AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052084

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052084.t1 MTR_2g097580 99.170 241 2 0 1 241 96 336 1.20e-178 494
MS.gene052084.t1 MTR_3g058630 55.336 253 99 5 1 241 99 349 2.31e-98 291
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052084.t1 AT1G55910 58.233 249 80 3 1 241 93 325 5.71e-103 301
MS.gene052084.t1 AT5G59520 60.324 247 91 4 1 241 108 353 4.63e-93 277
MS.gene052084.t1 AT2G04032 26.415 265 162 11 2 240 107 364 1.23e-11 63.9

Find 52 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCCTGCTGTTGTTATTAA+TGG 0.165665 2.2:-4896589 None:intergenic
GGCATCGCCGTTGGAATTTC+AGG 0.231489 2.2:+4895825 MS.gene052084:CDS
GCCTTCATGTTGGCTTGTTC+TGG 0.231810 2.2:+4895579 MS.gene052084:CDS
TAATTGCAGTTGTCATGATT+TGG 0.312381 2.2:+4896848 MS.gene052084:CDS
CCCTTCTGTTGTTGCGTCGA+TGG 0.338990 2.2:-4896662 None:intergenic
GTTTCGACACTCCATGGTTT+AGG 0.340853 2.2:+4896797 MS.gene052084:CDS
AGCCCAATTGGCGTAGGAAT+TGG 0.343250 2.2:+4896634 MS.gene052084:CDS
ATTCCAATTCCTACGCCAAT+TGG 0.349639 2.2:-4896637 None:intergenic
AATTGCAGTTGTCATGATTT+GGG 0.398612 2.2:+4896849 MS.gene052084:CDS
ATCAATCATTTAATCTCTAA+AGG 0.405525 2.2:+4896751 MS.gene052084:CDS
TTCATGAAGACTACTAATCT+TGG 0.413670 2.2:+4895753 MS.gene052084:CDS
TTTGCTATCTCTAGCCCAAT+TGG 0.420772 2.2:+4896622 MS.gene052084:CDS
CAAGCCAACATGAAGGCAAA+AGG 0.443986 2.2:-4895573 None:intergenic
TTGGATGTATGCAATATCAA+TGG 0.451469 2.2:+4896696 MS.gene052084:CDS
AAGAAGCATGGAGGAATTTG+TGG 0.466479 2.2:+4896494 MS.gene052084:CDS
TTCCAATTCCTACGCCAATT+GGG 0.476127 2.2:-4896636 None:intergenic
GAGAACACCTCAAGAAGAAG+AGG 0.481872 2.2:+4895692 MS.gene052084:CDS
GATATTTGCTGCAATAGCAA+TGG 0.517861 2.2:+4896534 MS.gene052084:CDS
ATATTTGCTGCAATAGCAAT+GGG 0.519706 2.2:+4896535 MS.gene052084:CDS
TGGATGTATGCAATATCAAT+GGG 0.524253 2.2:+4896697 MS.gene052084:CDS
GTCGTTCCCTCTTCTTCTTG+AGG 0.530005 2.2:-4895699 None:intergenic
AAATTAATGATCAGGTACTA+AGG 0.530087 2.2:+4896471 MS.gene052084:intron
CAGAAGGGAGAACAGCGGAT+TGG 0.535719 2.2:+4896677 MS.gene052084:CDS
AACCATGTTTGGTGATTGTG+TGG 0.549871 2.2:+4895611 MS.gene052084:CDS
GCCATCGACGCAACAACAGA+AGG 0.551024 2.2:+4896661 MS.gene052084:CDS
GCTAAAGTTGAGGAACTTGA+AGG 0.551786 2.2:+4895666 MS.gene052084:CDS
GCTCTCATCCATCGCCAACT+CGG 0.559618 2.2:-4895721 None:intergenic
TAAACCATGGAGTGTCGAAA+CGG 0.560955 2.2:-4896795 None:intergenic
