AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053291

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053291.t1 MTR_1g103380 95.833 120 3 1 3 120 163 282 1.23e-72 224
MS.gene053291.t1 MTR_7g018500 85.484 62 9 0 43 104 122 183 2.61e-29 109
MS.gene053291.t1 MTR_6g017055 64.045 89 24 2 15 103 108 188 1.20e-28 108
MS.gene053291.t1 MTR_4g111935 61.194 67 26 0 39 105 130 196 3.63e-21 87.4
MS.gene053291.t1 MTR_4g079580 53.226 62 29 0 40 101 21 82 3.91e-18 79.0
MS.gene053291.t1 MTR_8g463380 54.098 61 28 0 40 100 53 113 9.34e-18 78.2
MS.gene053291.t1 MTR_2g078200 55.738 61 27 0 40 100 19 79 1.13e-17 77.0
MS.gene053291.t1 MTR_2g090960 51.667 60 29 0 40 99 23 82 2.66e-17 76.6
MS.gene053291.t1 MTR_6g015350 50.000 60 30 0 40 99 48 107 3.40e-14 67.8
MS.gene053291.t1 MTR_7g015010 43.210 81 46 0 40 120 56 136 1.54e-13 66.2
MS.gene053291.t1 MTR_4g109660 50.000 62 30 1 38 99 54 114 1.56e-13 65.9
MS.gene053291.t1 MTR_3g026050 46.667 60 32 0 40 99 56 115 2.38e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053291.t1 AT1G67260 64.474 76 23 1 41 116 87 158 3.47e-25 98.2
MS.gene053291.t1 AT1G67260 64.474 76 23 1 41 116 87 158 3.47e-25 98.2
MS.gene053291.t1 AT1G67260 64.474 76 23 1 41 116 87 158 4.02e-25 98.2
MS.gene053291.t1 AT1G68800 76.271 59 14 0 41 99 112 170 5.46e-24 95.1
MS.gene053291.t1 AT1G68800 76.271 59 14 0 41 99 112 170 5.91e-24 94.7
MS.gene053291.t1 AT3G18550 36.752 117 51 2 21 114 106 222 2.05e-18 80.1
MS.gene053291.t1 AT3G18550 36.752 117 51 2 21 114 106 222 2.05e-18 80.1
MS.gene053291.t1 AT3G18550 36.752 117 51 2 21 114 106 222 2.05e-18 80.1
MS.gene053291.t1 AT3G18550 36.752 117 51 2 21 114 106 222 2.19e-18 80.1
MS.gene053291.t1 AT1G53230 54.839 62 28 0 40 101 48 109 2.73e-18 79.7
MS.gene053291.t1 AT1G53230 54.839 62 28 0 40 101 48 109 2.73e-18 79.7
MS.gene053291.t1 AT3G15030 55.738 61 27 0 40 100 44 104 5.61e-18 79.0
MS.gene053291.t1 AT3G15030 55.738 61 27 0 40 100 44 104 5.61e-18 79.0
MS.gene053291.t1 AT3G15030 55.738 61 27 0 40 100 44 104 5.61e-18 79.0
MS.gene053291.t1 AT3G15030 55.738 61 27 0 40 100 44 104 5.61e-18 79.0
MS.gene053291.t1 AT2G31070 55.000 60 27 0 40 99 28 87 2.61e-17 76.6
MS.gene053291.t1 AT4G18390 47.297 74 39 0 40 113 41 114 1.53e-16 74.7
MS.gene053291.t1 AT4G18390 47.297 74 39 0 40 113 41 114 1.53e-16 74.7
MS.gene053291.t1 AT1G30210 55.000 60 27 0 40 99 49 108 2.38e-16 73.9
MS.gene053291.t1 AT1G30210 55.000 60 27 0 40 99 49 108 2.38e-16 73.9
MS.gene053291.t1 AT3G02150 50.000 60 30 0 40 99 73 132 1.69e-13 65.5
MS.gene053291.t1 AT3G02150 50.000 60 30 0 40 99 73 132 2.29e-13 65.9
MS.gene053291.t1 AT5G60970 45.000 60 33 0 40 99 62 121 3.21e-12 62.4
MS.gene053291.t1 AT5G08070 50.000 50 25 0 40 89 32 81 4.04e-11 58.9
MS.gene053291.t1 AT5G08070 50.000 50 25 0 40 89 32 81 4.04e-11 58.9

