AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene072241

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene072241.t1 MTR_8g014210 78.037 214 9 1 1 176 1 214 2.36e-112 320
MS.gene072241.t1 MTR_4g024745 51.628 215 65 2 1 176 70 284 5.15e-64 199
MS.gene072241.t1 MTR_8g445780 56.216 185 43 1 1 147 206 390 4.96e-62 197
MS.gene072241.t1 MTR_4g024710 51.852 216 65 2 1 177 116 331 1.10e-60 192
MS.gene072241.t1 MTR_8g014260 47.436 234 77 3 1 188 220 453 2.68e-57 187
MS.gene072241.t1 MTR_2g083840 42.601 223 84 5 1 182 221 440 3.54e-41 144
MS.gene072241.t1 MTR_8g468840 42.478 226 81 5 6 182 221 446 1.95e-39 140
MS.gene072241.t1 MTR_8g058970 39.749 239 91 6 1 187 235 472 9.41e-37 133
MS.gene072241.t1 MTR_5g092960 40.435 230 81 5 9 182 229 458 2.09e-36 132
MS.gene072241.t1 MTR_8g062270 40.260 231 84 7 4 182 222 450 4.19e-34 125
MS.gene072241.t1 MTR_8g468810 41.063 207 76 5 1 162 224 429 2.69e-33 124
MS.gene072241.t1 MTR_8g077460 42.222 180 69 4 1 177 212 359 7.59e-33 121
MS.gene072241.t1 MTR_8g014230 68.831 77 24 0 101 177 13 89 2.38e-32 112
MS.gene072241.t1 MTR_8g014160 40.437 183 82 6 3 177 246 409 1.78e-29 113
MS.gene072241.t1 MTR_8g467800 36.596 235 86 6 6 182 220 449 8.02e-29 111
MS.gene072241.t1 MTR_8g468760 37.264 212 95 8 1 182 212 415 9.92e-25 100
MS.gene072241.t1 MTR_4g032730 35.124 242 83 8 10 182 227 463 2.31e-24 99.4
MS.gene072241.t1 MTR_8g062310 34.762 210 83 7 9 177 216 412 4.61e-21 90.1
MS.gene072241.t1 MTR_8g469020 49.000 100 41 4 93 182 348 447 1.17e-19 86.3
MS.gene072241.t1 MTR_2g086020 44.860 107 49 4 86 182 205 311 5.62e-19 83.2
MS.gene072241.t1 MTR_8g062010 35.000 180 95 9 21 182 251 426 1.65e-18 82.8
MS.gene072241.t1 MTR_5g092960 39.860 143 41 2 9 106 229 371 4.06e-17 78.6
MS.gene072241.t1 MTR_8g058965 44.000 100 46 4 93 182 353 452 1.60e-16 77.0
MS.gene072241.t1 MTR_8g062080 46.000 100 48 4 93 187 342 440 2.12e-16 76.6
MS.gene072241.t1 MTR_8g070950 47.727 88 43 3 93 177 331 418 3.06e-16 76.3
MS.gene072241.t1 MTR_8g062300 42.000 100 48 3 93 182 374 473 9.34e-15 72.0
MS.gene072241.t1 MTR_8g468810 35.570 149 52 3 1 106 224 371 3.07e-14 70.5
MS.gene072241.t1 MTR_8g468810 38.835 103 62 1 1 103 224 325 2.85e-13 67.4
MS.gene072241.t1 MTR_8g468810 44.828 87 47 1 1 87 224 309 4.72e-13 66.6
MS.gene072241.t1 MTR_8g468810 44.828 87 47 1 1 87 224 309 5.62e-13 66.6
MS.gene072241.t1 MTR_7g032380 28.718 195 122 7 8 187 159 351 4.02e-12 64.3
MS.gene072241.t1 MTR_7g032370 37.755 98 57 2 94 187 250 347 2.51e-11 62.0
