AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059853


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059853.t1 MTR_2g079630 97.143 280 8 0 6 285 110 389 0.0 551
MS.gene059853.t1 MTR_2g079650 82.206 281 45 2 6 285 109 385 2.38e-155 439
MS.gene059853.t1 MTR_2g013110 47.350 283 130 4 6 283 125 393 2.08e-77 241
MS.gene059853.t1 MTR_7g079680 29.936 314 146 13 5 275 114 396 7.21e-21 92.0
MS.gene059853.t1 MTR_7g079680 31.707 246 117 10 51 275 61 276 5.16e-19 85.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059853.t1 AT4G27460 53.147 286 119 6 6 283 110 388 1.64e-82 253
MS.gene059853.t1 AT5G53750 48.667 300 123 8 6 283 115 405 4.98e-70 222
MS.gene059853.t1 AT1G65320 27.302 315 153 11 5 275 117 399 2.33e-17 82.0

Find 77 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTTGATGATACAGCTTAT+TGG 0.263301 2.2:+15643550 MS.gene059853:intron
AAGGTTGAAGGAAAAGAATT+TGG 0.316598 2.2:+15644063 MS.gene059853:CDS
CGATGACCTTGCATACTTTC+CGG 0.330667 2.2:-15644188 None:intergenic
CACAGCAATCAAAGAGCTCT+TGG 0.367612 2.2:-15644260 None:intergenic
GAGGATGATTGGAGTTTAGT+TGG 0.388830 2.2:+15644328 MS.gene059853:CDS
GCCCTCCAGAGGATCTAGTT+AGG 0.395318 2.2:+15644029 MS.gene059853:CDS
TGTGGGTTATTGAGGATGAT+TGG 0.421114 2.2:+15644317 MS.gene059853:CDS
GCCATCACAACTTTGTCTGC+AGG 0.430978 2.2:+15643977 MS.gene059853:CDS
CTTCAACAGCAGAAGATGCC+TGG 0.431407 2.2:-15643838 None:intergenic
AGGTTCTTGCTTGGTTCCAT+TGG 0.451234 2.2:+15643734 MS.gene059853:CDS
CTCCATTGATTACTCTTCCC+AGG 0.458539 2.2:+15643820 MS.gene059853:CDS
TAATAGAGTGAATTACTTGT+GGG 0.472091 2.2:+15644300 MS.gene059853:CDS
GGTTGTAAAGGCAAGGTTGA+AGG 0.477069 2.2:+15644051 MS.gene059853:CDS
GCCATTGATCTCATACTTGA+GGG 0.480304 2.2:+15643575 MS.gene059853:CDS
CGAATTGATTGACATGGAAA+GGG 0.483775 2.2:+15643414 None:intergenic
GAATTACTTGTGGGTTATTG+AGG 0.486011 2.2:+15644309 MS.gene059853:CDS
GATGTGATCAGGTTCTTGCT+TGG 0.488754 2.2:+15643725 MS.gene059853:CDS
GCGAGGAGTTTGACACGGTC+CGG 0.494146 2.2:+15644169 MS.gene059853:CDS
TTCATCTGATGAGGACAGTC+CGG 0.496147 2.2:+15644147 MS.gene059853:CDS
CCGAATTGATTGACATGGAA+AGG 0.498180 2.2:+15643413 None:intergenic
CCCTCCAGAGGATCTAGTTA+GGG 0.498391 2.2:+15644030 MS.gene059853:CDS
AGACGATCGATGGATTGTGC+AGG 0.510025 2.2:-15643773 None:intergenic
TGCAAGGTCATCGAGCTACT+CGG 0.516553 2.2:+15644198 MS.gene059853:CDS
