AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42432

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42432.t1 MTR_7g077620 69.759 291 82 5 2 290 84 370 1.18e-136 392
MS.gene42432.t1 MTR_7g077660 69.521 292 81 6 3 292 83 368 1.83e-131 378
MS.gene42432.t1 MTR_7g077650 66.892 296 89 4 1 292 82 372 3.33e-129 372
MS.gene42432.t1 MTR_7g076110 55.369 298 118 6 4 292 22 313 2.79e-103 304
MS.gene42432.t1 MTR_7g076100 64.017 239 79 4 57 292 66 300 9.36e-96 285
MS.gene42432.t1 MTR_1g108740 43.051 295 139 11 1 290 74 344 3.88e-58 189
MS.gene42432.t1 MTR_5g038260 40.187 321 147 13 2 292 78 383 4.07e-55 183
MS.gene42432.t1 MTR_5g038230 37.539 317 131 12 2 290 76 353 4.68e-47 161
MS.gene42432.t1 MTR_5g082770 45.946 222 94 7 15 224 81 288 9.98e-45 153
MS.gene42432.t1 MTR_1g064570 36.578 339 151 15 3 292 77 400 2.34e-44 155
MS.gene42432.t1 MTR_7g076130 61.111 126 44 2 87 209 25 148 9.38e-43 144
MS.gene42432.t1 MTR_5g082780 39.912 228 104 8 34 248 2 209 9.88e-39 136
MS.gene42432.t1 MTR_1g016150 42.609 115 63 3 1 114 83 195 3.85e-21 90.1
MS.gene42432.t1 MTR_6g023955 48.000 75 38 1 60 133 74 148 2.13e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 59 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGGTGATAAGAAGCATTT+AGG 0.171183 7.2:-28492672 MS.gene42432:CDS
AAAGAGCAAGCCAATCATTT+TGG 0.202770 7.2:-28493151 MS.gene42432:CDS
CAAACTCCACATTCACAAAT+TGG 0.228464 7.2:-28492847 MS.gene42432:CDS
TTCTCGTAGTAAGTAAAATT+AGG 0.242633 7.2:+28492996 None:intergenic
TTCGAGAGGTGGCAGATTAA+TGG 0.291036 7.2:+28493268 None:intergenic
AATGAACAAACTTGAGAGTT+TGG 0.291432 7.2:-28492793 MS.gene42432:CDS
TGTTCACCTAATACAATATA+TGG 0.299029 7.2:+28492960 None:intergenic
AGTACTCCATATATTGTATT+AGG 0.310368 7.2:-28492966 MS.gene42432:CDS
CCATGGTTGGCTTGCATTAA+CGG 0.321484 7.2:-28493342 MS.gene42432:CDS
GGAGCTACACTGTACTTAAA+AGG 0.330559 7.2:+28493290 None:intergenic
GAAGGATGGGATAATTGAAT+AGG 0.335830 7.2:+28493401 None:intergenic
TAATCACTTGGGCTTGTAAT+GGG 0.338599 7.2:+28493215 None:intergenic
CTCCAAGTTGGAAAAGGATT+CGG 0.375437 7.2:-28492709 MS.gene42432:CDS
TTACACAAATCCAAAATGAT+TGG 0.383794 7.2:+28493141 None:intergenic
AAAAGGATTCACTAGAGTTA+TGG 0.384998 7.2:+28493307 None:intergenic
TCTCGTAGTAAGTAAAATTA+GGG 0.391917 7.2:+28492997 None:intergenic
AGCCTCTTGTTTCTCCAAGT+TGG 0.404761 7.2:-28492721 MS.gene42432:CDS
GGGTTCTACCACAATTTCAA+TGG 0.408660 7.2:-28492569 MS.gene42432:CDS
TCGAGAGGTGGCAGATTAAT+GGG 0.425947 7.2:+28493269 None:intergenic
