AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene055701


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055701.t1 MTR_1g057790 99.174 242 2 0 1 242 408 649 2.06e-177 502
MS.gene055701.t1 MTR_7g106320 63.424 257 63 9 1 242 420 660 3.31e-98 300
MS.gene055701.t1 MTR_4g051532 36.538 260 133 12 1 241 464 710 2.46e-29 115
MS.gene055701.t1 MTR_7g114930 91.892 37 3 0 120 156 9 45 5.28e-19 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene055701.t1 AT2G35940 45.989 187 61 9 85 242 505 680 1.22e-35 134
MS.gene055701.t1 AT2G35940 45.989 187 61 9 85 242 505 680 1.22e-35 134
MS.gene055701.t1 AT2G35940 45.989 187 61 9 85 242 505 680 1.22e-35 134

Find 53 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACAAATTTCAATGAAATT+TGG 0.179649 1.2:-45101932 MS.gene055701:CDS
CCTCATTGTGACACATTATC+AGG 0.219156 1.2:-45101743 MS.gene055701:CDS
TTCTTCCTAGTTGAATGTTT+TGG 0.253546 1.2:+45101696 None:intergenic
AATTGTGCGGCAAACCTCTT+TGG 0.296812 1.2:+45101602 None:intergenic
ACTAATTTCATTGCTGGTTT+CGG 0.310210 1.2:-45101863 MS.gene055701:CDS
AACCAAACTAATTTCATTGC+TGG 0.316269 1.2:-45101869 MS.gene055701:CDS
AACCAGCAATGAAATTAGTT+TGG 0.317050 1.2:+45101867 None:intergenic
ATTATTAGTTGTTGTTTCAT+TGG 0.321824 1.2:+45101955 None:intergenic
GTGAATGTTAGAAACAATTC+AGG 0.352767 1.2:-45102070 MS.gene055701:CDS
TAGAGATGGTTATTGTTTCA+TGG 0.358531 1.2:-45101894 MS.gene055701:CDS
TTGTTTGGAATTGAAACTTT+TGG 0.360991 1.2:+45102141 None:intergenic
CTTATTTATGCCACAAAATC+CGG 0.365359 1.2:+45101575 None:intergenic
GGAACTCTTTCTTGTGGAGT+TGG 0.373552 1.2:+45102181 None:intergenic
AACCATAGGAATGTCTTGTT+TGG 0.375205 1.2:+45102126 None:intergenic
TTTCTAACATTCACACCAAT+AGG 0.376813 1.2:+45102079 None:intergenic
ACACCATCAACTTCACCTAT+TGG 0.384849 1.2:-45102094 MS.gene055701:CDS
ATTAGCGAAACAAATGAGTT+TGG 0.384850 1.2:-45101665 MS.gene055701:CDS
TCATGGTTCCTCGTTCGCTT+TGG 0.399272 1.2:+45102007 None:intergenic
TTCAGCTTCACGGAACTTGA+TGG 0.410535 1.2:-45102046 MS.gene055701:CDS
GTTTGCCGCACAATTGTTAC+CGG 0.411095 1.2:-45101594 MS.gene055701:CDS
TTGGATTCTGTTTCCGAGGT+TGG 0.416477 1.2:+45102160 None:intergenic
TCATTGGACTTCACATGATT+CGG 0.418133 1.2:+45101971 None:intergenic
AATCTTCCGATTTCCTCCAT+TGG 0.452740 1.2:+45101833 None:intergenic
AGAGATGGTTATTGTTTCAT+GGG 0.464621 1.2:-45101893 MS.gene055701:CDS
AATGGTGTTTCACTCACTCT+TGG 0.469626 1.2:-45101770 MS.gene055701:CDS
TTTGCTTGATTTGTTGTCCT+CGG 0.470961 1.2:+45102234 None:intergenic
ATGTACATTTCCTCCACCAT+TGG 0.475080 1.2:+45102289 None:intergenic
CATTCAACTAGGAAGAAGAT+TGG 0.477777 1.2:-45101690 MS.gene055701:CDS
CAATATCCAATGGAGGAAAT+CGG 0.481438 1.2:-45101839 MS.gene055701:CDS
TCGGTGATTGAAGAATTTCA+TGG 0.493060 1.2:+45101990 None:intergenic
TTCCAAACAAGACATTCCTA+TGG 0.509814 1.2:-45102128 MS.gene055701:CDS
AATGTACATGGAAGAGATGA+AGG 0.518111 1.2:-45102275 MS.gene055701:CDS
CAATTCAGGATTCAGCTTCA+CGG 0.521074 1.2:-45102056 MS.gene055701:CDS
TTATTATTACCTGAAAACCT+TGG 0.548405 1.2:+45101791 None:intergenic
