AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene045598

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045598.t1 MTR_4g078350 94.231 208 11 1 1 207 1 208 1.09e-143 399
MS.gene045598.t1 MTR_2g090440 64.796 196 64 3 8 201 9 201 2.07e-83 246
MS.gene045598.t1 MTR_2g090480 64.500 200 60 4 8 201 9 203 6.73e-83 245
MS.gene045598.t1 MTR_2g090425 66.162 198 57 5 8 199 9 202 1.97e-79 240
MS.gene045598.t1 MTR_2g090500 59.615 156 60 2 48 201 60 214 1.26e-57 181
MS.gene045598.t1 MTR_2g013920 47.778 180 77 8 7 180 3 171 1.70e-43 144
MS.gene045598.t1 MTR_2g090515 70.000 50 12 1 8 57 9 55 2.36e-14 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045598.t1 AT4G20970 42.328 189 89 8 8 180 2 186 2.04e-32 116
MS.gene045598.t1 AT1G10585 27.429 175 116 6 10 182 10 175 1.76e-11 60.8

Find 42 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTCAAAACATGGTGATTT+TGG 0.176377 4.2:+31579126 None:intergenic
AGAACCTTGGGGTTATAGTT+AGG 0.280194 4.2:+31579431 None:intergenic
TATCTAATTATGGATCAAAT+TGG 0.283616 4.2:-31579563 None:intergenic
AGGGAGAAGAGAGTTGAGTT+TGG 0.296752 4.2:+31579451 None:intergenic
GAGAGTTGAGTTTGGAGTAG+AGG 0.397503 4.2:+31579459 None:intergenic
TGAATTATCTCCAACCTTAG+AGG 0.408147 4.2:+31578984 None:intergenic
GGAATTACCGTTGGCGCTAC+CGG 0.409114 4.2:-31579274 MS.gene045598:CDS
AACCAGCCTTCTTTCAACTT+TGG 0.410390 4.2:+31579511 None:intergenic
GAACCTTGGGGTTATAGTTA+GGG 0.410715 4.2:+31579432 None:intergenic
TGATTTCATAGAAAATGAAT+TGG 0.411346 4.2:+31579052 None:intergenic
AAGGAGTGTCAATTCCTCTA+AGG 0.421100 4.2:-31578998 MS.gene045598:CDS
ATCGCCTCATCTACTTGATC+CGG 0.457881 4.2:+31579255 None:intergenic
TGGCTAAGGAGAAGAAAGAA+AGG 0.476291 4.2:-31579197 MS.gene045598:CDS
AAGTGAGTGAGAGATTGAAA+AGG 0.491808 4.2:-31578808 MS.gene045598:CDS
TTGGTTGTATTAGAGCTAGA+AGG 0.500610 4.2:+31579530 None:intergenic
ATGAAGAGAATGTAGACATA+AGG 0.503791 4.2:-31579017 MS.gene045598:CDS
AGATTGAAAAGGTTTGTGTA+TGG 0.509660 4.2:-31578797 MS.gene045598:CDS
AGATCACGTGAATATTGCTT+AGG 0.510152 4.2:-31579153 MS.gene045598:CDS
TTGGAACTGATCATAATATG+TGG 0.512688 4.2:-31578727 MS.gene045598:CDS
AGGCTGTATTTCCACATCAC+TGG 0.522661 4.2:+31578769 None:intergenic
ATACAACCAAAGTTGAAAGA+AGG 0.526780 4.2:-31579517 MS.gene045598:CDS
TATAATTCAGGAATTACCGT+TGG 0.530375 4.2:-31579283 MS.gene045598:intron
ACTTGATCCGGTAGCGCCAA+CGG 0.534008 4.2:+31579267 None:intergenic
