AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054800

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054800.t1 MTR_3g099570 81.982 111 14 2 23 128 32 141 1.52e-56 175
MS.gene054800.t1 MTR_3g099580 74.107 112 22 2 24 128 33 144 9.05e-44 142
MS.gene054800.t1 MTR_3g099680 73.913 92 17 3 23 107 32 123 2.10e-37 127
MS.gene054800.t1 MTR_3g099980 73.913 92 17 3 23 107 32 123 6.92e-37 126
MS.gene054800.t1 MTR_3g099540 54.545 99 40 1 23 116 33 131 7.21e-30 105
MS.gene054800.t1 MTR_8g007035 52.222 90 36 2 24 106 31 120 2.91e-22 88.2
MS.gene054800.t1 MTR_8g007020 41.538 130 58 3 24 135 31 160 2.32e-21 85.5
MS.gene054800.t1 MTR_4g114870 39.815 108 54 3 24 121 36 142 1.79e-16 75.1
MS.gene054800.t1 MTR_4g114870 41.489 94 45 2 23 106 197 290 1.76e-15 72.4
MS.gene054800.t1 MTR_2g088990 38.793 116 59 3 24 127 33 148 2.19e-16 73.2
MS.gene054800.t1 MTR_1g090190 35.644 101 59 2 24 118 30 130 3.85e-15 68.9
MS.gene054800.t1 MTR_5g006040 38.393 112 58 4 24 126 33 142 4.82e-15 68.9
MS.gene054800.t1 MTR_6g080660 38.043 92 52 1 25 111 36 127 1.25e-14 68.2
MS.gene054800.t1 MTR_1g090420 31.776 107 61 3 24 118 35 141 3.14e-12 62.0
MS.gene054800.t1 MTR_2g025580 34.737 95 55 2 24 111 34 128 4.57e-12 60.8
MS.gene054800.t1 MTR_8g099220 35.106 94 52 2 23 107 35 128 7.32e-12 59.3
MS.gene054800.t1 MTR_6g023760 37.079 89 50 2 24 106 33 121 1.45e-11 59.7
MS.gene054800.t1 MTR_0334s0010 36.957 92 50 2 24 107 35 126 2.99e-11 58.9
MS.gene054800.t1 MTR_6g083240 33.858 127 62 5 23 127 33 159 3.70e-11 58.5
MS.gene054800.t1 MTR_2g101300 33.981 103 61 2 31 126 46 148 5.65e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054800.t1 AT1G72230 45.390 141 60 3 3 131 14 149 2.70e-31 110
MS.gene054800.t1 AT1G22480 55.319 94 37 1 23 111 25 118 1.06e-24 94.0
MS.gene054800.t1 AT2G32300 42.857 112 57 2 24 129 63 173 4.17e-21 87.0
MS.gene054800.t1 AT2G32300 42.857 112 57 2 24 129 33 143 5.65e-21 86.3
MS.gene054800.t1 AT3G60270 43.011 93 48 1 24 111 33 125 1.01e-18 78.6
MS.gene054800.t1 AT2G26720 35.433 127 74 3 1 120 13 138 1.28e-17 76.3
MS.gene054800.t1 AT2G44790 45.263 95 45 2 25 112 36 130 1.01e-16 73.6
MS.gene054800.t1 AT2G31050 40.385 104 54 3 24 120 36 138 2.34e-16 72.8
MS.gene054800.t1 AT5G07475 35.593 118 69 3 24 135 37 153 2.87e-15 69.7
MS.gene054800.t1 AT3G27200 39.326 89 48 2 24 106 33 121 1.78e-14 67.4
MS.gene054800.t1 AT3G17675 34.066 91 54 1 24 108 39 129 5.07e-12 59.7
MS.gene054800.t1 AT5G20230 38.679 106 56 3 31 127 42 147 2.68e-11 59.3
MS.gene054800.t1 AT3G60280 38.636 88 49 1 24 106 31 118 4.60e-11 58.9

