AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene77468

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77468.t1 MTR_3g083150 49.791 239 93 8 1 239 1 212 1.58e-53 172
MS.gene77468.t1 MTR_3g083030 37.339 233 121 8 12 239 18 230 6.86e-36 127
MS.gene77468.t1 MTR_3g083100 53.521 142 47 6 109 239 41 174 1.19e-35 125
MS.gene77468.t1 MTR_3g083050 38.919 185 94 6 57 239 40 207 1.48e-31 115
MS.gene77468.t1 MTR_3g083080 41.530 183 91 7 57 238 38 205 7.12e-30 110
MS.gene77468.t1 MTR_3g082340 34.818 247 127 9 1 238 1 222 1.95e-24 97.4
MS.gene77468.t1 MTR_3g082420 37.229 231 124 10 12 238 8 221 7.72e-24 95.5
MS.gene77468.t1 MTR_3g080680 35.610 205 108 9 45 239 9 199 1.01e-16 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 57 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 3.2:-71981081 None:intergenic
GGGATACGTTCTTGGGTTAT+AGG 0.311188 3.2:-71981528 None:intergenic
ATCGGAATTAAAAGTTGAAT+TGG 0.320482 3.2:+71981171 MS.gene77468:CDS
TGAGAAGAGGGATACGTTCT+TGG 0.339655 3.2:-71981536 None:intergenic
TCCGAGTCAGATTCTGATTC+CGG 0.343923 3.2:-71981106 None:intergenic
CACGACTTGACCTCAGGTTC+AGG 0.360780 3.2:-71981879 None:intergenic
TGACCTCTCAAAACTTGCTT+TGG 0.360948 3.2:+71981560 MS.gene77468:CDS
AAAGTACAATTGTGATAATC+AGG 0.367307 3.2:+71981584 MS.gene77468:CDS
AAGGAACTCATACTTGATAT+TGG 0.375702 3.2:-71981703 None:intergenic
TTGAGAGGTCAGTGAGAAGA+GGG 0.380708 3.2:-71981548 None:intergenic
CTCGCAAATGTCGATGGAAT+TGG 0.404270 3.2:+71981024 None:intergenic
GAGAAGAGGGATACGTTCTT+GGG 0.427166 3.2:-71981535 None:intergenic
ATCTGACTCGGAATCGGAAT+CGG 0.428389 3.2:+71981117 MS.gene77468:CDS
CTCGGAATCGGAATCGGAAT+CGG 0.431066 3.2:+71981123 MS.gene77468:CDS
ATCGGAATCGGAATCGGAAT+CGG 0.432857 3.2:+71981129 MS.gene77468:CDS
GATACCAGTGAAAGATTTGA+AGG 0.434630 3.2:+71981213 MS.gene77468:CDS
ATCAGAATCTGACTCGGAAT+CGG 0.435994 3.2:+71981111 MS.gene77468:CDS
ATGTGAACATGAACTAGAAC+CGG 0.449384 3.2:+71981087 MS.gene77468:CDS
GCCTGAAAAGTTGTTGGAGC+AGG 0.450019 3.2:-71981837 None:intergenic
TTGGGTTATAGGAAAGGGTC+TGG 0.453997 3.2:-71981517 None:intergenic
ATCGGAATCGGAATCGGAAT+CGG 0.468133 3.2:+71981135 MS.gene77468:CDS
CTCTCCTTCAAATCTTTCAC+TGG 0.480515 3.2:-71981217 None:intergenic
CGTTCTTGGGTTATAGGAAA+GGG 0.490176 3.2:-71981522 None:intergenic
TTTGAGAGGTCAGTGAGAAG+AGG 0.497199 3.2:-71981549 None:intergenic
TGCCGTGGATGCGTATTTGA+AGG 0.502058 3.2:+71981348 MS.gene77468:CDS
