AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060041

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060041.t1 MTR_3g011990 58.786 313 84 4 1 311 27 296 8.79e-115 333
MS.gene060041.t1 MTR_8g466760 58.917 314 83 5 1 311 27 297 5.16e-114 332
MS.gene060041.t1 MTR_3g011970 55.172 319 93 4 1 311 27 303 1.09e-95 285
MS.gene060041.t1 MTR_3g012010 51.852 324 98 7 1 311 27 305 1.74e-90 272
MS.gene060041.t1 MTR_3g009410 46.749 323 116 8 2 311 28 307 5.03e-78 240
MS.gene060041.t1 MTR_7g026977 42.073 328 144 11 1 301 28 336 7.23e-61 197
MS.gene060041.t1 MTR_5g008310 38.083 386 113 11 1 311 1 335 1.75e-58 191
MS.gene060041.t1 MTR_7g022960 40.000 325 120 8 4 311 22 288 3.26e-57 186
MS.gene060041.t1 MTR_5g008320 39.211 380 116 11 1 311 1 334 1.73e-55 183
MS.gene060041.t1 MTR_7g022980 48.611 216 90 5 106 311 68 272 7.98e-49 164
MS.gene060041.t1 MTR_7g023010 45.370 216 89 6 106 311 68 264 1.62e-48 163
MS.gene060041.t1 MTR_5g008280 34.354 294 88 10 39 273 14 261 3.20e-31 120
MS.gene060041.t1 MTR_5g008280 48.966 145 64 5 173 311 247 387 3.37e-22 95.9
MS.gene060041.t1 MTR_7g026710 44.586 157 78 6 161 311 7 160 7.84e-24 95.9
MS.gene060041.t1 MTR_7g026700 43.312 157 81 5 161 311 7 161 9.49e-23 93.2
MS.gene060041.t1 MTR_5g008390 42.593 108 41 2 93 200 3 89 2.88e-20 84.0
MS.gene060041.t1 MTR_1g106730 37.349 83 36 1 62 128 71 153 9.64e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060041.t1 AT2G37430 37.500 88 40 2 63 135 36 123 7.27e-12 63.5

Find 62 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGACGGTTCTTCTTCAATTT+TGG 0.138512 6.3:+39490377 None:intergenic
TTGGCGGCGCAGCTACTTTA+AGG 0.197167 6.3:-39490551 MS.gene060041:CDS
TCTTGTGTCGTTGAGAAATA+TGG 0.218334 6.3:-39490607 MS.gene060041:CDS
GATCGTGGTGCTATTGGTTT+AGG 0.256115 6.3:-39490792 MS.gene060041:CDS
ATCCCTAGATTGTTGTTATC+AGG 0.272526 6.3:+39491095 None:intergenic
CACGGGAACTGGATCGTCTT+TGG 0.284615 6.3:+39491178 None:intergenic
CATGGTTCAACTAATAAAAT+TGG 0.298289 6.3:-39490522 MS.gene060041:CDS
TAACCATAGGATCAAAATAA+TGG 0.322810 6.3:+39490688 None:intergenic
ATCGTATTTATTCTAATTAT+AGG 0.329066 6.3:-39490749 MS.gene060041:CDS
AACCATAGGATCAAAATAAT+GGG 0.333110 6.3:+39490689 None:intergenic
TTTCCTGATAACAACAATCT+AGG 0.336123 6.3:-39491098 MS.gene060041:CDS
AATATGGGAAGCGGTAATAA+TGG 0.341226 6.3:-39490591 MS.gene060041:CDS
GATAGCTTCACAAAATCAAT+AGG 0.350376 6.3:+39491200 None:intergenic
ATGGTTACCCCACACAGTTT+TGG 0.353666 6.3:-39490672 MS.gene060041:CDS
AGGTATGATCGTGGTGCTAT+TGG 0.362635 6.3:-39490798 MS.gene060041:CDS