GTTGCAATTGTCGACGGTGA+TGG 0.521762 2.2:+15643893 MS.gene059853:CDS
GGATCTAGTTAGGGTTGTAA+AGG 0.524022 2.2:+15644039 MS.gene059853:CDS
CCATCACAACTTTGTCTGCA+GGG 0.524200 2.2:+15643978 MS.gene059853:CDS
ACAGCAATCAAAGAGCTCTT+GGG 0.525945 2.2:-15644259 None:intergenic
TTGTGTGAGGGACTTTGAGA+TGG 0.531894 2.2:-15643861 None:intergenic
CCCCTCAAGTATGAGATCAA+TGG 0.534194 2.2:-15643576 None:intergenic
CTAATAGAGTGAATTACTTG+TGG 0.535417 2.2:+15644299 MS.gene059853:CDS
ACAACCCTAACTAGATCCTC+TGG 0.535562 2.2:-15644034 None:intergenic
TGCCATTGATCTCATACTTG+AGG 0.539564 2.2:+15643574 MS.gene059853:CDS
GCAAGGTCATCGAGCTACTC+GGG 0.541443 2.2:+15644199 MS.gene059853:CDS
TTCAACAGCAGAAGATGCCT+GGG 0.542048 2.2:-15643837 None:intergenic
TTGCAATTGTCGACGGTGAT+GGG 0.542443 2.2:+15643894 MS.gene059853:CDS
GACGGTGATGGGACATTCAT+CGG 0.542508 2.2:+15643905 MS.gene059853:CDS
CCCTGCAGACAAAGTTGTGA+TGG 0.549793 2.2:-15643978 None:intergenic
CATCACAACTTTGTCTGCAG+GGG 0.550293 2.2:+15643979 MS.gene059853:CDS
TAACACAAGAGGATGTGATC+AGG 0.550433 2.2:+15643714 MS.gene059853:CDS
GATAATATTGAGACGATCGA+TGG 0.553025 2.2:-15643783 None:intergenic
GAGTGCACTGAAGCGGCCAA+TGG 0.559548 2.2:-15643750 None:intergenic
ACAACGGTGTTGAGTTCTGT+TGG 0.560590 2.2:+15643690 MS.gene059853:CDS
ATCACAACATGCAAGTGTGA+AGG 0.567692 2.2:-15643939 None:intergenic
TAGTTAGGGTTGTAAAGGCA+AGG 0.569328 2.2:+15644044 MS.gene059853:CDS
CAACAGAAGTTTGTTGTGTG+AGG 0.577183 2.2:-15643874 None:intergenic
ATCCTCCTCTTCATCTGATG+AGG 0.578040 2.2:+15644138 MS.gene059853:CDS
GACCGTGTCAAACTCCTCGC+CGG 0.578167 2.2:-15644166 None:intergenic
TGCCTGGGAAGAGTAATCAA+TGG 0.580600 2.2:-15643822 None:intergenic
ATCACAACTTTGTCTGCAGG+GGG 0.584206 2.2:+15643980 MS.gene059853:CDS
GTTCTGTTGGTTAACACAAG+AGG 0.588395 2.2:+15643703 MS.gene059853:CDS
GTGCAGGGAGTGCACTGAAG+CGG 0.593463 2.2:-15643757 None:intergenic
GTCCTCATCAGATGAAGAGG+AGG 0.596841 2.2:-15644140 None:intergenic
TCACAACATGCAAGTGTGAA+GGG 0.596883 2.2:-15643938 None:intergenic
ACTGTCCTCATCAGATGAAG+AGG 0.604105 2.2:-15644143 None:intergenic
GACGATCGATGGATTGTGCA+GGG 0.604203 2.2:-15643772 None:intergenic
TGCAGACAAAGTTGTGATGG+CGG 0.609998 2.2:-15643975 None:intergenic
AACAGAAGTTTGTTGTGTGA+GGG 0.614439 2.2:-15643873 None:intergenic
CACGGTCCGGAAAGTATGCA+AGG 0.614793 2.2:+15644182 MS.gene059853:CDS
AGGGCGACCACAGTCAATGT+AGG 0.615124 2.2:-15644011 None:intergenic
