AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025629

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025629.t1 AT5G22250 64.179 268 91 4 23 287 12 277 8.79e-119 342
MS.gene025629.t1 AT3G44260 63.941 269 89 5 22 287 16 279 4.89e-116 335
MS.gene025629.t1 AT5G10960 53.933 267 114 5 22 287 9 267 2.58e-93 277
MS.gene025629.t1 AT2G32070 52.809 267 118 5 22 287 9 268 3.83e-93 277
MS.gene025629.t1 AT1G15920 48.727 275 134 4 15 286 6 276 9.23e-92 274
MS.gene025629.t1 AT1G15920 48.727 275 134 4 15 286 6 276 9.23e-92 274
MS.gene025629.t1 AT1G80780 51.504 266 122 4 22 287 9 267 1.26e-89 268
MS.gene025629.t1 AT1G80780 51.504 266 122 4 22 287 9 267 1.26e-89 268
MS.gene025629.t1 AT1G80780 51.504 266 122 4 22 287 9 267 1.86e-89 268
MS.gene025629.t1 AT1G06450 35.581 267 147 9 24 285 8 254 5.04e-42 148
MS.gene025629.t1 AT1G61470 33.333 246 141 6 24 264 1 228 1.41e-33 124
MS.gene025629.t1 AT1G27820 34.553 246 144 5 22 264 3 234 2.56e-33 124
MS.gene025629.t1 AT1G27890 34.167 240 141 5 28 264 4 229 4.20e-30 115
MS.gene025629.t1 AT3G44240 34.649 228 132 7 39 264 3 215 6.77e-29 110

Find 63 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCTGAAAATAGTTATATT+TGG 0.169182 7.3:-8680508 MS.gene025629:CDS
TTCATAGTGCGTATGATTTC+GGG 0.187035 7.3:-8680301 MS.gene025629:CDS
TTGAAGGTGGAGAGGCTTAT+AGG 0.219054 7.3:-8680119 MS.gene025629:CDS
TTTCATAGTGCGTATGATTT+CGG 0.233508 7.3:-8680302 MS.gene025629:CDS
TGAAGGTGGAGAGGCTTATA+GGG 0.242741 7.3:-8680118 MS.gene025629:CDS
TGCGTATGATTTCGGGTATT+TGG 0.263514 7.3:-8680294 MS.gene025629:CDS
TGTAAGAATGGAACCATTAC+TGG 0.287488 7.3:+8680778 None:intergenic
GAAGCTGTTACCGGATGATT+TGG 0.329254 7.3:-8680255 MS.gene025629:CDS
TGCTGAAAATAGTTATATTT+GGG 0.331814 7.3:-8680507 MS.gene025629:CDS
TTTGTGCTGATTCTGTTAGC+TGG 0.344952 7.3:-8680331 MS.gene025629:CDS
TCAAATCTTGATAACGAATT+CGG 0.346517 7.3:-8680740 MS.gene025629:CDS
TTAACTCTTTCTGATCATAA+AGG 0.384845 7.3:-8680548 MS.gene025629:CDS
GAAGGTGTATTTCGGTGATA+TGG 0.431170 7.3:-8680213 MS.gene025629:CDS
CTGATTCTGTTGAGTTGTTG+AGG 0.433052 7.3:-8680439 MS.gene025629:CDS
AAAGAGGAATCGATTCCGTT+AGG 0.437401 7.3:+8680810 None:intergenic
TCAATGGACACGGAGTTTCC+CGG 0.451307 7.3:-8680680 MS.gene025629:CDS
ATATCAGAGAGCTTTACTTC+GGG 0.453384 7.3:-8680043 MS.gene025629:CDS
AGGTTGAATTTGATTCAGAT+TGG 0.457708 7.3:-8680572 MS.gene025629:CDS
AGGCTGGTGAAGGTGTATTT+CGG 0.458544 7.3:-8680221 MS.gene025629:CDS
CCACACTGATCTTGTAAGAA+TGG 0.461921 7.3:+8680766 None:intergenic
