AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene70424

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70424.t1 MTR_3g083150 49.576 236 94 9 1 235 1 212 4.77e-51 165
MS.gene70424.t1 MTR_3g083030 37.069 232 119 10 12 235 18 230 9.68e-34 121
MS.gene70424.t1 MTR_3g083100 52.448 143 47 7 105 235 41 174 7.81e-32 115
MS.gene70424.t1 MTR_3g083050 38.172 186 94 7 53 235 40 207 1.40e-30 112
MS.gene70424.t1 MTR_3g083080 40.984 183 92 7 53 234 38 205 5.62e-27 103
MS.gene70424.t1 MTR_3g082340 34.156 243 130 9 1 234 1 222 1.16e-21 89.7
MS.gene70424.t1 MTR_3g082420 35.931 231 123 11 12 234 8 221 1.42e-19 84.3
MS.gene70424.t1 MTR_3g080680 34.466 206 107 9 41 234 9 198 4.37e-14 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 49 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGTTCATGTTCACATTTC+AGG 0.183501 3.1:+66121794 None:intergenic
TGAACTCTCAAAACTTGCTT+TGG 0.306108 3.1:-66121330 MS.gene70424:CDS
ATCATCAATGTTAATAGGTC+TGG 0.313972 3.1:+66121370 None:intergenic
ATCGGAATTAAAAGTTGAAT+TGG 0.320482 3.1:-66121716 MS.gene70424:CDS
TCCGAGTCAGATTCTGATTC+CGG 0.357769 3.1:+66121769 None:intergenic
CACGACTTGACCTCAGGTTC+AGG 0.360780 3.1:+66121008 None:intergenic
GTATTTGCTAAGCGTGGAAT+CGG 0.382503 3.1:+66121410 None:intergenic
TGACGATCATCAATGTTAAT+AGG 0.383800 3.1:+66121365 None:intergenic
AAAGTACAATCGTGATAATC+AGG 0.389640 3.1:-66121306 MS.gene70424:intron
AAGGAACTCATACATGATAT+TGG 0.390277 3.1:+66121187 None:intergenic
ATCAGAATCTGACTCGGATT+CGG 0.398939 3.1:-66121764 MS.gene70424:CDS
TTGAGAGTTCAATGAAAAGT+TGG 0.400007 3.1:+66121342 None:intergenic
CTCGCAAATGTCGATGGAAT+TGG 0.404270 3.1:-66121851 None:intergenic
ATCTGACTCGGATTCGGAAT+CGG 0.428389 3.1:-66121758 MS.gene70424:CDS
CTCGGATTCGGAATCGGAAT+CGG 0.433731 3.1:-66121752 MS.gene70424:CDS
ATGTGAACATGAACTAGAAC+CGG 0.449384 3.1:-66121788 MS.gene70424:CDS
TCATCAATGTTAATAGGTCT+GGG 0.487473 3.1:+66121371 None:intergenic
ATGGAACACGACTTGACCTC+AGG 0.499797 3.1:+66121002 None:intergenic
TGCCGTGGATGCGTATTTGA+AGG 0.502058 3.1:-66121539 MS.gene70424:CDS
AAGTTGAATTGGATCTGTAT+TGG 0.503636 3.1:-66121705 MS.gene70424:CDS
CTCTCCTTCAGATCTTTCAC+TGG 0.520708 3.1:+66121670 None:intergenic
ATTGGATGCACCGTTGTACC+AGG 0.522683 3.1:-66121833 MS.gene70424:CDS
TATTTGCTAAGCGTGGAATC+GGG 0.526940 3.1:+66121411 None:intergenic
GTCTGAAGGATCAGCATCGC+CGG 0.527036 3.1:+66121076 None:intergenic
TTATTCTTGTACACAAATTG+CGG 0.527845 3.1:+66121595 None:intergenic
ATCGGAAGCAGAATCAGAAT+CGG 0.540258 3.1:-66121734 MS.gene70424:CDS
TACAAGGGTGGTATTCATAC+CGG 0.542469 3.1:+66121635 None:intergenic
CACGCAAAATGAAAAGTACA+AGG 0.542670 3.1:+66121619 None:intergenic
ACGTACACTTATGTTCTTAG+CGG 0.550563 3.1:+66121516 None:intergenic
TGGAATCGGGATAGCATCGA+AGG 0.568011 3.1:+66121424 None:intergenic
CCACATGTATTTGCTAAGCG+TGG 0.570185 3.1:+66121404 None:intergenic
