCATA+TGG 0.448703 2.2:+55248668 None:intergenic
GGGGTTCCCAAGGCCATGTA+TGG 0.457536 2.2:-55248762 MS.gene058268:CDS
GGCCTTCTAGGAGTGGAATC+AGG 0.458196 2.2:-55248222 MS.gene058268:CDS
GGCCTGATTCCACTCCTAGA+AGG 0.458732 2.2:+55248220 None:intergenic
TCATTTGCATATGGATCAAA+AGG 0.461244 2.2:+55248677 None:intergenic
AGCAAGGATATTTCCTGAGA+TGG 0.467561 2.2:+55248059 None:intergenic
AAGGTGATGGATAGTGCCTT+TGG 0.473626 2.2:-55248716 MS.gene058268:CDS
TGCAAGAAGTTGGACATTTG+AGG 0.477314 2.2:-55248949 MS.gene058268:intron
TGGATCATTAGGTCATGGAT+TGG 0.491581 2.2:-55249074 None:intergenic
TCCTACAAAATGCTACTTCG+AGG 0.497607 2.2:-55248583 MS.gene058268:CDS
GTCGGTCTTACCGGCTATGT+TGG 0.505513 2.2:-55248617 MS.gene058268:CDS
TCTGCCACAGTTACTCCATA+AGG 0.507698 2.2:+55248144 None:intergenic
TTAGATCCATACATGGCCTT+GGG 0.510288 2.2:+55248756 None:intergenic
CTAATCGCATCTCAGCGCTT+AGG 0.514135 2.2:-55248116 MS.gene058268:CDS
GCTATAAAGAGCACAGTGAA+GGG 0.515388 2.2:-55248782 MS.gene058268:CDS
ATCATCATTTGCCAAGGTGA+TGG 0.516251 2.2:-55248729 MS.gene058268:CDS
CCTCTAGGGTAGAAGCCACC+TGG 0.517093 2.2:+55247955 None:intergenic
ATAACACCATCTCCTCCTCT+AGG 0.519512 2.2:+55247940 None:intergenic
ATAAAAGATGAACCCATCTC+AGG 0.525491 2.2:-55248072 MS.gene058268:CDS
GGCTATAAAGAGCACAGTGA+AGG 0.527779 2.2:-55248783 MS.gene058268:CDS
GCAAGGATATTTCCTGAGAT+GGG 0.529908 2.2:+55248060 None:intergenic
GGATCAAAAGGTGGGTGTAG+AGG 0.531869 2.2:+55248689 None:intergenic
TGTTATACGAACGACGTGCA+TGG 0.542914 2.2:-55248176 MS.gene058268:CDS
TGGATTGGTGCCAACATAGC+CGG 0.545039 2.2:+55248607 None:intergenic
TTGAGAATTGTATATGGAAG+TGG 0.548661 2.2:-55247991 MS.gene058268:CDS
GTTGATTCGGATTTAGCAGA+GGG 0.554995 2.2:-55249046 MS.gene058268:CDS
ATACGAACGACGTGCATGGA+AGG 0.556244 2.2:-55248172 MS.gene058268:CDS
TTCTACCCTAGAGGAGGAGA+TGG 0.561993 2.2:-55247946 MS.gene058268:CDS
ATGATCGTATAACTGCATCT+TGG 0.571142 2.2:+55248199 None:intergenic
TAGCCGGTAAGACCGACATA+AGG 0.572610 2.2:+55248623 None:intergenic
CTCTAGGGTAGAAGCCACCT+GGG 0.572783 2.2:+55247956 None:intergenic
GATTCGGATTTAGCAGAGGG+TGG 0.575302 2.2:-55249043 MS.gene058268:CDS
TCTTATGTGATTCCTTATGT+CGG 0.575588 2.2:-55248635 MS.gene058268:CDS
TTTGCATATGGATCAAAAGG+TGG 0.585853 2.2:+55248680 None:intergenic
AGTGGTGATGAACATGTCCC+AGG 0.596378 2.2:-55247973 MS.gene058268:CDS
TAACACCATCTCCTCCTCTA+GGG 0.597219 2.2:+55247941 None:intergenic
ACAAAATGCTACTTCGAGGA+AGG 0.597559 2.2:-55248579 MS.gene058268:intron
CCAGGTGGCTTCTACCCTAG+AGG 0.599664 2.2:-55247955 MS.gene058268:CDS
GCACAGTGAAGGGGTTCCCA+AGG 0.602015 2.2:-55248772 MS.gene058268:CDS
