AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene044376

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044376.t1 MTR_3g083150 49.160 238 94 8 1 237 1 212 3.01e-52 168
MS.gene044376.t1 MTR_3g083030 37.662 231 121 8 12 237 18 230 9.11e-36 127
MS.gene044376.t1 MTR_3g083100 53.521 142 47 6 107 237 41 174 1.26e-35 124
MS.gene044376.t1 MTR_3g083050 38.919 185 94 6 55 237 40 207 1.57e-31 115
MS.gene044376.t1 MTR_3g083080 41.530 183 91 7 55 236 38 205 8.00e-30 110
MS.gene044376.t1 MTR_3g082340 35.102 245 127 9 1 236 1 222 2.77e-25 99.4
MS.gene044376.t1 MTR_3g082420 37.662 231 121 11 12 236 8 221 1.38e-23 94.7
MS.gene044376.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 3.3:-69914894 None:intergenic
GGGATACGTTCTTGGGTTAT+AGG 0.311188 3.3:-69915335 None:intergenic
ATCGGAATTAAAAGTTGAAT+TGG 0.320482 3.3:+69914978 MS.gene044376:CDS
TGAGAAGAGGGATACGTTCT+TGG 0.339655 3.3:-69915343 None:intergenic
TCCGAGTCAGATTCTGATTC+CGG 0.357769 3.3:-69914919 None:intergenic
CACGACTTGACCTCAGGTTC+AGG 0.360780 3.3:-69915686 None:intergenic
TGACCTCTCAAAACTTGCTT+TGG 0.360948 3.3:+69915367 MS.gene044376:CDS
AAAGTACAATTGTGATAATC+AGG 0.367307 3.3:+69915391 MS.gene044376:CDS
AAGGAACTCATACTTGATAT+TGG 0.375702 3.3:-69915510 None:intergenic
TTGAGAGGTCAGTGAGAAGA+GGG 0.380708 3.3:-69915355 None:intergenic
ATCAGAATCTGACTCGGATT+CGG 0.398939 3.3:+69914924 MS.gene044376:CDS
CTCGCAAATGTCGATGGAAT+TGG 0.404270 3.3:+69914837 None:intergenic
CTCGGATTCGGAATCGGAAT+CGG 0.425215 3.3:+69914936 MS.gene044376:CDS
GAGAAGAGGGATACGTTCTT+GGG 0.427166 3.3:-69915342 None:intergenic
ATCTGACTCGGATTCGGAAT+CGG 0.428389 3.3:+69914930 MS.gene044376:CDS
GATACCAGTGAAAGATTTGA+AGG 0.434630 3.3:+69915020 MS.gene044376:CDS
ATGTGAACATGAACTAGAAC+CGG 0.449384 3.3:+69914900 MS.gene044376:CDS
GCCTGAAAAGTTGTTGGAGC+AGG 0.450019 3.3:-69915644 None:intergenic
TTCGGAATCGGAATCGGAAT+CGG 0.451635 3.3:+69914942 MS.gene044376:CDS
TTGGGTTATAGGAAAGGGTC+TGG 0.453997 3.3:-69915324 None:intergenic
CTCTCCTTCAAATCTTTCAC+TGG 0.480515 3.3:-69915024 None:intergenic
CGTTCTTGGGTTATAGGAAA+GGG 0.490176 3.3:-69915329 None:intergenic
TTTGAGAGGTCAGTGAGAAG+AGG 0.497199 3.3:-69915356 None:intergenic
TGCCGTGGATGCGTATTTGA+AGG 0.502058 3.3:+69915155 MS.gene044376:CDS
AAGTTGAATTGGATCTGTAT+TGG 0.503636 3.3:+69914989 MS.gene044376:CDS
ATAGAACACGACTTGACCTC+AGG 0.516661 3.3:-69915692 None:intergenic