Find 22 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTCTGTCACAACAAAATT+TGG 0.083599 1.2:-76907487 None:intergenic
AAACAACCAGCAGCAGTTAT+AGG 0.340022 1.2:+76907511 MS.gene053291:CDS
CAAGATAATGGCTACAACTT+TGG 0.372622 1.2:+76907442 MS.gene053291:CDS
GCAATGTTTGAACAAGATAA+TGG 0.390494 1.2:+76907430 MS.gene053291:CDS
TTCCGGCGGGGTGGCGGCGA+TGG 0.396490 1.2:+76907791 MS.gene053291:CDS
AGCCACTCAAGTGTGTTACT+TGG 0.429932 1.2:-76907658 None:intergenic
TTATAGGAGGAAAGAGAGAT+AGG 0.434649 1.2:+76907527 MS.gene053291:CDS
TTTCCTCCTATAACTGCTGC+TGG 0.449288 1.2:-76907517 None:intergenic
GTCACAACAAAATTTGGAAT+CGG 0.465229 1.2:-76907481 None:intergenic
ATCATGTTCCGGCGGGGTGG+CGG 0.498282 1.2:+76907785 MS.gene053291:CDS
TACCATCGCCGCCACCCCGC+CGG 0.508711 1.2:-76907793 None:intergenic
AAATAGCAACAATCATGTTC+CGG 0.520484 1.2:+76907774 MS.gene053291:CDS
AGCAACAATCATGTTCCGGC+GGG 0.530190 1.2:+76907778 MS.gene053291:CDS
CAGTAAGATTCACACATCAC+AGG 0.558791 1.2:+76907552 MS.gene053291:CDS
CACAGGGTTTGAGAGACAGA+AGG 0.612414 1.2:+76907569 MS.gene053291:CDS
ACAATCATGTTCCGGCGGGG+TGG 0.624688 1.2:+76907782 MS.gene053291:CDS
CAACCAGCAGCAGTTATAGG+AGG 0.626000 1.2:+76907514 MS.gene053291:CDS
ACAGGGTTTGAGAGACAGAA+GGG 0.629239 1.2:+76907570 MS.gene053291:CDS
TAGCAACAATCATGTTCCGG+CGG 0.636668 1.2:+76907777 MS.gene053291:CDS
AGTAAGATTCACACATCACA+GGG 0.651645 1.2:+76907553 MS.gene053291:CDS
AACCAAGTAACACACTTGAG+TGG 0.665918 1.2:+76907656 MS.gene053291:CDS
GCAACAATCATGTTCCGGCG+GGG 0.694107 1.2:+76907779 MS.gene053291:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGCTATTTGAATCAAAAAAT+GGG - chr1.2:76907762-76907781 None:intergenic 20.0%
!!! TTGCTATTTGAATCAAAAAA+TGG - chr1.2:76907763-76907782 None:intergenic 20.0%
AAATAGCAACAATCATGTTC+CGG + chr1.2:76907774-76907793 MS.gene053291:CDS 30.0%
GCAATGTTTGAACAAGATAA+TGG + chr1.2:76907430-76907449 MS.gene053291:CDS 30.0%
! GTCACAACAAAATTTGGAAT+CGG - chr1.2:76907484-76907503 None:intergenic 30.0%
AGTAAGATTCACACATCACA+GGG + chr1.2:76907553-76907572 MS.gene053291:CDS 35.0%
TGCTCTGTCACAACAAAATT+TGG - chr1.2:76907490-76907509 None:intergenic 35.0%
TTATAGGAGGAAAGAGAGAT+AGG + chr1.2:76907527-76907546 MS.gene053291:CDS 35.0%
