AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71528

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71528.t1 MTR_3g083150 49.160 238 94 8 1 237 1 212 3.01e-52 168
MS.gene71528.t1 MTR_3g083030 37.662 231 121 8 12 237 18 230 9.11e-36 127
MS.gene71528.t1 MTR_3g083100 53.521 142 47 6 107 237 41 174 1.26e-35 124
MS.gene71528.t1 MTR_3g083050 38.919 185 94 6 55 237 40 207 1.57e-31 115
MS.gene71528.t1 MTR_3g083080 41.530 183 91 7 55 236 38 205 8.00e-30 110
MS.gene71528.t1 MTR_3g082340 35.102 245 127 9 1 236 1 222 2.77e-25 99.4
MS.gene71528.t1 MTR_3g082420 37.662 231 121 11 12 236 8 221 1.38e-23 94.7
MS.gene71528.t1 MTR_3g080680 35.610 205 108 9 43 237 9 199 8.31e-17 76.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 56 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGTTCATGTTCACATTTC+AGG 0.183501 3.4:-78263595 None:intergenic
GGGATACGTTCTTGGGTTAT+AGG 0.311188 3.4:-78264036 None:intergenic
ATCGGAATTAAAAGTTGAAT+TGG 0.320482 3.4:+78263679 MS.gene71528:CDS
TGAGAAGAGGGATACGTTCT+TGG 0.339655 3.4:-78264044 None:intergenic
TCCGAGTCAGATTCTGATTC+CGG 0.357769 3.4:-78263620 None:intergenic
CACGACTTGACCTCAGGTTC+AGG 0.360780 3.4:-78264387 None:intergenic
TGACCTCTCAAAACTTGCTT+TGG 0.360948 3.4:+78264068 MS.gene71528:CDS
AAAGTACAATTGTGATAATC+AGG 0.367307 3.4:+78264092 MS.gene71528:CDS
AAGGAACTCATACTTGATAT+TGG 0.375702 3.4:-78264211 None:intergenic
TTGAGAGGTCAGTGAGAAGA+GGG 0.380708 3.4:-78264056 None:intergenic
ATCAGAATCTGACTCGGATT+CGG 0.398939 3.4:+78263625 MS.gene71528:CDS
CTCGCAAATGTCGATGGAAT+TGG 0.404270 3.4:+78263538 None:intergenic
CTCGGATTCGGAATCGGAAT+CGG 0.425215 3.4:+78263637 MS.gene71528:CDS
GAGAAGAGGGATACGTTCTT+GGG 0.427166 3.4:-78264043 None:intergenic
ATCTGACTCGGATTCGGAAT+CGG 0.428389 3.4:+78263631 MS.gene71528:CDS
GATACCAGTGAAAGATTTGA+AGG 0.434630 3.4:+78263721 MS.gene71528:CDS
ATGTGAACATGAACTAGAAC+CGG 0.449384 3.4:+78263601 MS.gene71528:CDS
GCCTGAAAAGTTGTTGGAGC+AGG 0.450019 3.4:-78264345 None:intergenic
TTCGGAATCGGAATCGGAAT+CGG 0.451635 3.4:+78263643 MS.gene71528:CDS
TTGGGTTATAGGAAAGGGTC+TGG 0.453997 3.4:-78264025 None:intergenic
CTCTCCTTCAAATCTTTCAC+TGG 0.480515 3.4:-78263725 None:intergenic
CGTTCTTGGGTTATAGGAAA+GGG 0.490176 3.4:-78264030 None:intergenic
TTTGAGAGGTCAGTGAGAAG+AGG 0.497199 3.4:-78264057 None:intergenic
TGCCGTGGATGCGTATTTGA+AGG 0.502058 3.4:+78263856 MS.gene71528:CDS