TGGGTTATAGGAAAGGGTCT+GGG 0.521892 3.3:-69915323 None:intergenic
ATTGGATGCACCGTTGTACC+AGG 0.522683 3.3:+69914855 MS.gene044376:CDS
TTATTCTTGTACACAAATTG+CGG 0.527845 3.3:-69915099 None:intergenic
ACGTGGGCCTGAAAAGTTGT+TGG 0.529875 3.3:-69915650 None:intergenic
ACGTTCTTGGGTTATAGGAA+AGG 0.530036 3.3:-69915330 None:intergenic
TACAAGGGTGGTCTTCATAC+CGG 0.532965 3.3:-69915059 None:intergenic
TGGAATCGAGATAGCATCAA+AGG 0.533400 3.3:-69915270 None:intergenic
ATCGGAAGCAGAATCAGAAT+CGG 0.540258 3.3:+69914960 MS.gene044376:CDS
CACGCAAAATGAAAAGTACA+AGG 0.542670 3.3:-69915075 None:intergenic
ACGTACACTTATGTTCTTAG+CGG 0.550563 3.3:-69915178 None:intergenic
CAGGCTTCGAATTCCAGACG+TGG 0.580636 3.3:-69915667 None:intergenic
CCTGAAAAGTTGTTGGAGCA+GGG 0.582135 3.3:-69915643 None:intergenic
GTTGGAGCAGGGCAGTCTGA+AGG 0.582271 3.3:-69915632 None:intergenic
AGGAGAGTGATTTCGCAAGC+CGG 0.584531 3.3:+69915040 MS.gene044376:CDS
TAAAGCCATGAGAAAAGAAG+AGG 0.588395 3.3:+69915119 MS.gene044376:CDS
TTGAATTGGATCTGTATTGG+TGG 0.596872 3.3:+69914992 MS.gene044376:CDS
CCACATGTATTTGCTGCGCG+TGG 0.600455 3.3:-69915290 None:intergenic
AGCCATGAGAAAAGAAGAGG+AGG 0.601644 3.3:+69915122 MS.gene044376:CDS
GGAATCGAGATAGCATCAAA+GGG 0.606574 3.3:-69915269 None:intergenic
GGCCTTCAAATACGCATCCA+CGG 0.611088 3.3:-69915157 None:intergenic
TGAGTTCCTTGAGCTTGTCA+AGG 0.613030 3.3:+69915523 MS.gene044376:CDS
GAATTCGAAGCCTGAACCTG+AGG 0.613285 3.3:+69915676 MS.gene044376:CDS
GCAGTCTGAAGGATCAGCAT+CGG 0.631805 3.3:-69915621 None:intergenic
AGGCTTCGAATTCCAGACGT+GGG 0.641698 3.3:-69915666 None:intergenic
TGAATTGGATCTGTATTGGT+GGG 0.648989 3.3:+69914993 MS.gene044376:CDS
GGGTTGCCTTGACAAGCTCA+AGG 0.655608 3.3:-69915529 None:intergenic
ACCGGAATCAGAATCTGACT+CGG 0.664080 3.3:+69914918 MS.gene044376:CDS
CAAAATGAAAAGTACAAGGG+TGG 0.680847 3.3:-69915071 None:intergenic
CCACGCGCAGCAAATACATG+TGG 0.685685 3.3:+69915290 MS.gene044376:CDS
ACGCAAAATGAAAAGTACAA+GGG 0.752956 3.3:-69915074 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTTTATCTTATTAATTTA+GGG + chr3.3:69915485-69915504 MS.gene044376:intron 10.0%
!! TTTGTTTATCTTATTAATTT+AGG + chr3.3:69915484-69915503 MS.gene044376:intron 10.0%
!! ATGTAGTAATTACCAAAAAT+AGG - chr3.3:69915566-69915585 None:intergenic 20.0%
!! TAATTACCAAAAATAGGAAT+AGG - chr3.3:69915560-69915579 None:intergenic 20.0%
! AAAGTACAATTGTGATAATC+AGG + chr3.3:69915391-69915410 MS.gene044376:CDS 25.0%
