AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028404

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028404.t1 MTR_4g094332 91.556 225 18 1 1 225 1 224 2.42e-129 364
MS.gene028404.t1 MTR_4g094328 90.222 225 21 1 1 225 1 224 1.74e-126 357
MS.gene028404.t1 MTR_4g094330 90.222 225 21 1 1 225 1 224 1.74e-126 357
MS.gene028404.t1 MTR_1g099010 64.851 202 66 1 24 225 21 217 5.36e-89 261
MS.gene028404.t1 MTR_6g034975 66.500 200 62 2 26 225 16 210 8.71e-84 248
MS.gene028404.t1 MTR_4g094325 63.402 194 67 1 32 225 50 239 5.33e-82 244
MS.gene028404.t1 MTR_0119s0010 59.686 191 67 1 30 220 27 207 2.62e-71 216
MS.gene028404.t1 MTR_0119s0020 59.686 191 67 1 30 220 27 207 2.62e-71 216
MS.gene028404.t1 MTR_2g008110 59.686 191 67 1 30 220 27 207 3.48e-71 216
MS.gene028404.t1 MTR_4g094335 59.278 194 77 1 29 220 32 225 7.08e-70 214
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028404.t1 AT3G43660 62.121 198 65 2 29 225 10 198 1.71e-89 262
MS.gene028404.t1 AT1G21140 60.000 205 70 2 24 225 5 200 6.56e-80 238
MS.gene028404.t1 AT3G43630 60.500 200 69 2 24 222 4 194 3.34e-79 236
MS.gene028404.t1 AT1G76800 61.500 200 67 1 26 225 7 196 1.45e-77 232
MS.gene028404.t1 AT3G25190 62.085 211 75 2 18 225 9 217 1.05e-71 218

Find 50 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCTATGGCCATTACTTT+TGG 0.296297 4.2:-18620495 MS.gene028404:CDS
ACCAAATTGATTGGCACTAC+TGG 0.296615 4.2:-18620468 MS.gene028404:CDS
TGTGGTTAGGTTTGCATTGT+TGG 0.312190 4.2:-18620595 MS.gene028404:CDS
TCTTGTGTTAGAGTTCTAAT+TGG 0.326616 4.2:-18620525 MS.gene028404:CDS
TCCAGTAGTGCCAATCAATT+TGG 0.330163 4.2:+18620467 None:intergenic
TTTGGTTTCACCAAATTGAT+TGG 0.341339 4.2:-18620477 MS.gene028404:CDS
TATCTCAATCTCAAAATTGC+TGG 0.375338 4.2:+18621076 None:intergenic
AGGTTTGCATTGTTGGTGTT+TGG 0.379958 4.2:-18620588 MS.gene028404:CDS
AGGGCTGCTTGAAATGGATT+TGG 0.388581 4.2:+18620714 None:intergenic
TGGCTTAGAGCAGCCATGTT+AGG 0.393100 4.2:-18620981 MS.gene028404:CDS
GTTTGGAGGAGTGGGTGCAT+TGG 0.412614 4.2:-18620571 MS.gene028404:CDS
GATGCTAGGGCTGCTTGAAA+TGG 0.413748 4.2:+18620708 None:intergenic
ACCGTTGCGTCGTTGATGAT+TGG 0.428147 4.2:-18620939 MS.gene028404:CDS
AGAGTACTACTGACATGAAT+AGG 0.444320 4.2:+18621053 None:intergenic
TGTGTTAGAGTTCTAATTGG+AGG 0.446628 4.2:-18620522 MS.gene028404:CDS
GGTTTCGCTGGTTTAGTAGC+AGG 0.462292 4.2:-18620873 MS.gene028404:CDS
CAACATTGATTACTTTCAAA+GGG 0.466059 4.2:-18621009 MS.gene028404:CDS
ATGCTCCGAGCTGGTTTCGC+TGG 0.471108 4.2:-18620885 MS.gene028404:CDS
TTGTTGGTGTTTGGAGGAGT+GGG 0.472009 4.2:-18620579 MS.gene028404:CDS
