AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41266

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41266.t1 MTR_1g048720 93.522 247 16 0 1 247 1 247 2.98e-171 472
MS.gene41266.t1 MTR_1g048720 93.117 247 16 1 1 247 1 246 9.95e-169 465
MS.gene41266.t1 MTR_1g048720 94.064 219 13 0 1 219 1 219 8.09e-153 424
MS.gene41266.t1 MTR_1g048720 93.607 219 13 1 1 219 1 218 2.24e-150 418
MS.gene41266.t1 MTR_1g048710 87.295 244 22 2 1 244 1 235 7.97e-146 407
MS.gene41266.t1 MTR_1g048750 86.697 218 21 1 1 218 1 210 2.99e-137 387
MS.gene41266.t1 MTR_7g090410 58.964 251 84 7 1 241 1 242 6.35e-66 205
MS.gene41266.t1 MTR_0007s0330 31.677 161 98 5 65 222 6 157 1.24e-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.gene41266.t1 AT3G56970 42.169 249 133 5 1 240 1 247 1.48e-56 181
MS.gene41266.t1 AT2G41240 39.216 255 125 6 1 242 1 238 1.25e-46 155
MS.gene41266.t1 AT3G56980 40.293 273 113 6 1 242 1 254 4.21e-46 154
MS.gene41266.t1 AT2G41240 38.824 255 125 7 1 242 1 237 3.46e-44 149
MS.gene41266.t1 AT5G04150 46.626 163 82 2 60 219 78 238 8.89e-37 130
MS.gene41266.t1 AT5G04150 44.809 183 93 4 60 237 78 257 2.81e-36 129

Find 42 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCACCTGTTTCTGTAATTC+TGG 0.155913 1.4:+34778338 None:intergenic
TGATGCTGGTTATGGCTTAT+TGG 0.196697 1.4:+34778831 None:intergenic
CTTCTATAATTTGCATTTCC+AGG 0.265122 1.4:-34778045 MS.gene41266:intron
TTCTGAGATCTTGATCTGTT+TGG 0.308189 1.4:-34778126 MS.gene41266:CDS
GTTTCTTCATCTCAGACCTT+TGG 0.353556 1.4:-34778077 MS.gene41266:CDS
AGGACTCTTGAAATTGTTGC+TGG 0.367920 1.4:+34778371 None:intergenic
ATGAATTCTGATGCTGGTTA+TGG 0.378267 1.4:+34778823 None:intergenic
TAGAATAACCTCTTCTACTT+GGG 0.395863 1.4:+34778271 None:intergenic
TCTTCATCTCAGACCTTTGG+AGG 0.399420 1.4:-34778074 MS.gene41266:CDS
TCTTCCTGTTTCTGATCAAA+TGG 0.413993 1.4:-34778616 MS.gene41266:intron
AGTACCATTTGATCAGAAAC+AGG 0.414053 1.4:+34778612 None:intergenic
CATACCAGAATTACAGAAAC+AGG 0.417584 1.4:-34778342 MS.gene41266:CDS
TTAGAATAACCTCTTCTACT+TGG 0.448901 1.4:+34778270 None:intergenic
AACAATTGGATGGCCCTTTG+AGG 0.464251 1.4:-34778856 MS.gene41266:CDS
TGGCTTATTGGCTCCTCAAA+GGG 0.478232 1.4:+34778843 None:intergenic
ATGGCTTATTGGCTCCTCAA+AGG 0.479279 1.4:+34778842 None:intergenic