AAGTTGAATTGGATCTGTAT+TGG 0.503636 3.2:+71981182 MS.gene77468:CDS
ATAGAACACGACTTGACCTC+AGG 0.516661 3.2:-71981885 None:intergenic
TGGGTTATAGGAAAGGGTCT+GGG 0.521892 3.2:-71981516 None:intergenic
ATTGGATGCACCGTTGTACC+AGG 0.522683 3.2:+71981042 MS.gene77468:CDS
TTATTCTTGTACACAAATTG+CGG 0.527845 3.2:-71981292 None:intergenic
ACGTGGGCCTGAAAAGTTGT+TGG 0.529875 3.2:-71981843 None:intergenic
ACGTTCTTGGGTTATAGGAA+AGG 0.530036 3.2:-71981523 None:intergenic
TACAAGGGTGGTCTTCATAC+CGG 0.532965 3.2:-71981252 None:intergenic
TGGAATCGAGATAGCATCAA+AGG 0.533400 3.2:-71981463 None:intergenic
ATCGGAAGCAGAATCAGAAT+CGG 0.540258 3.2:+71981153 MS.gene77468:CDS
CACGCAAAATGAAAAGTACA+AGG 0.542670 3.2:-71981268 None:intergenic
ACGTACACTTATGTTCTTAG+CGG 0.550563 3.2:-71981371 None:intergenic
CAGGCTTCGAATTCCAGACG+TGG 0.580636 3.2:-71981860 None:intergenic
CCTGAAAAGTTGTTGGAGCA+GGG 0.582135 3.2:-71981836 None:intergenic
GTTGGAGCAGGGCAGTCTGA+AGG 0.582271 3.2:-71981825 None:intergenic
AGGAGAGTGATTTCGCAAGC+CGG 0.584531 3.2:+71981233 MS.gene77468:CDS
TAAAGCCATGAGAAAAGAAG+AGG 0.588395 3.2:+71981312 MS.gene77468:CDS
TTGAATTGGATCTGTATTGG+TGG 0.596872 3.2:+71981185 MS.gene77468:CDS
CCACATGTATTTGCTGCGCG+TGG 0.600455 3.2:-71981483 None:intergenic
AGCCATGAGAAAAGAAGAGG+AGG 0.601644 3.2:+71981315 MS.gene77468:CDS
GGAATCGAGATAGCATCAAA+GGG 0.606574 3.2:-71981462 None:intergenic
GGCCTTCAAATACGCATCCA+CGG 0.611088 3.2:-71981350 None:intergenic
TGAGTTCCTTGAGCTTGTCA+AGG 0.613030 3.2:+71981716 MS.gene77468:CDS
GAATTCGAAGCCTGAACCTG+AGG 0.613285 3.2:+71981869 MS.gene77468:CDS
GCAGTCTGAAGGATCAGCAT+CGG 0.631805 3.2:-71981814 None:intergenic
AGGCTTCGAATTCCAGACGT+GGG 0.641698 3.2:-71981859 None:intergenic
TGAATTGGATCTGTATTGGT+GGG 0.648989 3.2:+71981186 MS.gene77468:CDS
GGGTTGCCTTGACAAGCTCA+AGG 0.655608 3.2:-71981722 None:intergenic
ACCGGAATCAGAATCTGACT+CGG 0.664080 3.2:+71981105 MS.gene77468:CDS
CAAAATGAAAAGTACAAGGG+TGG 0.680847 3.2:-71981264 None:intergenic
CCACGCGCAGCAAATACATG+TGG 0.685685 3.2:+71981483 MS.gene77468:CDS
ACGCAAAATGAAAAGTACAA+GGG 0.752956 3.2:-71981267 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTTTATCTTATTAATTTA+GGG + chr3.2:71981678-71981697 MS.gene77468:intron 10.0%
!! TTTGTTTATCTTATTAATTT+AGG + chr3.2:71981677-71981696 MS.gene77468:intron 10.0%
!! ATGTAGTAATTACCAAAAAT+AGG - chr3.2:71981759-71981778 None:intergenic 20.0%