AAGTTGAATTGGATCTGTAT+TGG 0.503636 3.4:+78263690 MS.gene71528:CDS
ATAGAACACGACTTGACCTC+AGG 0.516661 3.4:-78264393 None:intergenic
TGGGTTATAGGAAAGGGTCT+GGG 0.521892 3.4:-78264024 None:intergenic
ATTGGATGCACCGTTGTACC+AGG 0.522683 3.4:+78263556 MS.gene71528:CDS
TTATTCTTGTACACAAATTG+CGG 0.527845 3.4:-78263800 None:intergenic
ACGTGGGCCTGAAAAGTTGT+TGG 0.529875 3.4:-78264351 None:intergenic
ACGTTCTTGGGTTATAGGAA+AGG 0.530036 3.4:-78264031 None:intergenic
TACAAGGGTGGTCTTCATAC+CGG 0.532965 3.4:-78263760 None:intergenic
TGGAATCGAGATAGCATCAA+AGG 0.533400 3.4:-78263971 None:intergenic
ATCGGAAGCAGAATCAGAAT+CGG 0.540258 3.4:+78263661 MS.gene71528:CDS
CACGCAAAATGAAAAGTACA+AGG 0.542670 3.4:-78263776 None:intergenic
ACGTACACTTATGTTCTTAG+CGG 0.550563 3.4:-78263879 None:intergenic
CAGGCTTCGAATTCCAGACG+TGG 0.580636 3.4:-78264368 None:intergenic
CCTGAAAAGTTGTTGGAGCA+GGG 0.582135 3.4:-78264344 None:intergenic
GTTGGAGCAGGGCAGTCTGA+AGG 0.582271 3.4:-78264333 None:intergenic
AGGAGAGTGATTTCGCAAGC+CGG 0.584531 3.4:+78263741 MS.gene71528:CDS
TAAAGCCATGAGAAAAGAAG+AGG 0.588395 3.4:+78263820 MS.gene71528:CDS
TTGAATTGGATCTGTATTGG+TGG 0.596872 3.4:+78263693 MS.gene71528:CDS
CCACATGTATTTGCTGCGCG+TGG 0.600455 3.4:-78263991 None:intergenic
AGCCATGAGAAAAGAAGAGG+AGG 0.601644 3.4:+78263823 MS.gene71528:CDS
GGAATCGAGATAGCATCAAA+GGG 0.606574 3.4:-78263970 None:intergenic
GGCCTTCAAATACGCATCCA+CGG 0.611088 3.4:-78263858 None:intergenic
TGAGTTCCTTGAGCTTGTCA+AGG 0.613030 3.4:+78264224 MS.gene71528:CDS
GAATTCGAAGCCTGAACCTG+AGG 0.613285 3.4:+78264377 MS.gene71528:CDS
GCAGTCTGAAGGATCAGCAT+CGG 0.631805 3.4:-78264322 None:intergenic
AGGCTTCGAATTCCAGACGT+GGG 0.641698 3.4:-78264367 None:intergenic
TGAATTGGATCTGTATTGGT+GGG 0.648989 3.4:+78263694 MS.gene71528:CDS
GGGTTGCCTTGACAAGCTCA+AGG 0.655608 3.4:-78264230 None:intergenic
ACCGGAATCAGAATCTGACT+CGG 0.664080 3.4:+78263619 MS.gene71528:CDS
CAAAATGAAAAGTACAAGGG+TGG 0.680847 3.4:-78263772 None:intergenic
CCACGCGCAGCAAATACATG+TGG 0.685685 3.4:+78263991 MS.gene71528:CDS
ACGCAAAATGAAAAGTACAA+GGG 0.752956 3.4:-78263775 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTTTATCTTATTAATTTA+GGG + chr3.4:78264186-78264205 MS.gene71528:intron 10.0%
!! TTTGTTTATCTTATTAATTT+AGG + chr3.4:78264185-78264204 MS.gene71528:intron 10.0%
!! ATGTAGTAATTACCAAAAAT+AGG - chr3.4:78264267-78264286 None:intergenic 20.0%
!! TAATTACCAAAAATAGGAAT+AGG - chr3.4:78264261-78264280 None:intergenic 20.0%