CAGATCAAGATCTCAGAAAG+TGG 0.487534 1.4:+34778131 None:intergenic
TTGATCTGTTTGGAAAATGA+TGG 0.493817 1.4:-34778116 MS.gene41266:CDS
CATGCCAAGGTCACTGCTTG+TGG 0.499479 1.4:+34778719 None:intergenic
AAGAAACATTAAGCAGCAAA+AGG 0.506413 1.4:+34778093 None:intergenic
TGTAGAATGAATTCTGATGC+TGG 0.526407 1.4:+34778817 None:intergenic
ACAAATTATTGATCTTCTTG+CGG 0.529574 1.4:+34778658 None:intergenic
AGTGTAACATGAAATCTGAA+TGG 0.542718 1.4:+34778166 None:intergenic
GCTCTTATCAATAGTCGAGA+AGG 0.548655 1.4:-34777468 MS.gene41266:CDS
AAGAAGCATAGTTACAACTC+TGG 0.551749 1.4:-34778230 MS.gene41266:CDS
ACTTTCTCCCCAAGTAGAAG+AGG 0.556979 1.4:-34778279 MS.gene41266:CDS
CATCCAATTGTTGAAAACAT+AGG 0.558093 1.4:+34778867 None:intergenic
CTTCATCTCAGACCTTTGGA+GGG 0.563936 1.4:-34778073 MS.gene41266:CDS
AGGAAGAAGTGAACGAAGAG+AGG 0.567551 1.4:+34778632 None:intergenic
CAATCCACAAGCAGTGACCT+TGG 0.569748 1.4:-34778723 MS.gene41266:CDS
ACTAGTTAAAAGAAAAGAAG+AGG 0.575033 1.4:-34778312 MS.gene41266:CDS
CCAATTGTTGAAAACATAGG+AGG 0.582074 1.4:+34778870 None:intergenic
AGAATAACCTCTTCTACTTG+GGG 0.586846 1.4:+34778272 None:intergenic
GTCACTGCTTGTGGATTGTG+AGG 0.591686 1.4:+34778728 None:intergenic
ATAGAAGACTCTCCCTCCAA+AGG 0.594272 1.4:+34778061 None:intergenic
CACAAGCAGTGACCTTGGCA+TGG 0.602895 1.4:-34778718 MS.gene41266:CDS
TTATCAATAGTCGAGAAGGA+AGG 0.633485 1.4:-34777464 MS.gene41266:CDS
CAAGCTTCTTAACCATGCCA+AGG 0.655760 1.4:+34778706 None:intergenic
ACCAGAATTACAGAAACAGG+TGG 0.656125 1.4:-34778339 MS.gene41266:CDS
GAATTACAGAAACAGGTGGA+AGG 0.659206 1.4:-34778335 MS.gene41266:CDS
TTCTAAGCAAAGAATCACAA+AGG 0.666729 1.4:-34778253 MS.gene41266:CDS
TCACTGCTTGTGGATTGTGA+GGG 0.698792 1.4:+34778729 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATACAAATAATTGATTACTT+GGG - chr1.4:34778682-34778701 MS.gene41266:CDS 15.0%
!! GATCATATATAATTATGATT+TGG - chr1.4:34778456-34778475 MS.gene41266:intron 15.0%
!! TATACAAATAATTGATTACT+TGG - chr1.4:34778681-34778700 MS.gene41266:CDS 15.0%
! ACAAATTATTGATCTTCTTG+CGG + chr1.4:34777675-34777694 None:intergenic 25.0%
! ACAATTAGAAACAGATAGAA+GGG + chr1.4:34777752-34777771 None:intergenic 25.0%
! ACTAGTTAAAAGAAAAGAAG+AGG - chr1.4:34778018-34778037 MS.gene41266:intron 25.0%
! TCTAATTGTCAATAATGCTT+TGG - chr1.4:34777763-34777782 MS.gene41266:intron 25.0%