!! TAATTACCAAAAATAGGAAT+AGG - chr3.2:71981753-71981772 None:intergenic 20.0%
! AAAGTACAATTGTGATAATC+AGG + chr3.2:71981584-71981603 MS.gene77468:CDS 25.0%
! ATCGGAATTAAAAGTTGAAT+TGG + chr3.2:71981171-71981190 MS.gene77468:CDS 25.0%
! GAAAGATTAAGATATATCAG+CGG - chr3.2:71981625-71981644 None:intergenic 25.0%
! TTATTCTTGTACACAAATTG+CGG - chr3.2:71981295-71981314 None:intergenic 25.0%
AAGGAACTCATACTTGATAT+TGG - chr3.2:71981706-71981725 None:intergenic 30.0%
AAGTTGAATTGGATCTGTAT+TGG + chr3.2:71981182-71981201 MS.gene77468:CDS 30.0%
! ACGCAAAATGAAAAGTACAA+GGG - chr3.2:71981270-71981289 None:intergenic 30.0%
!!! TGTTTTTGGTTTTGCATGAA+AGG - chr3.2:71981784-71981803 None:intergenic 30.0%
AAAAATAGGAATAGGACGAC+GGG - chr3.2:71981745-71981764 None:intergenic 35.0%
ACGTACACTTATGTTCTTAG+CGG - chr3.2:71981374-71981393 None:intergenic 35.0%
ATGTGAACATGAACTAGAAC+CGG + chr3.2:71981087-71981106 MS.gene77468:CDS 35.0%
CAAAAATAGGAATAGGACGA+CGG - chr3.2:71981746-71981765 None:intergenic 35.0%
CTAGTTCATGTTCACATTTC+AGG - chr3.2:71981084-71981103 None:intergenic 35.0%
GATACCAGTGAAAGATTTGA+AGG + chr3.2:71981213-71981232 MS.gene77468:CDS 35.0%
TAAAGCCATGAGAAAAGAAG+AGG + chr3.2:71981312-71981331 MS.gene77468:CDS 35.0%
TTGAATTGGATCTGTATTGG+TGG + chr3.2:71981185-71981204 MS.gene77468:CDS 35.0%
! CAAAATGAAAAGTACAAGGG+TGG - chr3.2:71981267-71981286 None:intergenic 35.0%
! CACGCAAAATGAAAAGTACA+AGG - chr3.2:71981271-71981290 None:intergenic 35.0%
! TGAATTGGATCTGTATTGGT+GGG + chr3.2:71981186-71981205 MS.gene77468:CDS 35.0%
!!! TTTCCAAAGCAAGTTTTGAG+AGG - chr3.2:71981566-71981585 None:intergenic 35.0%
ACGTTCTTGGGTTATAGGAA+AGG - chr3.2:71981526-71981545 None:intergenic 40.0%
ATCGGAAGCAGAATCAGAAT+CGG + chr3.2:71981153-71981172 MS.gene77468:CDS 40.0%
CGTTCTTGGGTTATAGGAAA+GGG - chr3.2:71981525-71981544 None:intergenic 40.0%
CTCTCCTTCAAATCTTTCAC+TGG - chr3.2:71981220-71981239 None:intergenic 40.0%
GGAATCGAGATAGCATCAAA+GGG - chr3.2:71981465-71981484 None:intergenic 40.0%
TGGAATCGAGATAGCATCAA+AGG - chr3.2:71981466-71981485 None:intergenic 40.0%
! ATCCTCCTCTTCTTTTCTCA+TGG - chr3.2:71981320-71981339 None:intergenic 40.0%
! CGTCGTCCTATTCCTATTTT+TGG + chr3.2:71981744-71981763 MS.gene77468:CDS 40.0%
! TCGGTAGCATCTTCTGTTTT+TGG - chr3.2:71981798-71981817 None:intergenic 40.0%
! TGACCTCTCAAAACTTGCTT+TGG + chr3.2:71981560-71981579 MS.gene77468:CDS 40.0%
!! ATCAGAATCTGACTCGGAAT+CGG + chr3.2:71981111-71981130 MS.gene77468:CDS 40.0%
