AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059096

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059096.t1 MTR_1g009110 86.321 212 21 1 19 222 91 302 4.43e-135 387
MS.gene059096.t1 MTR_1g022105 50.222 225 54 7 19 233 99 275 2.31e-58 189
MS.gene059096.t1 MTR_1g023400 43.868 212 95 7 38 233 88 291 6.53e-46 158
MS.gene059096.t1 MTR_4g080200 44.344 221 101 8 28 234 73 285 8.67e-44 152
MS.gene059096.t1 MTR_1g022200 42.130 216 97 9 32 227 91 298 9.52e-35 129
MS.gene059096.t1 MTR_1g037540 38.182 220 108 10 28 227 113 324 9.00e-33 124
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 73 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTTGGTCACTTGATTCTA+TGG 0.211950 1.2:-10864810 MS.gene059096:CDS
CGAATTTCAAACTTATGTTT+TGG 0.285058 1.2:-10864171 MS.gene059096:CDS
AATGTTACAGTCGTCGTTAA+AGG 0.311664 1.2:+10864699 None:intergenic
AAGGATGGCGATCAAGTCTT+TGG 0.320162 1.2:-10864248 MS.gene059096:CDS
CGAACTGGGATGCGGTTAAA+AGG 0.324187 1.2:+10864559 None:intergenic
GTCCGACCCAGTTGGAAATC+TGG 0.346576 1.2:-10864348 MS.gene059096:CDS
CTGTTTGCATGTTAAACATA+AGG 0.366156 1.2:-10864407 MS.gene059096:CDS
CTTATGTTTAACATGCAAAC+AGG 0.379062 1.2:+10864408 None:intergenic
AAATACGATGATTCCATGTA+TGG 0.380419 1.2:-10864730 MS.gene059096:CDS
AGTGGACTTGTTTAGTTGTT+GGG 0.389103 1.2:+10864785 None:intergenic
TATGATGGATTGTATCGAAC+TGG 0.389997 1.2:+10864544 None:intergenic
AAAGGTGGAGGGTGATGGAC+AGG 0.392292 1.2:+10864577 None:intergenic
TTGTTAACTGCGTTTATCAT+TGG 0.394286 1.2:-10864513 MS.gene059096:CDS
GAGAAGATGATTATTTCTTC+AGG 0.395114 1.2:-10864637 MS.gene059096:CDS
TGATAAACGCAGTTAACAAC+CGG 0.421312 1.2:+10864517 None:intergenic
TGTTTGCATGTTAAACATAA+GGG 0.424384 1.2:-10864406 MS.gene059096:CDS
AAGTGGACTTGTTTAGTTGT+TGG 0.433206 1.2:+10864784 None:intergenic
AAGTCAAAGCAGATGATGTT+TGG 0.437710 1.2:+10864463 None:intergenic
CGGTCTACGGATTGATTAGC+TGG 0.445840 1.2:+10864895 None:intergenic
CAAGTCTTTGGAGGAAAGGT+TGG 0.455199 1.2:-10864236 MS.gene059096:CDS
ATTTCCAACTGGGTCGGACT+AGG 0.460982 1.2:+10864352 None:intergenic
TCGGTCCTCGCCACCGTCGC+AGG 0.468773 1.2:+10864952 None:intergenic
GCAGGAGAGAAGAGTGATGT+AGG 0.469702 1.2:+10864970 None:intergenic
TCATAATCCAGATTTCCAAC+TGG 0.477934 1.2:+10864341 None:intergenic
ATATGATTCGACTCGGTCTA+CGG 0.477983 1.2:+10864882 None:intergenic
ATGCAACAAGTCCACGGAAC+TGG 0.481178 1.2:+10864284 None:intergenic
GGTGGCGAGGACCGAGGAGT+TGG 0.482604 1.2:-10864944 MS.gene059096:CDS
AGGAAAGGTTGGACAACTGC+TGG 0.494743 1.2:-10864225 MS.gene059096:CDS
CGGATTGATTAGCTGGAAAG+AGG 0.525041 1.2:+10864902 None:intergenic
GTAGACCGAGTCGAATCATA+TGG 0.525200 1.2:-10864880 MS.gene059096:CDS
TCTCTCCTGCGACGGTGGCG+AGG 0.528113 1.2:-10864957 MS.gene059096:CDS