!! GTAATTCTGGTATGTATTTT+AGG + chr1.4:34777982-34778001 None:intergenic 25.0%
!!! ACACAAAGAGCTTTTAATTA+AGG + chr1.4:34778789-34778808 None:intergenic 25.0%
!!! TAATTTTCATGATCAAGTTG+AGG - chr1.4:34777558-34777577 MS.gene41266:intron 25.0%
AAGAAACATTAAGCAGCAAA+AGG + chr1.4:34778240-34778259 None:intergenic 30.0%
AGTGTAACATGAAATCTGAA+TGG + chr1.4:34778167-34778186 None:intergenic 30.0%
CATCCAATTGTTGAAAACAT+AGG + chr1.4:34777466-34777485 None:intergenic 30.0%
GACAATTAGAAACAGATAGA+AGG + chr1.4:34777753-34777772 None:intergenic 30.0%
GATGTATAGACTCATAAAAG+AGG - chr1.4:34778748-34778767 MS.gene41266:CDS 30.0%
TAGAATAACCTCTTCTACTT+GGG + chr1.4:34778062-34778081 None:intergenic 30.0%
TTAGAATAACCTCTTCTACT+TGG + chr1.4:34778063-34778082 None:intergenic 30.0%
TTCTAAGCAAAGAATCACAA+AGG - chr1.4:34778077-34778096 MS.gene41266:CDS 30.0%
TTGATCTGTTTGGAAAATGA+TGG - chr1.4:34778214-34778233 MS.gene41266:CDS 30.0%
! CTATGTTTTCAACAATTGGA+TGG - chr1.4:34777464-34777483 MS.gene41266:CDS 30.0%
! CTTCTATAATTTGCATTTCC+AGG - chr1.4:34778285-34778304 MS.gene41266:CDS 30.0%
! GTTTTGTAGTTTCAACAAGT+AGG - chr1.4:34778122-34778141 MS.gene41266:CDS 30.0%
!!! TCTAATTGTGATGTCGTTTT+TGG - chr1.4:34777860-34777879 MS.gene41266:intron 30.0%
AGAATAACCTCTTCTACTTG+GGG + chr1.4:34778061-34778080 None:intergenic 35.0%
AGTACCATTTGATCAGAAAC+AGG + chr1.4:34777721-34777740 None:intergenic 35.0%
CATACCAGAATTACAGAAAC+AGG - chr1.4:34777988-34778007 MS.gene41266:intron 35.0%
CCAATTGTTGAAAACATAGG+AGG + chr1.4:34777463-34777482 None:intergenic 35.0%
TGTAGAATGAATTCTGATGC+TGG + chr1.4:34777516-34777535 None:intergenic 35.0%
TTATCAATAGTCGAGAAGGA+AGG - chr1.4:34778866-34778885 MS.gene41266:CDS 35.0%
! AAGAAGCATAGTTACAACTC+TGG - chr1.4:34778100-34778119 MS.gene41266:CDS 35.0%
! ATGAATTCTGATGCTGGTTA+TGG + chr1.4:34777510-34777529 None:intergenic 35.0%
! CCTCCTATGTTTTCAACAAT+TGG - chr1.4:34777460-34777479 MS.gene41266:CDS 35.0%
! CTTGAAAACCTTGTGTTTTG+AGG - chr1.4:34777821-34777840 MS.gene41266:intron 35.0%
!! TCTTCCTGTTTCTGATCAAA+TGG - chr1.4:34777714-34777733 MS.gene41266:intron 35.0%
!! TTCTGAGATCTTGATCTGTT+TGG - chr1.4:34778204-34778223 MS.gene41266:CDS 35.0%
ACCAGAATTACAGAAACAGG+TGG - chr1.4:34777991-34778010 MS.gene41266:intron 40.0%