AAGCCAACATGAAGGCAAAA+GGG 0.565308 2.2:-4895572 None:intergenic
GGGAACGACCGAGTTGGCGA+TGG 0.565946 2.2:+4895713 MS.gene052084:CDS
CACCACACAATCACCAAACA+TGG 0.566132 2.2:-4895613 None:intergenic
AGACCATTAATAACAACAGC+AGG 0.566425 2.2:+4896586 MS.gene052084:CDS
CATGTTTGGTGATTGTGTGG+TGG 0.584077 2.2:+4895614 MS.gene052084:CDS
AGAGCCGTTTCGACACTCCA+TGG 0.586693 2.2:+4896791 MS.gene052084:CDS
TCCAGAACAAGCCAACATGA+AGG 0.595290 2.2:-4895580 None:intergenic
AAGTTGAGGAACTTGAAGGA+GGG 0.602436 2.2:+4895670 MS.gene052084:CDS
TGTAACAAGTAATAATCAGA+GGG 0.605818 2.2:+4895641 MS.gene052084:CDS
AGAAGAGGGAACGACCGAGT+TGG 0.611188 2.2:+4895707 MS.gene052084:CDS
AAAGTTGAGGAACTTGAAGG+AGG 0.613893 2.2:+4895669 MS.gene052084:CDS
ATGTAACAAGTAATAATCAG+AGG 0.621888 2.2:+4895640 MS.gene052084:CDS
AGAACACCTCAAGAAGAAGA+GGG 0.622606 2.2:+4895693 MS.gene052084:CDS
ATCTCTAGCCCAATTGGCGT+AGG 0.622666 2.2:+4896628 MS.gene052084:CDS
CAGGTACTAAGGAAGAAGCA+TGG 0.640699 2.2:+4896482 MS.gene052084:intron
CCATCGACGCAACAACAGAA+GGG 0.642467 2.2:+4896662 MS.gene052084:CDS
TCAGAGGGAAGCTAAAGTTG+AGG 0.644763 2.2:+4895656 MS.gene052084:CDS
TCGAAACGGCTCTTCCTCTG+CGG 0.648000 2.2:-4896781 None:intergenic
ATATCAATGGGTATTGCTTG+TGG 0.657971 2.2:+4896709 MS.gene052084:CDS
GAAATAACCTGAAATTCCAA+CGG 0.658581 2.2:-4895832 None:intergenic
CTAAAGGCTTCAAACCGCAG+AGG 0.686420 2.2:+4896767 MS.gene052084:CDS
ACAGCAAGAAACCTAAACCA+TGG 0.706576 2.2:-4896808 None:intergenic
AACAACAGAAGGGAGAACAG+CGG 0.747170 2.2:+4896672 MS.gene052084:CDS
GTACTAAGGAAGAAGCATGG+AGG 0.765390 2.2:+4896485 MS.gene052084:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATATACAAATTAATGATC+AGG + chr2.2:4896463-4896482 MS.gene052084:intron 15.0%
!!! ATTTTAACTATTCGTATATA+TGG - chr2.2:4896088-4896107 None:intergenic 15.0%
!!! TTTTAACTATTCGTATATAT+GGG - chr2.2:4896087-4896106 None:intergenic 15.0%
!! ATCAATCATTTAATCTCTAA+AGG + chr2.2:4896751-4896770 MS.gene052084:CDS 20.0%
!!! ATATGCATTTTCATATTGAA+AGG - chr2.2:4896386-4896405 None:intergenic 20.0%
!!! ATTTTAAATAGCATCAAAGT+GGG + chr2.2:4896187-4896206 MS.gene052084:intron 20.0%
!!! TATGCATTTTCATATTGAAA+GGG - chr2.2:4896385-4896404 None:intergenic 20.0%
!!! TATTTTAAATAGCATCAAAG+TGG + chr2.2:4896186-4896205 MS.gene052084:intron 20.0%
!!! TGATAGTCTTTTTCTTTTTT+CGG + chr2.2:4895883-4895902 MS.gene052084:intron 20.0%
!!! TGTATATATGATGTGTTTTA+GGG + chr2.2:4896214-4896233 MS.gene052084:intron 20.0%
