AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002931

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002931.t1 MTR_5g036670 86.170 94 13 0 3 96 77 170 1.41e-47 166
MS.gene002931.t1 MTR_8g062700 71.250 80 23 0 3 82 76 155 7.45e-32 120
MS.gene002931.t1 MTR_8g062700 71.250 80 23 0 3 82 76 155 7.52e-32 120
MS.gene002931.t1 MTR_6g008970 64.773 88 31 0 3 90 97 184 1.22e-30 117
MS.gene002931.t1 MTR_6g008995 63.636 88 30 2 3 90 14 99 2.85e-27 106
MS.gene002931.t1 MTR_6g008995 63.636 88 30 2 3 90 71 156 4.46e-27 106
MS.gene002931.t1 MTR_1g023820 100.000 36 0 0 3 38 21 56 3.33e-19 79.3
MS.gene002931.t1 MTR_7g013410 41.935 93 43 3 3 92 32 116 9.87e-16 70.5
MS.gene002931.t1 MTR_8g062350 32.374 139 52 4 8 107 53 188 1.14e-13 66.6
MS.gene002931.t1 MTR_1g105955 44.872 78 36 2 1 78 48 118 1.18e-12 63.5
MS.gene002931.t1 MTR_0091s0080 34.066 91 56 2 89 179 387 473 4.33e-12 63.9
MS.gene002931.t1 MTR_1g105960 56.818 44 19 0 3 46 35 78 5.65e-12 60.1
MS.gene002931.t1 MTR_4g133300 36.905 84 47 1 3 86 43 120 3.57e-11 60.5
MS.gene002931.t1 MTR_4g133470 38.750 80 43 1 3 82 43 116 3.91e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002931.t1 AT1G70060 70.787 89 25 1 3 90 48 136 3.57e-34 127
MS.gene002931.t1 AT1G70060 70.787 89 25 1 3 90 48 136 3.57e-34 127
MS.gene002931.t1 AT1G24190 71.591 88 25 0 3 90 48 135 9.96e-34 126
MS.gene002931.t1 AT1G24190 71.591 88 25 0 3 90 48 135 1.02e-33 126
MS.gene002931.t1 AT1G24190 71.591 88 25 0 3 90 48 135 1.06e-33 126
MS.gene002931.t1 AT3G01320 60.000 90 35 1 3 92 91 179 1.02e-26 106
MS.gene002931.t1 AT5G15020 62.791 86 30 1 4 89 87 170 1.05e-26 106
MS.gene002931.t1 AT5G15020 62.791 86 30 1 4 89 87 170 1.05e-26 106
MS.gene002931.t1 AT3G01320 60.000 90 35 1 3 92 91 179 1.05e-26 106
MS.gene002931.t1 AT1G59890 59.091 88 34 1 3 90 79 164 2.61e-26 105
MS.gene002931.t1 AT1G59890 59.091 88 34 1 3 90 79 164 2.77e-26 105
MS.gene002931.t1 AT1G59890 59.091 88 34 1 3 90 79 164 2.87e-26 105
MS.gene002931.t1 AT1G59890 59.091 88 34 1 3 90 79 164 2.91e-26 105
MS.gene002931.t1 AT1G10450 61.250 80 29 1 3 82 67 144 1.43e-25 103
MS.gene002931.t1 AT1G10450 61.250 80 29 1 3 82 67 144 1.43e-25 103
MS.gene002931.t1 AT1G10450 61.250 80 29 1 3 82 118 195 1.46e-25 103
MS.gene002931.t1 AT1G24200 57.500 80 31 1 3 82 48 124 3.00e-22 89.0
MS.gene002931.t1 AT1G70030 53.947 76 33 2 8 83 50 123 1.11e-17 76.3
MS.gene002931.t1 AT5G35610 35.965 114 58 3 3 105 44 153 1.98e-13 65.1
MS.gene002931.t1 AT1G70030 50.000 72 33 2 8 77 61 131 1.89e-12 62.0
MS.gene002931.t1 AT1G70030 56.140 57 24 1 8 64 61 116 3.63e-12 60.8

Find 45 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATGTTTACAAGTCATTTA+TGG 0.140196 2.1:-65380150 MS.gene002931:CDS