AAGGTGATAAGAAGCATTTA+GGG 0.432837 7.2:-28492671 MS.gene42432:CDS
TTGTTTCTCCAAGTTGGAAA+AGG 0.437802 7.2:-28492715 MS.gene42432:CDS
AAGCCAACCATGGCTACAAC+CGG 0.461155 7.2:+28493352 None:intergenic
TACTTTCAATGATGGAAGGA+TGG 0.467431 7.2:+28493387 None:intergenic
ATAATCACTTGGGCTTGTAA+TGG 0.476686 7.2:+28493214 None:intergenic
AAGGATGGGATAATTGAATA+GGG 0.479464 7.2:+28493402 None:intergenic
GGTTCTACCACAATTTCAAT+GGG 0.480142 7.2:-28492568 MS.gene42432:CDS
ATGAGGATTATTGAGCTTGA+AGG 0.482842 7.2:+28493037 None:intergenic
ACCTCTCGAAGCTGTTTACA+AGG 0.482941 7.2:-28493255 MS.gene42432:CDS
AATCATTGACCGGAGACATA+TGG 0.484616 7.2:-28492905 MS.gene42432:CDS
TGGCCGGTTGTAGCCATGGT+TGG 0.485159 7.2:-28493355 MS.gene42432:CDS
TACAAGCCCAAGTGATTATG+TGG 0.499442 7.2:-28493210 MS.gene42432:CDS
ACTTTCAATGATGGAAGGAT+GGG 0.503431 7.2:+28493388 None:intergenic
GAGATCTATAATGTGAAGGA+TGG 0.509549 7.2:-28492645 MS.gene42432:CDS
CGCGGCTATCAGCAAATACC+AGG 0.511548 7.2:+28493075 None:intergenic
TATTTCGTGAAATCATTGAC+CGG 0.532294 7.2:-28492915 MS.gene42432:CDS
TCTCACCATCCATATGTCTC+CGG 0.543961 7.2:+28492896 None:intergenic
GCTGCAACCACATAATCACT+TGG 0.549128 7.2:+28493203 None:intergenic
CTAGTTCCAATTTGTGAATG+TGG 0.551800 7.2:+28492841 None:intergenic
ATGTGAAGGATGGAAGCTTA+CGG 0.560055 7.2:-28492635 MS.gene42432:CDS
TGCATTCGCTCGAAGGAAAG+TGG 0.562548 7.2:+28492600 None:intergenic
TGTAATGGGGTCAGCAGACA+AGG 0.568289 7.2:+28493229 None:intergenic
GGTCAATCCCATTGAAATTG+TGG 0.574786 7.2:+28492561 None:intergenic
CCGTTAATGCAAGCCAACCA+TGG 0.592476 7.2:+28493342 None:intergenic
TTCCAACTTGGAGAAACAAG+AGG 0.597328 7.2:+28492719 None:intergenic
GTTGCAGCGATTTACAATTG+TGG 0.603650 7.2:-28493188 MS.gene42432:CDS
GTTAGAGATCTATAATGTGA+AGG 0.603732 7.2:-28492649 MS.gene42432:CDS
AATCACTTGGGCTTGTAATG+GGG 0.606028 7.2:+28493216 None:intergenic
AACTTGGAGAAACAAGAGGC+TGG 0.606698 7.2:+28492723 None:intergenic
TTGTAAACAGCTTCGAGAGG+TGG 0.615094 7.2:+28493257 None:intergenic
ATTGAGCTTGAAGGATACAA+TGG 0.615993 7.2:+28493046 None:intergenic
CTGGTATTTGCTGATAGCCG+CGG 0.626838 7.2:-28493074 MS.gene42432:CDS
CTGCAACCACATAATCACTT+GGG 0.636696 7.2:+28493204 None:intergenic
TCATTTGAGTCATCACAATG+AGG 0.645711 7.2:+28493020 None:intergenic
AGGATACAATGGTATTTCCG+CGG 0.667549 7.2:+28493057 None:intergenic
ATGATTTCACGAAATAAACA+TGG 0.673183 7.2:+28492922 None:intergenic
ACCTTGTAAACAGCTTCGAG+AGG 0.677454 7.2:+28493254 None:intergenic
GCATAGAAGTTGAATCACCA+CGG 0.688735 7.2:+28492745 None:intergenic