ATTTCTTGAATTTCAAAACA+TGG 0.541430 4.2:+31579117 None:intergenic
CCTTCATGTTGTTCATGCTG+AGG 0.541669 4.2:-31578959 MS.gene045598:intron
AACCAAAGTTGAAAGAAGGC+TGG 0.543583 4.2:-31579513 MS.gene045598:CDS
TTTAGAGGCAAATGTTGAGA+TGG 0.546113 4.2:-31579217 MS.gene045598:CDS
TACAAATCATTCTCACGTGT+GGG 0.548323 4.2:-31579083 MS.gene045598:CDS
TGGAACTGATCATAATATGT+GGG 0.553773 4.2:-31578726 MS.gene045598:CDS
CTACAAATCATTCTCACGTG+TGG 0.558837 4.2:-31579084 MS.gene045598:CDS
AGTGTCAATTCCTCTAAGGT+TGG 0.561526 4.2:-31578994 MS.gene045598:CDS
ATTTCAAAATCCCACAACTC+AGG 0.570407 4.2:+31578749 None:intergenic
GGAAATACAGCCTGAGTTGT+GGG 0.582012 4.2:-31578759 MS.gene045598:CDS
GCTCCAAATTGAAAACAAGA+TGG 0.586259 4.2:+31578836 None:intergenic
TGGAAATACAGCCTGAGTTG+TGG 0.593486 4.2:-31578760 MS.gene045598:CDS
GGCAAATGTTGAGATGGCTA+AGG 0.613070 4.2:-31579211 MS.gene045598:CDS
CCTCAGCATGAACAACATGA+AGG 0.636646 4.2:+31578959 None:intergenic
CCAAATTGAAAACAAGATGG+AGG 0.639764 4.2:+31578839 None:intergenic
GGAACTGATCATAATATGTG+GGG 0.640483 4.2:-31578725 MS.gene045598:CDS
GTATGGATCTTCCAGTGATG+TGG 0.643608 4.2:-31578780 MS.gene045598:CDS
TCTCCCTAACTATAACCCCA+AGG 0.657270 4.2:-31579435 MS.gene045598:intron
GCTACCGGATCAAGTAGATG+AGG 0.685176 4.2:-31579259 MS.gene045598:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAGTTAGTTACAA+TGG - chr4.2:31578932-31578951 MS.gene045598:intron 15.0%
!!! GATGTAATTTTTTATAATTC+AGG - chr4.2:31578977-31578996 MS.gene045598:CDS 15.0%
!! AAACTACATAAAAAGTTTAG+AGG - chr4.2:31579040-31579059 MS.gene045598:CDS 20.0%
!! ATTTCTTGAATTTCAAAACA+TGG + chr4.2:31579158-31579177 None:intergenic 20.0%
!! TGATTTCATAGAAAATGAAT+TGG + chr4.2:31579223-31579242 None:intergenic 20.0%
!!! TGTTTTGAAATTCAAGAAAT+TGG - chr4.2:31579158-31579177 MS.gene045598:CDS 20.0%
! AAAGAAAGAAATTAGAACCT+TGG + chr4.2:31578857-31578876 None:intergenic 25.0%
! AAGAAAGAAATTAGAACCTT+GGG + chr4.2:31578856-31578875 None:intergenic 25.0%
!! ATTTCAAAACATGGTGATTT+TGG + chr4.2:31579149-31579168 None:intergenic 25.0%
ACAATACTAGTTAGCTACAA+TGG - chr4.2:31578898-31578917 MS.gene045598:intron 30.0%
AGAAAGAAATTAGAACCTTG+GGG + chr4.2:31578855-31578874 None:intergenic 30.0%
AGATTGAAAAGGTTTGTGTA+TGG - chr4.2:31579475-31579494 MS.gene045598:CDS 30.0%
ATAAAGAGAGAGCAATTACT+AGG + chr4.2:31579406-31579425 None:intergenic 30.0%
ATACAACCAAAGTTGAAAGA+AGG - chr4.2:31578755-31578774 MS.gene045598:CDS 30.0%