CTCATGGCCCTTTGGCAAAA+AGG 0.248205 2.1:+65380382 None:intergenic
CAAGAAGATCCGGGTGGTTT+TGG 0.249415 2.1:+65379947 None:intergenic
TTCATCTGTGTCGTGTTGAT+TGG 0.378078 2.1:-65379915 MS.gene002931:CDS
AAGTTAACCATTACTTTATG+AGG 0.408474 2.1:-65379713 MS.gene002931:CDS
TTGTATGAGTGCACTGCAAA+GGG 0.421632 2.1:+65379784 None:intergenic
TCGTGTTGATTGGCGGTGAC+TGG 0.441416 2.1:-65379905 MS.gene002931:CDS
GAGTTATGTGAACACGATAA+AGG 0.446913 2.1:-65380294 MS.gene002931:intron
AGGGTAATCTCATGGCCCTT+TGG 0.451315 2.1:+65380374 None:intergenic
ACTCGGCATCAGTGGGGAAG+GGG 0.451431 2.1:-65379835 MS.gene002931:CDS
ACTGCAAAGGGGTATGTCTC+AGG 0.456330 2.1:+65379796 None:intergenic
AACCACCCGGATCTTCTTGA+AGG 0.457397 2.1:-65379943 MS.gene002931:CDS
TGGTTGAGGTTGCTCATCCT+CGG 0.459938 2.1:+65380346 None:intergenic
CAGGTACTTTCCCTCTTGGT+AGG 0.460534 2.1:+65379687 None:intergenic
GGTCATAGAGACTTGATCTT+GGG 0.467943 2.1:-65380413 MS.gene002931:CDS
ACATCAGGTACTTTCCCTCT+TGG 0.471918 2.1:+65379683 None:intergenic
ATAAACCCTTCAAGAAGATC+CGG 0.477187 2.1:+65379937 None:intergenic
TTTATGCAGACTCGGTTTCA+GGG 0.487740 2.1:-65380179 MS.gene002931:intron
AAACTCGGCATCAGTGGGGA+AGG 0.492373 2.1:-65379837 MS.gene002931:CDS
CTATAAAACTCGGCATCAGT+GGG 0.502922 2.1:-65379842 MS.gene002931:CDS
AGGTACTTTCCCTCTTGGTA+GGG 0.505190 2.1:+65379688 None:intergenic
GCTATAAAACTCGGCATCAG+TGG 0.506265 2.1:-65379843 MS.gene002931:CDS
ATCTGTGTCGTGTTGATTGG+CGG 0.509936 2.1:-65379912 MS.gene002931:CDS
AGGTCATAGAGACTTGATCT+TGG 0.513611 2.1:-65380414 MS.gene002931:CDS
CTCGGCATCAGTGGGGAAGG+GGG 0.515169 2.1:-65379834 MS.gene002931:CDS
AACTCGGCATCAGTGGGGAA+GGG 0.528339 2.1:-65379836 MS.gene002931:CDS
TTGCTCATCCTCGGACGAAA+GGG 0.539598 2.1:+65380355 None:intergenic
CTTGTATGAGTGCACTGCAA+AGG 0.547650 2.1:+65379783 None:intergenic
GTTGCTCATCCTCGGACGAA+AGG 0.549267 2.1:+65380354 None:intergenic
ACCACCCGGATCTTCTTGAA+GGG 0.554045 2.1:-65379942 MS.gene002931:CDS
TATATTCATCCTTCGAGCAA+TGG 0.563072 2.1:-65379759 MS.gene002931:CDS
CGGACGAAAGGGTAATCTCA+TGG 0.581909 2.1:+65380366 None:intergenic
TGAGATTACCCTTTCGTCCG+AGG 0.584557 2.1:-65380363 MS.gene002931:CDS
TAAACCCTTCAAGAAGATCC+GGG 0.599628 2.1:+65379938 None:intergenic
TGCATTCTTCCAAAACCACC+CGG 0.599692 2.1:-65379956 MS.gene002931:CDS
GTTGGTCATGCTATAAAACT+CGG 0.605058 2.1:-65379852 MS.gene002931:CDS
TCATTGACACCATTGCTCGA+AGG 0.620805 2.1:+65379750 None:intergenic
TAGGGCACCTCATAAAGTAA+TGG 0.626853 2.1:+65379706 None:intergenic
ATTTGTAGAGTTGATACTGA+TGG 0.633224 2.1:-65380467 MS.gene002931:intron
TATGAGGTGCCCTACCAAGA+GGG 0.635144 2.1:-65379697 MS.gene002931:CDS
TTATGAGGTGCCCTACCAAG+AGG 0.660657 2.1:-65379698 MS.gene002931:CDS
TGGTGTCATTGAAAGAGTGA+AGG 0.685356 2.1:-65380447 MS.gene002931:CDS