ATTGACCGGAGACATATGGA+TGG 0.696827 7.2:-28492901 MS.gene42432:CDS
TTGGAACTAGACGTCCAGAG+TGG 0.702846 7.2:-28492828 MS.gene42432:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAACATTTTACTTTCAATGA+TGG + chr7.2:28492606-28492625 None:intergenic 20.0%
!!! ACTCATGTTGTATTTTATAA+AGG - chr7.2:28492884-28492903 MS.gene42432:CDS 20.0%
!!! CATTGAAAGTAAAATGTTTT+TGG - chr7.2:28492607-28492626 MS.gene42432:CDS 20.0%
! AGTACTCCATATATTGTATT+AGG - chr7.2:28493016-28493035 MS.gene42432:CDS 25.0%
! ATGATTTCACGAAATAAACA+TGG + chr7.2:28493063-28493082 None:intergenic 25.0%
! TCTCGTAGTAAGTAAAATTA+GGG + chr7.2:28492988-28493007 None:intergenic 25.0%
! TGTTCACCTAATACAATATA+TGG + chr7.2:28493025-28493044 None:intergenic 25.0%
! TTACACAAATCCAAAATGAT+TGG + chr7.2:28492844-28492863 None:intergenic 25.0%
! TTCTCGTAGTAAGTAAAATT+AGG + chr7.2:28492989-28493008 None:intergenic 25.0%
!!! ATTTTACTTTCAATGATGGA+AGG + chr7.2:28492602-28492621 None:intergenic 25.0%
!!! GAAGACAACATTTTATTTGT+CGG - chr7.2:28493211-28493230 MS.gene42432:CDS 25.0%
AAAAGGATTCACTAGAGTTA+TGG + chr7.2:28492678-28492697 None:intergenic 30.0%
AAGGATGGGATAATTGAATA+GGG + chr7.2:28492583-28492602 None:intergenic 30.0%
AATGAACAAACTTGAGAGTT+TGG - chr7.2:28493189-28493208 MS.gene42432:CDS 30.0%
GTTAGAGATCTATAATGTGA+AGG - chr7.2:28493333-28493352 MS.gene42432:CDS 30.0%
TATTTCGTGAAATCATTGAC+CGG - chr7.2:28493067-28493086 MS.gene42432:CDS 30.0%
! TGTTGTATTTTATAAAGGCC+TGG - chr7.2:28492889-28492908 MS.gene42432:CDS 30.0%
!! AAGGTGATAAGAAGCATTTA+GGG - chr7.2:28493311-28493330 MS.gene42432:CDS 30.0%
!!! GAAAGTAAAATGTTTTTGGC+CGG - chr7.2:28492611-28492630 MS.gene42432:CDS 30.0%
!!! TCGGTTTATTTTGTTTGTGA+AGG - chr7.2:28493292-28493311 MS.gene42432:CDS 30.0%
ATAATCACTTGGGCTTGTAA+TGG + chr7.2:28492771-28492790 None:intergenic 35.0%
ATGAGGATTATTGAGCTTGA+AGG + chr7.2:28492948-28492967 None:intergenic 35.0%
ATTGAGCTTGAAGGATACAA+TGG + chr7.2:28492939-28492958 None:intergenic 35.0%
CAAACTCCACATTCACAAAT+TGG - chr7.2:28493135-28493154 MS.gene42432:CDS 35.0%
CTAGTTCCAATTTGTGAATG+TGG + chr7.2:28493144-28493163 None:intergenic 35.0%
GAAGGATGGGATAATTGAAT+AGG + chr7.2:28492584-28492603 None:intergenic 35.0%
GAGATCTATAATGTGAAGGA+TGG - chr7.2:28493337-28493356 MS.gene42432:CDS 35.0%
GGTTCTACCACAATTTCAAT+GGG - chr7.2:28493414-28493433 MS.gene42432:CDS 35.0%
TAATCACTTGGGCTTGTAAT+GGG + chr7.2:28492770-28492789 None:intergenic 35.0%