ACCATACTCCTCAAAACACA+AGG + chr1.4:34777832-34777851 None:intergenic 40.0%
AGGACTCTTGAAATTGTTGC+TGG + chr1.4:34777962-34777981 None:intergenic 40.0%
CAGATCAAGATCTCAGAAAG+TGG + chr1.4:34778202-34778221 None:intergenic 40.0%
CCAGGTGTGTTAATATCACT+AGG - chr1.4:34778303-34778322 MS.gene41266:CDS 40.0%
CCTAGTGATATTAACACACC+TGG + chr1.4:34778306-34778325 None:intergenic 40.0%
GAATTACAGAAACAGGTGGA+AGG - chr1.4:34777995-34778014 MS.gene41266:intron 40.0%
GCTCTTATCAATAGTCGAGA+AGG - chr1.4:34778862-34778881 MS.gene41266:CDS 40.0%
GTTTCTTCATCTCAGACCTT+TGG - chr1.4:34778253-34778272 MS.gene41266:CDS 40.0%
! AAGCTCTTTGTGTTTTCTGC+AGG - chr1.4:34778796-34778815 MS.gene41266:CDS 40.0%
! TGATGCTGGTTATGGCTTAT+TGG + chr1.4:34777502-34777521 None:intergenic 40.0%
!! TCCACCTGTTTCTGTAATTC+TGG + chr1.4:34777995-34778014 None:intergenic 40.0%
!!! ACCTTGTGTTTTGAGGAGTA+TGG - chr1.4:34777828-34777847 MS.gene41266:intron 40.0%
AACAATTGGATGGCCCTTTG+AGG - chr1.4:34777474-34777493 MS.gene41266:CDS 45.0%
ACTTTCTCCCCAAGTAGAAG+AGG - chr1.4:34778051-34778070 MS.gene41266:CDS 45.0%
AGGAAGAAGTGAACGAAGAG+AGG + chr1.4:34777701-34777720 None:intergenic 45.0%
ATAGAAGACTCTCCCTCCAA+AGG + chr1.4:34778272-34778291 None:intergenic 45.0%
CAAGCTTCTTAACCATGCCA+AGG + chr1.4:34777627-34777646 None:intergenic 45.0%
CTTCATCTCAGACCTTTGGA+GGG - chr1.4:34778257-34778276 MS.gene41266:CDS 45.0%
TCTTCATCTCAGACCTTTGG+AGG - chr1.4:34778256-34778275 MS.gene41266:CDS 45.0%
! CTCTTTGTGTTTTCTGCAGG+TGG - chr1.4:34778799-34778818 MS.gene41266:CDS 45.0%
! TCACTGCTTGTGGATTGTGA+GGG + chr1.4:34777604-34777623 None:intergenic 45.0%
!! ATGGCTTATTGGCTCCTCAA+AGG + chr1.4:34777491-34777510 None:intergenic 45.0%
!! TGGCTTATTGGCTCCTCAAA+GGG + chr1.4:34777490-34777509 None:intergenic 45.0%
CAATCCACAAGCAGTGACCT+TGG - chr1.4:34777607-34777626 MS.gene41266:intron 50.0%
! GTCACTGCTTGTGGATTGTG+AGG + chr1.4:34777605-34777624 None:intergenic 50.0%
CACAAGCAGTGACCTTGGCA+TGG - chr1.4:34777612-34777631 MS.gene41266:intron 55.0%
CATGCCAAGGTCACTGCTTG+TGG + chr1.4:34777614-34777633 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 34777445 34778907 34777445 ID=MS.gene41266
chr1.4 mRNA 34777445 34778907 34777445 ID=MS.gene41266.t1;Parent=MS.gene41266
chr1.4 exon 34778617 34778907 34778617 ID=MS.gene41266.t1.exon1;Parent=MS.gene41266.t1