! CAAGATAATGGCTACAACTT+TGG + chr1.2:76907442-76907461 MS.gene053291:CDS 35.0%
AAACAACCAGCAGCAGTTAT+AGG + chr1.2:76907511-76907530 MS.gene053291:CDS 40.0%
AACCAAGTAACACACTTGAG+TGG + chr1.2:76907656-76907675 MS.gene053291:CDS 40.0%
CAGTAAGATTCACACATCAC+AGG + chr1.2:76907552-76907571 MS.gene053291:CDS 40.0%
ACAGGGTTTGAGAGACAGAA+GGG + chr1.2:76907570-76907589 MS.gene053291:CDS 45.0%
TAGCAACAATCATGTTCCGG+CGG + chr1.2:76907777-76907796 MS.gene053291:CDS 45.0%
TTTCCTCCTATAACTGCTGC+TGG - chr1.2:76907520-76907539 None:intergenic 45.0%
! AGCCACTCAAGTGTGTTACT+TGG - chr1.2:76907661-76907680 None:intergenic 45.0%
AGCAACAATCATGTTCCGGC+GGG + chr1.2:76907778-76907797 MS.gene053291:CDS 50.0%
CAACCAGCAGCAGTTATAGG+AGG + chr1.2:76907514-76907533 MS.gene053291:CDS 50.0%
CACAGGGTTTGAGAGACAGA+AGG + chr1.2:76907569-76907588 MS.gene053291:CDS 50.0%
GCAACAATCATGTTCCGGCG+GGG + chr1.2:76907779-76907798 MS.gene053291:CDS 55.0%
ACAATCATGTTCCGGCGGGG+TGG + chr1.2:76907782-76907801 MS.gene053291:CDS 60.0%
ATCATGTTCCGGCGGGGTGG+CGG + chr1.2:76907785-76907804 MS.gene053291:CDS 65.0%
TACCATCGCCGCCACCCCGC+CGG - chr1.2:76907796-76907815 None:intergenic 75.0%
!! TTCCGGCGGGGTGGCGGCGA+TGG + chr1.2:76907791-76907810 MS.gene053291:CDS 80.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 76907418 76907816 76907418 ID=MS.gene053291
chr1.2 mRNA 76907418 76907816 76907418 ID=MS.gene053291.t1;Parent=MS.gene053291
chr1.2 exon 76907418 76907816 76907418 ID=MS.gene053291.t1.exon1;Parent=MS.gene053291.t1
chr1.2 CDS 76907418 76907816 76907418 ID=cds.MS.gene053291.t1;Parent=MS.gene053291.t1
Gene Sequence

>MS.gene053291

ATTGTAAACACTGCAATGTTTGAACAAGATAATGGCTACAACTTTGGTGTTAATAGTAGTTTTCCGATTCCAAATTTTGTTGTGACAGAGCAGAAACAACCAGCAGCAGTTATAGGAGGAAAGAGAGATAGGCACAGTAAGATTCACACATCACAGGGTTTGAGAGACAGAAGGGTAAGATTGTCAAGTGAAATAGCAAGAAAGTTCTTTGATCTTCAAGATATGTTAGAGTTTGACAAACCAAGTAACACACTTGAGTGGCTTTTCACTAAATCTGACACTGCAATCAAAGAACTAGCTAGAACTAAAAACGCTGCTTGTTACAACAACAACGACAACAGCCCATTTTTTGATTCAAATAGCAACAATCATGTTCCGGCGGGGTGGCGGCGATGGTAG
Protein sequence

>MS.gene053291.t1

IVNTAMFEQDNGYNFGVNSSFPIPNFVVTEQKQPAAVIGGKRDRHSKIHTSQGLRDRRVRLSSEIARKFFDLQDMLEFDKPSNTLEWLFTKSDTAIKELARTKNAACYNNNDNSPFFDSNSNNHVPAGWRRW