AGTTGCAGGCCTTCTAGGAG+TGG 0.603562 2.2:-55248229 MS.gene058268:CDS
GGGGCCAAAATGGCCAAACT+GGG 0.606123 2.2:-55249007 MS.gene058268:CDS
TTGCATATGGATCAAAAGGT+GGG 0.620461 2.2:+55248681 None:intergenic
AAGCTCATCATCATTTGCCA+AGG 0.621976 2.2:-55248735 MS.gene058268:CDS
AAAGGCACTATCCATCACCT+TGG 0.631525 2.2:+55248718 None:intergenic
AGGAATGAATTAGGAAACGA+TGG 0.646376 2.2:-55248096 MS.gene058268:CDS
GATGAGCTTAGATCCATACA+TGG 0.648355 2.2:+55248749 None:intergenic
AGTTGATTCGGATTTAGCAG+AGG 0.651747 2.2:-55249047 MS.gene058268:CDS
GGTGGCTTCTACCCTAGAGG+AGG 0.663458 2.2:-55247952 MS.gene058268:CDS
CTATAAAGAGCACAGTGAAG+GGG 0.666124 2.2:-55248781 MS.gene058268:CDS
GTATCCTTATGGAGTAACTG+TGG 0.688628 2.2:-55248148 MS.gene058268:CDS
GGTGATGAACATGTCCCAGG+TGG 0.767815 2.2:-55247970 MS.gene058268:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACATTAAAATTATTTTAGT+AGG + chr2.2:55248708-55248727 None:intergenic 10.0%
!!! TTGTATGAATCTTTATTTTA+GGG - chr2.2:55248171-55248190 MS.gene058268:CDS 15.0%
!! ACAATTCTCAATATTTCAAT+TGG + chr2.2:55248975-55248994 None:intergenic 20.0%
!! ATCTTACTTAGTACTTAATT+AGG - chr2.2:55249064-55249083 MS.gene058268:CDS 20.0%
!! GAAATATTGAGAATTGTATA+TGG - chr2.2:55248978-55248997 MS.gene058268:CDS 20.0%
!! GTTTACAAAACTAACTTAAA+AGG + chr2.2:55248626-55248645 None:intergenic 20.0%
!!! ACTTGTTAGTAATAAAAGAA+TGG - chr2.2:55248481-55248500 MS.gene058268:intron 20.0%
!!! ATGATAAAAAAAGTACTAGA+GGG + chr2.2:55248054-55248073 None:intergenic 20.0%
!!! GTTGTATGAATCTTTATTTT+AGG - chr2.2:55248170-55248189 MS.gene058268:CDS 20.0%
!!! GTTTTACTCGAAAATAAATA+AGG - chr2.2:55248575-55248594 MS.gene058268:intron 20.0%
! AAGGATATTATCTTGCAATT+TGG - chr2.2:55248001-55248020 MS.gene058268:CDS 25.0%
!!! ATTCACTTGCGATTTTATTT+AGG - chr2.2:55248542-55248561 MS.gene058268:intron 25.0%
!!! GATGATAAAAAAAGTACTAG+AGG + chr2.2:55248055-55248074 None:intergenic 25.0%
AAGTTGACATCATTTGCATA+TGG + chr2.2:55248310-55248329 None:intergenic 30.0%
CAAACTGGGTACATTTATTA+AGG - chr2.2:55247982-55248001 MS.gene058268:CDS 30.0%
CTTAATAAATGTACCCAGTT+TGG + chr2.2:55247984-55248003 None:intergenic 30.0%
TCATTTGCATATGGATCAAA+AGG + chr2.2:55248301-55248320 None:intergenic 30.0%
TCTTATGTGATTCCTTATGT+CGG - chr2.2:55248340-55248359 MS.gene058268:intron 30.0%
TTGAGAATTGTATATGGAAG+TGG - chr2.2:55248984-55249003 MS.gene058268:CDS 30.0%
AGGAATGAATTAGGAAACGA+TGG - chr2.2:55248879-55248898 MS.gene058268:intron 35.0%
ATAAAAGATGAACCCATCTC+AGG - chr2.2:55248903-55248922 MS.gene058268:intron 35.0%
ATGATCGTATAACTGCATCT+TGG + chr2.2:55248779-55248798 None:intergenic 35.0%