! ATCGGAATTAAAAGTTGAAT+TGG + chr3.3:69914978-69914997 MS.gene044376:CDS 25.0%
! GAAAGATTAAGATATATCAG+CGG - chr3.3:69915432-69915451 None:intergenic 25.0%
! TTATTCTTGTACACAAATTG+CGG - chr3.3:69915102-69915121 None:intergenic 25.0%
AAGGAACTCATACTTGATAT+TGG - chr3.3:69915513-69915532 None:intergenic 30.0%
AAGTTGAATTGGATCTGTAT+TGG + chr3.3:69914989-69915008 MS.gene044376:CDS 30.0%
! ACGCAAAATGAAAAGTACAA+GGG - chr3.3:69915077-69915096 None:intergenic 30.0%
!!! TGTTTTTGGTTTTGCATGAA+AGG - chr3.3:69915591-69915610 None:intergenic 30.0%
AAAAATAGGAATAGGACGAC+GGG - chr3.3:69915552-69915571 None:intergenic 35.0%
ACGTACACTTATGTTCTTAG+CGG - chr3.3:69915181-69915200 None:intergenic 35.0%
ATGTGAACATGAACTAGAAC+CGG + chr3.3:69914900-69914919 MS.gene044376:CDS 35.0%
CAAAAATAGGAATAGGACGA+CGG - chr3.3:69915553-69915572 None:intergenic 35.0%
CTAGTTCATGTTCACATTTC+AGG - chr3.3:69914897-69914916 None:intergenic 35.0%
GATACCAGTGAAAGATTTGA+AGG + chr3.3:69915020-69915039 MS.gene044376:CDS 35.0%
TAAAGCCATGAGAAAAGAAG+AGG + chr3.3:69915119-69915138 MS.gene044376:CDS 35.0%
TTGAATTGGATCTGTATTGG+TGG + chr3.3:69914992-69915011 MS.gene044376:CDS 35.0%
! CAAAATGAAAAGTACAAGGG+TGG - chr3.3:69915074-69915093 None:intergenic 35.0%
! CACGCAAAATGAAAAGTACA+AGG - chr3.3:69915078-69915097 None:intergenic 35.0%
! TGAATTGGATCTGTATTGGT+GGG + chr3.3:69914993-69915012 MS.gene044376:CDS 35.0%
!!! TTTCCAAAGCAAGTTTTGAG+AGG - chr3.3:69915373-69915392 None:intergenic 35.0%
ACGTTCTTGGGTTATAGGAA+AGG - chr3.3:69915333-69915352 None:intergenic 40.0%
ATCGGAAGCAGAATCAGAAT+CGG + chr3.3:69914960-69914979 MS.gene044376:CDS 40.0%
CGTTCTTGGGTTATAGGAAA+GGG - chr3.3:69915332-69915351 None:intergenic 40.0%
CTCTCCTTCAAATCTTTCAC+TGG - chr3.3:69915027-69915046 None:intergenic 40.0%
GGAATCGAGATAGCATCAAA+GGG - chr3.3:69915272-69915291 None:intergenic 40.0%
TGGAATCGAGATAGCATCAA+AGG - chr3.3:69915273-69915292 None:intergenic 40.0%
! ATCCTCCTCTTCTTTTCTCA+TGG - chr3.3:69915127-69915146 None:intergenic 40.0%
! CGTCGTCCTATTCCTATTTT+TGG + chr3.3:69915551-69915570 MS.gene044376:CDS 40.0%
! TCGGTAGCATCTTCTGTTTT+TGG - chr3.3:69915605-69915624 None:intergenic 40.0%
! TGACCTCTCAAAACTTGCTT+TGG + chr3.3:69915367-69915386 MS.gene044376:CDS 40.0%
!! ATCAGAATCTGACTCGGATT+CGG + chr3.3:69914924-69914943 MS.gene044376:CDS 40.0%
ACCGGAATCAGAATCTGACT+CGG + chr3.3:69914918-69914937 MS.gene044376:CDS 45.0%