GGTTGAATTTGATTCAGATT+GGG 0.466535 7.3:-8680571 MS.gene025629:CDS
GTTGATGATGTCGTCCGGTT+TGG 0.470458 7.3:-8680354 MS.gene025629:CDS
ATTTGCATGGTGGATTGGAT+AGG 0.470548 7.3:-8680154 MS.gene025629:CDS
TGTTGAAAGCGAATGTTGAT+AGG 0.470879 7.3:-8680592 MS.gene025629:CDS
AAGAGGAATCGATTCCGTTA+GGG 0.475020 7.3:+8680811 None:intergenic
TACGAATTTGCATGGTGGAT+TGG 0.478435 7.3:-8680159 MS.gene025629:CDS
TTGTGCTGATTCTGTTAGCT+GGG 0.481953 7.3:-8680330 MS.gene025629:CDS
TCAGTATCCGCTAATTTCAA+TGG 0.486009 7.3:-8680696 MS.gene025629:CDS
GTTCTTGAACGGCGAATCAC+AGG 0.491118 7.3:+8680637 None:intergenic
CTTTCACCACGATCCAGTAA+TGG 0.491979 7.3:-8680791 MS.gene025629:CDS
TTGAGAAGAATCGTGAGTGT+GGG 0.492422 7.3:-8680400 MS.gene025629:CDS
AATATCAGAGAGCTTTACTT+CGG 0.499438 7.3:-8680044 MS.gene025629:CDS
TAGGGTTTGCAAGAGTTTGA+AGG 0.503822 7.3:-8680135 MS.gene025629:CDS
GCTGACGCAGAAGCTGTTAC+CGG 0.505236 7.3:-8680264 MS.gene025629:CDS
TTTGCATGGTGGATTGGATA+GGG 0.507227 7.3:-8680153 MS.gene025629:CDS
AAATATGCCGGTGTATTGTA+TGG 0.511609 7.3:-8680002 MS.gene025629:CDS
AGTTTCCCGGTGTGATTGTG+AGG 0.516131 7.3:-8680667 MS.gene025629:CDS
AGAATCAGCACAAACCAAAC+CGG 0.520363 7.3:+8680340 None:intergenic
TTTACTTCGGGAAAGCAGAC+GGG 0.525168 7.3:-8680031 MS.gene025629:CDS
GGTTTGCAAGAGTTTGAAGG+TGG 0.534617 7.3:-8680132 MS.gene025629:CDS
CTTTACTTCGGGAAAGCAGA+CGG 0.534703 7.3:-8680032 MS.gene025629:CDS
GCTGTTACCGGATGATTTGG+AGG 0.539995 7.3:-8680252 MS.gene025629:CDS
GACGGGTTTGTCAAATATGC+CGG 0.543121 7.3:-8680014 MS.gene025629:CDS
GCTGAGTTGATGATGTCGTC+CGG 0.548614 7.3:-8680359 MS.gene025629:CDS
CACGCGCCACGGTTCTTGAA+CGG 0.548659 7.3:+8680626 None:intergenic
TTACTGGATCGTGGTGAAAG+AGG 0.558261 7.3:+8680794 None:intergenic
GTTGAGTTGTTGAGGAGACA+AGG 0.563888 7.3:-8680431 MS.gene025629:CDS
GTTTCCCGGTGTGATTGTGA+GGG 0.568400 7.3:-8680666 MS.gene025629:CDS
TTTGAGAAGAATCGTGAGTG+TGG 0.568643 7.3:-8680401 MS.gene025629:CDS
TCCCGGTGTGATTGTGAGGG+CGG 0.571114 7.3:-8680663 MS.gene025629:CDS
GCAAGAGTTTGAAGGTGGAG+AGG 0.582586 7.3:-8680127 MS.gene025629:CDS
TCCGTGTCCATTGAAATTAG+CGG 0.591513 7.3:+8680689 None:intergenic
TTGAGTTGTTGAGGAGACAA+GGG 0.608645 7.3:-8680430 MS.gene025629:CDS
TCGATGTGAAGCATTTGATG+AGG 0.612916 7.3:-8680187 MS.gene025629:CDS
TTCTAATCCATACAATACAC+CGG 0.622880 7.3:+8679995 None:intergenic
ATCCGCCCTCACAATCACAC+CGG 0.632148 7.3:+8680661 None:intergenic
TCCGCTAATTTCAATGGACA+CGG 0.632987 7.3:-8680690 MS.gene025629:CDS
CTGCATAGAGACACGCGCCA+CGG 0.638041 7.3:+8680615 None:intergenic
TCCGCCCTCACAATCACACC+GGG 0.638539 7.3:+8680662 None:intergenic
