AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004268

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004268.t1 MTR_0722s0020 87.218 133 2 1 1 133 359 476 3.42e-77 237
MS.gene004268.t1 MTR_4g065087 76.562 128 30 0 6 133 303 430 1.58e-66 212
MS.gene004268.t1 MTR_8g086490 76.562 128 30 0 6 133 303 430 1.58e-66 212
MS.gene004268.t1 MTR_4g130920 52.066 121 57 1 13 133 499 618 9.52e-39 138
MS.gene004268.t1 MTR_1g100787 39.806 103 62 0 31 133 964 1066 1.25e-18 81.3
MS.gene004268.t1 MTR_3g009400 34.746 118 76 1 17 133 862 979 7.38e-15 70.5
MS.gene004268.t1 MTR_7g080810 33.043 115 76 1 19 133 262 375 1.11e-14 69.7
MS.gene004268.t1 MTR_3g095100 35.398 113 72 1 22 133 836 948 9.40e-14 67.0
MS.gene004268.t1 MTR_8g010180 32.174 115 77 1 19 133 266 379 1.00e-13 67.0
MS.gene004268.t1 MTR_6g009370 33.333 108 71 1 26 133 270 376 2.27e-13 65.9
MS.gene004268.t1 MTR_7g092910 35.632 87 54 1 49 133 381 467 1.65e-11 60.5
MS.gene004268.t1 MTR_8g041660 34.831 89 58 0 45 133 321 409 2.02e-11 60.5
MS.gene004268.t1 MTR_8g041660 34.831 89 58 0 45 133 321 409 2.19e-11 60.5
MS.gene004268.t1 MTR_8g445800 37.647 85 53 0 49 133 691 775 8.53e-11 58.5
MS.gene004268.t1 MTR_8g445800 37.647 85 53 0 49 133 493 577 8.63e-11 58.5
MS.gene004268.t1 MTR_8g445800 37.647 85 53 0 49 133 546 630 8.93e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004268.t1 AT5G45800 70.339 118 35 0 9 126 344 461 1.07e-54 178
MS.gene004268.t1 AT5G45800 67.200 125 41 0 9 133 344 468 2.91e-54 180
MS.gene004268.t1 AT2G24230 50.388 129 61 2 7 133 492 619 8.46e-39 138
MS.gene004268.t1 AT5G58150 40.000 105 63 0 29 133 490 594 2.52e-21 89.0
MS.gene004268.t1 AT5G07280 38.835 103 63 0 31 133 888 990 8.91e-19 81.6
MS.gene004268.t1 AT4G39400 36.290 124 78 1 11 133 833 956 7.18e-17 76.3
MS.gene004268.t1 AT1G69990 28.800 125 89 0 9 133 244 368 4.75e-15 70.9
MS.gene004268.t1 AT3G13380 39.216 102 62 0 32 133 830 931 2.51e-14 68.9
MS.gene004268.t1 AT1G55610 34.746 118 76 1 17 133 815 932 3.17e-14 68.6
MS.gene004268.t1 AT1G55610 34.746 118 76 1 17 133 815 932 3.17e-14 68.6
MS.gene004268.t1 AT5G48380 34.513 113 69 2 23 133 266 375 8.56e-14 67.4
MS.gene004268.t1 AT1G27190 31.707 123 83 1 11 133 252 373 2.40e-13 65.9
MS.gene004268.t1 AT2G01950 35.398 113 72 1 22 133 799 911 1.46e-12 63.9
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 525 610 9.41e-12 61.2
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 525 610 9.41e-12 61.2
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 525 610 9.82e-12 61.2
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 525 610 9.82e-12 61.2
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 525 610 1.02e-11 61.2
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 456 541 1.28e-11 60.8
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 525 610 1.30e-11 60.8
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 456 541 1.31e-11 60.8
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 525 610 1.40e-11 60.8
MS.gene004268.t1 AT4G11900 36.047 86 55 0 48 133 525 610 1.40e-11 60.8
MS.gene004268.t1 AT4G22130 36.145 83 51 1 53 133 247 329 1.57e-11 60.8
MS.gene004268.t1 AT4G22130 36.145 83 51 1 53 133 388 470 1.78e-11 60.5
MS.gene004268.t1 AT3G45410 38.961 77 47 0 47 123 329 405 1.89e-11 60.5
MS.gene004268.t1 AT4G03230 34.568 81 53 0 53 133 583 663 3.02e-11 60.1
MS.gene004268.t1 AT4G03230 34.568 81 53 0 53 133 583 663 3.02e-11 60.1
MS.gene004268.t1 AT4G03230 34.568 81 53 0 53 133 611 691 3.06e-11 60.1
MS.gene004268.t1 AT4G03230 34.568 81 53 0 53 133 525 605 3.21e-11 60.1
MS.gene004268.t1 AT4G03230 34.568 81 53 0 53 133 526 606 3.28e-11 59.7
MS.gene004268.t1 AT4G03230 34.568 81 53 0 53 133 683 763 3.33e-11 59.7
MS.gene004268.t1 AT4G03230 34.568 81 53 0 53 133 683 763 3.33e-11 59.7
MS.gene004268.t1 AT3G28450 31.304 115 77 2 20 133 266 379 4.01e-11 59.7
MS.gene004268.t1 AT3G45420 36.905 84 53 0 49 132 339 422 7.47e-11 58.9
MS.gene004268.t1 AT4G03230 34.568 81 53 0 53 133 518 598 7.59e-11 58.9