Find 38 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACTATGGCATTGCCGACTA+TGG 0.299229 3.3:-79498084 MS.gene054800:CDS
CCACATTGTTGGAGATTGTT+AGG 0.307944 3.3:-79498054 MS.gene054800:CDS
ATTCCTAGACATTGCACATT+TGG 0.319782 3.3:-79497710 MS.gene054800:CDS
TGGCATGAAACTCTCTGTTA+AGG 0.390798 3.3:-79497690 MS.gene054800:CDS
AGATTGTTAGGTTGGACAAT+TGG 0.438687 3.3:-79498042 MS.gene054800:CDS
CTAGCCCATGTAGTGTAATC+AGG 0.453147 3.3:+79498018 None:intergenic
TTCCAGCTGTGCATAATGTA+TGG 0.484126 3.3:+79497810 None:intergenic
ATTGTTGGAGATTGTTAGGT+TGG 0.488096 3.3:-79498050 MS.gene054800:CDS
ATCGGAAGGTGAACCTTTCG+TGG 0.489155 3.3:+79497622 None:intergenic
GTTGCGGCAGCGGTGCGGAT+CGG 0.492950 3.3:+79497604 None:intergenic
ATGGCAACAACCCACATTGT+TGG 0.499388 3.3:-79498065 MS.gene054800:CDS
ATGCCAAATGTGCAATGTCT+AGG 0.500016 3.3:+79497707 None:intergenic
GACCATACATTATGCACAGC+TGG 0.503333 3.3:-79497812 MS.gene054800:CDS
TTGGTCCTGATTACACTACA+TGG 0.504799 3.3:-79498023 MS.gene054800:CDS
GGTGGTGGTTGTTGCGGCAG+CGG 0.517819 3.3:+79497594 None:intergenic
CGGCAGCGGTGCGGATCGGA+AGG 0.536655 3.3:+79497608 None:intergenic
GAAGGTGAACCTTTCGTGGA+TGG 0.547718 3.3:+79497626 None:intergenic
TTTGCAGTTGGTGACAGTCT+CGG 0.554211 3.3:-79497985 MS.gene054800:intron
GAAGGAGCGGCAGAAGAAGA+AGG 0.554641 3.3:+79497662 None:intergenic
TGTGGTAGGAGTAGTGGTGG+TGG 0.559960 3.3:+79497579 None:intergenic
ATGTGGGTTGTTGCCATAGT+CGG 0.565131 3.3:+79498071 None:intergenic
GAAGATGCACTTTGTGTGGT+AGG 0.585213 3.3:+79497565 None:intergenic
AGTGACAAAACCTTTGCAGT+TGG 0.590211 3.3:-79497997 MS.gene054800:CDS
GAACCTTTCGTGGATGGTGA+TGG 0.595492 3.3:+79497632 None:intergenic
AGTAGTGGTGGTGGTTGTTG+CGG 0.603984 3.3:+79497588 None:intergenic
GATGGTGATGGTGTTGCAGA+AGG 0.618024 3.3:+79497644 None:intergenic
ACTTTGTGTGGTAGGAGTAG+TGG 0.618884 3.3:+79497573 None:intergenic
GAGACTGTCACCAACTGCAA+AGG 0.629029 3.3:+79497987 None:intergenic
TGGTCCTGATTACACTACAT+GGG 0.630389 3.3:-79498022 MS.gene054800:CDS
ACACCATCACCATCCACGAA+AGG 0.636152 3.3:-79497635 MS.gene054800:CDS
CTAACAATCTCCAACAATGT+GGG 0.638468 3.3:+79498055 None:intergenic
CCTAACAATCTCCAACAATG+TGG 0.639240 3.3:+79498054 None:intergenic
GGCTGAAGATGCACTTTGTG+TGG 0.645311 3.3:+79497561 None:intergenic
TTGTGTGGTAGGAGTAGTGG+TGG 0.649594 3.3:+79497576 None:intergenic
TGGTTGTTGCGGCAGCGGTG+CGG 0.669330 3.3:+79497599 None:intergenic
TCAATTAATACAGACAGCAG+TGG 0.671855 3.3:-79497785 MS.gene054800:CDS
TGATGGTGTTGCAGAAGGAG+CGG 0.712627 3.3:+79497649 None:intergenic