MS.gene072241.t1 MTR_7g034115 37.363 91 54 1 94 181 281 371 2.56e-11 62.0
MS.gene072241.t1 MTR_1g041245 36.634 101 58 2 94 188 282 382 3.06e-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

Find 42 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATATTTCCGTGGACTTAA+AGG 0.241780 8.3:-74504201 MS.gene072241:CDS
CTTTAAATTGAATAAAAGTT+AGG 0.323748 8.3:+74504306 None:intergenic
AACCTCCTTGGCAATCTCTC+TGG 0.356546 8.3:-74504878 MS.gene072241:CDS
AGGTGTGATACAAGACAATT+AGG 0.379881 8.3:+74504326 None:intergenic
TCTGATGTGCCAAGGGCCTC+TGG 0.399227 8.3:-74504153 MS.gene072241:CDS
GATCCGGTGCGTTCATTTCA+AGG 0.404732 8.3:+74505026 None:intergenic
CAGGAACAGTCATCTTTACT+AGG 0.411116 8.3:-74504371 MS.gene072241:CDS
GCGTCCCACCTTCTTTGAAA+AGG 0.432637 8.3:-74505084 MS.gene072241:CDS
ACCTCCTTGGCAATCTCTCT+GGG 0.462671 8.3:-74504877 MS.gene072241:CDS
TGCCAAGGAGGTTGTTCAAA+GGG 0.470637 8.3:+74504888 None:intergenic
ATCCCTTTGAACAACCTCCT+TGG 0.481592 8.3:-74504890 MS.gene072241:CDS
ATGTGATTCCGTTGATGTAA+AGG 0.489313 8.3:+74504996 None:intergenic
ATTCAATTTAAAGGATTTCG+TGG 0.496055 8.3:-74504296 MS.gene072241:CDS
GGGACTAAACATCTAGTGTT+GGG 0.507850 8.3:-74504857 MS.gene072241:CDS
TACATCAACGGAATCACATC+CGG 0.515817 8.3:-74504992 MS.gene072241:CDS
GGATGACGGAAGAAAACGGC+TGG 0.517452 8.3:+74504909 None:intergenic
AACAGTCATCTTTACTAGGA+TGG 0.526478 8.3:-74504367 MS.gene072241:CDS
TGGGACTAAACATCTAGTGT+TGG 0.530389 8.3:-74504858 MS.gene072241:CDS
ATGTAAAGGTACTCAAGATC+CGG 0.531961 8.3:+74505010 None:intergenic
TGACACATTCCAGAGGCCCT+TGG 0.534109 8.3:+74504144 None:intergenic
ATTATTAGAACTTGAAGCAT+AGG 0.536850 8.3:+74504547 None:intergenic
CAATTAGGAACACATGGTGT+TGG 0.539182 8.3:+74504341 None:intergenic
TTGACTGAACTGTATGCATA+AGG 0.554292 8.3:-74504113 None:intergenic
TTGCCAAGGAGGTTGTTCAA+AGG 0.562217 8.3:+74504887 None:intergenic
GATTATTGCTGATATTTCCG+TGG 0.562279 8.3:-74504210 MS.gene072241:CDS
CATCATTGATAATGAAGTTG+AGG 0.566259 8.3:-74505053 MS.gene072241:CDS
AAAGGGATGACGGAAGAAAA+CGG 0.567288 8.3:+74504905 None:intergenic
CTTGAGTACCTTTACATCAA+CGG 0.572815 8.3:-74505004 MS.gene072241:CDS
TCCCAGAGAGATTGCCAAGG+AGG 0.576483 8.3:+74504876 None:intergenic
GTACTTCTCCTTTAAGTCCA+CGG 0.580895 8.3:+74504193 None:intergenic
GAGGTTGTTCAAAGGGATGA+CGG 0.605555 8.3:+74504895 None:intergenic
ATGACGGAAGAAAACGGCTG+GGG 0.611934 8.3:+74504911 None:intergenic
TCTAATAATTCATAATGACA+AGG 0.613723 8.3:-74504533 MS.gene072241:intron
TTACCTTGAAATGAACGCAC+CGG 0.629323 8.3:-74505029 MS.gene072241:CDS
GTTGGGTCGTTCAACAACCA+AGG 0.635068 8.3:-74504840 MS.gene072241:intron