TGACTGTGGTCGCCCTCCAG+AGG 0.619657 2.2:+15644018 MS.gene059853:CDS
ATGTTGTGATGAGACGGTTG+CGG 0.621625 2.2:+15643952 MS.gene059853:CDS
ACTTCTGTTGCAATTGTCGA+CGG 0.622534 2.2:+15643887 MS.gene059853:CDS
AACAGAACTCAACACCGTTG+TGG 0.629524 2.2:-15643688 None:intergenic
GCTACTCGGGCAAGTATGTG+AGG 0.642862 2.2:+15644212 MS.gene059853:CDS
TGATTGACATGGAAAGGGGA+CGG 0.643465 2.2:+15643419 None:intergenic
ACCCTAACTAGATCCTCTGG+AGG 0.646675 2.2:-15644031 None:intergenic
AGAGGAGGATGACATATCAC+CGG 0.649223 2.2:-15644125 None:intergenic
GAATTGATTGACATGGAAAG+GGG 0.650322 2.2:+15643415 None:intergenic
CATTGATCTCATACTTGAGG+GGG 0.653452 2.2:+15643577 MS.gene059853:CDS
CAAGTATGTGAGGAATGTAG+AGG 0.658949 2.2:+15644222 MS.gene059853:CDS
ACTTGCATGTTGTGATGAGA+CGG 0.665678 2.2:+15643946 MS.gene059853:CDS
CCATTGATCTCATACTTGAG+GGG 0.673886 2.2:+15643576 MS.gene059853:CDS
CCCTAACTAGATCCTCTGGA+GGG 0.680964 2.2:-15644030 None:intergenic
TTGATGGCCTACATTGACTG+TGG 0.683351 2.2:+15644004 MS.gene059853:CDS
GTCCGGCGAGGAGTTTGACA+CGG 0.708960 2.2:+15644164 MS.gene059853:CDS
TTAACAATCAACAGCCACAA+CGG 0.709558 2.2:+15643674 MS.gene059853:CDS
CTGATGAGGACAGTCCGGCG+AGG 0.730013 2.2:+15644152 MS.gene059853:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACTTTTTCTAATATCTTGA+AGG + chr2.2:15644357-15644376 MS.gene059853:CDS 20.0%
! TAATAGAGTGAATTACTTGT+GGG + chr2.2:15644300-15644319 MS.gene059853:CDS 25.0%
!! AATTTGATGATACAGCTTAT+TGG + chr2.2:15643550-15643569 MS.gene059853:intron 25.0%
AAGGTTGAAGGAAAAGAATT+TGG + chr2.2:15644063-15644082 MS.gene059853:CDS 30.0%
ATTTCGCAAACAAAAAAAGG+TGG + chr2.2:15643620-15643639 MS.gene059853:CDS 30.0%
CATCAAATTAACAAGAAGCA+AGG - chr2.2:15643539-15643558 None:intergenic 30.0%
CCAATTTCGCAAACAAAAAA+AGG + chr2.2:15643617-15643636 MS.gene059853:CDS 30.0%
CTAATAGAGTGAATTACTTG+TGG + chr2.2:15644299-15644318 MS.gene059853:CDS 30.0%
!!! CCTTTTTTTGTTTGCGAAAT+TGG - chr2.2:15643620-15643639 None:intergenic 30.0%
CAAAAAAAGGTGGTCTTTCT+AGG + chr2.2:15643630-15643649 MS.gene059853:CDS 35.0%
GATAATATTGAGACGATCGA+TGG - chr2.2:15643786-15643805 None:intergenic 35.0%
TTAACAATCAACAGCCACAA+CGG + chr2.2:15643674-15643693 MS.gene059853:CDS 35.0%
! GAATTACTTGTGGGTTATTG+AGG + chr2.2:15644309-15644328 MS.gene059853:CDS 35.0%
!! AACAGAAGTTTGTTGTGTGA+GGG - chr2.2:15643876-15643895 None:intergenic 35.0%