GATGATAGACAAAGTAGAGA+TGG 0.562540 1.2:-45101908 MS.gene055701:CDS
ACACCAATAGGTGAAGTTGA+TGG 0.562831 1.2:+45102091 None:intergenic
TCTTTGGAAACCAATGGTGG+AGG 0.574109 1.2:-45102299 None:intergenic
ATGAAGGATCAAGAGCTGAA+TGG 0.575119 1.2:-45102259 MS.gene055701:CDS
CCAAACCAAAACATTCAACT+AGG 0.581717 1.2:-45101701 MS.gene055701:CDS
AAGCAAGTCCAAAGCGAACG+AGG 0.604196 1.2:-45102015 MS.gene055701:CDS
AATGGTGGAGGAAATGTACA+TGG 0.609719 1.2:-45102287 MS.gene055701:CDS
TGGTTTCGGTCAATATCCAA+TGG 0.615136 1.2:-45101849 MS.gene055701:CDS
TTTCATCGAAGGATCGTCAT+CGG 0.623127 1.2:+45102207 None:intergenic
GAGGTTGGAACTCTTTCTTG+TGG 0.623921 1.2:+45102175 None:intergenic
ATGCGGAACAATTTGCACCA+AGG 0.636094 1.2:-45101808 MS.gene055701:CDS
TCAACATGCAGAATCCAAAG+AGG 0.639986 1.2:-45101616 MS.gene055701:CDS
GGTGTTGAAACTGAAACCAT+AGG 0.645975 1.2:+45102112 None:intergenic
TCAAGAGCTGAATGGTTCCG+AGG 0.663324 1.2:-45102251 MS.gene055701:CDS
GGAAATCGGAAGATTTGATG+CGG 0.664371 1.2:-45101825 MS.gene055701:CDS
CCTGATAATGTGTCACAATG+AGG 0.665244 1.2:+45101743 None:intergenic
ACAAGAAAGAGTTCCAACCT+CGG 0.675024 1.2:-45102173 MS.gene055701:CDS
AAAATCCGGTAACAATTGTG+CGG 0.678724 1.2:+45101589 None:intergenic
TTTCGGTCAATATCCAATGG+AGG 0.697787 1.2:-45101846 MS.gene055701:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAACAAATTTCAATGAAATT+TGG - chr1.2:45101934-45101953 MS.gene055701:CDS 20.0%
!!! ATTATTAGTTGTTGTTTCAT+TGG + chr1.2:45101914-45101933 None:intergenic 20.0%
! TTATTATTACCTGAAAACCT+TGG + chr1.2:45102078-45102097 None:intergenic 25.0%
!!! AGGTTTTCAGGTAATAATAA+TGG - chr1.2:45102078-45102097 MS.gene055701:CDS 25.0%
!!! TTGTTTGGAATTGAAACTTT+TGG + chr1.2:45101728-45101747 None:intergenic 25.0%
AACCAAACTAATTTCATTGC+TGG - chr1.2:45101997-45102016 MS.gene055701:CDS 30.0%
AACCAGCAATGAAATTAGTT+TGG + chr1.2:45102002-45102021 None:intergenic 30.0%
AGAGATGGTTATTGTTTCAT+GGG - chr1.2:45101973-45101992 MS.gene055701:CDS 30.0%
ATTAGCGAAACAAATGAGTT+TGG - chr1.2:45102201-45102220 MS.gene055701:CDS 30.0%
GTGAATGTTAGAAACAATTC+AGG - chr1.2:45101796-45101815 MS.gene055701:CDS 30.0%
TAGAGATGGTTATTGTTTCA+TGG - chr1.2:45101972-45101991 MS.gene055701:CDS 30.0%
TTTCTAACATTCACACCAAT+AGG + chr1.2:45101790-45101809 None:intergenic 30.0%
! TTCTTCCTAGTTGAATGTTT+TGG + chr1.2:45102173-45102192 None:intergenic 30.0%
!! ACTAATTTCATTGCTGGTTT+CGG - chr1.2:45102003-45102022 MS.gene055701:CDS 30.0%
AAAATCCGGTAACAATTGTG+CGG + chr1.2:45102280-45102299 None:intergenic 35.0%
AATGTACATGGAAGAGATGA+AGG - chr1.2:45101591-45101610 MS.gene055701:CDS 35.0%
CAATATCCAATGGAGGAAAT+CGG - chr1.2:45102027-45102046 MS.gene055701:CDS 35.0%
CATTCAACTAGGAAGAAGAT+TGG - chr1.2:45102176-45102195 MS.gene055701:CDS 35.0%
CCAAACCAAAACATTCAACT+AGG - chr1.2:45102165-45102184 MS.gene055701:CDS 35.0%
GATGATAGACAAAGTAGAGA+TGG - chr1.2:45101958-45101977 MS.gene055701:CDS 35.0%
TCATTGGACTTCACATGATT+CGG + chr1.2:45101898-45101917 None:intergenic 35.0%