ACAAGACAATTAGGAACACA+TGG 0.644694 8.3:+74504335 None:intergenic
GATGACGGAAGAAAACGGCT+GGG 0.652963 8.3:+74504910 None:intergenic
TAGTCCCAGAGAGATTGCCA+AGG 0.657681 8.3:+74504873 None:intergenic
GTACAACTTGCACAATGTGG+TGG 0.667122 8.3:-74504954 MS.gene072241:CDS
TGGGACGCAAACTTTACCCA+TGG 0.667733 8.3:+74505099 None:intergenic
TTTAAGTTGACACATTCCAG+AGG 0.695966 8.3:+74504137 None:intergenic
CATGTACAACTTGCACAATG+TGG 0.728594 8.3:-74504957 MS.gene072241:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTAATTTATTTCATAAAAAA+TGG + chr8.3:74504756-74504775 None:intergenic 10.0%
!! AAATTATAAATTGCATCTTA+TGG - chr8.3:74504778-74504797 MS.gene072241:intron 15.0%
!! ATAAAATAAAACTTAAACCT+TGG + chr8.3:74504392-74504411 None:intergenic 15.0%
!! CTTTAAATTGAATAAAAGTT+AGG + chr8.3:74504909-74504928 None:intergenic 15.0%
!! TGAAAATTAATTTAGATCAT+GGG + chr8.3:74504563-74504582 None:intergenic 15.0%
!! TTGAAAATTAATTTAGATCA+TGG + chr8.3:74504564-74504583 None:intergenic 15.0%
!!! CTAACTTTTATTCAATTTAA+AGG - chr8.3:74504907-74504926 MS.gene072241:CDS 15.0%
!! GAAAATTAATTTAGATCATG+GGG + chr8.3:74504562-74504581 None:intergenic 20.0%
!! TCTAATAATTCATAATGACA+AGG - chr8.3:74504679-74504698 MS.gene072241:intron 20.0%
! AATATATATGACATCAGAGA+TGG + chr8.3:74504485-74504504 None:intergenic 25.0%
! ATTATTAGAACTTGAAGCAT+AGG + chr8.3:74504668-74504687 None:intergenic 25.0%
! ATTCAATTTAAAGGATTTCG+TGG - chr8.3:74504916-74504935 MS.gene072241:CDS 25.0%
AAAAAATATCTGATGTGCCA+AGG - chr8.3:74505051-74505070 MS.gene072241:CDS 30.0%
AAAAATATCTGATGTGCCAA+GGG - chr8.3:74505052-74505071 MS.gene072241:CDS 30.0%
ATAAATTGCATCTTATGGTC+TGG - chr8.3:74504783-74504802 MS.gene072241:intron 30.0%
TTGATGTCATGTACAAATAG+TGG - chr8.3:74504524-74504543 MS.gene072241:intron 30.0%
! ATTGTCAACCTTTTCAAAGA+AGG + chr8.3:74504139-74504158 None:intergenic 30.0%
! GCTGAGTATGTTTTACAAAA+AGG - chr8.3:74504961-74504980 MS.gene072241:CDS 30.0%
! TGTTTTGTCGAAGCTTAATT+TGG - chr8.3:74504704-74504723 MS.gene072241:intron 30.0%
!! CATCATTGATAATGAAGTTG+AGG - chr8.3:74504159-74504178 MS.gene072241:CDS 30.0%
AACAGTCATCTTTACTAGGA+TGG - chr8.3:74504845-74504864 MS.gene072241:CDS 35.0%
ACAAGACAATTAGGAACACA+TGG + chr8.3:74504880-74504899 None:intergenic 35.0%
AGGTGTGATACAAGACAATT+AGG + chr8.3:74504889-74504908 None:intergenic 35.0%
ATGTGATTCCGTTGATGTAA+AGG + chr8.3:74504219-74504238 None:intergenic 35.0%
CTTGAGTACCTTTACATCAA+CGG - chr8.3:74504208-74504227 MS.gene072241:CDS 35.0%