TTAACAACCGGGGTATATGA+TGG 0.531903 1.2:+10864529 None:intergenic
ACTCTTCTCTCCTGCGACGG+TGG 0.534629 1.2:-10864962 MS.gene059096:CDS
CTGGCTTTATATGAAGATCA+AGG 0.535518 1.2:-10864206 MS.gene059096:CDS
CGATCAAGTCTTTGGAGGAA+AGG 0.536754 1.2:-10864240 MS.gene059096:CDS
CATAATCCAGATTTCCAACT+GGG 0.537214 1.2:+10864342 None:intergenic
ACGATCTAAGCACTAAATCA+TGG 0.541598 1.2:-10864603 MS.gene059096:CDS
GGTTAAAAGGTGGAGGGTGA+TGG 0.541875 1.2:+10864572 None:intergenic
GAGTCACAAAATGAGGGTGC+AGG 0.546607 1.2:+10864754 None:intergenic
CAGGAGAGAAGAGTGATGTA+GGG 0.550066 1.2:+10864971 None:intergenic
GCAAACAGGGAGCTTTGAGT+TGG 0.555369 1.2:+10864422 None:intergenic
GTCGATGCGTTCCAACTCCT+CGG 0.558741 1.2:+10864933 None:intergenic
GAGAGAAGAGTGATGTAGGG+AGG 0.559362 1.2:+10864974 None:intergenic
ATCACTCTTCTCTCCTGCGA+CGG 0.566825 1.2:-10864965 MS.gene059096:CDS
GATGGCGATCAAGTCTTTGG+AGG 0.568823 1.2:-10864245 MS.gene059096:CDS
GTATTTAGAGTCACAAAATG+AGG 0.569672 1.2:+10864747 None:intergenic
TCATCCTAGTCCGACCCAGT+TGG 0.573989 1.2:-10864356 MS.gene059096:CDS
GATACTTCAAAACATAAGCA+AGG 0.575880 1.2:+10864380 None:intergenic
GATTGTATCGAACTGGGATG+CGG 0.586322 1.2:+10864551 None:intergenic
GGGATGCGGTTAAAAGGTGG+AGG 0.586358 1.2:+10864565 None:intergenic
GAATCATATGGCAATTGCAA+TGG 0.596106 1.2:-10864868 MS.gene059096:CDS
AGGGTGCAGGAGGTATAAAG+TGG 0.598291 1.2:+10864767 None:intergenic
GGATTGATTAGCTGGAAAGA+GGG 0.601844 1.2:+10864903 None:intergenic
AAGGTGGAGGGTGATGGACA+GGG 0.604225 1.2:+10864578 None:intergenic
ATCCAGATTTCCAACTGGGT+CGG 0.606074 1.2:+10864346 None:intergenic
ACTGGGATGCGGTTAAAAGG+TGG 0.613040 1.2:+10864562 None:intergenic
AGGTGGAGGGTGATGGACAG+GGG 0.617953 1.2:+10864579 None:intergenic
ATACTTCAAAACATAAGCAA+GGG 0.623300 1.2:+10864381 None:intergenic
TGCGACGGTGGCGAGGACCG+AGG 0.624717 1.2:-10864950 MS.gene059096:CDS
TCACAAAATGAGGGTGCAGG+AGG 0.625154 1.2:+10864757 None:intergenic
TCACGTATGCAACAAGTCCA+CGG 0.629328 1.2:+10864278 None:intergenic
TGGAGCAGTATGCAAATCGA+CGG 0.633685 1.2:+10864483 None:intergenic
AATTGCCATATGATTCGACT+CGG 0.634347 1.2:+10864875 None:intergenic
TTATGTTTAACATGCAAACA+GGG 0.637814 1.2:+10864409 None:intergenic
AAAGGCACAGAAACCATACA+TGG 0.639071 1.2:+10864717 None:intergenic
TATTTAGAGTCACAAAATGA+GGG 0.639125 1.2:+10864748 None:intergenic
ACAACATTGGACCAGTTCCG+TGG 0.656417 1.2:-10864295 MS.gene059096:CDS
GATAAACGCAGTTAACAACC+GGG 0.662346 1.2:+10864518 None:intergenic
TGGATTATGATCAAAGCCAG+TGG 0.672827 1.2:-10864328 MS.gene059096:CDS
GGATGCGGTTAAAAGGTGGA+GGG 0.677010 1.2:+10864566 None:intergenic
ATACAATCCATCATATACCC+CGG 0.677642 1.2:-10864536 MS.gene059096:CDS
ATGATGGATTGTATCGAACT+GGG 0.683119 1.2:+10864545 None:intergenic