ATGAAGAGAATGTAGACATA+AGG - chr4.2:31579255-31579274 MS.gene045598:CDS 30.0%
TATAATTCAGGAATTACCGT+TGG - chr4.2:31578989-31579008 MS.gene045598:CDS 30.0%
TGGAACTGATCATAATATGT+GGG - chr4.2:31579546-31579565 MS.gene045598:CDS 30.0%
TTGGAACTGATCATAATATG+TGG - chr4.2:31579545-31579564 MS.gene045598:CDS 30.0%
AAGTGAGTGAGAGATTGAAA+AGG - chr4.2:31579464-31579483 MS.gene045598:CDS 35.0%
AGATCACGTGAATATTGCTT+AGG - chr4.2:31579119-31579138 MS.gene045598:CDS 35.0%
ATTTCAAAATCCCACAACTC+AGG + chr4.2:31579526-31579545 None:intergenic 35.0%
CCAAATTGAAAACAAGATGG+AGG + chr4.2:31579436-31579455 None:intergenic 35.0%
GCTCCAAATTGAAAACAAGA+TGG + chr4.2:31579439-31579458 None:intergenic 35.0%
GGAACTGATCATAATATGTG+GGG - chr4.2:31579547-31579566 MS.gene045598:CDS 35.0%
TACAAATCATTCTCACGTGT+GGG - chr4.2:31579189-31579208 MS.gene045598:CDS 35.0%
TGAATTATCTCCAACCTTAG+AGG + chr4.2:31579291-31579310 None:intergenic 35.0%
TTGGTTGTATTAGAGCTAGA+AGG + chr4.2:31578745-31578764 None:intergenic 35.0%
TTTAGAGGCAAATGTTGAGA+TGG - chr4.2:31579055-31579074 MS.gene045598:CDS 35.0%
!!! CCTCCATCTTGTTTTCAATT+TGG - chr4.2:31579433-31579452 MS.gene045598:intron 35.0%
!!! GAGTTGTGGGATTTTGAAAT+TGG - chr4.2:31579526-31579545 MS.gene045598:CDS 35.0%
AACCAAAGTTGAAAGAAGGC+TGG - chr4.2:31578759-31578778 MS.gene045598:CDS 40.0%
AACCAGCCTTCTTTCAACTT+TGG + chr4.2:31578764-31578783 None:intergenic 40.0%
AGAACCTTGGGGTTATAGTT+AGG + chr4.2:31578844-31578863 None:intergenic 40.0%
CTACAAATCATTCTCACGTG+TGG - chr4.2:31579188-31579207 MS.gene045598:CDS 40.0%
GAACCTTGGGGTTATAGTTA+GGG + chr4.2:31578843-31578862 None:intergenic 40.0%
TGGCTAAGGAGAAGAAAGAA+AGG - chr4.2:31579075-31579094 MS.gene045598:CDS 40.0%
!! AAGGAGTGTCAATTCCTCTA+AGG - chr4.2:31579274-31579293 MS.gene045598:CDS 40.0%
!! AGTGTCAATTCCTCTAAGGT+TGG - chr4.2:31579278-31579297 MS.gene045598:intron 40.0%
AGGCTGTATTTCCACATCAC+TGG + chr4.2:31579506-31579525 None:intergenic 45.0%
AGGGAGAAGAGAGTTGAGTT+TGG + chr4.2:31578824-31578843 None:intergenic 45.0%
ATCGCCTCATCTACTTGATC+CGG + chr4.2:31579020-31579039 None:intergenic 45.0%
CCTCAGCATGAACAACATGA+AGG + chr4.2:31579316-31579335 None:intergenic 45.0%
CCTTCATGTTGTTCATGCTG+AGG - chr4.2:31579313-31579332 MS.gene045598:intron 45.0%
GGAAATACAGCCTGAGTTGT+GGG - chr4.2:31579513-31579532 MS.gene045598:CDS 45.0%
GGCAAATGTTGAGATGGCTA+AGG - chr4.2:31579061-31579080 MS.gene045598:CDS 45.0%