TTGCATATGGATCAAAAGGT+GGG + chr2.2:55248297-55248316 None:intergenic 35.0%
TTTGCATATGGATCAAAAGG+TGG + chr2.2:55248298-55248317 None:intergenic 35.0%
! TGGATTGGATGTAGTTGATT+CGG - chr2.2:55247916-55247935 MS.gene058268:CDS 35.0%
!! CAATTTGGTTTGCAAGAAGT+TGG - chr2.2:55248016-55248035 MS.gene058268:CDS 35.0%
!! GAATTTTAACAGCTAGTTGC+AGG - chr2.2:55248732-55248751 MS.gene058268:CDS 35.0%
AAGCTCATCATCATTTGCCA+AGG - chr2.2:55248240-55248259 MS.gene058268:intron 40.0%
AGCAAGGATATTTCCTGAGA+TGG + chr2.2:55248919-55248938 None:intergenic 40.0%
AGTGAATAACACGCGTCAAT+CGG + chr2.2:55248529-55248548 None:intergenic 40.0%
ATCATCATTTGCCAAGGTGA+TGG - chr2.2:55248246-55248265 MS.gene058268:intron 40.0%
ATCTCAGGAAATATCCTTGC+TGG - chr2.2:55248918-55248937 MS.gene058268:intron 40.0%
ATTCCTTATGTCGGTCTTAC+CGG - chr2.2:55248349-55248368 MS.gene058268:intron 40.0%
GATGAGCTTAGATCCATACA+TGG + chr2.2:55248229-55248248 None:intergenic 40.0%
GCAAGGATATTTCCTGAGAT+GGG + chr2.2:55248918-55248937 None:intergenic 40.0%
GTATCCTTATGGAGTAACTG+TGG - chr2.2:55248827-55248846 MS.gene058268:intron 40.0%
TCAGCGCTTAGGAATGAATT+AGG - chr2.2:55248870-55248889 MS.gene058268:intron 40.0%
TGCAAGAAGTTGGACATTTG+AGG - chr2.2:55248026-55248045 MS.gene058268:CDS 40.0%
TTAGATCCATACATGGCCTT+GGG + chr2.2:55248222-55248241 None:intergenic 40.0%
! ACAAAATGCTACTTCGAGGA+AGG - chr2.2:55248396-55248415 MS.gene058268:intron 40.0%
! AGCATTTTGTAGGAGTGGAT+TGG + chr2.2:55248386-55248405 None:intergenic 40.0%
! CTATAAAGAGCACAGTGAAG+GGG - chr2.2:55248194-55248213 MS.gene058268:CDS 40.0%
! GAAGTAGCATTTTGTAGGAG+TGG + chr2.2:55248391-55248410 None:intergenic 40.0%
! GCTATAAAGAGCACAGTGAA+GGG - chr2.2:55248193-55248212 MS.gene058268:CDS 40.0%
! GTGAATTTTCATCACCAGCA+AGG + chr2.2:55248935-55248954 None:intergenic 40.0%
! TCCTACAAAATGCTACTTCG+AGG - chr2.2:55248392-55248411 MS.gene058268:intron 40.0%
! TCCTCGAAGTAGCATTTTGT+AGG + chr2.2:55248396-55248415 None:intergenic 40.0%
!! AGTTGATTCGGATTTAGCAG+AGG - chr2.2:55247928-55247947 MS.gene058268:CDS 40.0%
!! GTTGATTCGGATTTAGCAGA+GGG - chr2.2:55247929-55247948 MS.gene058268:CDS 40.0%
AGTAGGTCGCGATGAAATCA+TGG + chr2.2:55248691-55248710 None:intergenic 45.0%
ATAACACCATCTCCTCCTCT+AGG + chr2.2:55249038-55249057 None:intergenic 45.0%
CTTAGATCCATACATGGCCT+TGG + chr2.2:55248223-55248242 None:intergenic 45.0%
GTGAATAACACGCGTCAATC+GGG + chr2.2:55248528-55248547 None:intergenic 45.0%
TAACACCATCTCCTCCTCTA+GGG + chr2.2:55249037-55249056 None:intergenic 45.0%
TCTGCCACAGTTACTCCATA+AGG + chr2.2:55248834-55248853 None:intergenic 45.0%