GATTATTGCTGATATTTCCG+TGG - chr8.3:74505002-74505021 MS.gene072241:CDS 35.0%
TGATATTTCCGTGGACTTAA+AGG - chr8.3:74505011-74505030 MS.gene072241:CDS 35.0%
! TCAACCTTTTCAAAGAAGGT+GGG + chr8.3:74504135-74504154 None:intergenic 35.0%
!! ATGTAAAGGTACTCAAGATC+CGG + chr8.3:74504205-74504224 None:intergenic 35.0%
!! TTTAAGTTGACACATTCCAG+AGG + chr8.3:74505078-74505097 None:intergenic 35.0%
ATGTACAAATAGTGGCTGCT+TGG - chr8.3:74504532-74504551 MS.gene072241:intron 40.0%
CAATTAGGAACACATGGTGT+TGG + chr8.3:74504874-74504893 None:intergenic 40.0%
CAGGAACAGTCATCTTTACT+AGG - chr8.3:74504841-74504860 MS.gene072241:CDS 40.0%
CATGTACAACTTGCACAATG+TGG - chr8.3:74504255-74504274 MS.gene072241:CDS 40.0%
GGGACTAAACATCTAGTGTT+GGG - chr8.3:74504355-74504374 MS.gene072241:CDS 40.0%
GTAAAGATGACTGTTCCTGT+AGG + chr8.3:74504840-74504859 None:intergenic 40.0%
GTACATGCTAAAAACTTCGC+CGG + chr8.3:74504242-74504261 None:intergenic 40.0%
GTACTTCTCCTTTAAGTCCA+CGG + chr8.3:74505022-74505041 None:intergenic 40.0%
TACATCAACGGAATCACATC+CGG - chr8.3:74504220-74504239 MS.gene072241:CDS 40.0%
TGGGACTAAACATCTAGTGT+TGG - chr8.3:74504354-74504373 MS.gene072241:CDS 40.0%
TTACCTTGAAATGAACGCAC+CGG - chr8.3:74504183-74504202 MS.gene072241:CDS 40.0%
! AGGATTTCGTGGATTTTCAG+AGG - chr8.3:74504927-74504946 MS.gene072241:CDS 40.0%
! ATTTCGTGGATTTTCAGAGG+AGG - chr8.3:74504930-74504949 MS.gene072241:CDS 40.0%
! GTCAACCTTTTCAAAGAAGG+TGG + chr8.3:74504136-74504155 None:intergenic 40.0%
!! AAAGGGATGACGGAAGAAAA+CGG + chr8.3:74504310-74504329 None:intergenic 40.0%
!! GAACATGTTTTGTTGCCTAC+AGG - chr8.3:74504822-74504841 MS.gene072241:intron 40.0%
ACCGATAAAGAGTGAGCTCT+AGG + chr8.3:74504607-74504626 None:intergenic 45.0%
ATCCCTTTGAACAACCTCCT+TGG - chr8.3:74504322-74504341 MS.gene072241:CDS 45.0%
GAGGTTGTTCAAAGGGATGA+CGG + chr8.3:74504320-74504339 None:intergenic 45.0%
GCCTAGAGCTCACTCTTTAT+CGG - chr8.3:74504603-74504622 MS.gene072241:intron 45.0%
GTACAACTTGCACAATGTGG+TGG - chr8.3:74504258-74504277 MS.gene072241:CDS 45.0%
TGCCAAGGAGGTTGTTCAAA+GGG + chr8.3:74504327-74504346 None:intergenic 45.0%
TTGCCAAGGAGGTTGTTCAA+AGG + chr8.3:74504328-74504347 None:intergenic 45.0%
AACCTCCTTGGCAATCTCTC+TGG - chr8.3:74504334-74504353 MS.gene072241:CDS 50.0%
ACCTCCTTGGCAATCTCTCT+GGG - chr8.3:74504335-74504354 MS.gene072241:CDS 50.0%
GATCCGGTGCGTTCATTTCA+AGG + chr8.3:74504189-74504208 None:intergenic 50.0%
GTTGGGTCGTTCAACAACCA+AGG - chr8.3:74504372-74504391 MS.gene072241:intron 50.0%
TAGTCCCAGAGAGATTGCCA+AGG + chr8.3:74504342-74504361 None:intergenic 50.0%