TCATTTGAGTCATCACAATG+AGG + chr7.2:28492965-28492984 None:intergenic 35.0%
! AAAGAGCAAGCCAATCATTT+TGG - chr7.2:28492831-28492850 MS.gene42432:CDS 35.0%
! ACTTTCAATGATGGAAGGAT+GGG + chr7.2:28492597-28492616 None:intergenic 35.0%
! TACTTTCAATGATGGAAGGA+TGG + chr7.2:28492598-28492617 None:intergenic 35.0%
! TTGTTTCTCCAAGTTGGAAA+AGG - chr7.2:28493267-28493286 MS.gene42432:CDS 35.0%
!! ATTTTATTTGTCGGAAACCG+TGG - chr7.2:28493220-28493239 MS.gene42432:CDS 35.0%
!! GAAGGTGATAAGAAGCATTT+AGG - chr7.2:28493310-28493329 MS.gene42432:CDS 35.0%
!! TTTGTTCAAGTTTTCCACTC+TGG + chr7.2:28493171-28493190 None:intergenic 35.0%
AAAAAGTTGCATTCGCTCGA+AGG + chr7.2:28493392-28493411 None:intergenic 40.0%
AATCACTTGGGCTTGTAATG+GGG + chr7.2:28492769-28492788 None:intergenic 40.0%
AATCATTGACCGGAGACATA+TGG - chr7.2:28493077-28493096 MS.gene42432:CDS 40.0%
AGGATACAATGGTATTTCCG+CGG + chr7.2:28492928-28492947 None:intergenic 40.0%
ATGTGAAGGATGGAAGCTTA+CGG - chr7.2:28493347-28493366 MS.gene42432:CDS 40.0%
CTGCAACCACATAATCACTT+GGG + chr7.2:28492781-28492800 None:intergenic 40.0%
GCATAGAAGTTGAATCACCA+CGG + chr7.2:28493240-28493259 None:intergenic 40.0%
GGAGCTACACTGTACTTAAA+AGG + chr7.2:28492695-28492714 None:intergenic 40.0%
GGGTTCTACCACAATTTCAA+TGG - chr7.2:28493413-28493432 MS.gene42432:CDS 40.0%
GTTGCAGCGATTTACAATTG+TGG - chr7.2:28492794-28492813 MS.gene42432:CDS 40.0%
TACAAGCCCAAGTGATTATG+TGG - chr7.2:28492772-28492791 MS.gene42432:CDS 40.0%
TTCCAACTTGGAGAAACAAG+AGG + chr7.2:28493266-28493285 None:intergenic 40.0%
! AACCGAATCCTTTTCCAACT+TGG + chr7.2:28493278-28493297 None:intergenic 40.0%
! CTCCAAGTTGGAAAAGGATT+CGG - chr7.2:28493273-28493292 MS.gene42432:CDS 40.0%
!!! CGAGCGAATGCAACTTTTTT+GGG - chr7.2:28493393-28493412 MS.gene42432:CDS 40.0%
!!! TCGAGCGAATGCAACTTTTT+TGG - chr7.2:28493392-28493411 MS.gene42432:CDS 40.0%
AACTTGGAGAAACAAGAGGC+TGG + chr7.2:28493262-28493281 None:intergenic 45.0%
ACCTCTCGAAGCTGTTTACA+AGG - chr7.2:28492727-28492746 MS.gene42432:CDS 45.0%
ACCTTGTAAACAGCTTCGAG+AGG + chr7.2:28492731-28492750 None:intergenic 45.0%
ATTGACCGGAGACATATGGA+TGG - chr7.2:28493081-28493100 MS.gene42432:CDS 45.0%
GCTGCAACCACATAATCACT+TGG + chr7.2:28492782-28492801 None:intergenic 45.0%
TCGAGAGGTGGCAGATTAAT+GGG + chr7.2:28492716-28492735 None:intergenic 45.0%
TCTCACCATCCATATGTCTC+CGG + chr7.2:28493089-28493108 None:intergenic 45.0%
TTCGAGAGGTGGCAGATTAA+TGG + chr7.2:28492717-28492736 None:intergenic 45.0%
TTGTAAACAGCTTCGAGAGG+TGG + chr7.2:28492728-28492747 None:intergenic 45.0%