ATAAACGCAGTTAACAACCG+GGG 0.757950 1.2:+10864519 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTATTTTAGATGTTTATG+GGG - chr1.2:10864962-10864981 MS.gene059096:CDS 20.0%
!!! GGATTATTTTAGATGTTTAT+GGG - chr1.2:10864961-10864980 MS.gene059096:CDS 20.0%
!!! TCTTCTTAAAAGCTTTTTAT+AGG - chr1.2:10864271-10864290 MS.gene059096:CDS 20.0%
!!! TGGATTATTTTAGATGTTTA+TGG - chr1.2:10864960-10864979 MS.gene059096:CDS 20.0%
! ATACTTCAAAACATAAGCAA+GGG + chr1.2:10864733-10864752 None:intergenic 25.0%
! TGTTTGCATGTTAAACATAA+GGG - chr1.2:10864705-10864724 MS.gene059096:CDS 25.0%
! TTATGTTTAACATGCAAACA+GGG + chr1.2:10864705-10864724 None:intergenic 25.0%
!! CGAATTTCAAACTTATGTTT+TGG - chr1.2:10864940-10864959 MS.gene059096:CDS 25.0%
!! TATTTAGAGTCACAAAATGA+GGG + chr1.2:10864366-10864385 None:intergenic 25.0%
!! TTTTATAGGAATTCAACTCT+TGG - chr1.2:10864285-10864304 MS.gene059096:CDS 25.0%
AAATACGATGATTCCATGTA+TGG - chr1.2:10864381-10864400 MS.gene059096:CDS 30.0%
CTGTTTGCATGTTAAACATA+AGG - chr1.2:10864704-10864723 MS.gene059096:CDS 30.0%
CTTATGTTTAACATGCAAAC+AGG + chr1.2:10864706-10864725 None:intergenic 30.0%
GATACTTCAAAACATAAGCA+AGG + chr1.2:10864734-10864753 None:intergenic 30.0%
TTGTTAACTGCGTTTATCAT+TGG - chr1.2:10864598-10864617 MS.gene059096:CDS 30.0%
! GAGAAGATGATTATTTCTTC+AGG - chr1.2:10864474-10864493 MS.gene059096:CDS 30.0%
! GTATTTAGAGTCACAAAATG+AGG + chr1.2:10864367-10864386 None:intergenic 30.0%
AAGTCAAAGCAGATGATGTT+TGG + chr1.2:10864651-10864670 None:intergenic 35.0%
AATGTTACAGTCGTCGTTAA+AGG + chr1.2:10864415-10864434 None:intergenic 35.0%
AATTGCCATATGATTCGACT+CGG + chr1.2:10864239-10864258 None:intergenic 35.0%
ACGATCTAAGCACTAAATCA+TGG - chr1.2:10864508-10864527 MS.gene059096:CDS 35.0%
ATACAATCCATCATATACCC+CGG - chr1.2:10864575-10864594 MS.gene059096:CDS 35.0%
CATAATCCAGATTTCCAACT+GGG + chr1.2:10864772-10864791 None:intergenic 35.0%
GAATCATATGGCAATTGCAA+TGG - chr1.2:10864243-10864262 MS.gene059096:CDS 35.0%
TCATAATCCAGATTTCCAAC+TGG + chr1.2:10864773-10864792 None:intergenic 35.0%
TGATAAACGCAGTTAACAAC+CGG + chr1.2:10864597-10864616 None:intergenic 35.0%
! AAGTGGACTTGTTTAGTTGT+TGG + chr1.2:10864330-10864349 None:intergenic 35.0%
! AGTGGACTTGTTTAGTTGTT+GGG + chr1.2:10864329-10864348 None:intergenic 35.0%
! CTTGTTGCATACGTGATTTT+TGG - chr1.2:10864840-10864859 MS.gene059096:CDS 35.0%
! TGGACCAAAAAGTACAACAT+TGG - chr1.2:10864803-10864822 MS.gene059096:CDS 35.0%
! TGGTCCAATGTTGTACTTTT+TGG + chr1.2:10864810-10864829 None:intergenic 35.0%
!! ATACGTGATTTTTGGAAGGA+TGG - chr1.2:10864848-10864867 MS.gene059096:CDS 35.0%
!! ATGATGGATTGTATCGAACT+GGG + chr1.2:10864569-10864588 None:intergenic 35.0%
!! CTGGCTTTATATGAAGATCA+AGG - chr1.2:10864905-10864924 MS.gene059096:CDS 35.0%