TGTATGAGTGCACTGCAAAG+GGG 0.718580 2.1:+65379785 None:intergenic
ACCCTTCAAGAAGATCCGGG+TGG 0.747614 2.1:+65379941 None:intergenic
TATAAAACTCGGCATCAGTG+GGG 0.747744 2.1:-65379841 MS.gene002931:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTGTTTTTGTATATATATT+GGG - chr2.1:65379698-65379717 MS.gene002931:CDS 15.0%
!! ATATATATACAAAAACAACG+TGG + chr2.1:65379697-65379716 None:intergenic 20.0%
!!! AATTGATTTGTTTATCCTTT+TGG - chr2.1:65379747-65379766 MS.gene002931:CDS 20.0%
!!! CGTTGTTTTTGTATATATAT+TGG - chr2.1:65379697-65379716 MS.gene002931:CDS 20.0%
!!! TAAAATTCAACCTTCTTTTT+TGG + chr2.1:65379917-65379936 None:intergenic 20.0%
! AAGTTAACCATTACTTTATG+AGG - chr2.1:65380527-65380546 MS.gene002931:intron 25.0%
! TAGAATGTTTGTGAGTTTAA+TGG - chr2.1:65379970-65379989 MS.gene002931:intron 25.0%
! TCATGTTTACAAGTCATTTA+TGG - chr2.1:65380090-65380109 MS.gene002931:intron 25.0%
! TTTGTATATATATTGGGAGA+GGG - chr2.1:65379704-65379723 MS.gene002931:CDS 25.0%
!! TTTTGTATATATATTGGGAG+AGG - chr2.1:65379703-65379722 MS.gene002931:CDS 25.0%
!!! AGTTTTAGTTTTGAGCTTAA+TGG - chr2.1:65380032-65380051 MS.gene002931:intron 25.0%
CATATTGAATACGTACAGAA+AGG - chr2.1:65380114-65380133 MS.gene002931:intron 30.0%
! ATTTAACACCTTTTTGCCAA+AGG - chr2.1:65379850-65379869 MS.gene002931:CDS 30.0%
! TTTAACACCTTTTTGCCAAA+GGG - chr2.1:65379851-65379870 MS.gene002931:CDS 30.0%
!! ATTTGTAGAGTTGATACTGA+TGG - chr2.1:65379773-65379792 MS.gene002931:CDS 30.0%
AACTCTACAAATGCACCAAA+AGG + chr2.1:65379765-65379784 None:intergenic 35.0%
ATAAACCCTTCAAGAAGATC+CGG + chr2.1:65380306-65380325 None:intergenic 35.0%
GAGTTATGTGAACACGATAA+AGG - chr2.1:65379946-65379965 MS.gene002931:CDS 35.0%
GTCAGGAAAATCTGTAATGT+TGG - chr2.1:65380184-65380203 MS.gene002931:intron 35.0%
GTTGGTCATGCTATAAAACT+CGG - chr2.1:65380388-65380407 MS.gene002931:CDS 35.0%
TATATTCATCCTTCGAGCAA+TGG - chr2.1:65380481-65380500 MS.gene002931:intron 35.0%
! AGAGTGAAGGAACTTTTTAG+AGG - chr2.1:65379806-65379825 MS.gene002931:CDS 35.0%
!!! TCAACCTTCTTTTTTGGTTG+AGG + chr2.1:65379911-65379930 None:intergenic 35.0%
AATCATGATTGCACTTCTCC+AGG - chr2.1:65380257-65380276 MS.gene002931:intron 40.0%
ACATACCTCTTTGTAGACCA+GGG + chr2.1:65380155-65380174 None:intergenic 40.0%
AGGTCATAGAGACTTGATCT+TGG - chr2.1:65379826-65379845 MS.gene002931:CDS 40.0%
CACAGCAATATGTCAAGTAC+TGG + chr2.1:65380226-65380245 None:intergenic 40.0%
CTATAAAACTCGGCATCAGT+GGG - chr2.1:65380398-65380417 MS.gene002931:CDS 40.0%
GAAACCGAGTCTGCATAAAA+AGG + chr2.1:65380060-65380079 None:intergenic 40.0%
GCAACCTCAACCAAAAAAGA+AGG - chr2.1:65379904-65379923 MS.gene002931:CDS 40.0%
GGTCATAGAGACTTGATCTT+GGG - chr2.1:65379827-65379846 MS.gene002931:CDS 40.0%