ACAGCAATCAAAGAGCTCTT+GGG - chr2.2:15644262-15644281 None:intergenic 40.0%
ACTTCTGTTGCAATTGTCGA+CGG + chr2.2:15643887-15643906 MS.gene059853:CDS 40.0%
ACTTGCATGTTGTGATGAGA+CGG + chr2.2:15643946-15643965 MS.gene059853:CDS 40.0%
ATCACAACATGCAAGTGTGA+AGG - chr2.2:15643942-15643961 None:intergenic 40.0%
CAAGTATGTGAGGAATGTAG+AGG + chr2.2:15644222-15644241 MS.gene059853:CDS 40.0%
CATTGATCTCATACTTGAGG+GGG + chr2.2:15643577-15643596 MS.gene059853:CDS 40.0%
CCATTGATCTCATACTTGAG+GGG + chr2.2:15643576-15643595 MS.gene059853:CDS 40.0%
GAGGATGATTGGAGTTTAGT+TGG + chr2.2:15644328-15644347 MS.gene059853:CDS 40.0%
GCCATTGATCTCATACTTGA+GGG + chr2.2:15643575-15643594 MS.gene059853:CDS 40.0%
GGATCTAGTTAGGGTTGTAA+AGG + chr2.2:15644039-15644058 MS.gene059853:CDS 40.0%
TAACACAAGAGGATGTGATC+AGG + chr2.2:15643714-15643733 MS.gene059853:CDS 40.0%
TAGTTAGGGTTGTAAAGGCA+AGG + chr2.2:15644044-15644063 MS.gene059853:CDS 40.0%
TCACAACATGCAAGTGTGAA+GGG - chr2.2:15643941-15643960 None:intergenic 40.0%
TGCCATTGATCTCATACTTG+AGG + chr2.2:15643574-15643593 MS.gene059853:CDS 40.0%
! GTTCTGTTGGTTAACACAAG+AGG + chr2.2:15643703-15643722 MS.gene059853:CDS 40.0%
! TGTGGGTTATTGAGGATGAT+TGG + chr2.2:15644317-15644336 MS.gene059853:CDS 40.0%
!! CAACAGAAGTTTGTTGTGTG+AGG - chr2.2:15643877-15643896 None:intergenic 40.0%
!!! ACGCTTTTGACTTCTTTGAC+CGG + chr2.2:15644106-15644125 MS.gene059853:CDS 40.0%
AACAGAACTCAACACCGTTG+TGG - chr2.2:15643691-15643710 None:intergenic 45.0%
ACAACCCTAACTAGATCCTC+TGG - chr2.2:15644037-15644056 None:intergenic 45.0%
ACTGTCCTCATCAGATGAAG+AGG - chr2.2:15644146-15644165 None:intergenic 45.0%
AGAGGAGGATGACATATCAC+CGG - chr2.2:15644128-15644147 None:intergenic 45.0%
AGGTTCTTGCTTGGTTCCAT+TGG + chr2.2:15643734-15643753 MS.gene059853:CDS 45.0%
ATCACAACTTTGTCTGCAGG+GGG + chr2.2:15643980-15643999 MS.gene059853:CDS 45.0%
ATCCTCCTCTTCATCTGATG+AGG + chr2.2:15644138-15644157 MS.gene059853:CDS 45.0%
ATGTTGTGATGAGACGGTTG+CGG + chr2.2:15643952-15643971 MS.gene059853:CDS 45.0%
CACAGCAATCAAAGAGCTCT+TGG - chr2.2:15644263-15644282 None:intergenic 45.0%
CATCACAACTTTGTCTGCAG+GGG + chr2.2:15643979-15643998 MS.gene059853:CDS 45.0%
CCATCACAACTTTGTCTGCA+GGG + chr2.2:15643978-15643997 MS.gene059853:CDS 45.0%
CCCCTCAAGTATGAGATCAA+TGG - chr2.2:15643579-15643598 None:intergenic 45.0%
CGATGACCTTGCATACTTTC+CGG - chr2.2:15644191-15644210 None:intergenic 45.0%