TCGGTGATTGAAGAATTTCA+TGG + chr1.2:45101879-45101898 None:intergenic 35.0%
TTCCAAACAAGACATTCCTA+TGG - chr1.2:45101738-45101757 MS.gene055701:CDS 35.0%
! AACCATAGGAATGTCTTGTT+TGG + chr1.2:45101743-45101762 None:intergenic 35.0%
! ACAATTGTTACCGGATTTTG+TGG - chr1.2:45102281-45102300 MS.gene055701:CDS 35.0%
!! TTTGCTTGATTTGTTGTCCT+CGG + chr1.2:45101635-45101654 None:intergenic 35.0%
!!! CCTAGTTGAATGTTTTGGTT+TGG + chr1.2:45102168-45102187 None:intergenic 35.0%
AATCTTCCGATTTCCTCCAT+TGG + chr1.2:45102036-45102055 None:intergenic 40.0%
AATGGTGTTTCACTCACTCT+TGG - chr1.2:45102096-45102115 MS.gene055701:CDS 40.0%
ACAAGAAAGAGTTCCAACCT+CGG - chr1.2:45101693-45101712 MS.gene055701:CDS 40.0%
ACACCAATAGGTGAAGTTGA+TGG + chr1.2:45101778-45101797 None:intergenic 40.0%
ACACCATCAACTTCACCTAT+TGG - chr1.2:45101772-45101791 MS.gene055701:CDS 40.0%
ATGAAGGATCAAGAGCTGAA+TGG - chr1.2:45101607-45101626 MS.gene055701:CDS 40.0%
CAATTCAGGATTCAGCTTCA+CGG - chr1.2:45101810-45101829 MS.gene055701:CDS 40.0%
CCTCATTGTGACACATTATC+AGG - chr1.2:45102123-45102142 MS.gene055701:CDS 40.0%
GGAAATCGGAAGATTTGATG+CGG - chr1.2:45102041-45102060 MS.gene055701:CDS 40.0%
TCAACATGCAGAATCCAAAG+AGG - chr1.2:45102250-45102269 MS.gene055701:CDS 40.0%
TGGTTTCGGTCAATATCCAA+TGG - chr1.2:45102017-45102036 MS.gene055701:CDS 40.0%
TTTCATCGAAGGATCGTCAT+CGG + chr1.2:45101662-45101681 None:intergenic 40.0%
TTTCGGTCAATATCCAATGG+AGG - chr1.2:45102020-45102039 MS.gene055701:CDS 40.0%
! ACTTTTGGATTCTGTTTCCG+AGG + chr1.2:45101713-45101732 None:intergenic 40.0%
! CAATTTGCACCAAGGTTTTC+AGG - chr1.2:45102066-45102085 MS.gene055701:CDS 40.0%
! CCTGATAATGTGTCACAATG+AGG + chr1.2:45102126-45102145 None:intergenic 40.0%
! GGTGTTGAAACTGAAACCAT+AGG + chr1.2:45101757-45101776 None:intergenic 40.0%
AATTGTGCGGCAAACCTCTT+TGG + chr1.2:45102267-45102286 None:intergenic 45.0%
ATGCGGAACAATTTGCACCA+AGG - chr1.2:45102058-45102077 MS.gene055701:CDS 45.0%
GAGGTTGGAACTCTTTCTTG+TGG + chr1.2:45101694-45101713 None:intergenic 45.0%
GGAACTCTTTCTTGTGGAGT+TGG + chr1.2:45101688-45101707 None:intergenic 45.0%
GTTTGCCGCACAATTGTTAC+CGG - chr1.2:45102272-45102291 MS.gene055701:CDS 45.0%
TTCAGCTTCACGGAACTTGA+TGG - chr1.2:45101820-45101839 MS.gene055701:CDS 45.0%
TTGGATTCTGTTTCCGAGGT+TGG + chr1.2:45101709-45101728 None:intergenic 45.0%
!!! GGAGTTGGTGTTTTCATCGA+AGG + chr1.2:45101673-45101692 None:intergenic 45.0%
AAGCAAGTCCAAAGCGAACG+AGG - chr1.2:45101851-45101870 MS.gene055701:CDS 50.0%
TCAAGAGCTGAATGGTTCCG+AGG - chr1.2:45101615-45101634 MS.gene055701:CDS 50.0%
TCATGGTTCCTCGTTCGCTT+TGG + chr1.2:45101862-45101881 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 45101580 45102308 45101580 ID=MS.gene055701
chr1.2 mRNA 45101580 45102308 45101580 ID=MS.gene055701.t1;Parent=MS.gene055701
chr1.2 exon 45101580 45102308 45101580 ID=MS.gene055701.t1.exon1;Parent=MS.gene055701.t1
chr1.2 CDS 45101580 45102308 45101580 ID=cds.MS.gene055701.t1;Parent=MS.gene055701.t1
Gene Sequence