AACGGTGATTAGTCCATCAT+TGG 0.472628 4.2:+18620956 None:intergenic
GTGTTGTTGCTGCTGTGGTT+AGG 0.476689 4.2:-18620608 MS.gene028404:CDS
GGAGGAGTGGGTGCATTGGT+TGG 0.478561 4.2:-18620567 MS.gene028404:CDS
ACAACATTGATTACTTTCAA+AGG 0.489039 4.2:-18621010 MS.gene028404:CDS
TTTGCATTGTTGGTGTTTGG+AGG 0.490032 4.2:-18620585 MS.gene028404:CDS
GGAGCTTGTAGCATGGCAAT+TGG 0.492067 4.2:-18620852 MS.gene028404:CDS
AAAGAATCACAAAATCAGAA+TGG 0.497688 4.2:-18620631 MS.gene028404:CDS
AAGAATCACAAAATCAGAAT+GGG 0.499997 4.2:-18620630 MS.gene028404:CDS
TTCAATATGGCCTCCCACCT+TGG 0.500245 4.2:-18621122 None:intergenic
ATTGTTGGTGTTTGGAGGAG+TGG 0.501761 4.2:-18620580 MS.gene028404:CDS
AAAATGCAAGTGCTGATGCT+AGG 0.501770 4.2:+18620694 None:intergenic
AATTGGAGGTTGGATGGCTA+TGG 0.510325 4.2:-18620508 MS.gene028404:CDS
ATCTCAATCTCAAAATTGCT+GGG 0.516463 4.2:+18621077 None:intergenic
AGTTCTAATTGGAGGTTGGA+TGG 0.519543 4.2:-18620514 MS.gene028404:CDS
TTAGAGTTCTAATTGGAGGT+TGG 0.521312 4.2:-18620518 MS.gene028404:CDS
GCGTCGTTGATGATTGGTGT+TGG 0.527815 4.2:-18620933 MS.gene028404:CDS
AATGGGTGTTGTTGCTGCTG+TGG 0.531269 4.2:-18620613 MS.gene028404:CDS
TAAATGCAGCTGCTAGCAAT+GGG 0.531631 4.2:+18620655 None:intergenic
ATAAATGCAGCTGCTAGCAA+TGG 0.533922 4.2:+18620654 None:intergenic
AAATGCAAGTGCTGATGCTA+GGG 0.534060 4.2:+18620695 None:intergenic
TTTGGTGAAACCAAAAGTAA+TGG 0.542621 4.2:+18620485 None:intergenic
TCCATCATTGGCTCCTAACA+TGG 0.543290 4.2:+18620968 None:intergenic
ACCAATCATCAACGACGCAA+CGG 0.550619 4.2:+18620938 None:intergenic
ATCAAAGTAATGCTCCGAGC+TGG 0.567968 4.2:-18620894 MS.gene028404:CDS
GCCATGTTAGGAGCCAATGA+TGG 0.577904 4.2:-18620969 MS.gene028404:CDS
ATGATGATGAAAGTAGTGAA+AGG 0.610585 4.2:-18620746 MS.gene028404:CDS
TGATGATGAAAGTAGTGAAA+GGG 0.611622 4.2:-18620745 MS.gene028404:CDS
ATTACTTTCAAAGGGCACAA+TGG 0.615521 4.2:-18621001 MS.gene028404:CDS
CTAAACCAGCGAAACCAGCT+CGG 0.629821 4.2:+18620880 None:intergenic
AGTAGCAGGAGCTTGTAGCA+TGG 0.637161 4.2:-18620859 MS.gene028404:CDS
CTAACACAAGACCTCATCAG+AGG 0.675054 4.2:+18620537 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGAATCACAAAATCAGAA+TGG - chr4.2:18620946-18620965 MS.gene028404:CDS 25.0%
! AAGAATCACAAAATCAGAAT+GGG - chr4.2:18620947-18620966 MS.gene028404:CDS 25.0%
!! ACAACATTGATTACTTTCAA+AGG - chr4.2:18620567-18620586 MS.gene028404:CDS 25.0%
!! CAACATTGATTACTTTCAAA+GGG - chr4.2:18620568-18620587 MS.gene028404:CDS 25.0%
ATCTCAATCTCAAAATTGCT+GGG + chr4.2:18620503-18620522 None:intergenic 30.0%
TATCTCAATCTCAAAATTGC+TGG + chr4.2:18620504-18620523 None:intergenic 30.0%
TTTGGTGAAACCAAAAGTAA+TGG + chr4.2:18621095-18621114 None:intergenic 30.0%