CAGGCTTCGAATTCCAGACG+TGG 0.570772 3.1:+66121027 None:intergenic
GTTGGAGCAGGGCAGTCTGA+AGG 0.582271 3.1:+66121062 None:intergenic
TAAAGCCATGAGAAAAGAAG+AGG 0.588395 3.1:-66121575 MS.gene70424:CDS
AGGAGAGTGATTTCGCAAGC+CGG 0.596688 3.1:-66121654 MS.gene70424:CDS
TTGAATTGGATCTGTATTGG+TGG 0.596872 3.1:-66121702 MS.gene70424:CDS
AGCCATGAGAAAAGAAGAGG+AGG 0.601644 3.1:-66121572 MS.gene70424:CDS
GGCCTTCAAATACGCATCCA+CGG 0.611088 3.1:+66121537 None:intergenic
TGAGTTCCTTGAGCTTGTCA+AGG 0.613030 3.1:-66121174 MS.gene70424:CDS
GAATTCGAAGCCTGAACCTG+AGG 0.613285 3.1:-66121018 MS.gene70424:CDS
GATACCAGTGAAAGATCTGA+AGG 0.615773 3.1:-66121674 MS.gene70424:CDS
AGGCTTCGAATTCCAGACGT+GGG 0.643260 3.1:+66121028 None:intergenic
TGAATTGGATCTGTATTGGT+GGG 0.648989 3.1:-66121701 MS.gene70424:CDS
GGGTTGCCTTGACAAGCTCA+AGG 0.655608 3.1:+66121168 None:intergenic
CAAAATGAAAAGTACAAGGG+TGG 0.658227 3.1:+66121623 None:intergenic
ACCGGAATCAGAATCTGACT+CGG 0.664080 3.1:-66121770 MS.gene70424:CDS
GGAATCGGGATAGCATCGAA+GGG 0.678801 3.1:+66121425 None:intergenic
CCACGCTTAGCAAATACATG+TGG 0.691589 3.1:-66121404 MS.gene70424:CDS
ACGCAAAATGAAAAGTACAA+GGG 0.752956 3.1:+66121620 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTTTATCTTATTAATTTA+GGG - chr3.1:66121624-66121643 MS.gene70424:CDS 10.0%
!! TTTGTTTATCTTATTAATTT+AGG - chr3.1:66121623-66121642 MS.gene70424:CDS 10.0%
!! ATGTAGTAATTACCAAAAAT+AGG + chr3.1:66121705-66121724 None:intergenic 20.0%
!! TAATTACCAAAAATAGGAAT+AGG + chr3.1:66121699-66121718 None:intergenic 20.0%
! ATCGGAATTAAAAGTTGAAT+TGG - chr3.1:66121120-66121139 MS.gene70424:CDS 25.0%
! TTATTCTTGTACACAAATTG+CGG + chr3.1:66121244-66121263 None:intergenic 25.0%
!!! TGTTTTTGGTTTTGCATAAA+AGG + chr3.1:66121730-66121749 None:intergenic 25.0%
AAAGTACAATCGTGATAATC+AGG - chr3.1:66121530-66121549 MS.gene70424:CDS 30.0%
AAGGAACTCATACATGATAT+TGG + chr3.1:66121652-66121671 None:intergenic 30.0%
AAGTTGAATTGGATCTGTAT+TGG - chr3.1:66121131-66121150 MS.gene70424:CDS 30.0%
ATCATCAATGTTAATAGGTC+TGG + chr3.1:66121469-66121488 None:intergenic 30.0%
GAAAGGTTAAGATATATCAG+CGG + chr3.1:66121571-66121590 None:intergenic 30.0%
TAATGAAGCTGATGAATGAA+AGG + chr3.1:66121588-66121607 None:intergenic 30.0%
TCATCAATGTTAATAGGTCT+GGG + chr3.1:66121468-66121487 None:intergenic 30.0%
TGACGATCATCAATGTTAAT+AGG + chr3.1:66121474-66121493 None:intergenic 30.0%
TTGAGAGTTCAATGAAAAGT+TGG + chr3.1:66121497-66121516 None:intergenic 30.0%
! ACGCAAAATGAAAAGTACAA+GGG + chr3.1:66121219-66121238 None:intergenic 30.0%
AAAAATAGGAATAGGACGAC+GGG + chr3.1:66121691-66121710 None:intergenic 35.0%
ACGTACACTTATGTTCTTAG+CGG + chr3.1:66121323-66121342 None:intergenic 35.0%
ATGTGAACATGAACTAGAAC+CGG - chr3.1:66121048-66121067 MS.gene70424:CDS 35.0%