! AAAGTACAATTGTGATAATC+AGG + chr3.4:78264092-78264111 MS.gene71528:CDS 25.0%
! ATCGGAATTAAAAGTTGAAT+TGG + chr3.4:78263679-78263698 MS.gene71528:CDS 25.0%
! GAAAGATTAAGATATATCAG+CGG - chr3.4:78264133-78264152 None:intergenic 25.0%
! TTATTCTTGTACACAAATTG+CGG - chr3.4:78263803-78263822 None:intergenic 25.0%
AAGGAACTCATACTTGATAT+TGG - chr3.4:78264214-78264233 None:intergenic 30.0%
AAGTTGAATTGGATCTGTAT+TGG + chr3.4:78263690-78263709 MS.gene71528:CDS 30.0%
! ACGCAAAATGAAAAGTACAA+GGG - chr3.4:78263778-78263797 None:intergenic 30.0%
!!! TGTTTTTGGTTTTGCATGAA+AGG - chr3.4:78264292-78264311 None:intergenic 30.0%
AAAAATAGGAATAGGACGAC+GGG - chr3.4:78264253-78264272 None:intergenic 35.0%
ACGTACACTTATGTTCTTAG+CGG - chr3.4:78263882-78263901 None:intergenic 35.0%
ATGTGAACATGAACTAGAAC+CGG + chr3.4:78263601-78263620 MS.gene71528:CDS 35.0%
CAAAAATAGGAATAGGACGA+CGG - chr3.4:78264254-78264273 None:intergenic 35.0%
CTAGTTCATGTTCACATTTC+AGG - chr3.4:78263598-78263617 None:intergenic 35.0%
GATACCAGTGAAAGATTTGA+AGG + chr3.4:78263721-78263740 MS.gene71528:CDS 35.0%
TAAAGCCATGAGAAAAGAAG+AGG + chr3.4:78263820-78263839 MS.gene71528:CDS 35.0%
TTGAATTGGATCTGTATTGG+TGG + chr3.4:78263693-78263712 MS.gene71528:CDS 35.0%
! CAAAATGAAAAGTACAAGGG+TGG - chr3.4:78263775-78263794 None:intergenic 35.0%
! CACGCAAAATGAAAAGTACA+AGG - chr3.4:78263779-78263798 None:intergenic 35.0%
! TGAATTGGATCTGTATTGGT+GGG + chr3.4:78263694-78263713 MS.gene71528:CDS 35.0%
!!! TTTCCAAAGCAAGTTTTGAG+AGG - chr3.4:78264074-78264093 None:intergenic 35.0%
ACGTTCTTGGGTTATAGGAA+AGG - chr3.4:78264034-78264053 None:intergenic 40.0%
ATCGGAAGCAGAATCAGAAT+CGG + chr3.4:78263661-78263680 MS.gene71528:CDS 40.0%
CGTTCTTGGGTTATAGGAAA+GGG - chr3.4:78264033-78264052 None:intergenic 40.0%
CTCTCCTTCAAATCTTTCAC+TGG - chr3.4:78263728-78263747 None:intergenic 40.0%
GGAATCGAGATAGCATCAAA+GGG - chr3.4:78263973-78263992 None:intergenic 40.0%
TGGAATCGAGATAGCATCAA+AGG - chr3.4:78263974-78263993 None:intergenic 40.0%
! ATCCTCCTCTTCTTTTCTCA+TGG - chr3.4:78263828-78263847 None:intergenic 40.0%
! CGTCGTCCTATTCCTATTTT+TGG + chr3.4:78264252-78264271 MS.gene71528:CDS 40.0%
! TCGGTAGCATCTTCTGTTTT+TGG - chr3.4:78264306-78264325 None:intergenic 40.0%
! TGACCTCTCAAAACTTGCTT+TGG + chr3.4:78264068-78264087 MS.gene71528:CDS 40.0%
!! ATCAGAATCTGACTCGGATT+CGG + chr3.4:78263625-78263644 MS.gene71528:CDS 40.0%
