AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene067686

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067686.t1 MTR_3g083080 54.595 185 84 0 2 186 23 207 4.05e-65 199
MS.gene067686.t1 MTR_3g083030 52.660 188 84 3 2 186 46 231 2.07e-59 185
MS.gene067686.t1 MTR_3g083050 55.357 168 72 2 20 186 43 208 2.86e-57 179
MS.gene067686.t1 MTR_3g082420 36.224 196 107 7 2 184 31 221 1.76e-26 100
MS.gene067686.t1 MTR_3g082340 36.585 164 91 5 30 184 63 222 1.12e-24 96.3
MS.gene067686.t1 MTR_3g080680 35.263 190 104 8 9 184 14 198 3.58e-24 94.4
MS.gene067686.t1 MTR_3g083150 38.220 191 101 5 10 184 22 211 8.50e-24 93.6
MS.gene067686.t1 MTR_3g086030 46.535 101 52 1 9 109 5 103 2.53e-21 85.5
MS.gene067686.t1 MTR_8g461300 36.788 193 93 12 10 184 17 198 1.77e-20 84.7
MS.gene067686.t1 MTR_3g083100 43.200 125 55 4 76 184 49 173 4.54e-16 72.4
MS.gene067686.t1 MTR_4g055800 33.566 143 75 5 34 168 143 273 6.60e-15 71.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCACTTTGTGTATAGGAATA+AGG 0.280516 4.1:-68487915 MS.gene067686:CDS
CCGCATAAACGCGCAATTGC+TGG 0.285411 4.1:+68487700 None:intergenic
GGCGTGTCCGGTTCCGATTT+TGG 0.288134 4.1:+68488025 None:intergenic
TCCCCTCTGCAAGCTTGCTT+TGG 0.301525 4.1:-68487629 MS.gene067686:CDS
GATACGCAATGAAGAACTTA+TGG 0.316755 4.1:-68487993 MS.gene067686:CDS
GATGCTTACAGTTAGGTTAC+AGG 0.342671 4.1:+68487835 None:intergenic
TGCGAACACATAAACATATA+AGG 0.360061 4.1:+68487935 None:intergenic
GAAATACAATGCCGAGAATC+AGG 0.370063 4.1:-68487605 MS.gene067686:intron
TGTGTTCGCACTTTGTGTAT+AGG 0.382348 4.1:-68487922 MS.gene067686:CDS
CATGAGCTAGGTAGGCTTCA+TGG 0.407712 4.1:+68487320 None:intergenic
ATCGATTCACACGGCGTGTC+CGG 0.417902 4.1:+68488013 None:intergenic
ACCGACGATGGAGCCAAAAT+CGG 0.429034 4.1:-68488038 MS.gene067686:CDS
TATTGAACCTACCTGATTCT+CGG 0.452481 4.1:+68487594 None:intergenic
TGCAGAGGGGAGTGAGTTCA+AGG 0.476525 4.1:+68487641 None:intergenic
TGGCTCCATCGTCGGTGGTA+AGG 0.478145 4.1:+68488045 None:intergenic
AGATCATCGTCCATGCGATC+AGG 0.496351 4.1:+68487667 None:intergenic
AGCAGGGCAGTTGGAAGGAT+GGG 0.501180 4.1:+68487404 None:intergenic
TCAGCCTGAAAAGTTATAGC+AGG 0.514365 4.1:+68487387 None:intergenic
CCAGCAATTGCGCGTTTATG+CGG 0.515594 4.1:-68487700 MS.gene067686:CDS
CTCCAAAGCAAGCTTGCAGA+GGG 0.518878 4.1:+68487627 None:intergenic
AGACTCGACTACAGGCGGTT+CGG 0.519469 4.1:+68487347 None:intergenic
AATACACAATATTACCTCCA+TGG 0.530348 4.1:+68487454 None:intergenic
GATGGAGCCAAAATCGGAAC+CGG 0.533510 4.1:-68488032 MS.gene067686:CDS