TGTTATACGAACGACGTGCA+TGG - chr2.2:55248799-55248818 MS.gene058268:intron 45.0%
! GCATGGAAGGTGTATCCTTA+TGG - chr2.2:55248816-55248835 MS.gene058268:intron 45.0%
! GGCTATAAAGAGCACAGTGA+AGG - chr2.2:55248192-55248211 MS.gene058268:CDS 45.0%
! TGGGTGTAGAGGTTTTCCAA+AGG + chr2.2:55248278-55248297 None:intergenic 45.0%
! TGTACCCAGTTTGGCCATTT+TGG + chr2.2:55247975-55247994 None:intergenic 45.0%
!! AAAGGCACTATCCATCACCT+TGG + chr2.2:55248260-55248279 None:intergenic 45.0%
!! AAGGTGATGGATAGTGCCTT+TGG - chr2.2:55248259-55248278 MS.gene058268:intron 45.0%
ATACGAACGACGTGCATGGA+AGG - chr2.2:55248803-55248822 MS.gene058268:intron 50.0%
CTAATCGCATCTCAGCGCTT+AGG - chr2.2:55248859-55248878 MS.gene058268:intron 50.0%
GATTCGGATTTAGCAGAGGG+TGG - chr2.2:55247932-55247951 MS.gene058268:CDS 50.0%
GGATCAAAAGGTGGGTGTAG+AGG + chr2.2:55248289-55248308 None:intergenic 50.0%
TAGCCGGTAAGACCGACATA+AGG + chr2.2:55248355-55248374 None:intergenic 50.0%
TTCTACCCTAGAGGAGGAGA+TGG - chr2.2:55249029-55249048 MS.gene058268:CDS 50.0%
! AGTGGTGATGAACATGTCCC+AGG - chr2.2:55249002-55249021 MS.gene058268:CDS 50.0%
!! ATTTTGGCCCCAATAGGTGG+GGG + chr2.2:55247959-55247978 None:intergenic 50.0%
!! CATTTTGGCCCCAATAGGTG+GGG + chr2.2:55247960-55247979 None:intergenic 50.0%
!! CCATTTTGGCCCCAATAGGT+GGG + chr2.2:55247961-55247980 None:intergenic 50.0%
!! TGGATTGGTGCCAACATAGC+CGG + chr2.2:55248371-55248390 None:intergenic 50.0%
!! TTGGCCATTTTGGCCCCAAT+AGG + chr2.2:55247965-55247984 None:intergenic 50.0%
CAGCTAGTTGCAGGCCTTCT+AGG - chr2.2:55248741-55248760 MS.gene058268:CDS 55.0%
CCCACCTATTGGGGCCAAAA+TGG - chr2.2:55247958-55247977 MS.gene058268:CDS 55.0%
GGCCTGATTCCACTCCTAGA+AGG + chr2.2:55248758-55248777 None:intergenic 55.0%
GGGGCCAAAATGGCCAAACT+GGG - chr2.2:55247968-55247987 MS.gene058268:CDS 55.0%
GGTGATGAACATGTCCCAGG+TGG - chr2.2:55249005-55249024 MS.gene058268:CDS 55.0%
TGGGGCCAAAATGGCCAAAC+TGG - chr2.2:55247967-55247986 MS.gene058268:CDS 55.0%
! AGTTGCAGGCCTTCTAGGAG+TGG - chr2.2:55248746-55248765 MS.gene058268:CDS 55.0%
! GGCCTTCTAGGAGTGGAATC+AGG - chr2.2:55248753-55248772 MS.gene058268:CDS 55.0%
! GTCGGTCTTACCGGCTATGT+TGG - chr2.2:55248358-55248377 MS.gene058268:intron 55.0%
!! CTCTAGGGTAGAAGCCACCT+GGG + chr2.2:55249022-55249041 None:intergenic 55.0%
!! GCCATTTTGGCCCCAATAGG+TGG + chr2.2:55247962-55247981 None:intergenic 55.0%
AGGGTGGACCCCCACCTATT+GGG - chr2.2:55247948-55247967 MS.gene058268:CDS 60.0%
CCAGGTGGCTTCTACCCTAG+AGG - chr2.2:55249020-55249039 MS.gene058268:CDS 60.0%
GCACAGTGAAGGGGTTCCCA+AGG - chr2.2:55248203-55248222 MS.gene058268:CDS 60.0%