CTATGTAGCTGGGCACACAG+TGG 0.727318 3.3:-79497852 MS.gene054800:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATGTAACTTTACTATGACAG+TGG - chr3.3:79497778-79497797 MS.gene054800:CDS 30.0%
!! CATCTTTTTAGCAATCACTA+TGG - chr3.3:79497559-79497578 MS.gene054800:CDS 30.0%
!!! AATGTGTTCCTGCTTTTTTT+AGG + chr3.3:79497914-79497933 None:intergenic 30.0%
!!! ATGTGTTCCTGCTTTTTTTA+GGG + chr3.3:79497913-79497932 None:intergenic 30.0%
ATTCCTAGACATTGCACATT+TGG - chr3.3:79497948-79497967 MS.gene054800:intron 35.0%
ATTGTTGGAGATTGTTAGGT+TGG - chr3.3:79497608-79497627 MS.gene054800:CDS 35.0%
CTAACAATCTCCAACAATGT+GGG + chr3.3:79497606-79497625 None:intergenic 35.0%
TCAATTAATACAGACAGCAG+TGG - chr3.3:79497873-79497892 MS.gene054800:intron 35.0%
!! AGATTGTTAGGTTGGACAAT+TGG - chr3.3:79497616-79497635 MS.gene054800:CDS 35.0%
!!! TGTGTTCCTGCTTTTTTTAG+GGG + chr3.3:79497912-79497931 None:intergenic 35.0%
!!! TTTTTTTAGGGGAATGGTTG+TGG + chr3.3:79497901-79497920 None:intergenic 35.0%
ACCATTCCCCTAAAAAAAGC+AGG - chr3.3:79497903-79497922 MS.gene054800:intron 40.0%
AGTGACAAAACCTTTGCAGT+TGG - chr3.3:79497661-79497680 MS.gene054800:CDS 40.0%
AGTGGTTCAACTATGTAGCT+GGG - chr3.3:79497796-79497815 MS.gene054800:CDS 40.0%
ATGCCAAATGTGCAATGTCT+AGG + chr3.3:79497954-79497973 None:intergenic 40.0%
CCACATTGTTGGAGATTGTT+AGG - chr3.3:79497604-79497623 MS.gene054800:CDS 40.0%
CCTAACAATCTCCAACAATG+TGG + chr3.3:79497607-79497626 None:intergenic 40.0%
TGGCATGAAACTCTCTGTTA+AGG - chr3.3:79497968-79497987 MS.gene054800:intron 40.0%
TGGTCCTGATTACACTACAT+GGG - chr3.3:79497636-79497655 MS.gene054800:CDS 40.0%
TTCCAGCTGTGCATAATGTA+TGG + chr3.3:79497851-79497870 None:intergenic 40.0%
TTGGTCCTGATTACACTACA+TGG - chr3.3:79497635-79497654 MS.gene054800:CDS 40.0%
!!! TCCTGCTTTTTTTAGGGGAA+TGG + chr3.3:79497907-79497926 None:intergenic 40.0%
ACTTTGTGTGGTAGGAGTAG+TGG + chr3.3:79498088-79498107 None:intergenic 45.0%
ATGGCAACAACCCACATTGT+TGG - chr3.3:79497593-79497612 MS.gene054800:CDS 45.0%
CAGTGGTTCAACTATGTAGC+TGG - chr3.3:79497795-79497814 MS.gene054800:CDS 45.0%
CTAGCCCATGTAGTGTAATC+AGG + chr3.3:79497643-79497662 None:intergenic 45.0%
GAAGATGCACTTTGTGTGGT+AGG + chr3.3:79498096-79498115 None:intergenic 45.0%
GACCATACATTATGCACAGC+TGG - chr3.3:79497846-79497865 MS.gene054800:CDS 45.0%
! ATGTGGGTTGTTGCCATAGT+CGG + chr3.3:79497590-79497609 None:intergenic 45.0%
!! TTTGCAGTTGGTGACAGTCT+CGG - chr3.3:79497673-79497692 MS.gene054800:CDS 45.0%
ACACCATCACCATCCACGAA+AGG - chr3.3:79498023-79498042 MS.gene054800:CDS 50.0%
ATCGGAAGGTGAACCTTTCG+TGG + chr3.3:79498039-79498058 None:intergenic 50.0%