TTCAACTTCGACACGGGAAC+TGG 0.370674 6.3:+39491167 None:intergenic
ATTGTTGTTATCAGGAAAAC+AGG 0.375833 6.3:+39491103 None:intergenic
TAATTAGAATAAATACGATA+TGG 0.376851 6.3:+39490753 None:intergenic
ATCGTGGTGCTATTGGTTTA+GGG 0.377319 6.3:-39490791 MS.gene060041:CDS
ATATGGGAAGCGGTAATAAT+GGG 0.397385 6.3:-39490590 MS.gene060041:CDS
AGAATATCGTTTATTGCAAA+AGG 0.407785 6.3:+39491019 None:intergenic
AATAATGGGGTTGAAAATCT+AGG 0.417861 6.3:-39490576 MS.gene060041:CDS
TGCTCTTTCAACTTCGACAC+GGG 0.451823 6.3:+39491161 None:intergenic
GATGATGAACAAATTCGAAT+AGG 0.454167 6.3:+39491125 None:intergenic
TATTCTAATTATAGGTCACT+TGG 0.459145 6.3:-39490741 MS.gene060041:CDS
GGGGTTGAAAATCTAGGTAT+TGG 0.472243 6.3:-39490570 MS.gene060041:CDS
TATTCTACTGCACAAGCGTT+GGG 0.488486 6.3:-39490906 MS.gene060041:CDS
TATTCTACTGCACAAGCGTT+GGG 0.488486 6.3:-39491002 MS.gene060041:CDS
AAAGGAGCATGAGAAAGATC+TGG 0.489039 6.3:+39491037 None:intergenic
ATTCTAATTATAGGTCACTT+GGG 0.501963 6.3:-39490740 MS.gene060041:CDS
AAGACCCGAAGATTCAAAAT+CGG 0.513744 6.3:+39490356 None:intergenic
CTTGTGTCGTTGAGAAATAT+GGG 0.514306 6.3:-39490606 MS.gene060041:CDS
TTCCTGATAACAACAATCTA+GGG 0.520512 6.3:-39491097 MS.gene060041:CDS
TCTCCTTCCTATGAGCGCTC+TGG 0.526806 6.3:+39490973 None:intergenic
GAGGACACCAGAGCGCTCAT+AGG 0.532993 6.3:-39490980 MS.gene060041:CDS
GTTGAAAATCTAGGTATTGG+CGG 0.536047 6.3:-39490567 MS.gene060041:CDS
TACAGAAAAGCAAATTATTG+TGG 0.538998 6.3:-39490442 MS.gene060041:CDS
GTGGACATGAAGGAGAAAGA+AGG 0.546251 6.3:-39491254 None:intergenic
GAGGACACAAGACCGCTCAT+AGG 0.547668 6.3:-39490884 MS.gene060041:CDS
ATATTCTACTGCACAAGCGT+TGG 0.562358 6.3:-39490907 MS.gene060041:CDS
ATATTCTACTGCACAAGCGT+TGG 0.562358 6.3:-39491003 MS.gene060041:CDS
ACACCAGAGCGCTCATAGGA+AGG 0.562791 6.3:-39490976 MS.gene060041:CDS
GACCATACCCAAAACTGTGT+GGG 0.565543 6.3:+39490664 None:intergenic
TTCTAATTATAGGTCACTTG+GGG 0.573154 6.3:-39490739 MS.gene060041:CDS
ACACAAGACCGCTCATAGGA+AGG 0.576634 6.3:-39490880 MS.gene060041:CDS
TCGTTGAGAAATATGGGAAG+CGG 0.607350 6.3:-39490600 MS.gene060041:CDS
AAACTGTGTGGGGTAACCAT+AGG 0.609760 6.3:+39490675 None:intergenic
GTGCTCTTTCAACTTCGACA+CGG 0.612007 6.3:+39491160 None:intergenic
GCTACTTTAAGGATCGAACA+TGG 0.613690 6.3:-39490540 MS.gene060041:CDS
TCGATCACGAATGTCATCCT+CGG 0.622785 6.3:+39490407 None:intergenic
ATACGATATGGATCAAAGCA+AGG 0.624663 6.3:+39490765 None:intergenic
ATATTTCTCAACGACACAAG+AGG 0.626986 6.3:+39490609 None:intergenic
AGCAAGTTCCTTCCTATGAG+CGG 0.633160 6.3:+39490872 None:intergenic