Find 29 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTAATCTCTTGCCACTTTC+TGG 0.085890 2.4:-68645761 MS.gene004268:CDS
ATGAATGCCACGTCATATTT+TGG 0.098926 2.4:-68645941 MS.gene004268:CDS
CTTTCTGGCTATTGCATTGC+AGG 0.239690 2.4:-68645746 MS.gene004268:CDS
TTTGATGAACATTAGTTTCA+TGG 0.278423 2.4:-68645969 MS.gene004268:CDS
AGGTAAAACAGCACGGTAAA+CGG 0.359171 2.4:+68645883 None:intergenic
TTTGCATTTGAGACAGAATC+TGG 0.364194 2.4:-68646055 MS.gene004268:CDS
TCCAGATTTCTCCATCTTAA+CGG 0.383948 2.4:+68646081 None:intergenic
CCAGAAAGTGGCAAGAGATT+AGG 0.384955 2.4:+68645761 None:intergenic
GTTGTTGTTAATCCTGTCAT+TGG 0.401185 2.4:+68646103 None:intergenic
GGTAAAACAGCACGGTAAAC+GGG 0.405346 2.4:+68645884 None:intergenic
GGAGTTACACGTGGCAATTA+AGG 0.406038 2.4:-68645858 MS.gene004268:CDS
ACCGTTAAGATGGAGAAATC+TGG 0.466381 2.4:-68646082 MS.gene004268:CDS
GAGATTAGGATGTTTAAGCT+TGG 0.476885 2.4:+68645775 None:intergenic
ATTAACAACAACCGTTAAGA+TGG 0.482546 2.4:-68646092 MS.gene004268:CDS
TCAATATCAAAACCAATGAC+AGG 0.512119 2.4:-68646115 None:intergenic
AGACAGAATCTGGAACATCA+TGG 0.538537 2.4:-68646045 MS.gene004268:CDS
CAGCTAGCTGAAGGTAGATG+TGG 0.542978 2.4:-68645908 MS.gene004268:CDS
GGTTCTTGAAAATGCTAGAG+AGG 0.544825 2.4:-68645837 MS.gene004268:CDS
GCAATGCAATAGCCAGAAAG+TGG 0.553743 2.4:+68645749 None:intergenic
ATGAAACTAATGTTCATCAA+AGG 0.554158 2.4:+68645971 None:intergenic
GATTCTGTCTCAAATGCAAA+CGG 0.572633 2.4:+68646058 None:intergenic
ATGACAACTGATGCTGAAGT+TGG 0.574292 2.4:+68646004 None:intergenic
GACAGAATCTGGAACATCAT+GGG 0.581209 2.4:-68646044 MS.gene004268:CDS
AGCTAGCTGAAGGTAGATGT+GGG 0.584184 2.4:-68645907 MS.gene004268:CDS
AAAGATTCTCAGCTAGCTGA+AGG 0.588956 2.4:-68645917 MS.gene004268:CDS
ATTGCCACGTGTAACTCCCC+AGG 0.593098 2.4:+68645863 None:intergenic
ATCTTTCCCAAAATATGACG+TGG 0.677492 2.4:+68645934 None:intergenic
TTTACCTGGGGAGTTACACG+TGG 0.686026 2.4:-68645867 MS.gene004268:CDS
ACTCCCCAGGTAAAACAGCA+CGG 0.692386 2.4:+68645876 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATGAAACTAATGTTCATCAA+AGG + chr2.4:68645853-68645872 None:intergenic 25.0%
!! TTTGATGAACATTAGTTTCA+TGG - chr2.4:68645852-68645871 MS.gene004268:CDS 25.0%
ATTAACAACAACCGTTAAGA+TGG - chr2.4:68645729-68645748 MS.gene004268:CDS 30.0%
ATCTTTCCCAAAATATGACG+TGG + chr2.4:68645890-68645909 None:intergenic 35.0%
GAGATTAGGATGTTTAAGCT+TGG + chr2.4:68646049-68646068 None:intergenic 35.0%
GATTCTGTCTCAAATGCAAA+CGG + chr2.4:68645766-68645785 None:intergenic 35.0%
TCCAGATTTCTCCATCTTAA+CGG + chr2.4:68645743-68645762 None:intergenic 35.0%
! ATGAATGCCACGTCATATTT+TGG - chr2.4:68645880-68645899 MS.gene004268:CDS 35.0%
! TGAATGCCACGTCATATTTT+GGG - chr2.4:68645881-68645900 MS.gene004268:CDS 35.0%