GAACCTTTCGTGGATGGTGA+TGG + chr3.3:79498029-79498048 None:intergenic 50.0%
GAAGGTGAACCTTTCGTGGA+TGG + chr3.3:79498035-79498054 None:intergenic 50.0%
GAGACTGTCACCAACTGCAA+AGG + chr3.3:79497674-79497693 None:intergenic 50.0%
GGCTGAAGATGCACTTTGTG+TGG + chr3.3:79498100-79498119 None:intergenic 50.0%
TTGTGTGGTAGGAGTAGTGG+TGG + chr3.3:79498085-79498104 None:intergenic 50.0%
! CACTATGGCATTGCCGACTA+TGG - chr3.3:79497574-79497593 MS.gene054800:CDS 50.0%
!! AGTAGTGGTGGTGGTTGTTG+CGG + chr3.3:79498073-79498092 None:intergenic 50.0%
!! GATGGTGATGGTGTTGCAGA+AGG + chr3.3:79498017-79498036 None:intergenic 50.0%
!! TGATGGTGTTGCAGAAGGAG+CGG + chr3.3:79498012-79498031 None:intergenic 50.0%
CTATGTAGCTGGGCACACAG+TGG - chr3.3:79497806-79497825 MS.gene054800:CDS 55.0%
GAAGGAGCGGCAGAAGAAGA+AGG + chr3.3:79497999-79498018 None:intergenic 55.0%
TGTGGTAGGAGTAGTGGTGG+TGG + chr3.3:79498082-79498101 None:intergenic 55.0%
TGGTTGTTGCGGCAGCGGTG+CGG + chr3.3:79498062-79498081 None:intergenic 65.0%
! GGTGGTGGTTGTTGCGGCAG+CGG + chr3.3:79498067-79498086 None:intergenic 65.0%
GTTGCGGCAGCGGTGCGGAT+CGG + chr3.3:79498057-79498076 None:intergenic 70.0%
CGGCAGCGGTGCGGATCGGA+AGG + chr3.3:79498053-79498072 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 79497556 79498124 79497556 ID=MS.gene054800
chr3.3 mRNA 79497556 79498124 79497556 ID=MS.gene054800.t1;Parent=MS.gene054800
chr3.3 exon 79497986 79498124 79497986 ID=MS.gene054800.t1.exon1;Parent=MS.gene054800.t1
chr3.3 CDS 79497986 79498124 79497986 ID=cds.MS.gene054800.t1;Parent=MS.gene054800.t1
chr3.3 exon 79497556 79497866 79497556 ID=MS.gene054800.t1.exon2;Parent=MS.gene054800.t1
chr3.3 CDS 79497556 79497866 79497556 ID=cds.MS.gene054800.t1;Parent=MS.gene054800.t1
Gene Sequence

>MS.gene054800

ATGCATCTTTTTAGCAATCACTATGGCATTGCCGACTATGGCAACAACCCACATTGTTGGAGATTGTTAGGTTGGACAATTGGTCCTGATTACACTACATGGGCTAGTGACAAAACCTTTGCAGTTGGTGACAGTCTCGGTAAGTATAATAATTTAACGAACTTTTATCAATTTCATTTTTTTTTAGTTTTAAATTGCAATCACAATTTACGAAACTAATGTATGTAACTTTACTATGACAGTGGTTCAACTATGTAGCTGGGCACACAGTGGATGAAGTTAAAGAAAGTGACCATACATTATGCACAGCTGGAAATTCAATTAATACAGACAGCAGTGGTGCCACAACCATTCCCCTAAAAAAAGCAGGAACACATTACTTCATATGTGCTATTCCTAGACATTGCACATTTGGCATGAAACTCTCTGTTAAGGTTAATCCTTCTTCTTCTGCCGCTCCTTCTGCAACACCATCACCATCCACGAAAGGTTCACCTTCCGATCCGCACCGCTGCCGCAACAACCACCACCACTACTCCTACCACACAAAGTGCATCTTCAGCCACTAA
Protein sequence

>MS.gene054800.t1

MHLFSNHYGIADYGNNPHCWRLLGWTIGPDYTTWASDKTFAVGDSLAGHTVDEVKESDHTLCTAGNSINTDSSGATTIPLKKAGTHYFICAIPRHCTFGMKLSVKVNPSSSAAPSATPSPSTKGSPSDPHRCRNNHHHYSYHTKCIFSH