GATGTGATCAGGTTCTTGCT+TGG + chr2.2:15643725-15643744 MS.gene059853:CDS 45.0%
GGTTGTAAAGGCAAGGTTGA+AGG + chr2.2:15644051-15644070 MS.gene059853:CDS 45.0%
TGCAGACAAAGTTGTGATGG+CGG - chr2.2:15643978-15643997 None:intergenic 45.0%
TGCCTGGGAAGAGTAATCAA+TGG - chr2.2:15643825-15643844 None:intergenic 45.0%
TTCAACAGCAGAAGATGCCT+GGG - chr2.2:15643840-15643859 None:intergenic 45.0%
TTCATCTGATGAGGACAGTC+CGG + chr2.2:15644147-15644166 MS.gene059853:CDS 45.0%
TTGCAATTGTCGACGGTGAT+GGG + chr2.2:15643894-15643913 MS.gene059853:CDS 45.0%
! ACAACGGTGTTGAGTTCTGT+TGG + chr2.2:15643690-15643709 MS.gene059853:CDS 45.0%
! CTCCATTGATTACTCTTCCC+AGG + chr2.2:15643820-15643839 MS.gene059853:CDS 45.0%
! TTGATGGCCTACATTGACTG+TGG + chr2.2:15644004-15644023 MS.gene059853:CDS 45.0%
! TTGTGTGAGGGACTTTGAGA+TGG - chr2.2:15643864-15643883 None:intergenic 45.0%
ACCCTAACTAGATCCTCTGG+AGG - chr2.2:15644034-15644053 None:intergenic 50.0%
CCCTAACTAGATCCTCTGGA+GGG - chr2.2:15644033-15644052 None:intergenic 50.0%
CCCTCCAGAGGATCTAGTTA+GGG + chr2.2:15644030-15644049 MS.gene059853:CDS 50.0%
CCCTGCAGACAAAGTTGTGA+TGG - chr2.2:15643981-15644000 None:intergenic 50.0%
CTTCAACAGCAGAAGATGCC+TGG - chr2.2:15643841-15643860 None:intergenic 50.0%
GCCATCACAACTTTGTCTGC+AGG + chr2.2:15643977-15643996 MS.gene059853:CDS 50.0%
GTCCTCATCAGATGAAGAGG+AGG - chr2.2:15644143-15644162 None:intergenic 50.0%
GTTGCAATTGTCGACGGTGA+TGG + chr2.2:15643893-15643912 MS.gene059853:CDS 50.0%
TGCAAGGTCATCGAGCTACT+CGG + chr2.2:15644198-15644217 MS.gene059853:CDS 50.0%
!! AGACGATCGATGGATTGTGC+AGG - chr2.2:15643776-15643795 None:intergenic 50.0%
!! GACGATCGATGGATTGTGCA+GGG - chr2.2:15643775-15643794 None:intergenic 50.0%
!! GACGGTGATGGGACATTCAT+CGG + chr2.2:15643905-15643924 MS.gene059853:CDS 50.0%
AGGGCGACCACAGTCAATGT+AGG - chr2.2:15644014-15644033 None:intergenic 55.0%
GCAAGGTCATCGAGCTACTC+GGG + chr2.2:15644199-15644218 MS.gene059853:CDS 55.0%
GCCCTCCAGAGGATCTAGTT+AGG + chr2.2:15644029-15644048 MS.gene059853:CDS 55.0%
GCTACTCGGGCAAGTATGTG+AGG + chr2.2:15644212-15644231 MS.gene059853:CDS 55.0%
TTTGTCTGCAGGGGGCTTGA+TGG + chr2.2:15643988-15644007 MS.gene059853:CDS 55.0%
! CACGGTCCGGAAAGTATGCA+AGG + chr2.2:15644182-15644201 MS.gene059853:CDS 55.0%
! TGAGGGGGCACAGAATCTTG+TGG + chr2.2:15643592-15643611 MS.gene059853:CDS 55.0%
GACCGTGTCAAACTCCTCGC+CGG - chr2.2:15644169-15644188 None:intergenic 60.0%