ATAGGGAAGAGTCATCAAGC+AGG 0.666021 7.3:-8680101 MS.gene025629:CDS
ATGGAACCATTACTGGATCG+TGG 0.673080 7.3:+8680785 None:intergenic
GATTCGCCGTTCAAGAACCG+TGG 0.687694 7.3:-8680632 MS.gene025629:CDS
CCATTCTTACAAGATCAGTG+TGG 0.730924 7.3:-8680766 MS.gene025629:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGCTGAAAATAGTTATATT+TGG - chr7.3:8680308-8680327 MS.gene025629:CDS 20.0%
!! TGCTGAAAATAGTTATATTT+GGG - chr7.3:8680309-8680328 MS.gene025629:CDS 20.0%
!!! TAATTTTAAGGATTTTGATG+TGG - chr7.3:8680336-8680355 MS.gene025629:CDS 20.0%
!!! TATTTGGGAGTTTAATTTTA+AGG - chr7.3:8680324-8680343 MS.gene025629:CDS 20.0%
! TTAACTCTTTCTGATCATAA+AGG - chr7.3:8680268-8680287 MS.gene025629:CDS 25.0%
!!! TCAAATCTTGATAACGAATT+CGG - chr7.3:8680076-8680095 MS.gene025629:CDS 25.0%
AATATCAGAGAGCTTTACTT+CGG - chr7.3:8680772-8680791 MS.gene025629:CDS 30.0%
AGGTTGAATTTGATTCAGAT+TGG - chr7.3:8680244-8680263 MS.gene025629:CDS 30.0%
GGTTGAATTTGATTCAGATT+GGG - chr7.3:8680245-8680264 MS.gene025629:CDS 30.0%
TTCTAATCCATACAATACAC+CGG + chr7.3:8680824-8680843 None:intergenic 30.0%
TTTCATAGTGCGTATGATTT+CGG - chr7.3:8680514-8680533 MS.gene025629:CDS 30.0%
! CTATTTTCAGCATCTAACAT+TGG + chr7.3:8680301-8680320 None:intergenic 30.0%
AAAAACTCCTCCAAATCATC+CGG + chr7.3:8680574-8680593 None:intergenic 35.0%
AAATATGCCGGTGTATTGTA+TGG - chr7.3:8680814-8680833 MS.gene025629:CDS 35.0%
ATATCAGAGAGCTTTACTTC+GGG - chr7.3:8680773-8680792 MS.gene025629:CDS 35.0%
TAACCGCAAAAAAACCCTAA+CGG - chr7.3:8679991-8680010 MS.gene025629:CDS 35.0%
TCAGTATCCGCTAATTTCAA+TGG - chr7.3:8680120-8680139 MS.gene025629:CDS 35.0%
TGTAAGAATGGAACCATTAC+TGG + chr7.3:8680041-8680060 None:intergenic 35.0%
TGTTGAAAGCGAATGTTGAT+AGG - chr7.3:8680224-8680243 MS.gene025629:CDS 35.0%
TTCATAGTGCGTATGATTTC+GGG - chr7.3:8680515-8680534 MS.gene025629:CDS 35.0%
! TTTTGTACGAATTTGCATGG+TGG - chr7.3:8680652-8680671 MS.gene025629:CDS 35.0%
!! AGGTTTTGTACGAATTTGCA+TGG - chr7.3:8680649-8680668 MS.gene025629:CDS 35.0%
!! ATGATTTGGAGGAGTTTTTG+AGG - chr7.3:8680575-8680594 MS.gene025629:CDS 35.0%
!!! ATTCCGTTAGGGTTTTTTTG+CGG + chr7.3:8679997-8680016 None:intergenic 35.0%
AGAATCAGCACAAACCAAAC+CGG + chr7.3:8680479-8680498 None:intergenic 40.0%
CCACACTGATCTTGTAAGAA+TGG + chr7.3:8680053-8680072 None:intergenic 40.0%
CCATTCTTACAAGATCAGTG+TGG - chr7.3:8680050-8680069 MS.gene025629:CDS 40.0%
TAGGGTTTGCAAGAGTTTGA+AGG - chr7.3:8680681-8680700 MS.gene025629:CDS 40.0%
TCCGCTAATTTCAATGGACA+CGG - chr7.3:8680126-8680145 MS.gene025629:CDS 40.0%