>MS.gene055701

ATGGTGGAGGAAATGTACATGGAAGAGATGAAGGATCAAGAGCTGAATGGTTCCGAGGACAACAAATCAAGCAAAAATACCGATGACGATCCTTCGATGAAAACACCAACTCCACAAGAAAGAGTTCCAACCTCGGAAACAGAATCCAAAAGTTTCAATTCCAAACAAGACATTCCTATGGTTTCAGTTTCAACACCATCAACTTCACCTATTGGTGTGAATGTTAGAAACAATTCAGGATTCAGCTTCACGGAACTTGATGGAATAACACAAGCAAGTCCAAAGCGAACGAGGAACCATGAAATTCTTCAATCACCGAATCATGTGAAGTCCAATGAAACAACAACTAATAATGAACAAATTTCAATGAAATTTGGTGATGATAGACAAAGTAGAGATGGTTATTGTTTCATGGGAAACCAAACTAATTTCATTGCTGGTTTCGGTCAATATCCAATGGAGGAAATCGGAAGATTTGATGCGGAACAATTTGCACCAAGGTTTTCAGGTAATAATAATGGTGTTTCACTCACTCTTGGTTTGCCTCATTGTGACACATTATCAGGAACACATCAAAGTTTTATGCCAAACCAAAACATTCAACTAGGAAGAAGATTGGACATTAGCGAAACAAATGAGTTTGGTGACTCTTCAGCTGCGTTTGAGAGTATCAACATGCAGAATCCAAAGAGGTTTGCCGCACAATTGTTACCGGATTTTGTGGCATAA

Protein sequence

>MS.gene055701.t1

MVEEMYMEEMKDQELNGSEDNKSSKNTDDDPSMKTPTPQERVPTSETESKSFNSKQDIPMVSVSTPSTSPIGVNVRNNSGFSFTELDGITQASPKRTRNHEILQSPNHVKSNETTTNNEQISMKFGDDRQSRDGYCFMGNQTNFIAGFGQYPMEEIGRFDAEQFAPRFSGNNNGVSLTLGLPHCDTLSGTHQSFMPNQNIQLGRRLDISETNEFGDSSAAFESINMQNPKRFAAQLLPDFVA