TATGGGAAGCGGTAATAATG+GGG 0.634473 6.3:-39490589 MS.gene060041:CDS
CCCGAAGATTCAAAATCGGA+CGG 0.636092 6.3:+39490360 None:intergenic
ACCATACCCAAAACTGTGTG+GGG 0.637496 6.3:+39490665 None:intergenic
TTCTCAACGACACAAGAGGA+TGG 0.643937 6.3:+39490613 None:intergenic
ACCATAGGATCAAAATAATG+GGG 0.649020 6.3:+39490690 None:intergenic
TGACCATACCCAAAACTGTG+TGG 0.662490 6.3:+39490663 None:intergenic
CATAAACAAAGGTATGATCG+TGG 0.678901 6.3:-39490807 MS.gene060041:CDS
TCTACTGCACAAGCGTTGGG+AGG 0.691089 6.3:-39490903 MS.gene060041:CDS
TCTACTGCACAAGCGTTGGG+AGG 0.691089 6.3:-39490999 MS.gene060041:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCGTATTTATTCTAATTAT+AGG - chr6.3:39490834-39490853 MS.gene060041:CDS 15.0%
!! TAATTAGAATAAATACGATA+TGG + chr6.3:39490833-39490852 None:intergenic 15.0%
!! TAGAAAAACAACATAAACAA+AGG - chr6.3:39490765-39490784 MS.gene060041:CDS 20.0%
! AACCATAGGATCAAAATAAT+GGG + chr6.3:39490897-39490916 None:intergenic 25.0%
! AGAATATCGTTTATTGCAAA+AGG + chr6.3:39490567-39490586 None:intergenic 25.0%
! ATTCTAATTATAGGTCACTT+GGG - chr6.3:39490843-39490862 MS.gene060041:CDS 25.0%
! CATGGTTCAACTAATAAAAT+TGG - chr6.3:39491061-39491080 MS.gene060041:CDS 25.0%
! TAACCATAGGATCAAAATAA+TGG + chr6.3:39490898-39490917 None:intergenic 25.0%
! TACAGAAAAGCAAATTATTG+TGG - chr6.3:39491141-39491160 MS.gene060041:CDS 25.0%
! TATTCTAATTATAGGTCACT+TGG - chr6.3:39490842-39490861 MS.gene060041:CDS 25.0%
ACCATAGGATCAAAATAATG+GGG + chr6.3:39490896-39490915 None:intergenic 30.0%
GATAGCTTCACAAAATCAAT+AGG + chr6.3:39490386-39490405 None:intergenic 30.0%
GATGATGAACAAATTCGAAT+AGG + chr6.3:39490461-39490480 None:intergenic 30.0%
TTCCTGATAACAACAATCTA+GGG - chr6.3:39490486-39490505 MS.gene060041:CDS 30.0%
TTCTAATTATAGGTCACTTG+GGG - chr6.3:39490844-39490863 MS.gene060041:CDS 30.0%
TTTCCTGATAACAACAATCT+AGG - chr6.3:39490485-39490504 MS.gene060041:CDS 30.0%
! AATAATGGGGTTGAAAATCT+AGG - chr6.3:39491007-39491026 MS.gene060041:CDS 30.0%
! ATTGTTGTTATCAGGAAAAC+AGG + chr6.3:39490483-39490502 None:intergenic 30.0%
! CACAAAATCAATAGGCTTTT+TGG + chr6.3:39490378-39490397 None:intergenic 30.0%
!!! AGGCTTTTTGGATTTTGATT+TGG + chr6.3:39490366-39490385 None:intergenic 30.0%
!!! CTTTTTGGATTTTGATTTGG+AGG + chr6.3:39490363-39490382 None:intergenic 30.0%
AAGACCCGAAGATTCAAAAT+CGG + chr6.3:39491230-39491249 None:intergenic 35.0%
AATATGGGAAGCGGTAATAA+TGG - chr6.3:39490992-39491011 MS.gene060041:CDS 35.0%
ATACGATATGGATCAAAGCA+AGG + chr6.3:39490821-39490840 None:intergenic 35.0%