TCCGTGTCCATTGAAATTAG+CGG + chr7.3:8680130-8680149 None:intergenic 40.0%
TTGAGAAGAATCGTGAGTGT+GGG - chr7.3:8680416-8680435 MS.gene025629:CDS 40.0%
TTTGAGAAGAATCGTGAGTG+TGG - chr7.3:8680415-8680434 MS.gene025629:CDS 40.0%
! AAAGAGGAATCGATTCCGTT+AGG + chr7.3:8680009-8680028 None:intergenic 40.0%
! AAGAGGAATCGATTCCGTTA+GGG + chr7.3:8680008-8680027 None:intergenic 40.0%
! CTGATTCTGTTGAGTTGTTG+AGG - chr7.3:8680377-8680396 MS.gene025629:CDS 40.0%
! GAAGGTGTATTTCGGTGATA+TGG - chr7.3:8680603-8680622 MS.gene025629:CDS 40.0%
! TCGATGTGAAGCATTTGATG+AGG - chr7.3:8680629-8680648 MS.gene025629:CDS 40.0%
! TGCGTATGATTTCGGGTATT+TGG - chr7.3:8680522-8680541 MS.gene025629:CDS 40.0%
! TTGAGTTGTTGAGGAGACAA+GGG - chr7.3:8680386-8680405 MS.gene025629:CDS 40.0%
!! ATTTGCATGGTGGATTGGAT+AGG - chr7.3:8680662-8680681 MS.gene025629:CDS 40.0%
!! TACGAATTTGCATGGTGGAT+TGG - chr7.3:8680657-8680676 MS.gene025629:CDS 40.0%
!! TTGTGCTGATTCTGTTAGCT+GGG - chr7.3:8680486-8680505 MS.gene025629:CDS 40.0%
!! TTTGCATGGTGGATTGGATA+GGG - chr7.3:8680663-8680682 MS.gene025629:CDS 40.0%
!! TTTGTGCTGATTCTGTTAGC+TGG - chr7.3:8680485-8680504 MS.gene025629:CDS 40.0%
ATAGGGAAGAGTCATCAAGC+AGG - chr7.3:8680715-8680734 MS.gene025629:CDS 45.0%
ATGGAACCATTACTGGATCG+TGG + chr7.3:8680034-8680053 None:intergenic 45.0%
CTTTACTTCGGGAAAGCAGA+CGG - chr7.3:8680784-8680803 MS.gene025629:CDS 45.0%
CTTTCACCACGATCCAGTAA+TGG - chr7.3:8680025-8680044 MS.gene025629:CDS 45.0%
GAAGCTGTTACCGGATGATT+TGG - chr7.3:8680561-8680580 MS.gene025629:CDS 45.0%
GGTTTGCAAGAGTTTGAAGG+TGG - chr7.3:8680684-8680703 MS.gene025629:CDS 45.0%
TGAAGGTGGAGAGGCTTATA+GGG - chr7.3:8680698-8680717 MS.gene025629:CDS 45.0%
TTACTGGATCGTGGTGAAAG+AGG + chr7.3:8680025-8680044 None:intergenic 45.0%
TTGAAGGTGGAGAGGCTTAT+AGG - chr7.3:8680697-8680716 MS.gene025629:CDS 45.0%
TTTACTTCGGGAAAGCAGAC+GGG - chr7.3:8680785-8680804 MS.gene025629:CDS 45.0%
! AGGCTGGTGAAGGTGTATTT+CGG - chr7.3:8680595-8680614 MS.gene025629:CDS 45.0%
! GACGGGTTTGTCAAATATGC+CGG - chr7.3:8680802-8680821 MS.gene025629:CDS 45.0%
! GTTGAGTTGTTGAGGAGACA+AGG - chr7.3:8680385-8680404 MS.gene025629:CDS 45.0%
!!! TTTGGAGGAGTTTTTGAGGC+TGG - chr7.3:8680579-8680598 MS.gene025629:CDS 45.0%
AGTTTCCCGGTGTGATTGTG+AGG - chr7.3:8680149-8680168 MS.gene025629:CDS 50.0%
GCAAGAGTTTGAAGGTGGAG+AGG - chr7.3:8680689-8680708 MS.gene025629:CDS 50.0%
GTTCTTGAACGGCGAATCAC+AGG + chr7.3:8680182-8680201 None:intergenic 50.0%
GTTTCCCGGTGTGATTGTGA+GGG - chr7.3:8680150-8680169 MS.gene025629:CDS 50.0%