TAGCAGGGCAGTTGGAAGGA+TGG 0.540470 4.1:+68487403 None:intergenic
ATGGCACAAGACTCGACTAC+AGG 0.541204 4.1:+68487339 None:intergenic
AAAAGTTATAGCAGGGCAGT+TGG 0.545343 4.1:+68487395 None:intergenic
TATTAATGCATGAGCTAGGT+AGG 0.547710 4.1:+68487312 None:intergenic
TAAACGCGCAATTGCTGGAG+GGG 0.549997 4.1:+68487705 None:intergenic
ATACACAATATTACCTCCAT+GGG 0.562952 4.1:+68487455 None:intergenic
CATAAACGCGCAATTGCTGG+AGG 0.575760 4.1:+68487703 None:intergenic
GACATTCTTAAGTCAACCCA+TGG 0.577711 4.1:-68487471 MS.gene067686:CDS
GTTATAGCAGGGCAGTTGGA+AGG 0.582712 4.1:+68487399 None:intergenic
GCAATTGCGCGTTTATGCGG+CGG 0.590566 4.1:-68487697 MS.gene067686:CDS
TGAAGAAATTCGAGTCGCCA+TGG 0.603715 4.1:-68487876 MS.gene067686:CDS
CGGTATCAGACCTGATCGCA+TGG 0.607640 4.1:-68487677 MS.gene067686:CDS
TCTCCAAAGCAAGCTTGCAG+AGG 0.618622 4.1:+68487626 None:intergenic
AGCTACCTTACCACCGACGA+TGG 0.624415 4.1:-68488050 MS.gene067686:CDS
GCGCTTTCTATGCTCAGCCA+TGG 0.631329 4.1:+68487859 None:intergenic
CAGCCTGAAAAGTTATAGCA+GGG 0.635889 4.1:+68487388 None:intergenic
ATAAACGCGCAATTGCTGGA+GGG 0.641638 4.1:+68487704 None:intergenic
TCATTGCGTATCGATTCACA+CGG 0.690513 4.1:+68488004 None:intergenic
GCACAAGACTCGACTACAGG+CGG 0.694421 4.1:+68487342 None:intergenic
ATTCTTAAGTCAACCCATGG+AGG 0.706999 4.1:-68487468 MS.gene067686:CDS
TCCAAAGCAAGCTTGCAGAG+GGG 0.721977 4.1:+68487628 None:intergenic
AGAGGGGAGTGAGTTCAAGG+CGG 0.771754 4.1:+68487644 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTATTCTTGTTAATTATTA+GGG - chr4.1:68487868-68487887 MS.gene067686:CDS 15.0%
!! TAGTATTCTTGTTAATTATT+AGG - chr4.1:68487867-68487886 MS.gene067686:CDS 15.0%
! AATTAAGTGAAACGCAAAAT+TGG + chr4.1:68487596-68487615 None:intergenic 25.0%
! ATAAATAGATGCTTACAGTT+AGG + chr4.1:68487556-68487575 None:intergenic 25.0%
AATACACAATATTACCTCCA+TGG + chr4.1:68487930-68487949 None:intergenic 30.0%
ATACACAATATTACCTCCAT+GGG + chr4.1:68487929-68487948 None:intergenic 30.0%
TGCGAACACATAAACATATA+AGG + chr4.1:68487449-68487468 None:intergenic 30.0%
!! TAATCTCTTGATTTTGATCC+TGG - chr4.1:68487633-68487652 MS.gene067686:CDS 30.0%
GATACGCAATGAAGAACTTA+TGG - chr4.1:68487388-68487407 MS.gene067686:CDS 35.0%
GCACTTTGTGTATAGGAATA+AGG - chr4.1:68487466-68487485 MS.gene067686:CDS 35.0%
TATTGAACCTACCTGATTCT+CGG + chr4.1:68487790-68487809 None:intergenic 35.0%
AAAAGTTATAGCAGGGCAGT+TGG + chr4.1:68487989-68488008 None:intergenic 40.0%
ATAGCATCAAATACCTGTCC+AGG + chr4.1:68487654-68487673 None:intergenic 40.0%