ATATGGGAAGCGGTAATAAT+GGG - chr6.3:39490993-39491012 MS.gene060041:CDS 35.0%
ATATTTCTCAACGACACAAG+AGG + chr6.3:39490977-39490996 None:intergenic 35.0%
! ATCCCTAGATTGTTGTTATC+AGG + chr6.3:39490491-39490510 None:intergenic 35.0%
! CATAAACAAAGGTATGATCG+TGG - chr6.3:39490776-39490795 MS.gene060041:CDS 35.0%
! CTTGTGTCGTTGAGAAATAT+GGG - chr6.3:39490977-39490996 MS.gene060041:CDS 35.0%
! TCTTGTGTCGTTGAGAAATA+TGG - chr6.3:39490976-39490995 MS.gene060041:CDS 35.0%
!! GTTGAAAATCTAGGTATTGG+CGG - chr6.3:39491016-39491035 MS.gene060041:CDS 35.0%
ATATTCTACTGCACAAGCGT+TGG - chr6.3:39490580-39490599 MS.gene060041:CDS 40.0%
GGGGTTGAAAATCTAGGTAT+TGG - chr6.3:39491013-39491032 MS.gene060041:CDS 40.0%
TATGGGAAGCGGTAATAATG+GGG - chr6.3:39490994-39491013 MS.gene060041:CDS 40.0%
TATTCTACTGCACAAGCGTT+GGG - chr6.3:39490581-39490600 MS.gene060041:CDS 40.0%
TCGTTGAGAAATATGGGAAG+CGG - chr6.3:39490983-39491002 MS.gene060041:CDS 40.0%
! AAAGGAGCATGAGAAAGATC+TGG + chr6.3:39490549-39490568 None:intergenic 40.0%
! ACCGTCCGATTTTGAATCTT+CGG - chr6.3:39491222-39491241 MS.gene060041:CDS 40.0%
! GCTACTTTAAGGATCGAACA+TGG - chr6.3:39491043-39491062 MS.gene060041:CDS 40.0%
! GGACGGTTCTTCTTCAATTT+TGG + chr6.3:39491209-39491228 None:intergenic 40.0%
! TGTGGCTTCTAATTTTTCCG+AGG - chr6.3:39491159-39491178 MS.gene060041:CDS 40.0%
!! ATCGTGGTGCTATTGGTTTA+GGG - chr6.3:39490792-39490811 MS.gene060041:CDS 40.0%
!!! GCCCCATTATTTTGATCCTA+TGG - chr6.3:39490892-39490911 MS.gene060041:CDS 40.0%
AAACTGTGTGGGGTAACCAT+AGG + chr6.3:39490911-39490930 None:intergenic 45.0%
ACCATACCCAAAACTGTGTG+GGG + chr6.3:39490921-39490940 None:intergenic 45.0%
AGCAAGTTCCTTCCTATGAG+CGG + chr6.3:39490714-39490733 None:intergenic 45.0%
CCCGAAGATTCAAAATCGGA+CGG + chr6.3:39491226-39491245 None:intergenic 45.0%
GACCATACCCAAAACTGTGT+GGG + chr6.3:39490922-39490941 None:intergenic 45.0%
GTGCTCTTTCAACTTCGACA+CGG + chr6.3:39490426-39490445 None:intergenic 45.0%
TCGATCACGAATGTCATCCT+CGG + chr6.3:39491179-39491198 None:intergenic 45.0%
TGACCATACCCAAAACTGTG+TGG + chr6.3:39490923-39490942 None:intergenic 45.0%
TGCTCTTTCAACTTCGACAC+GGG + chr6.3:39490425-39490444 None:intergenic 45.0%
TTCTCAACGACACAAGAGGA+TGG + chr6.3:39490973-39490992 None:intergenic 45.0%
! ATGGTTACCCCACACAGTTT+TGG - chr6.3:39490911-39490930 MS.gene060041:CDS 45.0%
! CCGTCCGATTTTGAATCTTC+GGG - chr6.3:39491223-39491242 MS.gene060041:CDS 45.0%
! TGGTTACCCCACACAGTTTT+GGG - chr6.3:39490912-39490931 MS.gene060041:CDS 45.0%
!! AGGTATGATCGTGGTGCTAT+TGG - chr6.3:39490785-39490804 MS.gene060041:CDS 45.0%