AGCCATGAGAAAAGAAGAGG+AGG + chr3.3:69915122-69915141 MS.gene044376:CDS 45.0%
ATAGAACACGACTTGACCTC+AGG - chr3.3:69915695-69915714 None:intergenic 45.0%
CCTGAAAAGTTGTTGGAGCA+GGG - chr3.3:69915646-69915665 None:intergenic 45.0%
GAGAAGAGGGATACGTTCTT+GGG - chr3.3:69915345-69915364 None:intergenic 45.0%
GGGATACGTTCTTGGGTTAT+AGG - chr3.3:69915338-69915357 None:intergenic 45.0%
TACAAGGGTGGTCTTCATAC+CGG - chr3.3:69915062-69915081 None:intergenic 45.0%
TCCGAGTCAGATTCTGATTC+CGG - chr3.3:69914922-69914941 None:intergenic 45.0%
TGAGAAGAGGGATACGTTCT+TGG - chr3.3:69915346-69915365 None:intergenic 45.0%
TGAGTTCCTTGAGCTTGTCA+AGG + chr3.3:69915523-69915542 MS.gene044376:CDS 45.0%
TGGGTTATAGGAAAGGGTCT+GGG - chr3.3:69915326-69915345 None:intergenic 45.0%
TTCGGAATCGGAATCGGAAT+CGG + chr3.3:69914942-69914961 MS.gene044376:CDS 45.0%
TTGAGAGGTCAGTGAGAAGA+GGG - chr3.3:69915358-69915377 None:intergenic 45.0%
TTGGGTTATAGGAAAGGGTC+TGG - chr3.3:69915327-69915346 None:intergenic 45.0%
TTTGAGAGGTCAGTGAGAAG+AGG - chr3.3:69915359-69915378 None:intergenic 45.0%
! ATACGCATCCACGGCATTTT+TGG - chr3.3:69915151-69915170 None:intergenic 45.0%
! TCGCAGTTTTCCTGGTACAA+CGG - chr3.3:69914868-69914887 None:intergenic 45.0%
!! ATCTGACTCGGATTCGGAAT+CGG + chr3.3:69914930-69914949 MS.gene044376:CDS 45.0%
ACGTGGGCCTGAAAAGTTGT+TGG - chr3.3:69915653-69915672 None:intergenic 50.0%
AGGAGAGTGATTTCGCAAGC+CGG + chr3.3:69915040-69915059 MS.gene044376:CDS 50.0%
AGGCTTCGAATTCCAGACGT+GGG - chr3.3:69915669-69915688 None:intergenic 50.0%
ATTGGATGCACCGTTGTACC+AGG + chr3.3:69914855-69914874 MS.gene044376:CDS 50.0%
CTCGGATTCGGAATCGGAAT+CGG + chr3.3:69914936-69914955 MS.gene044376:CDS 50.0%
GAATTCGAAGCCTGAACCTG+AGG + chr3.3:69915676-69915695 MS.gene044376:CDS 50.0%
GCAGTCTGAAGGATCAGCAT+CGG - chr3.3:69915624-69915643 None:intergenic 50.0%
GCCTGAAAAGTTGTTGGAGC+AGG - chr3.3:69915647-69915666 None:intergenic 50.0%
GGAGGATACCAAAAATGCCG+TGG + chr3.3:69915140-69915159 MS.gene044376:CDS 50.0%
GGCCTTCAAATACGCATCCA+CGG - chr3.3:69915160-69915179 None:intergenic 50.0%
TGCCGTGGATGCGTATTTGA+AGG + chr3.3:69915155-69915174 MS.gene044376:CDS 50.0%
! CCCTGCTCCAACAACTTTTC+AGG + chr3.3:69915643-69915662 MS.gene044376:CDS 50.0%
! GGCATTCTTCGCAGTTTTCC+TGG - chr3.3:69914876-69914895 None:intergenic 50.0%
CACGACTTGACCTCAGGTTC+AGG - chr3.3:69915689-69915708 None:intergenic 55.0%