ACCGGAATCAGAATCTGACT+CGG + chr3.2:71981105-71981124 MS.gene77468:CDS 45.0%
AGCCATGAGAAAAGAAGAGG+AGG + chr3.2:71981315-71981334 MS.gene77468:CDS 45.0%
ATAGAACACGACTTGACCTC+AGG - chr3.2:71981888-71981907 None:intergenic 45.0%
ATCGGAATCGGAATCGGAAT+CGG + chr3.2:71981129-71981148 MS.gene77468:CDS 45.0%
CCTGAAAAGTTGTTGGAGCA+GGG - chr3.2:71981839-71981858 None:intergenic 45.0%
GAGAAGAGGGATACGTTCTT+GGG - chr3.2:71981538-71981557 None:intergenic 45.0%
GGGATACGTTCTTGGGTTAT+AGG - chr3.2:71981531-71981550 None:intergenic 45.0%
TACAAGGGTGGTCTTCATAC+CGG - chr3.2:71981255-71981274 None:intergenic 45.0%
TCCGAGTCAGATTCTGATTC+CGG - chr3.2:71981109-71981128 None:intergenic 45.0%
TGAGAAGAGGGATACGTTCT+TGG - chr3.2:71981539-71981558 None:intergenic 45.0%
TGAGTTCCTTGAGCTTGTCA+AGG + chr3.2:71981716-71981735 MS.gene77468:CDS 45.0%
TGGGTTATAGGAAAGGGTCT+GGG - chr3.2:71981519-71981538 None:intergenic 45.0%
TTGAGAGGTCAGTGAGAAGA+GGG - chr3.2:71981551-71981570 None:intergenic 45.0%
TTGGGTTATAGGAAAGGGTC+TGG - chr3.2:71981520-71981539 None:intergenic 45.0%
TTTGAGAGGTCAGTGAGAAG+AGG - chr3.2:71981552-71981571 None:intergenic 45.0%
! ATACGCATCCACGGCATTTT+TGG - chr3.2:71981344-71981363 None:intergenic 45.0%
! TCGCAGTTTTCCTGGTACAA+CGG - chr3.2:71981055-71981074 None:intergenic 45.0%
!! ATCTGACTCGGAATCGGAAT+CGG + chr3.2:71981117-71981136 MS.gene77468:CDS 45.0%
ACGTGGGCCTGAAAAGTTGT+TGG - chr3.2:71981846-71981865 None:intergenic 50.0%
AGGAGAGTGATTTCGCAAGC+CGG + chr3.2:71981233-71981252 MS.gene77468:CDS 50.0%
AGGCTTCGAATTCCAGACGT+GGG - chr3.2:71981862-71981881 None:intergenic 50.0%
ATTGGATGCACCGTTGTACC+AGG + chr3.2:71981042-71981061 MS.gene77468:CDS 50.0%
CTCGGAATCGGAATCGGAAT+CGG + chr3.2:71981123-71981142 MS.gene77468:CDS 50.0%
GAATTCGAAGCCTGAACCTG+AGG + chr3.2:71981869-71981888 MS.gene77468:CDS 50.0%
GCAGTCTGAAGGATCAGCAT+CGG - chr3.2:71981817-71981836 None:intergenic 50.0%
GCCTGAAAAGTTGTTGGAGC+AGG - chr3.2:71981840-71981859 None:intergenic 50.0%
GGAGGATACCAAAAATGCCG+TGG + chr3.2:71981333-71981352 MS.gene77468:CDS 50.0%
GGCCTTCAAATACGCATCCA+CGG - chr3.2:71981353-71981372 None:intergenic 50.0%
TGCCGTGGATGCGTATTTGA+AGG + chr3.2:71981348-71981367 MS.gene77468:CDS 50.0%
! CCCTGCTCCAACAACTTTTC+AGG + chr3.2:71981836-71981855 MS.gene77468:CDS 50.0%
! GGCATTCTTCGCAGTTTTCC+TGG - chr3.2:71981063-71981082 None:intergenic 50.0%