ATTCTTAAGTCAACCCATGG+AGG - chr4.1:68487913-68487932 MS.gene067686:CDS 40.0%
CAGCCTGAAAAGTTATAGCA+GGG + chr4.1:68487996-68488015 None:intergenic 40.0%
GAAATACAATGCCGAGAATC+AGG - chr4.1:68487776-68487795 MS.gene067686:intron 40.0%
GACATTCTTAAGTCAACCCA+TGG - chr4.1:68487910-68487929 MS.gene067686:CDS 40.0%
GATGCTTACAGTTAGGTTAC+AGG + chr4.1:68487549-68487568 None:intergenic 40.0%
TCAGCCTGAAAAGTTATAGC+AGG + chr4.1:68487997-68488016 None:intergenic 40.0%
TGTGTTCGCACTTTGTGTAT+AGG - chr4.1:68487459-68487478 MS.gene067686:CDS 40.0%
!! TCATTGCGTATCGATTCACA+CGG + chr4.1:68487380-68487399 None:intergenic 40.0%
!! TCTTGATTTTGATCCTGGAC+AGG - chr4.1:68487638-68487657 MS.gene067686:CDS 40.0%
ATAAACGCGCAATTGCTGGA+GGG + chr4.1:68487680-68487699 None:intergenic 45.0%
TACAATGCCGAGAATCAGGT+AGG - chr4.1:68487780-68487799 MS.gene067686:intron 45.0%
TGAAGAAATTCGAGTCGCCA+TGG - chr4.1:68487505-68487524 MS.gene067686:intron 45.0%
! AGGCTGAAGTCTTTTGCAGT+AGG - chr4.1:68488010-68488029 MS.gene067686:CDS 45.0%
! CTGCCCTGCTATAACTTTTC+AGG - chr4.1:68487990-68488009 MS.gene067686:CDS 45.0%
! GGCAGCATCTTTTGCTTGAA+AGG + chr4.1:68487959-68487978 None:intergenic 45.0%
ACCGACGATGGAGCCAAAAT+CGG - chr4.1:68487343-68487362 MS.gene067686:CDS 50.0%
AGATCATCGTCCATGCGATC+AGG + chr4.1:68487717-68487736 None:intergenic 50.0%
ATGGCACAAGACTCGACTAC+AGG + chr4.1:68488045-68488064 None:intergenic 50.0%
CATAAACGCGCAATTGCTGG+AGG + chr4.1:68487681-68487700 None:intergenic 50.0%
CCAGCAATTGCGCGTTTATG+CGG - chr4.1:68487681-68487700 MS.gene067686:CDS 50.0%
CTCCAAAGCAAGCTTGCAGA+GGG + chr4.1:68487757-68487776 None:intergenic 50.0%
GATGGAGCCAAAATCGGAAC+CGG - chr4.1:68487349-68487368 MS.gene067686:CDS 50.0%
GTTATAGCAGGGCAGTTGGA+AGG + chr4.1:68487985-68488004 None:intergenic 50.0%
TAAACGCGCAATTGCTGGAG+GGG + chr4.1:68487679-68487698 None:intergenic 50.0%
TCCAAAGCAAGCTTGCAGAG+GGG + chr4.1:68487756-68487775 None:intergenic 50.0%
TCTCCAAAGCAAGCTTGCAG+AGG + chr4.1:68487758-68487777 None:intergenic 50.0%
!!! TCCGATTTTGGCTCCATCGT+CGG + chr4.1:68487347-68487366 None:intergenic 50.0%
AGACTCGACTACAGGCGGTT+CGG + chr4.1:68488037-68488056 None:intergenic 55.0%
AGAGGGGAGTGAGTTCAAGG+CGG + chr4.1:68487740-68487759 None:intergenic 55.0%
AGCAGGGCAGTTGGAAGGAT+GGG + chr4.1:68487980-68487999 None:intergenic 55.0%
AGCTACCTTACCACCGACGA+TGG - chr4.1:68487331-68487350 MS.gene067686:CDS 55.0%
CCGCATAAACGCGCAATTGC+TGG + chr4.1:68487684-68487703 None:intergenic 55.0%
CGGTATCAGACCTGATCGCA+TGG - chr4.1:68487704-68487723 MS.gene067686:CDS 55.0%