CAGGCTTCGAATTCCAGACG+TGG - chr3.3:69915670-69915689 None:intergenic 55.0%
CCACGCGCAGCAAATACATG+TGG + chr3.3:69915290-69915309 MS.gene044376:CDS 55.0%
GGGTTGCCTTGACAAGCTCA+AGG - chr3.3:69915532-69915551 None:intergenic 55.0%
! CCACATGTATTTGCTGCGCG+TGG - chr3.3:69915293-69915312 None:intergenic 55.0%
!! CAACTTTTCAGGCCCACGTC+TGG + chr3.3:69915654-69915673 MS.gene044376:CDS 55.0%
GTTGGAGCAGGGCAGTCTGA+AGG - chr3.3:69915635-69915654 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 69914844 69915724 69914844 ID=MS.gene044376
chr3.3 mRNA 69914844 69915724 69914844 ID=MS.gene044376.t1;Parent=MS.gene044376
chr3.3 exon 69914844 69915194 69914844 ID=MS.gene044376.t1.exon1;Parent=MS.gene044376.t1
chr3.3 CDS 69914844 69915194 69914844 ID=cds.MS.gene044376.t1;Parent=MS.gene044376.t1
chr3.3 exon 69915269 69915412 69915269 ID=MS.gene044376.t1.exon2;Parent=MS.gene044376.t1
chr3.3 CDS 69915269 69915412 69915269 ID=cds.MS.gene044376.t1;Parent=MS.gene044376.t1
chr3.3 exon 69915506 69915724 69915506 ID=MS.gene044376.t1.exon3;Parent=MS.gene044376.t1
chr3.3 CDS 69915506 69915724 69915506 ID=cds.MS.gene044376.t1;Parent=MS.gene044376.t1
Gene Sequence

>MS.gene044376

ATGTCGATGGAATTGGATGCACCGTTGTACCAGGAAAACTGCGAAGAATGCCTGAAATGTGAACATGAACTAGAACCGGAATCAGAATCTGACTCGGATTCGGAATCGGAATCGGAATCGGAAGCAGAATCAGAATCGGAATTAAAAGTTGAATTGGATCTGTATTGGTGGGAATCGATACCAGTGAAAGATTTGAAGGAGAGTGATTTCGCAAGCCGGTATGAAGACCACCCTTGTACTTTTCATTTTGCGTGTCCGCAATTTGTGTACAAGAATAAAGCCATGAGAAAAGAAGAGGAGGATACCAAAAATGCCGTGGATGCGTATTTGAAGGCCGCTAAGAACATAAGTGTACGTTTCTCTCTTTTAATTTTGCTTTTAATTTTGTGTTTAACTCTCTTAATCTGTTTCTGTACTCTGCACAGCCCTTTGATGCTATCTCGATTCCACGCGCAGCAAATACATGTGGCAATAACTTTCCCAGACCCTTTCCTATAACCCAAGAACGTATCCCTCTTCTCACTGACCTCTCAAAACTTGCTTTGGAAAAGTACAATTGTGATAATCAGGTTCTAAACTACTTCACCGCTGATATATCTTAATCTTTCATTCATCAGCTTCATTATTCTTTCTCTTAATTTTTGTTTATCTTATTAATTTAGGGTACCAATATCAAGTATGAGTTCCTTGAGCTTGTCAAGGCAACCCGTCGTCCTATTCCTATTTTTGGTAATTACTACATTACCTTTCATGCAAAACCAAAAACAGAAGATGCTACCGATGCTGATCCTTCAGACTGCCCTGCTCCAACAACTTTTCAGGCCCACGTCTGGAATTCGAAGCCTGAACCTGAGGTCAAGTCGTGTTCTATTAAAACCTAA
Protein sequence

>MS.gene044376.t1

MSMELDAPLYQENCEECLKCEHELEPESESDSDSESESESEAESESELKVELDLYWWESIPVKDLKESDFASRYEDHPCTFHFACPQFVYKNKAMRKEEEDTKNAVDAYLKAAKNISPFDAISIPRAANTCGNNFPRPFPITQERIPLLTDLSKLALEKYNCDNQGTNIKYEFLELVKATRRPIPIFGNYYITFHAKPKTEDATDADPSDCPAPTTFQAHVWNSKPEPEVKSCSIKT