GTATGGATCTTCCAGTGATG+TGG - chr4.2:31579492-31579511 MS.gene045598:CDS 45.0%
TCTCCCTAACTATAACCCCA+AGG - chr4.2:31578837-31578856 MS.gene045598:CDS 45.0%
TGGAAATACAGCCTGAGTTG+TGG - chr4.2:31579512-31579531 MS.gene045598:CDS 45.0%
! GAGAGTTGAGTTTGGAGTAG+AGG + chr4.2:31578816-31578835 None:intergenic 45.0%
GCTACCGGATCAAGTAGATG+AGG - chr4.2:31579013-31579032 MS.gene045598:CDS 50.0%
ACTTGATCCGGTAGCGCCAA+CGG + chr4.2:31579008-31579027 None:intergenic 55.0%
GGAATTACCGTTGGCGCTAC+CGG - chr4.2:31578998-31579017 MS.gene045598:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 31578718 31579576 31578718 ID=MS.gene045598
chr4.2 mRNA 31578718 31579576 31578718 ID=MS.gene045598.t1;Parent=MS.gene045598
chr4.2 exon 31579436 31579576 31579436 ID=MS.gene045598.t1.exon1;Parent=MS.gene045598.t1
chr4.2 CDS 31579436 31579576 31579436 ID=cds.MS.gene045598.t1;Parent=MS.gene045598.t1
chr4.2 exon 31578960 31579295 31578960 ID=MS.gene045598.t1.exon2;Parent=MS.gene045598.t1
chr4.2 CDS 31578960 31579295 31578960 ID=cds.MS.gene045598.t1;Parent=MS.gene045598.t1
chr4.2 exon 31578718 31578864 31578718 ID=MS.gene045598.t1.exon3;Parent=MS.gene045598.t1
chr4.2 CDS 31578718 31578864 31578718 ID=cds.MS.gene045598.t1;Parent=MS.gene045598.t1
Gene Sequence

>MS.gene045598

ATGGATCAAATTGGAAGTGATCAACCTTCTAGCTCTAATACAACCAAAGTTGAAAGAAGGCTGGTTGAGAAAAACAGAAGAAATCAGATGAAGATCCTCTACTCCAAACTCAACTCTCTTCTCCCTAACTATAACCCCAAGGTTCTAATTTCTTTCTTTATATAGATGTAAAAGTTAGTTACAATACTAGTTAGCTACAATGGTTTTGTCACAAAAAAAAAAAGTTAGTTACAATGGTTATTAGTAGTTTTCTTTGTTTGATGTAATTTTTTATAATTCAGGAATTACCGTTGGCGCTACCGGATCAAGTAGATGAGGCGATAAACTACATAAAAAGTTTAGAGGCAAATGTTGAGATGGCTAAGGAGAAGAAAGAAAGGTTATTAGCAGTAAAGAAGAAAAGATCACGTGAATATTGCTTAGGTCTACCAAAATCACCATGTTTTGAAATTCAAGAAATTGGTTCTTCTCTACAAATCATTCTCACGTGTGGGTTTGATAACCAATTCATTTTCTATGAAATCATTCGTGTGTTACATGAAGAGAATGTAGACATAAGGAGTGTCAATTCCTCTAAGGTTGGAGATAATTCACTCCTTCATGTTGTTCATGCTGAGGTATATATCTAAATCAATATTTGTTACTTAATTAATTGAACTTTCTTTAATTTTATGAAATTTAATTACCTAGTAATTGCTCTCTCTTTATGCAGATTCCTCCATCTTGTTTTCAATTTGGAGCGACGAAAGTGAGTGAGAGATTGAAAAGGTTTGTGTATGGATCTTCCAGTGATGTGGAAATACAGCCTGAGTTGTGGGATTTTGAAATTGGAACTGATCATAATATGTGGGGTTTCTAG
Protein sequence

>MS.gene045598.t1

MDQIGSDQPSSSNTTKVERRLVEKNRRNQMKILYSKLNSLLPNYNPKELPLALPDQVDEAINYIKSLEANVEMAKEKKERLLAVKKKRSREYCLGLPKSPCFEIQEIGSSLQIILTCGFDNQFIFYEIIRVLHEENVDIRSVNSSKVGDNSLLHVVHAEIPPSCFQFGATKVSERLKRFVYGSSSDVEIQPELWDFEIGTDHNMWGF