! AGCCTCTTGTTTCTCCAAGT+TGG - chr7.2:28493261-28493280 MS.gene42432:CDS 45.0%
!! CCATGGTTGGCTTGCATTAA+CGG - chr7.2:28492640-28492659 MS.gene42432:CDS 45.0%
AAGCCAACCATGGCTACAAC+CGG + chr7.2:28492633-28492652 None:intergenic 50.0%
CCGTTAATGCAAGCCAACCA+TGG + chr7.2:28492643-28492662 None:intergenic 50.0%
TGCATTCGCTCGAAGGAAAG+TGG + chr7.2:28493385-28493404 None:intergenic 50.0%
TTGGAACTAGACGTCCAGAG+TGG - chr7.2:28493154-28493173 MS.gene42432:CDS 50.0%
! CTGGTATTTGCTGATAGCCG+CGG - chr7.2:28492908-28492927 MS.gene42432:CDS 50.0%
! TGTAATGGGGTCAGCAGACA+AGG + chr7.2:28492756-28492775 None:intergenic 50.0%
!! TTTTTGGCCGGTTGTAGCCA+TGG - chr7.2:28492623-28492642 MS.gene42432:CDS 50.0%
CGCGGCTATCAGCAAATACC+AGG + chr7.2:28492910-28492929 None:intergenic 55.0%
TGGCCGGTTGTAGCCATGGT+TGG - chr7.2:28492627-28492646 MS.gene42432:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 28492563 28493441 28492563 ID=MS.gene42432
chr7.2 mRNA 28492563 28493441 28492563 ID=MS.gene42432.t1;Parent=MS.gene42432
chr7.2 exon 28492563 28493441 28492563 ID=MS.gene42432.t1.exon1;Parent=MS.gene42432.t1
chr7.2 CDS 28492563 28493441 28492563 ID=cds.MS.gene42432.t1;Parent=MS.gene42432.t1
Gene Sequence

>MS.gene42432

ATGAGTGAGAAAGAGTACCCTATTCAATTATCCCATCCTTCCATCATTGAAAGTAAAATGTTTTTGGCCGGTTGTAGCCATGGTTGGCTTGCATTAACGGATGATAACAAAGCCATAACTCTAGTGAATCCTTTTAAGTACAGTGTAGCTCCCATTAATCTGCCACCTCTCGAAGCTGTTTACAAGGTTACCTTGTCTGCTGACCCCATTACAAGCCCAAGTGATTATGTGGTTGCAGCGATTTACAATTGTGGTTTTCTCGCTTTCAAAAGAGCAAGCCAATCATTTTGGATTTGTGTAAACAGAAATGAATTTCGTTTCACTCATGTTGTATTTTATAAAGGCCTGGTATTTGCTGATAGCCGCGGAAATACCATTGTATCCTTCAAGCTCAATAATCCTCATTGTGATGACTCAAATGACCCTAATTTTACTTACTACGAGAAGATAGCTAGTACTCCATATATTGTATTAGGTGAACAGTATTATTATAGCTGCCATGTTTATTTCGTGAAATCATTGACCGGAGACATATGGATGGTGAGAAGATGTAACGTTGACAATCATTCGTTCAAACTCCACATTCACAAATTGGAACTAGACGTCCAGAGTGGAAAACTTGAACAAATGAACAAACTTGAGAGTTTGGAAGACAACATTTTATTTGTCGGAAACCGTGGTGATTCAACTTCTATGCCAGCCTCTTGTTTCTCCAAGTTGGAAAAGGATTCGGTTTATTTTGTTTGTGAAGGTGATAAGAAGCATTTAGGGTTAGAGATCTATAATGTGAAGGATGGAAGCTTACGGAGACAATCTTTACCACTTTCCTTCGAGCGAATGCAACTTTTTTGGGTTCTACCACAATTTCAATGGGATTGA
Protein sequence

>MS.gene42432.t1

MSEKEYPIQLSHPSIIESKMFLAGCSHGWLALTDDNKAITLVNPFKYSVAPINLPPLEAVYKVTLSADPITSPSDYVVAAIYNCGFLAFKRASQSFWICVNRNEFRFTHVVFYKGLVFADSRGNTIVSFKLNNPHCDDSNDPNFTYYEKIASTPYIVLGEQYYYSCHVYFVKSLTGDIWMVRRCNVDNHSFKLHIHKLELDVQSGKLEQMNKLESLEDNILFVGNRGDSTSMPASCFSKLEKDSVYFVCEGDKKHLGLEIYNVKDGSLRRQSLPLSFERMQLFWVLPQFQWD