ACCGGAATCAGAATCTGACT+CGG + chr3.4:78263619-78263638 MS.gene71528:CDS 45.0%
AGCCATGAGAAAAGAAGAGG+AGG + chr3.4:78263823-78263842 MS.gene71528:CDS 45.0%
ATAGAACACGACTTGACCTC+AGG - chr3.4:78264396-78264415 None:intergenic 45.0%
CCTGAAAAGTTGTTGGAGCA+GGG - chr3.4:78264347-78264366 None:intergenic 45.0%
GAGAAGAGGGATACGTTCTT+GGG - chr3.4:78264046-78264065 None:intergenic 45.0%
GGGATACGTTCTTGGGTTAT+AGG - chr3.4:78264039-78264058 None:intergenic 45.0%
TACAAGGGTGGTCTTCATAC+CGG - chr3.4:78263763-78263782 None:intergenic 45.0%
TCCGAGTCAGATTCTGATTC+CGG - chr3.4:78263623-78263642 None:intergenic 45.0%
TGAGAAGAGGGATACGTTCT+TGG - chr3.4:78264047-78264066 None:intergenic 45.0%
TGAGTTCCTTGAGCTTGTCA+AGG + chr3.4:78264224-78264243 MS.gene71528:CDS 45.0%
TGGGTTATAGGAAAGGGTCT+GGG - chr3.4:78264027-78264046 None:intergenic 45.0%
TTCGGAATCGGAATCGGAAT+CGG + chr3.4:78263643-78263662 MS.gene71528:CDS 45.0%
TTGAGAGGTCAGTGAGAAGA+GGG - chr3.4:78264059-78264078 None:intergenic 45.0%
TTGGGTTATAGGAAAGGGTC+TGG - chr3.4:78264028-78264047 None:intergenic 45.0%
TTTGAGAGGTCAGTGAGAAG+AGG - chr3.4:78264060-78264079 None:intergenic 45.0%
! ATACGCATCCACGGCATTTT+TGG - chr3.4:78263852-78263871 None:intergenic 45.0%
! TCGCAGTTTTCCTGGTACAA+CGG - chr3.4:78263569-78263588 None:intergenic 45.0%
!! ATCTGACTCGGATTCGGAAT+CGG + chr3.4:78263631-78263650 MS.gene71528:CDS 45.0%
ACGTGGGCCTGAAAAGTTGT+TGG - chr3.4:78264354-78264373 None:intergenic 50.0%
AGGAGAGTGATTTCGCAAGC+CGG + chr3.4:78263741-78263760 MS.gene71528:CDS 50.0%
AGGCTTCGAATTCCAGACGT+GGG - chr3.4:78264370-78264389 None:intergenic 50.0%
ATTGGATGCACCGTTGTACC+AGG + chr3.4:78263556-78263575 MS.gene71528:CDS 50.0%
CTCGGATTCGGAATCGGAAT+CGG + chr3.4:78263637-78263656 MS.gene71528:CDS 50.0%
GAATTCGAAGCCTGAACCTG+AGG + chr3.4:78264377-78264396 MS.gene71528:CDS 50.0%
GCAGTCTGAAGGATCAGCAT+CGG - chr3.4:78264325-78264344 None:intergenic 50.0%
GCCTGAAAAGTTGTTGGAGC+AGG - chr3.4:78264348-78264367 None:intergenic 50.0%
GGAGGATACCAAAAATGCCG+TGG + chr3.4:78263841-78263860 MS.gene71528:CDS 50.0%
GGCCTTCAAATACGCATCCA+CGG - chr3.4:78263861-78263880 None:intergenic 50.0%
TGCCGTGGATGCGTATTTGA+AGG + chr3.4:78263856-78263875 MS.gene71528:CDS 50.0%
! CCCTGCTCCAACAACTTTTC+AGG + chr3.4:78264344-78264363 MS.gene71528:CDS 50.0%
! GGCATTCTTCGCAGTTTTCC+TGG - chr3.4:78263577-78263596 None:intergenic 50.0%