! ATGATGATGAAAGTAGTGAA+AGG - chr4.2:18620831-18620850 MS.gene028404:CDS 30.0%
! TCTTGTGTTAGAGTTCTAAT+TGG - chr4.2:18621052-18621071 MS.gene028404:CDS 30.0%
! TGATGATGAAAGTAGTGAAA+GGG - chr4.2:18620832-18620851 MS.gene028404:CDS 30.0%
! TTTGGTTTCACCAAATTGAT+TGG - chr4.2:18621100-18621119 MS.gene028404:CDS 30.0%
! AGAGTACTACTGACATGAAT+AGG + chr4.2:18620527-18620546 None:intergenic 35.0%
! ATTACTTTCAAAGGGCACAA+TGG - chr4.2:18620576-18620595 MS.gene028404:CDS 35.0%
! TCAGCACTTGCATTTTCTAT+TGG - chr4.2:18620890-18620909 MS.gene028404:CDS 35.0%
! TGTGTTAGAGTTCTAATTGG+AGG - chr4.2:18621055-18621074 MS.gene028404:CDS 35.0%
! TTAGAGTTCTAATTGGAGGT+TGG - chr4.2:18621059-18621078 MS.gene028404:CDS 35.0%
!!! ATTAGTTTTTGCTCCAAGGT+GGG + chr4.2:18620471-18620490 None:intergenic 35.0%
!!! TTCCATTAGTTTTTGCTCCA+AGG + chr4.2:18620475-18620494 None:intergenic 35.0%
ACCAAATTGATTGGCACTAC+TGG - chr4.2:18621109-18621128 MS.gene028404:CDS 40.0%
ATAAATGCAGCTGCTAGCAA+TGG + chr4.2:18620926-18620945 None:intergenic 40.0%
CACCTTGGAGCAAAAACTAA+TGG - chr4.2:18620470-18620489 MS.gene028404:CDS 40.0%
TAAATGCAGCTGCTAGCAAT+GGG + chr4.2:18620925-18620944 None:intergenic 40.0%
TCCAGTAGTGCCAATCAATT+TGG + chr4.2:18621113-18621132 None:intergenic 40.0%
TGTGGTTAGGTTTGCATTGT+TGG - chr4.2:18620982-18621001 MS.gene028404:CDS 40.0%
TTGGAAAAACTCCTCTGATG+AGG - chr4.2:18621029-18621048 MS.gene028404:CDS 40.0%
! AACGGTGATTAGTCCATCAT+TGG + chr4.2:18620624-18620643 None:intergenic 40.0%
! AGGTTTGCATTGTTGGTGTT+TGG - chr4.2:18620989-18621008 MS.gene028404:CDS 40.0%
! AGTTCTAATTGGAGGTTGGA+TGG - chr4.2:18621063-18621082 MS.gene028404:CDS 40.0%
! ATGGCTATGGCCATTACTTT+TGG - chr4.2:18621082-18621101 MS.gene028404:CDS 40.0%
! TTTGCATTGTTGGTGTTTGG+AGG - chr4.2:18620992-18621011 MS.gene028404:CDS 40.0%
!! AAAATGCAAGTGCTGATGCT+AGG + chr4.2:18620886-18620905 None:intergenic 40.0%
!! AAATGCAAGTGCTGATGCTA+GGG + chr4.2:18620885-18620904 None:intergenic 40.0%
!!! CATTAGTTTTTGCTCCAAGG+TGG + chr4.2:18620472-18620491 None:intergenic 40.0%
AATTGGAGGTTGGATGGCTA+TGG - chr4.2:18621069-18621088 MS.gene028404:CDS 45.0%
ACCAATCATCAACGACGCAA+CGG + chr4.2:18620642-18620661 None:intergenic 45.0%
ATCAAAGTAATGCTCCGAGC+TGG - chr4.2:18620683-18620702 MS.gene028404:CDS 45.0%
CTAACACAAGACCTCATCAG+AGG + chr4.2:18621043-18621062 None:intergenic 45.0%
! AGGGCTGCTTGAAATGGATT+TGG + chr4.2:18620866-18620885 None:intergenic 45.0%
! ATTGTTGGTGTTTGGAGGAG+TGG - chr4.2:18620997-18621016 MS.gene028404:CDS 45.0%
! TTGTTGGTGTTTGGAGGAGT+GGG - chr4.2:18620998-18621017 MS.gene028404:CDS 45.0%