CACGACTTGACCTCAGGTTC+AGG - chr3.2:71981882-71981901 None:intergenic 55.0%
CAGGCTTCGAATTCCAGACG+TGG - chr3.2:71981863-71981882 None:intergenic 55.0%
CCACGCGCAGCAAATACATG+TGG + chr3.2:71981483-71981502 MS.gene77468:CDS 55.0%
GGGTTGCCTTGACAAGCTCA+AGG - chr3.2:71981725-71981744 None:intergenic 55.0%
! CCACATGTATTTGCTGCGCG+TGG - chr3.2:71981486-71981505 None:intergenic 55.0%
!! CAACTTTTCAGGCCCACGTC+TGG + chr3.2:71981847-71981866 MS.gene77468:CDS 55.0%
GTTGGAGCAGGGCAGTCTGA+AGG - chr3.2:71981828-71981847 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 71981031 71981917 71981031 ID=MS.gene77468
chr3.2 mRNA 71981031 71981917 71981031 ID=MS.gene77468.t1;Parent=MS.gene77468
chr3.2 exon 71981031 71981387 71981031 ID=MS.gene77468.t1.exon1;Parent=MS.gene77468.t1
chr3.2 CDS 71981031 71981387 71981031 ID=cds.MS.gene77468.t1;Parent=MS.gene77468.t1
chr3.2 exon 71981462 71981605 71981462 ID=MS.gene77468.t1.exon2;Parent=MS.gene77468.t1
chr3.2 CDS 71981462 71981605 71981462 ID=cds.MS.gene77468.t1;Parent=MS.gene77468.t1
chr3.2 exon 71981699 71981917 71981699 ID=MS.gene77468.t1.exon3;Parent=MS.gene77468.t1
chr3.2 CDS 71981699 71981917 71981699 ID=cds.MS.gene77468.t1;Parent=MS.gene77468.t1
Gene Sequence

>MS.gene77468

ATGTCGATGGAATTGGATGCACCGTTGTACCAGGAAAACTGCGAAGAATGCCTGAAATGTGAACATGAACTAGAACCGGAATCAGAATCTGACTCGGAATCGGAATCGGAATCGGAATCGGAATCGGAAGCAGAATCAGAATCGGAATTAAAAGTTGAATTGGATCTGTATTGGTGGGAATCGATACCAGTGAAAGATTTGAAGGAGAGTGATTTCGCAAGCCGGTATGAAGACCACCCTTGTACTTTTCATTTTGCGTGTCCGCAATTTGTGTACAAGAATAAAGCCATGAGAAAAGAAGAGGAGGATACCAAAAATGCCGTGGATGCGTATTTGAAGGCCGCTAAGAACATAAGTGTACGTTTCTCTCTTTTAATTTTGCTTTTAATTTTGTGTTTAACTCTCTTAATCTGTTTCTGTACTCTGCACAGCCCTTTGATGCTATCTCGATTCCACGCGCAGCAAATACATGTGGCAATAACTTTCCCAGACCCTTTCCTATAACCCAAGAACGTATCCCTCTTCTCACTGACCTCTCAAAACTTGCTTTGGAAAAGTACAATTGTGATAATCAGGTTCTAAACTACTTCACCGCTGATATATCTTAATCTTTCATTCATCAGCTTCATTATTCTTTCTCTTAATTTTTGTTTATCTTATTAATTTAGGGTACCAATATCAAGTATGAGTTCCTTGAGCTTGTCAAGGCAACCCGTCGTCCTATTCCTATTTTTGGTAATTACTACATTACCTTTCATGCAAAACCAAAAACAGAAGATGCTACCGATGCTGATCCTTCAGACTGCCCTGCTCCAACAACTTTTCAGGCCCACGTCTGGAATTCGAAGCCTGAACCTGAGGTCAAGTCGTGTTCTATTAAAACCTAA
Protein sequence

>MS.gene77468.t1

MSMELDAPLYQENCEECLKCEHELEPESESDSESESESESESEAESESELKVELDLYWWESIPVKDLKESDFASRYEDHPCTFHFACPQFVYKNKAMRKEEEDTKNAVDAYLKAAKNISPFDAISIPRAANTCGNNFPRPFPITQERIPLLTDLSKLALEKYNCDNQGTNIKYEFLELVKATRRPIPIFGNYYITFHAKPKTEDATDADPSDCPAPTTFQAHVWNSKPEPEVKSCSIKT