CAAAAATAGGAATAGGACGA+CGG + chr3.1:66121692-66121711 None:intergenic 35.0%
CTAGTTCATGTTCACATTTC+AGG + chr3.1:66121045-66121064 None:intergenic 35.0%
TAAAGCCATGAGAAAAGAAG+AGG - chr3.1:66121261-66121280 MS.gene70424:intron 35.0%
TCTGAAAAATTGTTGGAGCA+GGG + chr3.1:66121788-66121807 None:intergenic 35.0%
TTGAATTGGATCTGTATTGG+TGG - chr3.1:66121134-66121153 MS.gene70424:CDS 35.0%
! CAAAATGAAAAGTACAAGGG+TGG + chr3.1:66121216-66121235 None:intergenic 35.0%
! CACGCAAAATGAAAAGTACA+AGG + chr3.1:66121220-66121239 None:intergenic 35.0%
! TGAACTCTCAAAACTTGCTT+TGG - chr3.1:66121506-66121525 MS.gene70424:intron 35.0%
! TGAATTGGATCTGTATTGGT+GGG - chr3.1:66121135-66121154 MS.gene70424:CDS 35.0%
ACGTGGGTCTGAAAAATTGT+TGG + chr3.1:66121795-66121814 None:intergenic 40.0%
ATCGGAAGCAGAATCAGAAT+CGG - chr3.1:66121102-66121121 MS.gene70424:CDS 40.0%
CCAAAAACAGAAGATGCTAC+CGG - chr3.1:66121741-66121760 MS.gene70424:CDS 40.0%
GATACCAGTGAAAGATCTGA+AGG - chr3.1:66121162-66121181 MS.gene70424:CDS 40.0%
GTCTGAAAAATTGTTGGAGC+AGG + chr3.1:66121789-66121808 None:intergenic 40.0%
TACAAGGGTGGTATTCATAC+CGG + chr3.1:66121204-66121223 None:intergenic 40.0%
! ATCCTCCTCTTCTTTTCTCA+TGG + chr3.1:66121269-66121288 None:intergenic 40.0%
! CGTCGTCCTATTCCTATTTT+TGG - chr3.1:66121690-66121709 MS.gene70424:CDS 40.0%
! GTATTTGCTAAGCGTGGAAT+CGG + chr3.1:66121429-66121448 None:intergenic 40.0%
! TATTTGCTAAGCGTGGAATC+GGG + chr3.1:66121428-66121447 None:intergenic 40.0%
!! ATCAGAATCTGACTCGGATT+CGG - chr3.1:66121072-66121091 MS.gene70424:CDS 40.0%
ACCGGAATCAGAATCTGACT+CGG - chr3.1:66121066-66121085 MS.gene70424:CDS 45.0%
AGCCATGAGAAAAGAAGAGG+AGG - chr3.1:66121264-66121283 MS.gene70424:intron 45.0%
CCACGCTTAGCAAATACATG+TGG - chr3.1:66121432-66121451 MS.gene70424:intron 45.0%
CTCTCCTTCAGATCTTTCAC+TGG + chr3.1:66121169-66121188 None:intergenic 45.0%
TCCGAGTCAGATTCTGATTC+CGG + chr3.1:66121070-66121089 None:intergenic 45.0%
TGAGTTCCTTGAGCTTGTCA+AGG - chr3.1:66121662-66121681 MS.gene70424:CDS 45.0%
! ATACGCATCCACGGCATTTT+TGG + chr3.1:66121293-66121312 None:intergenic 45.0%
! CCACATGTATTTGCTAAGCG+TGG + chr3.1:66121435-66121454 None:intergenic 45.0%
! CCGGTAGCATCTTCTGTTTT+TGG + chr3.1:66121744-66121763 None:intergenic 45.0%
! TCGCAGTTTTCCTGGTACAA+CGG + chr3.1:66121016-66121035 None:intergenic 45.0%
!! ATCTGACTCGGATTCGGAAT+CGG - chr3.1:66121078-66121097 MS.gene70424:CDS 45.0%
!! CAATTTTTCAGACCCACGTC+TGG - chr3.1:66121796-66121815 MS.gene70424:CDS 45.0%
AGGAGAGTGATTTCGCAAGC+CGG - chr3.1:66121182-66121201 MS.gene70424:CDS 50.0%
AGGCTTCGAATTCCAGACGT+GGG + chr3.1:66121811-66121830 None:intergenic 50.0%
ATGGAACACGACTTGACCTC+AGG + chr3.1:66121837-66121856 None:intergenic 50.0%
ATTGGATGCACCGTTGTACC+AGG - chr3.1:66121003-66121022 MS.gene70424:CDS 50.0%
CTCGGATTCGGAATCGGAAT+CGG - chr3.1:66121084-66121103 MS.gene70424:CDS 50.0%