GAGTGCACTGAAGCGGCCAA+TGG - chr2.2:15643753-15643772 None:intergenic 60.0%
GCGAGGAGTTTGACACGGTC+CGG + chr2.2:15644169-15644188 MS.gene059853:CDS 60.0%
GTCCGGCGAGGAGTTTGACA+CGG + chr2.2:15644164-15644183 MS.gene059853:CDS 60.0%
! GTGCAGGGAGTGCACTGAAG+CGG - chr2.2:15643760-15643779 None:intergenic 60.0%
CTGATGAGGACAGTCCGGCG+AGG + chr2.2:15644152-15644171 MS.gene059853:CDS 65.0%
TGACTGTGGTCGCCCTCCAG+AGG + chr2.2:15644018-15644037 MS.gene059853:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 15643427 15644408 15643427 ID=MS.gene059853
chr2.2 mRNA 15643427 15644408 15643427 ID=MS.gene059853.t1;Parent=MS.gene059853
chr2.2 exon 15643427 15643440 15643427 ID=MS.gene059853.t1.exon1;Parent=MS.gene059853.t1
chr2.2 CDS 15643427 15643440 15643427 ID=cds.MS.gene059853.t1;Parent=MS.gene059853.t1
chr2.2 exon 15643565 15644408 15643565 ID=MS.gene059853.t1.exon2;Parent=MS.gene059853.t1
chr2.2 CDS 15643565 15644408 15643565 ID=cds.MS.gene059853.t1;Parent=MS.gene059853.t1
Gene Sequence

>MS.gene059853

ATGGAAAGGGGACGGTAATTATATATCTGTAATTTCTTGTTGAAGCTTGAAATTCTGTTTTAATGTGTTTGTTTTAATATGATCAAAATTAAGAATTTTAGTTAATTAACCTTGCTTCTTGTTAATTTGATGATACAGCTTATTGGATGCCATTGATCTCATACTTGAGGGGGCACAGAATCTTGTGGTGCCAATTTCGCAAACAAAAAAAGGTGGTCTTTCTAGGAGAAAATTGCAACAGAAGTCATTAACAATCAACAGCCACAACGGTGTTGAGTTCTGTTGGTTAACACAAGAGGATGTGATCAGGTTCTTGCTTGGTTCCATTGGCCGCTTCAGTGCACTCCCTGCACAATCCATCGATCGTCTCAATATTATCAGCTCGAATGTGCTCTCCATTGATTACTCTTCCCAGGCATCTTCTGCTGTTGAAGCCATCTCAAAGTCCCTCACACAACAAACTTCTGTTGCAATTGTCGACGGTGATGGGACATTCATCGGTGAGATATCACCCTTCACACTTGCATGTTGTGATGAGACGGTTGCGGCCGCCATCACAACTTTGTCTGCAGGGGGCTTGATGGCCTACATTGACTGTGGTCGCCCTCCAGAGGATCTAGTTAGGGTTGTAAAGGCAAGGTTGAAGGAAAAGAATTTGGAAAAACTGCTACAAGAGTTTACGCTTTTGACTTCTTTGACCGGTGATATGTCATCCTCCTCTTCATCTGATGAGGACAGTCCGGCGAGGAGTTTGACACGGTCCGGAAAGTATGCAAGGTCATCGAGCTACTCGGGCAAGTATGTGAGGAATGTAGAGGCTATAGTTTGTCATCCCAAGAGCTCTTTGATTGCTGTGATGATGCAAGCAATTGCTAATAGAGTGAATTACTTGTGGGTTATTGAGGATGATTGGAGTTTAGTTGGCATTGTTACTTTTTCTAATATCTTGAAGGTGTTCAAAGAGCGTTTAGAAGTTATTTAG

Protein sequence

>MS.gene059853.t1

MERGRLLDAIDLILEGAQNLVVPISQTKKGGLSRRKLQQKSLTINSHNGVEFCWLTQEDVIRFLLGSIGRFSALPAQSIDRLNIISSNVLSIDYSSQASSAVEAISKSLTQQTSVAIVDGDGTFIGEISPFTLACCDETVAAAITTLSAGGLMAYIDCGRPPEDLVRVVKARLKEKNLEKLLQEFTLLTSLTGDMSSSSSSDEDSPARSLTRSGKYARSSSYSGKYVRNVEAIVCHPKSSLIAVMMQAIANRVNYLWVIEDDWSLVGIVTFSNILKVFKERLEVI