TAAACCCTTCAAGAAGATCC+GGG + chr2.1:65380305-65380324 None:intergenic 40.0%
TATAAAACTCGGCATCAGTG+GGG - chr2.1:65380399-65380418 MS.gene002931:CDS 40.0%
TTGTATGAGTGCACTGCAAA+GGG + chr2.1:65380459-65380478 None:intergenic 40.0%
! AGGTATGTGCTGTTATAGTC+AGG - chr2.1:65380167-65380186 MS.gene002931:CDS 40.0%
! GGTTCCTTTTTATGCAGACT+CGG - chr2.1:65380053-65380072 MS.gene002931:intron 40.0%
! GTGTTGCGTAATTTTCGTGT+TGG - chr2.1:65380370-65380389 MS.gene002931:CDS 40.0%
! TAGGGCACCTCATAAAGTAA+TGG + chr2.1:65380537-65380556 None:intergenic 40.0%
! TTCATCTGTGTCGTGTTGAT+TGG - chr2.1:65380325-65380344 MS.gene002931:CDS 40.0%
! TTTATGCAGACTCGGTTTCA+GGG - chr2.1:65380061-65380080 MS.gene002931:intron 40.0%
!! AGCAATATGTCAAGTACTGG+AGG + chr2.1:65380223-65380242 None:intergenic 40.0%
!! TGGTGTCATTGAAAGAGTGA+AGG - chr2.1:65379793-65379812 MS.gene002931:CDS 40.0%
!! TTTTATGCAGACTCGGTTTC+AGG - chr2.1:65380060-65380079 MS.gene002931:intron 40.0%
AGGTACTTTCCCTCTTGGTA+GGG + chr2.1:65380555-65380574 None:intergenic 45.0%
CACATACCTCTTTGTAGACC+AGG + chr2.1:65380156-65380175 None:intergenic 45.0%
CTTGTATGAGTGCACTGCAA+AGG + chr2.1:65380460-65380479 None:intergenic 45.0%
GCTATAAAACTCGGCATCAG+TGG - chr2.1:65380397-65380416 MS.gene002931:CDS 45.0%
TATCACCCTGGTCTACAAAG+AGG - chr2.1:65380147-65380166 MS.gene002931:CDS 45.0%
TCATTGACACCATTGCTCGA+AGG + chr2.1:65380493-65380512 None:intergenic 45.0%
TCTTTGTAGACCAGGGTGAT+AGG + chr2.1:65380148-65380167 None:intergenic 45.0%
TGCATTCTTCCAAAACCACC+CGG - chr2.1:65380284-65380303 MS.gene002931:intron 45.0%
TGTATGAGTGCACTGCAAAG+GGG + chr2.1:65380458-65380477 None:intergenic 45.0%
TTTGGAAGAATGCAGCAACC+TGG + chr2.1:65380278-65380297 None:intergenic 45.0%
!! ATCTGTGTCGTGTTGATTGG+CGG - chr2.1:65380328-65380347 MS.gene002931:CDS 45.0%
AACCACCCGGATCTTCTTGA+AGG - chr2.1:65380297-65380316 MS.gene002931:CDS 50.0%
ACCACCCGGATCTTCTTGAA+GGG - chr2.1:65380298-65380317 MS.gene002931:CDS 50.0%
AGGGTAATCTCATGGCCCTT+TGG + chr2.1:65379869-65379888 None:intergenic 50.0%
CAGGTACTTTCCCTCTTGGT+AGG + chr2.1:65380556-65380575 None:intergenic 50.0%
CGGACGAAAGGGTAATCTCA+TGG + chr2.1:65379877-65379896 None:intergenic 50.0%
CTCATGGCCCTTTGGCAAAA+AGG + chr2.1:65379861-65379880 None:intergenic 50.0%
GGAAAGTAAGCCTATCACCC+TGG - chr2.1:65380135-65380154 MS.gene002931:intron 50.0%
TGAGATTACCCTTTCGTCCG+AGG - chr2.1:65379877-65379896 MS.gene002931:CDS 50.0%
TGGTTGAGGTTGCTCATCCT+CGG + chr2.1:65379897-65379916 None:intergenic 50.0%
TTGCTCATCCTCGGACGAAA+GGG + chr2.1:65379888-65379907 None:intergenic 50.0%
! ACTGCAAAGGGGTATGTCTC+AGG + chr2.1:65380447-65380466 None:intergenic 50.0%
! CAAGAAGATCCGGGTGGTTT+TGG + chr2.1:65380296-65380315 None:intergenic 50.0%