GCAATTGCGCGTTTATGCGG+CGG - chr4.1:68487684-68487703 MS.gene067686:CDS 55.0%
GCACAAGACTCGACTACAGG+CGG + chr4.1:68488042-68488061 None:intergenic 55.0%
GCGCTTTCTATGCTCAGCCA+TGG + chr4.1:68487525-68487544 None:intergenic 55.0%
TAGCAGGGCAGTTGGAAGGA+TGG + chr4.1:68487981-68488000 None:intergenic 55.0%
TGCAGAGGGGAGTGAGTTCA+AGG + chr4.1:68487743-68487762 None:intergenic 55.0%
! ATCGATTCACACGGCGTGTC+CGG + chr4.1:68487371-68487390 None:intergenic 55.0%
! TCCCCTCTGCAAGCTTGCTT+TGG - chr4.1:68487752-68487771 MS.gene067686:intron 55.0%
!!! GATTTTGGCTCCATCGTCGG+TGG + chr4.1:68487344-68487363 None:intergenic 55.0%
TGGCTCCATCGTCGGTGGTA+AGG + chr4.1:68487339-68487358 None:intergenic 60.0%
! GGCGTGTCCGGTTCCGATTT+TGG + chr4.1:68487359-68487378 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 68487326 68488077 68487326 ID=MS.gene067686
chr4.1 mRNA 68487326 68488077 68487326 ID=MS.gene067686.t1;Parent=MS.gene067686
chr4.1 exon 68487844 68488077 68487844 ID=MS.gene067686.t1.exon1;Parent=MS.gene067686.t1
chr4.1 CDS 68487844 68488077 68487844 ID=cds.MS.gene067686.t1;Parent=MS.gene067686.t1
chr4.1 exon 68487606 68487743 68487606 ID=MS.gene067686.t1.exon2;Parent=MS.gene067686.t1
chr4.1 CDS 68487606 68487743 68487606 ID=cds.MS.gene067686.t1;Parent=MS.gene067686.t1
chr4.1 exon 68487326 68487514 68487326 ID=MS.gene067686.t1.exon3;Parent=MS.gene067686.t1
chr4.1 CDS 68487326 68487514 68487326 ID=cds.MS.gene067686.t1;Parent=MS.gene067686.t1
Gene Sequence

>MS.gene067686

ATGGAAGCTACCTTACCACCGACGATGGAGCCAAAATCGGAACCGGACACGCCGTGTGAATCGATACGCAATGAAGAACTTATGGAAAGTGACTTTTCTATCTACGACGATCTCGATTATCCTTATATGTTTATGTGTTCGCACTTTGTGTATAGGAATAAGGTTCAGATAAAAAAAGATGAAGAAATTCGAGTCGCCATGGCTGAGCATAGAAAGCGCTCCTGTAACCTAACTGTAAGCATCTATTTATCTATCTCATTTTGCTTTCCAATTTTGCGTTTCACTTAATTTGTTATTAAAATAATCATAATCTCTTGATTTTGATCCTGGACAGGTATTTGATGCTATTTCCCCTCCAGCAATTGCGCGTTTATGCGGCGGTATCAGACCTGATCGCATGGACGATGATCTCCGCCTTGAACTCACTCCCCTCTGCAAGCTTGCTTTGGAGAAATACAATGCCGAGAATCAGGTAGGTTCAATACTTTTTAGAGTAAACTTATGAATATAGTTTATTTATTCATTCATTGATCAACTAATATAGTATTCTTGTTAATTATTAGGGTGCAAATTTTGTGTTTGATGACATTCTTAAGTCAACCCATGGAGGTAATATTGTGTATTACATGACCTTTCAAGCAAAAGATGCTGCCCATCCTTCCAACTGCCCTGCTATAACTTTTCAGGCTGAAGTCTTTTGCAGTAGGTCCGAACCGCCTGTAGTCGAGTCTTGTGCCATGAAGCCTACCTAG
Protein sequence

>MS.gene067686.t1

MEATLPPTMEPKSEPDTPCESIRNEELMESDFSIYDDLDYPYMFMCSHFVYRNKVQIKKDEEIRVAMAEHRKRSCNLTVFDAISPPAIARLCGGIRPDRMDDDLRLELTPLCKLALEKYNAENQGANFVFDDILKSTHGGNIVYYMTFQAKDAAHPSNCPAITFQAEVFCSRSEPPVVESCAMKPT