TCAATGGACACGGAGTTTCC+CGG - chr7.3:8680136-8680155 MS.gene025629:CDS 50.0%
! GCTGTTACCGGATGATTTGG+AGG - chr7.3:8680564-8680583 MS.gene025629:CDS 50.0%
!! GCTGAGTTGATGATGTCGTC+CGG - chr7.3:8680457-8680476 MS.gene025629:CDS 50.0%
!! GTTGATGATGTCGTCCGGTT+TGG - chr7.3:8680462-8680481 MS.gene025629:CDS 50.0%
!!! GGAGTTTTTGAGGCTGGTGA+AGG - chr7.3:8680585-8680604 MS.gene025629:CDS 50.0%
ATCCGCCCTCACAATCACAC+CGG + chr7.3:8680158-8680177 None:intergenic 55.0%
GATTCGCCGTTCAAGAACCG+TGG - chr7.3:8680184-8680203 MS.gene025629:CDS 55.0%
GCTGACGCAGAAGCTGTTAC+CGG - chr7.3:8680552-8680571 MS.gene025629:CDS 55.0%
CACGCGCCACGGTTCTTGAA+CGG + chr7.3:8680193-8680212 None:intergenic 60.0%
CTGCATAGAGACACGCGCCA+CGG + chr7.3:8680204-8680223 None:intergenic 60.0%
TCCCGGTGTGATTGTGAGGG+CGG - chr7.3:8680153-8680172 MS.gene025629:CDS 60.0%
TCCGCCCTCACAATCACACC+GGG + chr7.3:8680157-8680176 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 8679986 8680852 8679986 ID=MS.gene025629
chr7.3 mRNA 8679986 8680852 8679986 ID=MS.gene025629.t1;Parent=MS.gene025629
chr7.3 exon 8679986 8680852 8679986 ID=MS.gene025629.t1.exon1;Parent=MS.gene025629.t1
chr7.3 CDS 8679986 8680852 8679986 ID=cds.MS.gene025629.t1;Parent=MS.gene025629.t1
Gene Sequence

>MS.gene025629

ATGTGTAACCGCAAAAAAACCCTAACGGAATCGATTCCTCTTTCACCACGATCCAGTAATGGTTCCATTCTTACAAGATCAGTGTGGAGTTCAAATCTTGATAACGAATTCGGTTTGATTCGATCGTTAATCGATCAGTATCCGCTAATTTCAATGGACACGGAGTTTCCCGGTGTGATTGTGAGGGCGGATTCCTGTGATTCGCCGTTCAAGAACCGTGGCGCGTGTCTCTATGCAGTGTTGAAAGCGAATGTTGATAGGTTGAATTTGATTCAGATTGGGTTAACTCTTTCTGATCATAAAGGTAATCTTCCAATGTTAGATGCTGAAAATAGTTATATTTGGGAGTTTAATTTTAAGGATTTTGATGTGGCGCGTGATGATCACGCTGCTGATTCTGTTGAGTTGTTGAGGAGACAAGGGATTGATTTTGAGAAGAATCGTGAGTGTGGGATTGATTCTGTTAAGTTTGCTGAGTTGATGATGTCGTCCGGTTTGGTTTGTGCTGATTCTGTTAGCTGGGTAACGTTTCATAGTGCGTATGATTTCGGGTATTTGGTGAAATTGCTGACGCAGAAGCTGTTACCGGATGATTTGGAGGAGTTTTTGAGGCTGGTGAAGGTGTATTTCGGTGATATGGTATTCGATGTGAAGCATTTGATGAGGTTTTGTACGAATTTGCATGGTGGATTGGATAGGGTTTGCAAGAGTTTGAAGGTGGAGAGGCTTATAGGGAAGAGTCATCAAGCAGGTTCAGATAGTTTGCTTACTTTGCATGCTTTTCAGAATATCAGAGAGCTTTACTTCGGGAAAGCAGACGGGTTTGTCAAATATGCCGGTGTATTGTATGGATTAGAAGTTTGCTGA
Protein sequence

>MS.gene025629.t1

MCNRKKTLTESIPLSPRSSNGSILTRSVWSSNLDNEFGLIRSLIDQYPLISMDTEFPGVIVRADSCDSPFKNRGACLYAVLKANVDRLNLIQIGLTLSDHKGNLPMLDAENSYIWEFNFKDFDVARDDHAADSVELLRRQGIDFEKNRECGIDSVKFAELMMSSGLVCADSVSWVTFHSAYDFGYLVKLLTQKLLPDDLEEFLRLVKVYFGDMVFDVKHLMRFCTNLHGGLDRVCKSLKVERLIGKSHQAGSDSLLTLHAFQNIRELYFGKADGFVKYAGVLYGLEVC