! ATGACGGAAGAAAACGGCTG+GGG + chr8.3:74504304-74504323 None:intergenic 50.0%
! GCGTCCCACCTTCTTTGAAA+AGG - chr8.3:74504128-74504147 MS.gene072241:CDS 50.0%
!! GATGACGGAAGAAAACGGCT+GGG + chr8.3:74504305-74504324 None:intergenic 50.0%
TCCCAGAGAGATTGCCAAGG+AGG + chr8.3:74504339-74504358 None:intergenic 55.0%
TGACACATTCCAGAGGCCCT+TGG + chr8.3:74505071-74505090 None:intergenic 55.0%
!! GGATGACGGAAGAAAACGGC+TGG + chr8.3:74504306-74504325 None:intergenic 55.0%
TCTGATGTGCCAAGGGCCTC+TGG - chr8.3:74505059-74505078 MS.gene072241:CDS 60.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 74504115 74505119 74504115 ID=MS.gene072241
chr8.3 mRNA 74504115 74505119 74504115 ID=MS.gene072241.t1;Parent=MS.gene072241
chr8.3 exon 74504841 74505119 74504841 ID=MS.gene072241.t1.exon1;Parent=MS.gene072241.t1
chr8.3 CDS 74504841 74505119 74504841 ID=cds.MS.gene072241.t1;Parent=MS.gene072241.t1
chr8.3 exon 74504534 74504572 74504534 ID=MS.gene072241.t1.exon2;Parent=MS.gene072241.t1
chr8.3 CDS 74504534 74504572 74504534 ID=cds.MS.gene072241.t1;Parent=MS.gene072241.t1
chr8.3 exon 74504115 74504390 74504115 ID=MS.gene072241.t1.exon3;Parent=MS.gene072241.t1
chr8.3 CDS 74504115 74504390 74504115 ID=cds.MS.gene072241.t1;Parent=MS.gene072241.t1
Gene Sequence

>MS.gene072241

ATGGGTAAAGTTTGCGTCCCACCTTCTTTGAAAAGGTTGACAATCATCATTGATAATGAAGTTGAGGCTTACCTTGAAATGAACGCACCGGATCTTGAGTACCTTTACATCAACGGAATCACATCCGGCGAAGTTTTTAGCATGTACAACTTGCACAATGTGGTGGAAGCACATCTTAATGTTTTTCCCCAGCCGTTTTCTTCCGTCATCCCTTTGAACAACCTCCTTGGCAATCTCTCTGGGACTAAACATCTAGTGTTGGGTCGTTCAACAACCAAGGTTTAAGTTTTATTTTATATTTTCATCAAATGTTATCTCACTTATATAGAGATTAAGTTCAAACTAGTTACAAACTATTGATTAACTACCATCTCTGATGTCATATATATTGTTTTGTACTAATTACTATTTGATGTCATGTACAAATAGTGGCTGCTTGGAGAGCCCCATGATCTAAATTAATTTTCAAGAACTTCGCTATTTGCTTCGCCTAGAGCTCACTCTTTATCGGTACAACTTCAATTCTGTACTGAACTTGCTTCAAAAGTGTCCTATGCTTCAAGTTCTAATAATTCATAATGACAAGGTTTGTTTTGTCGAAGCTTAATTTGGTTTATATAACTTTGATGTGAAAATTACCATTTTTTATGAAATAAATTACAAAAATTATAAATTGCATCTTATGGTCTGGTACACAACTTAACATAGAACATGTTTTGTTGCCTACAGGAACAGTCATCTTTACTAGGATGGACTCCAACACCATGTGTTCCTAATTGTCTTGTATCACACCTAACTTTTATTCAATTTAAAGGATTTCGTGGATTTTCAGAGGAGGTGTCATTTGCTGAGTATGTTTTACAAAAAGGACTTGTTTTAAAGACAGTGATTATTGCTGATATTTCCGTGGACTTAAAGGAGAAGTACGACATTCTCAAAAAATATCTGATGTGCCAAGGGCCTCTGGAATGTGTCAACTTAAATTTGACTGAACTGTATGCATAA
Protein sequence

>MS.gene072241.t1

MGKVCVPPSLKRLTIIIDNEVEAYLEMNAPDLEYLYINGITSGEVFSMYNLHNVVEAHLNVFPQPFSSVIPLNNLLGNLSGTKHLVLGRSTTKCPMLQVLIIHNDKEQSSLLGWTPTPCVPNCLVSHLTFIQFKGFRGFSEEVSFAEYVLQKGLVLKTVIIADISVDLKEKYDILKKYLMCQGPLECVNLNLTELYA