!! GATCGTGGTGCTATTGGTTT+AGG - chr6.3:39490791-39490810 MS.gene060041:CDS 45.0%
ACACAAGACCGCTCATAGGA+AGG - chr6.3:39490703-39490722 MS.gene060041:CDS 50.0%
TTCAACTTCGACACGGGAAC+TGG + chr6.3:39490419-39490438 None:intergenic 50.0%
!!! ACCCCACACAGTTTTGGGTA+TGG - chr6.3:39490917-39490936 MS.gene060041:CDS 50.0%
CACGGGAACTGGATCGTCTT+TGG + chr6.3:39490408-39490427 None:intergenic 55.0%
GAGGACACAAGACCGCTCAT+AGG - chr6.3:39490699-39490718 MS.gene060041:CDS 55.0%
TCTCCTTCCTATGAGCGCTC+TGG + chr6.3:39490613-39490632 None:intergenic 55.0%
! ACACCAGAGCGCTCATAGGA+AGG - chr6.3:39490607-39490626 MS.gene060041:CDS 55.0%
! TTGGCGGCGCAGCTACTTTA+AGG - chr6.3:39491032-39491051 MS.gene060041:CDS 55.0%
!! TCTACTGCACAAGCGTTGGG+AGG - chr6.3:39490584-39490603 MS.gene060041:CDS 55.0%
! GAGGACACCAGAGCGCTCAT+AGG - chr6.3:39490603-39490622 MS.gene060041:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 39490335 39491270 39490335 ID=MS.gene060041
chr6.3 mRNA 39490335 39491270 39490335 ID=MS.gene060041.t1;Parent=MS.gene060041
chr6.3 exon 39490335 39491270 39490335 ID=MS.gene060041.t1.exon1;Parent=MS.gene060041.t1
chr6.3 CDS 39490335 39491270 39490335 ID=cds.MS.gene060041.t1;Parent=MS.gene060041.t1
Gene Sequence

>MS.gene060041

ATGAAGGAGAAAGAAGGAGTTCAATCCTCCAAATCAAAATCCAAAAAGCCTATTGATTTTGTGAAGCTATCCAAAGACGATCCAGTTCCCGTGTCGAAGTTGAAAGAGCACAATTATTTTCAGCCTATTCGAATTTGTTCATCATCCTGTTTTCCTGATAACAACAATCTAGGGATAGATGAGAACAACAAAGAAGAGAAGAATTCGTATTCCAGATCTTTCTCATGCTCCTTTTGCAATAAACGATATTCTACTGCACAAGCGTTGGGAGGACACCAGAGCGCTCATAGGAAGGAGAATTCAGATTCAAGATCTTTCTCATGCTCGTTTTGCAAGAAACGATATTCTACTGCACAAGCGTTGGGAGGACACAAGACCGCTCATAGGAAGGAACTTGCTTTAGAAAAAGCTCACAAGAAGAAACAAGCTTTAGAAAAACAACATAAACAAAGGTATGATCGTGGTGCTATTGGTTTAGGGAAACCTTGCTTTGATCCATATCGTATTTATTCTAATTATAGGTCACTTGGGGTTAGCACAAACTCAATGATTCGAAAGCCCCATTATTTTGATCCTATGGTTACCCCACACAGTTTTGGGTATGGTCATTCTGCTTTGTTGCAAGAGATAACACACCATCCTCTTGTGTCGTTGAGAAATATGGGAAGCGGTAATAATGGGGTTGAAAATCTAGGTATTGGCGGCGCAGCTACTTTAAGGATCGAACATGGTTCAACTAATAAAATTGGTGCTATTATGAAATTTAGAGATTCTTCTACAAATATTGCTACAAGTTCAAATTCAAATACAGAAAAGCAAATTATTGTGGCTTCTAATTTTTCCGAGGATGACATTCGTGATCGATCAAAGTCCAAAATTGAAGAAGAACCGTCCGATTTTGAATCTTCGGGTCTTGATTTATCACTTAAGCTTTAA
Protein sequence

>MS.gene060041.t1

MKEKEGVQSSKSKSKKPIDFVKLSKDDPVPVSKLKEHNYFQPIRICSSSCFPDNNNLGIDENNKEEKNSYSRSFSCSFCNKRYSTAQALGGHQSAHRKENSDSRSFSCSFCKKRYSTAQALGGHKTAHRKELALEKAHKKKQALEKQHKQRYDRGAIGLGKPCFDPYRIYSNYRSLGVSTNSMIRKPHYFDPMVTPHSFGYGHSALLQEITHHPLVSLRNMGSGNNGVENLGIGGAATLRIEHGSTNKIGAIMKFRDSSTNIATSSNSNTEKQIIVASNFSEDDIRDRSKSKIEEEPSDFESSGLDLSLKL