! TATGAGGTGCCCTACCAAGA+GGG - chr2.1:65380543-65380562 MS.gene002931:intron 50.0%
! TTATGAGGTGCCCTACCAAG+AGG - chr2.1:65380542-65380561 MS.gene002931:intron 50.0%
AAACTCGGCATCAGTGGGGA+AGG - chr2.1:65380403-65380422 MS.gene002931:CDS 55.0%
AACTCGGCATCAGTGGGGAA+GGG - chr2.1:65380404-65380423 MS.gene002931:CDS 55.0%
ACCCTTCAAGAAGATCCGGG+TGG + chr2.1:65380302-65380321 None:intergenic 55.0%
GTTGCTCATCCTCGGACGAA+AGG + chr2.1:65379889-65379908 None:intergenic 55.0%
!! TCGTGTTGATTGGCGGTGAC+TGG - chr2.1:65380335-65380354 MS.gene002931:CDS 55.0%
ACTCGGCATCAGTGGGGAAG+GGG - chr2.1:65380405-65380424 MS.gene002931:CDS 60.0%
CTCGGCATCAGTGGGGAAGG+GGG - chr2.1:65380406-65380425 MS.gene002931:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 65379686 65380576 65379686 ID=MS.gene002931
chr2.1 mRNA 65379686 65380576 65379686 ID=MS.gene002931.t1;Parent=MS.gene002931
chr2.1 exon 65380572 65380576 65380572 ID=MS.gene002931.t1.exon1;Parent=MS.gene002931.t1
chr2.1 CDS 65380572 65380576 65380572 ID=cds.MS.gene002931.t1;Parent=MS.gene002931.t1
chr2.1 exon 65380295 65380481 65380295 ID=MS.gene002931.t1.exon2;Parent=MS.gene002931.t1
chr2.1 CDS 65380295 65380481 65380295 ID=cds.MS.gene002931.t1;Parent=MS.gene002931.t1
chr2.1 exon 65380137 65380192 65380137 ID=MS.gene002931.t1.exon3;Parent=MS.gene002931.t1
chr2.1 CDS 65380137 65380192 65380137 ID=cds.MS.gene002931.t1;Parent=MS.gene002931.t1
chr2.1 exon 65379686 65379983 65379686 ID=MS.gene002931.t1.exon4;Parent=MS.gene002931.t1
chr2.1 CDS 65379686 65379983 65379686 ID=cds.MS.gene002931.t1;Parent=MS.gene002931.t1
Gene Sequence

>MS.gene002931

ATGTTGTACCACGTTGTTTTTGTATATATATTGGGAGAGGGATTATGAATTTGTTAGTTGTAATTGATTTGTTTATCCTTTTGGTGCATTTGTAGAGTTGATACTGATGGTGTCATTGAAAGAGTGAAGGAACTTTTTAGAGGTCATAGAGACTTGATCTTGGGATTTAACACCTTTTTGCCAAAGGGCCATGAGATTACCCTTTCGTCCGAGGATGAGCAACCTCAACCAAAAAAGAAGGTTGAATTTTATGAAGCTACGAGTTATGTGAACACGATAAAGGTTAGAATGTTTGTGAGTTTAATGGATTCTCTTCATGCAGATTTGTTTGCAATGTAGAATTAATAGTTTTAGTTTTGAGCTTAATGGTTCCTTTTTATGCAGACTCGGTTTCAGGGCGATGTTCATGTTTACAAGTCATTTATGGACATATTGAATACGTACAGAAAGGAAAGTAAGCCTATCACCCTGGTCTACAAAGAGGTATGTGCTGTTATAGTCAGGAAAATCTGTAATGTTGGTTTTTTTTTATTTCCTCCAGTACTTGACATATTGCTGTGATACACATTTTAATCATGATTGCACTTCTCCAGGTTGCTGCATTCTTCCAAAACCACCCGGATCTTCTTGAAGGGTTTATTCATCTGTGTCGTGTTGATTGGCGGTGACTGGAAAGCTATCTGTGTGTTGCGTAATTTTCGTGTTGGTCATGCTATAAAACTCGGCATCAGTGGGGAAGGGGGTGCTGATGTTGTGTACCTGAGACATACCCCTTTGCAGTGCACTCATACAAGCTATATTCATCCTTCGAGCAATGGTGTCAATGAGAAATTTGTATATCAAGTTAACCATTACTTTATGAGGTGCCCTACCAAGAGGGAAAGTACCTGA
Protein sequence

>MS.gene002931.t1

MLVDTDGVIERVKELFRGHRDLILGFNTFLPKGHEITLSSEDEQPQPKKKVEFYEATSYVNTIKTRFQGDVHVYKSFMDILNTLLHSSKTTRIFLKGLFICVVLIGGDWKAICVLRNFRVGHAIKLGISGEGGADVVYLRHTPLQCTHTSYIHPSSNGVNEKFVYQVNHYFMRCPTKREST