!! TATGATGGATTGTATCGAAC+TGG + chr1.2:10864570-10864589 None:intergenic 35.0%
!! TTGCATACGTGATTTTTGGA+AGG - chr1.2:10864844-10864863 MS.gene059096:CDS 35.0%
ATAAACGCAGTTAACAACCG+GGG + chr1.2:10864595-10864614 None:intergenic 40.0%
CTCTTGGTCACTTGATTCTA+TGG - chr1.2:10864301-10864320 MS.gene059096:CDS 40.0%
GATAAACGCAGTTAACAACC+GGG + chr1.2:10864596-10864615 None:intergenic 40.0%
TGGATTATGATCAAAGCCAG+TGG - chr1.2:10864783-10864802 MS.gene059096:CDS 40.0%
TTAACAACCGGGGTATATGA+TGG + chr1.2:10864585-10864604 None:intergenic 40.0%
! AAAGGCACAGAAACCATACA+TGG + chr1.2:10864397-10864416 None:intergenic 40.0%
! GGATTGATTAGCTGGAAAGA+GGG + chr1.2:10864211-10864230 None:intergenic 40.0%
!! ATATGATTCGACTCGGTCTA+CGG + chr1.2:10864232-10864251 None:intergenic 40.0%
!! TGTTGTACTTTTTGGTCCAC+TGG + chr1.2:10864802-10864821 None:intergenic 40.0%
AAGGATGGCGATCAAGTCTT+TGG - chr1.2:10864863-10864882 MS.gene059096:CDS 45.0%
ATCCAGATTTCCAACTGGGT+CGG + chr1.2:10864768-10864787 None:intergenic 45.0%
CAGGAGAGAAGAGTGATGTA+GGG + chr1.2:10864143-10864162 None:intergenic 45.0%
GATTGTATCGAACTGGGATG+CGG + chr1.2:10864563-10864582 None:intergenic 45.0%
GTAGACCGAGTCGAATCATA+TGG - chr1.2:10864231-10864250 MS.gene059096:CDS 45.0%
TCACGTATGCAACAAGTCCA+CGG + chr1.2:10864836-10864855 None:intergenic 45.0%
TGGAGCAGTATGCAAATCGA+CGG + chr1.2:10864631-10864650 None:intergenic 45.0%
! CAAGTCTTTGGAGGAAAGGT+TGG - chr1.2:10864875-10864894 MS.gene059096:CDS 45.0%
! CGATCAAGTCTTTGGAGGAA+AGG - chr1.2:10864871-10864890 MS.gene059096:CDS 45.0%
! CGGATTGATTAGCTGGAAAG+AGG + chr1.2:10864212-10864231 None:intergenic 45.0%
ACAACATTGGACCAGTTCCG+TGG - chr1.2:10864816-10864835 MS.gene059096:CDS 50.0%
ACTGGGATGCGGTTAAAAGG+TGG + chr1.2:10864552-10864571 None:intergenic 50.0%
AGGAAAGGTTGGACAACTGC+TGG - chr1.2:10864886-10864905 MS.gene059096:CDS 50.0%
ATCACTCTTCTCTCCTGCGA+CGG - chr1.2:10864146-10864165 MS.gene059096:CDS 50.0%
ATGCAACAAGTCCACGGAAC+TGG + chr1.2:10864830-10864849 None:intergenic 50.0%
ATTTCCAACTGGGTCGGACT+AGG + chr1.2:10864762-10864781 None:intergenic 50.0%
CGAACTGGGATGCGGTTAAA+AGG + chr1.2:10864555-10864574 None:intergenic 50.0%
GAGAGAAGAGTGATGTAGGG+AGG + chr1.2:10864140-10864159 None:intergenic 50.0%
GATGGCGATCAAGTCTTTGG+AGG - chr1.2:10864866-10864885 MS.gene059096:CDS 50.0%
GCAGGAGAGAAGAGTGATGT+AGG + chr1.2:10864144-10864163 None:intergenic 50.0%
GGATGCGGTTAAAAGGTGGA+GGG + chr1.2:10864548-10864567 None:intergenic 50.0%
GGTTAAAAGGTGGAGGGTGA+TGG + chr1.2:10864542-10864561 None:intergenic 50.0%
! AGGGTGCAGGAGGTATAAAG+TGG + chr1.2:10864347-10864366 None:intergenic 50.0%
! CGGTCTACGGATTGATTAGC+TGG + chr1.2:10864219-10864238 None:intergenic 50.0%
! GAGTCACAAAATGAGGGTGC+AGG + chr1.2:10864360-10864379 None:intergenic 50.0%