CACGACTTGACCTCAGGTTC+AGG - chr3.4:78264390-78264409 None:intergenic 55.0%
CAGGCTTCGAATTCCAGACG+TGG - chr3.4:78264371-78264390 None:intergenic 55.0%
CCACGCGCAGCAAATACATG+TGG + chr3.4:78263991-78264010 MS.gene71528:CDS 55.0%
GGGTTGCCTTGACAAGCTCA+AGG - chr3.4:78264233-78264252 None:intergenic 55.0%
! CCACATGTATTTGCTGCGCG+TGG - chr3.4:78263994-78264013 None:intergenic 55.0%
!! CAACTTTTCAGGCCCACGTC+TGG + chr3.4:78264355-78264374 MS.gene71528:CDS 55.0%
GTTGGAGCAGGGCAGTCTGA+AGG - chr3.4:78264336-78264355 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 78263545 78264425 78263545 ID=MS.gene71528
chr3.4 mRNA 78263545 78264425 78263545 ID=MS.gene71528.t1;Parent=MS.gene71528
chr3.4 exon 78263545 78263895 78263545 ID=MS.gene71528.t1.exon1;Parent=MS.gene71528.t1
chr3.4 CDS 78263545 78263895 78263545 ID=cds.MS.gene71528.t1;Parent=MS.gene71528.t1
chr3.4 exon 78263970 78264113 78263970 ID=MS.gene71528.t1.exon2;Parent=MS.gene71528.t1
chr3.4 CDS 78263970 78264113 78263970 ID=cds.MS.gene71528.t1;Parent=MS.gene71528.t1
chr3.4 exon 78264207 78264425 78264207 ID=MS.gene71528.t1.exon3;Parent=MS.gene71528.t1
chr3.4 CDS 78264207 78264425 78264207 ID=cds.MS.gene71528.t1;Parent=MS.gene71528.t1
Gene Sequence

>MS.gene71528

ATGTCGATGGAATTGGATGCACCGTTGTACCAGGAAAACTGCGAAGAATGCCTGAAATGTGAACATGAACTAGAACCGGAATCAGAATCTGACTCGGATTCGGAATCGGAATCGGAATCGGAAGCAGAATCAGAATCGGAATTAAAAGTTGAATTGGATCTGTATTGGTGGGAATCGATACCAGTGAAAGATTTGAAGGAGAGTGATTTCGCAAGCCGGTATGAAGACCACCCTTGTACTTTTCATTTTGCGTGTCCGCAATTTGTGTACAAGAATAAAGCCATGAGAAAAGAAGAGGAGGATACCAAAAATGCCGTGGATGCGTATTTGAAGGCCGCTAAGAACATAAGTGTACGTTTCTCTCTTTTAATTTTGCTTTTAATTTTGTGTTTAACTCTCTTAATCTGTTTCTGTACTCTGCACAGCCCTTTGATGCTATCTCGATTCCACGCGCAGCAAATACATGTGGCAATAACTTTCCCAGACCCTTTCCTATAACCCAAGAACGTATCCCTCTTCTCACTGACCTCTCAAAACTTGCTTTGGAAAAGTACAATTGTGATAATCAGGTTCTAAACTACTTCACCGCTGATATATCTTAATCTTTCATTCATCAGCTTCATTATTCTTTCTCTTAATTTTTGTTTATCTTATTAATTTAGGGTACCAATATCAAGTATGAGTTCCTTGAGCTTGTCAAGGCAACCCGTCGTCCTATTCCTATTTTTGGTAATTACTACATTACCTTTCATGCAAAACCAAAAACAGAAGATGCTACCGATGCTGATCCTTCAGACTGCCCTGCTCCAACAACTTTTCAGGCCCACGTCTGGAATTCGAAGCCTGAACCTGAGGTCAAGTCGTGTTCTATTAAAACCTAA
Protein sequence

>MS.gene71528.t1

MSMELDAPLYQENCEECLKCEHELEPESESDSDSESESESEAESESELKVELDLYWWESIPVKDLKESDFASRYEDHPCTFHFACPQFVYKNKAMRKEEEDTKNAVDAYLKAAKNISPFDAISIPRAANTCGNNFPRPFPITQERIPLLTDLSKLALEKYNCDNQGTNIKYEFLELVKATRRPIPIFGNYYITFHAKPKTEDATDADPSDCPAPTTFQAHVWNSKPEPEVKSCSIKT