GGGGTTCCCAAGGCCATGTA+TGG - chr2.2:55248213-55248232 MS.gene058268:CDS 60.0%
GGTGGCTTCTACCCTAGAGG+AGG - chr2.2:55249023-55249042 MS.gene058268:CDS 60.0%
!! CCTCTAGGGTAGAAGCCACC+TGG + chr2.2:55249023-55249042 None:intergenic 60.0%
GAGGGTGGACCCCCACCTAT+TGG - chr2.2:55247947-55247966 MS.gene058268:CDS 65.0%
GGGTGGACCCCCACCTATTG+GGG - chr2.2:55247949-55247968 MS.gene058268:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 55247912 55249085 55247912 ID=MS.gene058268
chr2.2 mRNA 55247912 55249085 55247912 ID=MS.gene058268.t1;Parent=MS.gene058268
chr2.2 exon 55248950 55249085 55248950 ID=MS.gene058268.t1.exon1;Parent=MS.gene058268.t1
chr2.2 CDS 55248950 55249085 55248950 ID=cds.MS.gene058268.t1;Parent=MS.gene058268.t1
chr2.2 exon 55248580 55248805 55248580 ID=MS.gene058268.t1.exon2;Parent=MS.gene058268.t1
chr2.2 CDS 55248580 55248805 55248580 ID=cds.MS.gene058268.t1;Parent=MS.gene058268.t1
chr2.2 exon 55247912 55248253 55247912 ID=MS.gene058268.t1.exon3;Parent=MS.gene058268.t1
chr2.2 CDS 55247912 55248253 55247912 ID=cds.MS.gene058268.t1;Parent=MS.gene058268.t1
Gene Sequence

>MS.gene058268

GTCATGGATTGGATGTAGTTGATTCGGATTTAGCAGAGGGTGGACCCCCACCTATTGGGGCCAAAATGGCCAAACTGGGTACATTTATTAAGGATATTATCTTGCAATTTGGTTTGCAAGAAGTTGGACATTTGAGGTACCCTCTAGTACTTTTTTTATCATCATCTCTTTCGTACTTTTTGAATCTTATAATTTGACATATATAGTGTTTTATTATGTCAATATATCTTGAGAGTCAAGTTTATTGTTTAAAGTGAAGTTGTATGAATCTTTATTTTAGGGCTATAAAGAGCACAGTGAAGGGGTTCCCAAGGCCATGTATGGATCTAAGCTCATCATCATTTGCCAAGGTGATGGATAGTGCCTTTGGAAAACCTCTACACCCACCTTTTGATCCATATGCAAATGATGTCAACTTTCTGCTTGCATCTTATGTGATTCCTTATGTCGGTCTTACCGGCTATGTTGGCACCAATCCACTCCTACAAAATGCTACTTCGAGGAAGGTATATCATCATACTCATCATATTAAAACTTTTCAAAACTATAGAAAAATCGATCAAGCATGTACTTGTTAGTAATAAAAGAATGGCACAATTCTATTTAAAAAATACCCGATTGACGCGTGTTATTCACTTGCGATTTTATTTAGGAAAATTTCAAGTTTTACTCGAAAATAAATAAGGCTGAAAATAGTTTATTAATAGATCACCTTTTAAGTTAGTTTTGTAAACATTAGTTAGACTCGATATAAAAAACTTCATAATTTTTTTTTACCATGATTTCATCGCGACCTACTAAAATAATTTTAATGTTGTGTGAATTTTAACAGCTAGTTGCAGGCCTTCTAGGAGTGGAATCAGGCCAAGATGCAGTTATACGATCATTGTTATACGAACGACGTGCATGGAAGGTGTATCCTTATGGAGTAACTGTGGCAGAGTTCACTAATCGCATCTCAGCGCTTAGGAATGAATTAGGAAACGATGGTATAAAAGATGAACCCATCTCAGGAAATATCCTTGCTGGTGATGAAAATTCACTATCATATTCAAGAACTCCAATTGAAATATTGAGAATTGTATATGGAAGTGGTGATGAACATGTCCCAGGTGGCTTCTACCCTAGAGGAGGAGATGGTGTTATAGCAAAATCTTACTTAGTACTTAATTAG

Protein sequence

>MS.gene058268.t1

VMDWMULIRIUQRVDPHLLGPKWPNWVHLLRILSCNLVCKKLDIUGLURAQURGSQGHVWIUAHHHLPRUWIVPLENLYTHLLIHMQMMSTFCLHLMUFLMSVLPAMLAPIHSYKMLLRGSULQAFUEWNQAKMQLYDHCYTNDVHGRCILMEULWQSSLIASQRLGMNUETMVUKMNPSQEISLLVMKIHYHIQELQLKYUELYMEVVMNMSQVASTLEEEMVLUQNLTUYLI