! TTTGCATTTGAGACAGAATC+TGG - chr2.4:68645766-68645785 MS.gene004268:CDS 35.0%
AAAGATTCTCAGCTAGCTGA+AGG - chr2.4:68645904-68645923 MS.gene004268:CDS 40.0%
ACCGTTAAGATGGAGAAATC+TGG - chr2.4:68645739-68645758 MS.gene004268:CDS 40.0%
AGGTAAAACAGCACGGTAAA+CGG + chr2.4:68645941-68645960 None:intergenic 40.0%
ATGACAACTGATGCTGAAGT+TGG + chr2.4:68645820-68645839 None:intergenic 40.0%
GGTTCTTGAAAATGCTAGAG+AGG - chr2.4:68645984-68646003 MS.gene004268:CDS 40.0%
! AGACAGAATCTGGAACATCA+TGG - chr2.4:68645776-68645795 MS.gene004268:CDS 40.0%
! GACAGAATCTGGAACATCAT+GGG - chr2.4:68645777-68645796 MS.gene004268:CDS 40.0%
!!! TTTACCGTGCTGTTTTACCT+GGG - chr2.4:68645941-68645960 MS.gene004268:CDS 40.0%
AGCTAGCTGAAGGTAGATGT+GGG - chr2.4:68645914-68645933 MS.gene004268:CDS 45.0%
CCAGAAAGTGGCAAGAGATT+AGG + chr2.4:68646063-68646082 None:intergenic 45.0%
GCAATGCAATAGCCAGAAAG+TGG + chr2.4:68646075-68646094 None:intergenic 45.0%
GGAGTTACACGTGGCAATTA+AGG - chr2.4:68645963-68645982 MS.gene004268:CDS 45.0%
GGTAAAACAGCACGGTAAAC+GGG + chr2.4:68645940-68645959 None:intergenic 45.0%
!! CCTAATCTCTTGCCACTTTC+TGG - chr2.4:68646060-68646079 MS.gene004268:CDS 45.0%
!! CTTTCTGGCTATTGCATTGC+AGG - chr2.4:68646075-68646094 MS.gene004268:CDS 45.0%
!!! GTTTACCGTGCTGTTTTACC+TGG - chr2.4:68645940-68645959 MS.gene004268:CDS 45.0%
!!! TTACCGTGCTGTTTTACCTG+GGG - chr2.4:68645942-68645961 MS.gene004268:CDS 45.0%
ACTCCCCAGGTAAAACAGCA+CGG + chr2.4:68645948-68645967 None:intergenic 50.0%
CAGCTAGCTGAAGGTAGATG+TGG - chr2.4:68645913-68645932 MS.gene004268:CDS 50.0%
TTTACCTGGGGAGTTACACG+TGG - chr2.4:68645954-68645973 MS.gene004268:CDS 50.0%
ATTGCCACGTGTAACTCCCC+AGG + chr2.4:68645961-68645980 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 68645721 68646122 68645721 ID=MS.gene004268
chr2.4 mRNA 68645721 68646122 68645721 ID=MS.gene004268.t1;Parent=MS.gene004268
chr2.4 exon 68645721 68646122 68645721 ID=MS.gene004268.t1.exon1;Parent=MS.gene004268.t1
chr2.4 CDS 68645721 68646122 68645721 ID=cds.MS.gene004268.t1;Parent=MS.gene004268.t1
Gene Sequence

>MS.gene004268

ATGACAGGATTAACAACAACCGTTAAGATGGAGAAATCTGGACCGTTTGCATTTGAGACAGAATCTGGAACATCATGGGTAGCTGATCTAAAAGAACCAACTTCAGCATCAGTTGTCATGTTTGAGAAACCTTTGATGAACATTAGTTTCATGGATCTTATGAATGCCACGTCATATTTTGGGAAAGATTCTCAGCTAGCTGAAGGTAGATGTGGGCCCGTTTACCGTGCTGTTTTACCTGGGGAGTTACACGTGGCAATTAAGGTTCTTGAAAATGCTAGAGAGGTTGATCATGATGATGCTGTTGATACTTTTGTTGACTTGTCCAAGCTTAAACATCCTAATCTCTTGCCACTTTCTGGCTATTGCATTGCAGGTAATCATTTTCTCTACGTTTTTTAA
Protein sequence

>MS.gene004268.t1

MTGLTTTVKMEKSGPFAFETESGTSWVADLKEPTSASVVMFEKPLMNISFMDLMNATSYFGKDSQLAEGRCGPVYRAVLPGELHVAIKVLENAREVDHDDAVDTFVDLSKLKHPNLLPLSGYCIAGNHFLYVF