! TCACAAAATGAGGGTGCAGG+AGG + chr1.2:10864357-10864376 None:intergenic 50.0%
!! GCAAACAGGGAGCTTTGAGT+TGG + chr1.2:10864692-10864711 None:intergenic 50.0%
GGGATGCGGTTAAAAGGTGG+AGG + chr1.2:10864549-10864568 None:intergenic 55.0%
GTCCGACCCAGTTGGAAATC+TGG - chr1.2:10864763-10864782 MS.gene059096:CDS 55.0%
GTCGATGCGTTCCAACTCCT+CGG + chr1.2:10864181-10864200 None:intergenic 55.0%
TCATCCTAGTCCGACCCAGT+TGG - chr1.2:10864755-10864774 MS.gene059096:CDS 55.0%
!! AAAGGTGGAGGGTGATGGAC+AGG + chr1.2:10864537-10864556 None:intergenic 55.0%
!! AAGGTGGAGGGTGATGGACA+GGG + chr1.2:10864536-10864555 None:intergenic 55.0%
ACTCTTCTCTCCTGCGACGG+TGG - chr1.2:10864149-10864168 MS.gene059096:CDS 60.0%
!! AGGTGGAGGGTGATGGACAG+GGG + chr1.2:10864535-10864554 None:intergenic 60.0%
GGTGGCGAGGACCGAGGAGT+TGG - chr1.2:10864167-10864186 MS.gene059096:CDS 70.0%
TCTCTCCTGCGACGGTGGCG+AGG - chr1.2:10864154-10864173 MS.gene059096:CDS 70.0%
TCGGTCCTCGCCACCGTCGC+AGG + chr1.2:10864162-10864181 None:intergenic 75.0%
TGCGACGGTGGCGAGGACCG+AGG - chr1.2:10864161-10864180 MS.gene059096:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 10864126 10865007 10864126 ID=MS.gene059096
chr1.2 mRNA 10864126 10865007 10864126 ID=MS.gene059096.t1;Parent=MS.gene059096
chr1.2 exon 10864126 10865007 10864126 ID=MS.gene059096.t1.exon1;Parent=MS.gene059096.t1
chr1.2 CDS 10864126 10865007 10864126 ID=cds.MS.gene059096.t1;Parent=MS.gene059096.t1
Gene Sequence

>MS.gene059096

ATGGATTCAAACCTCCCTACATCACTCTTCTCTCCTGCGACGGTGGCGAGGACCGAGGAGTTGGAACGCATCGACTTCTGCTCCCTCTTTCCAGCTAATCAATCCGTAGACCGAGTCGAATCATATGGCAATTGCAATGGTGTTTTCTTCTTAAAAGCTTTTTATAGGAATTCAACTCTTGGTCACTTGATTCTATGGAACCCAACAACTAAACAAGTCCACTTTATACCTCCTGCACCCTCATTTTGTGACTCTAAATACGATGATTCCATGTATGGTTTCTGTGCCTTTAACGACGACTGTAACATTAATTTCAAAGTTGTTAGACTTCAACAATGTGCACATGTTGAGAAGATGATTATTTCTTCAGGCGCAGAAGTGTACGATCTAAGCACTAAATCATGGACCCCTGTCCATCACCCTCCACCTTTTAACCGCATCCCAGTTCGATACAATCCATCATATACCCCGGTTGTTAACTGCGTTTATCATTGGATTGTTGCCGTCGATTTGCATACTGCTCCAAACATCATCTGCTTTGACTTTCACAACAATCAGTTTCACCAACTCAAAGCTCCCTGTTTGCATGTTAAACATAAGGGCTCCCTTGCTTATGTTTTGAAGTATCATCATCCTAGTCCGACCCAGTTGGAAATCTGGATTATGATCAAAGCCAGTGGACCAAAAAGTACAACATTGGACCAGTTCCGTGGACTTGTTGCATACGTGATTTTTGGAAGGATGGCGATCAAGTCTTTGGAGGAAAGGTTGGACAACTGCTGGCTTTATATGAAGATCAAGGCAACTCTCTTAGCGAATTTCAAACTTATGTTTTGGATTATTTTAGATGTTTATGGGGTTCTGAGTATTTGCAGACCATAA
Protein sequence

>MS.gene059096.t1

MDSNLPTSLFSPATVARTEELERIDFCSLFPANQSVDRVESYGNCNGVFFLKAFYRNSTLGHLILWNPTTKQVHFIPPAPSFCDSKYDDSMYGFCAFNDDCNINFKVVRLQQCAHVEKMIISSGAEVYDLSTKSWTPVHHPPPFNRIPVRYNPSYTPVVNCVYHWIVAVDLHTAPNIICFDFHNNQFHQLKAPCLHVKHKGSLAYVLKYHHPSPTQLEIWIMIKASGPKSTTLDQFRGLVAYVIFGRMAIKSLEERLDNCWLYMKIKATLLANFKLMFWIILDVYGVLSICRP