!! TCCATCATTGGCTCCTAACA+TGG + chr4.2:18620612-18620631 None:intergenic 45.0%
AGTAGCAGGAGCTTGTAGCA+TGG - chr4.2:18620718-18620737 MS.gene028404:CDS 50.0%
CTAAACCAGCGAAACCAGCT+CGG + chr4.2:18620700-18620719 None:intergenic 50.0%
GATGCTAGGGCTGCTTGAAA+TGG + chr4.2:18620872-18620891 None:intergenic 50.0%
GCCATGTTAGGAGCCAATGA+TGG - chr4.2:18620608-18620627 MS.gene028404:CDS 50.0%
GGAGCTTGTAGCATGGCAAT+TGG - chr4.2:18620725-18620744 MS.gene028404:CDS 50.0%
TGGCTTAGAGCAGCCATGTT+AGG - chr4.2:18620596-18620615 MS.gene028404:CDS 50.0%
! AGTTTTTGCTCCAAGGTGGG+AGG + chr4.2:18620468-18620487 None:intergenic 50.0%
! GTGTTGTTGCTGCTGTGGTT+AGG - chr4.2:18620969-18620988 MS.gene028404:CDS 50.0%
!! AATGGGTGTTGTTGCTGCTG+TGG - chr4.2:18620964-18620983 MS.gene028404:CDS 50.0%
!! ACCGTTGCGTCGTTGATGAT+TGG - chr4.2:18620638-18620657 MS.gene028404:CDS 50.0%
!! GCGTCGTTGATGATTGGTGT+TGG - chr4.2:18620644-18620663 MS.gene028404:CDS 50.0%
!! GGTTTCGCTGGTTTAGTAGC+AGG - chr4.2:18620704-18620723 MS.gene028404:CDS 50.0%
GTTTGGAGGAGTGGGTGCAT+TGG - chr4.2:18621006-18621025 MS.gene028404:CDS 55.0%
! ATGCTCCGAGCTGGTTTCGC+TGG - chr4.2:18620692-18620711 MS.gene028404:CDS 60.0%
! GGAGGAGTGGGTGCATTGGT+TGG - chr4.2:18621010-18621029 MS.gene028404:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 18620461 18621138 18620461 ID=MS.gene028404
chr4.2 mRNA 18620461 18621138 18620461 ID=MS.gene028404.t1;Parent=MS.gene028404
chr4.2 exon 18620461 18621138 18620461 ID=MS.gene028404.t1.exon1;Parent=MS.gene028404.t1
chr4.2 CDS 18620461 18621138 18620461 ID=cds.MS.gene028404.t1;Parent=MS.gene028404.t1
Gene Sequence

>MS.gene028404

ATGGCCTCCCACCTTGGAGCAAAAACTAATGGAATTTCACCCAGCAATTTTGAGATTGAGATACCTATTCATGTCAGTAGTACTCTCAAAATTGAAAAAGAGAGCAACAACATTGATTACTTTCAAAGGGCACAATGGCTTAGAGCAGCCATGTTAGGAGCCAATGATGGACTAATCACCGTTGCGTCGTTGATGATTGGTGTTGGAGCTATAAAAGAAGACATCAAAGTAATGCTCCGAGCTGGTTTCGCTGGTTTAGTAGCAGGAGCTTGTAGCATGGCAATTGGTGAGTTTGTGTCTGTTTATACTCAATATGACATTGAGATAGCTCAGATAAATAGAGAAAGTGAAGCTAATAATAATAATGATGATGATGATGAAAGTAGTGAAAGGGAGAAATTGCCAAATCCATTTCAAGCAGCCCTAGCATCAGCACTTGCATTTTCTATTGGTGCAGTGATCCCATTGCTAGCAGCTGCATTTATAAAGAATCACAAAATCAGAATGGGTGTTGTTGCTGCTGTGGTTAGGTTTGCATTGTTGGTGTTTGGAGGAGTGGGTGCATTGGTTGGAAAAACTCCTCTGATGAGGTCTTGTGTTAGAGTTCTAATTGGAGGTTGGATGGCTATGGCCATTACTTTTGGTTTCACCAAATTGATTGGCACTACTGGACTTTGA
Protein sequence

>MS.gene028404.t1

MASHLGAKTNGISPSNFEIEIPIHVSSTLKIEKESNNIDYFQRAQWLRAAMLGANDGLITVASLMIGVGAIKEDIKVMLRAGFAGLVAGACSMAIGEFVSVYTQYDIEIAQINRESEANNNNDDDDESSEREKLPNPFQAALASALAFSIGAVIPLLAAAFIKNHKIRMGVVAAVVRFALLVFGGVGALVGKTPLMRSCVRVLIGGWMAMAITFGFTKLIGTTGL