chr1.4 CDS 34778617 34778907 34778617 ID=cds.MS.gene41266.t1;Parent=MS.gene41266.t1
chr1.4 exon 34778046 34778408 34778046 ID=MS.gene41266.t1.exon2;Parent=MS.gene41266.t1
chr1.4 CDS 34778046 34778408 34778046 ID=cds.MS.gene41266.t1;Parent=MS.gene41266.t1
chr1.4 exon 34777445 34777534 34777445 ID=MS.gene41266.t1.exon3;Parent=MS.gene41266.t1
chr1.4 CDS 34777445 34777534 34777445 ID=cds.MS.gene41266.t1;Parent=MS.gene41266.t1
Gene Sequence

>MS.gene41266

ATGTTAGCGATATCTCCTCCTATGTTTTCAACAATTGGATGGCCCTTTGAGGAGCCAATAAGCCATAACCAGCATCAGAATTCATTCTACAAAGACACTGTTGATCAATTATTTAATTTTCATGATCAAGTTGAGGCAGAAATTAATTCAACAGATCCCTCACAATCCACAAGCAGTGACCTTGGCATGGTTAAGAAGCTTGTTCATAATGCTAGTGAACGCGATCGCCGCAAGAAGATCAATAATTTGTATTCCTCTCTTCGTTCACTTCTTCCTGTTTCTGATCAAATGGTACTTAATTAATCCCTTCTATCTGTTTCTAATTGTCAATAATGCTTTGGTCATTTCTTTGTCTTTTTTTTTTTTTTTTTTTAATCTTGAAAACCTTGTGTTTTGAGGAGTATGGTTGCAATTGTCTAATTGTGATGTCGTTTTTGGAACTTGCATATCTCTTGTTAGAACTATTGTCTTAGTATTAATTTATACATATATGTTGCAGAAGAAATTGAGCATTCCAGCAACAATTTCAAGAGTCCTAAAATACATACCAGAATTACAGAAACAGGTGGAAGGACTAGTTAAAAGAAAAGAAGAGGTCTTATTGAGACTTTCTCCCCAAGTAGAAGAGGTTATTCTAAGCAAAGAATCACAAAGGAAGAAGCATAGTTACAACTCTGGTTTTGTAGTTTCAACAAGTAGGCTCAGTGATTGTGAAATTACCATTCAGATTTCATGTTACACTGTACACAAGATTCCACTTTCTGAGATCTTGATCTGTTTGGAAAATGATGGCCTTTTGCTGCTTAATGTTTCTTCATCTCAGACCTTTGGAGGGAGAGTCTTCTATAATTTGCATTTCCAGGTGTGTTAATATCACTAGGCTTGTTTATTTTTTTAAAATATTTTGTCATTTATTATTGAGTGAAGTCTTTATTAAATATTTTTTTAAAATTATAAAATAAGCTTAATAACTATTGTGATCATGTATTTTTGAAAGAAAAAAACTATTTTGATCATATATAATTATGATTTGGTTTTTTGAAGCATCATATATAATTATGATGTTACTTTATTATATTCATTATAAAATTATTTTCACAAATGTTAATTTAGAAATACTCTTAGATGCATATTTTATTTTATTTTTATCATTAAATTATTTTAAGAATATTATGTTAATAACATGTAAGAAGTAACGAACTAATAATATAAGAAATTATGAAAACTATATTTTATTATACAAATAATTGATTACTTGGGAAAAAATAAAAAATAAATAATTTAAAAGTTAACTTTTTCTCAAGATGTATAGACTCATAAAAGAGGTACAACAAACATTTTCCTTAATTAAAAGCTCTTTGTGTTTTCTGCAGGTGGATAAAGCACAGAGATTAGAATCTCATATTCTAAATGAGAAGCTCTTATCAATAGTCGAGAAGGAAGGAGAGTTTTTAAAACAATAA
Protein sequence

>MS.gene41266.t1

MLAISPPMFSTIGWPFEEPISHNQHQNSFYKDTVDQLFNFHDQVEAEINSTDPSQSTSSDLGMVKKLVHNASERDRRKKINNLYSSLRSLLPVSDQMKKLSIPATISRVLKYIPELQKQVEGLVKRKEEVLLRLSPQVEEVILSKESQRKKHSYNSGFVVSTSRLSDCEITIQISCYTVHKIPLSEILICLENDGLLLLNVSSSQTFGGRVFYNLHFQVDKAQRLESHILNEKLLSIVEKEGEFLKQ