GAATTCGAAGCCTGAACCTG+AGG - chr3.1:66121818-66121837 MS.gene70424:CDS 50.0%
GGAGGATACCAAAAATGCCG+TGG - chr3.1:66121282-66121301 MS.gene70424:intron 50.0%
GGCCTTCAAATACGCATCCA+CGG + chr3.1:66121302-66121321 None:intergenic 50.0%
TGCCGTGGATGCGTATTTGA+AGG - chr3.1:66121297-66121316 MS.gene70424:intron 50.0%
! GGAATCGGGATAGCATCGAA+GGG + chr3.1:66121414-66121433 None:intergenic 50.0%
! GGCATTCTTCGCAGTTTTCC+TGG + chr3.1:66121024-66121043 None:intergenic 50.0%
! TGGAATCGGGATAGCATCGA+AGG + chr3.1:66121415-66121434 None:intergenic 50.0%
CACGACTTGACCTCAGGTTC+AGG + chr3.1:66121831-66121850 None:intergenic 55.0%
CAGGCTTCGAATTCCAGACG+TGG + chr3.1:66121812-66121831 None:intergenic 55.0%
GGGTTGCCTTGACAAGCTCA+AGG + chr3.1:66121671-66121690 None:intergenic 55.0%
GTCTGAAGGATCAGCATCGC+CGG + chr3.1:66121763-66121782 None:intergenic 55.0%
GTTGGAGCAGGGCAGTCTGA+AGG + chr3.1:66121777-66121796 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 66120992 66121866 66120992 ID=MS.gene70424
chr3.1 mRNA 66120992 66121866 66120992 ID=MS.gene70424.t1;Parent=MS.gene70424
chr3.1 exon 66121522 66121866 66121522 ID=MS.gene70424.t1.exon1;Parent=MS.gene70424.t1
chr3.1 CDS 66121522 66121866 66121522 ID=cds.MS.gene70424.t1;Parent=MS.gene70424.t1
chr3.1 exon 66121307 66121447 66121307 ID=MS.gene70424.t1.exon2;Parent=MS.gene70424.t1
chr3.1 CDS 66121307 66121447 66121307 ID=cds.MS.gene70424.t1;Parent=MS.gene70424.t1
chr3.1 exon 66120992 66121213 66120992 ID=MS.gene70424.t1.exon3;Parent=MS.gene70424.t1
chr3.1 CDS 66120992 66121213 66120992 ID=cds.MS.gene70424.t1;Parent=MS.gene70424.t1
Gene Sequence

>MS.gene70424

ATGTCGATGGAATTGGATGCACCGTTGTACCAGGAAAACTGCGAAGAATGCCTGAAATGTGAACATGAACTAGAACCGGAATCAGAATCTGACTCGGATTCGGAATCGGAATCGGAAGCAGAATCAGAATCGGAATTAAAAGTTGAATTGGATCTGTATTGGTGGGAATCGATACCAGTGAAAGATCTGAAGGAGAGTGATTTCGCAAGCCGGTATGAATACCACCCTTGTACTTTTCATTTTGCGTGTCCGCAATTTGTGTACAAGAATAAAGCCATGAGAAAAGAAGAGGAGGATACCAAAAATGCCGTGGATGCGTATTTGAAGGCCGCTAAGAACATAAGTGTACGTTTCTCTCTTTTAATTTTGCTTTTAATTTTGTGTTTAACTCTCTTAATCTGTTTCTGTACTCTGCACAGCCCTTCGATGCTATCCCGATTCCACGCTTAGCAAATACATGTGGCAATAACTTTCCCAGACCTATTAACATTGATGATCGTCACCAACTTTTCATTGAACTCTCAAAACTTGCTTTGGAAAAGTACAATCGTGATAATCAGGTTCTAAACTTCTTCACCGCTGATATATCTTAACCTTTCATTCATCAGCTTCATTATTCTTACTCTTAATTTTTGTTTATCTTATTAATTTAGGGTACCAATATCATGTATGAGTTCCTTGAGCTTGTCAAGGCAACCCGTCGTCCTATTCCTATTTTTGGTAATTACTACATTACCTTTTATGCAAAACCAAAAACAGAAGATGCTACCGGCGATGCTGATCCTTCAGACTGCCCTGCTCCAACAATTTTTCAGACCCACGTCTGGAATTCGAAGCCTGAACCTGAGGTCAAGTCGTGTTCCATTAAAACCTAA
Protein sequence

>MS.gene70424.t1

MSMELDAPLYQENCEECLKCEHELEPESESDSDSESESEAESESELKVELDLYWWESIPVKDLKESDFASRYEYHPCTFHFACPQFVYKNKAMRKEEEDTKNAVDAYLKAAKNISPFDAIPIPRLANTCGNNFPRPINIDDRHQLFIELSKLALEKYNRDNQGTNIMYEFLELVKATRRPIPIFGNYYITFYAKPKTEDATGDADPSDCPAPTIFQTHVWNSKPEPEVKSCSIKT