! AAATTAATGATCAGGTACTA+AGG + chr2.2:4896471-4896490 MS.gene052084:intron 25.0%
! AAGAAAAAGACTATCAAGAA+AGG - chr2.2:4895879-4895898 None:intergenic 25.0%
! ATGTAACAAGTAATAATCAG+AGG + chr2.2:4895640-4895659 MS.gene052084:CDS 25.0%
! GAAAATTTGATCTTCAACAT+TGG - chr2.2:4895936-4895955 None:intergenic 25.0%
! TGTAACAAGTAATAATCAGA+GGG + chr2.2:4895641-4895660 MS.gene052084:CDS 25.0%
!! CTGTATATATGATGTGTTTT+AGG + chr2.2:4896213-4896232 MS.gene052084:intron 25.0%
!! GATAGTCTTTTTCTTTTTTC+GGG + chr2.2:4895884-4895903 MS.gene052084:intron 25.0%
!!! GTTGTTATTAATGGTCTTTT+TGG - chr2.2:4896583-4896602 None:intergenic 25.0%
AATTGCAGTTGTCATGATTT+GGG + chr2.2:4896849-4896868 MS.gene052084:CDS 30.0%
AGAAAGGATGAAATAAACGA+TGG - chr2.2:4895863-4895882 None:intergenic 30.0%
GAAATAACCTGAAATTCCAA+CGG - chr2.2:4895835-4895854 None:intergenic 30.0%
TAATTGCAGTTGTCATGATT+TGG + chr2.2:4896848-4896867 MS.gene052084:CDS 30.0%
TGACTGTTATGTTACTGTAT+TGG + chr2.2:4896237-4896256 MS.gene052084:intron 30.0%
TGGATGTATGCAATATCAAT+GGG + chr2.2:4896697-4896716 MS.gene052084:CDS 30.0%
TTATGCATTCTTCTCTTTCT+TGG + chr2.2:4896131-4896150 MS.gene052084:intron 30.0%
TTCATGAAGACTACTAATCT+TGG + chr2.2:4895753-4895772 MS.gene052084:CDS 30.0%
TTGGATGTATGCAATATCAA+TGG + chr2.2:4896696-4896715 MS.gene052084:CDS 30.0%
! AAGTTTGGCATGTGATTTTT+AGG + chr2.2:4896337-4896356 MS.gene052084:intron 30.0%
! AGTGTTAAAGTATCAAACCT+AGG + chr2.2:4895907-4895926 MS.gene052084:intron 30.0%
! ATATTTGCTGCAATAGCAAT+GGG + chr2.2:4896535-4896554 MS.gene052084:CDS 30.0%
! CATTTTCATATTGAAAGGGA+TGG - chr2.2:4896381-4896400 None:intergenic 30.0%
! GGATATCTTTTAACCATGTT+TGG + chr2.2:4895600-4895619 MS.gene052084:CDS 30.0%
! TATCCTGCTGTTGTTATTAA+TGG - chr2.2:4896592-4896611 None:intergenic 30.0%
! TGTTTTCATTCGGTTTTTGA+AGG + chr2.2:4895804-4895823 MS.gene052084:CDS 30.0%
!!! TCTTGCACTTTGTTTTCATT+CGG + chr2.2:4895794-4895813 MS.gene052084:CDS 30.0%
AGACCATTAATAACAACAGC+AGG + chr2.2:4896586-4896605 MS.gene052084:CDS 35.0%
AGACTACCAAGAAATGATGT+TGG - chr2.2:4895980-4895999 None:intergenic 35.0%
TGAAGACCAACATCATTTCT+TGG + chr2.2:4895971-4895990 MS.gene052084:intron 35.0%
! ATATCAATGGGTATTGCTTG+TGG + chr2.2:4896709-4896728 MS.gene052084:CDS 35.0%
! GATATTTGCTGCAATAGCAA+TGG + chr2.2:4896534-4896553 MS.gene052084:CDS 35.0%
!! ATTGAAAGGGATGGACTATA+TGG - chr2.2:4896372-4896391 None:intergenic 35.0%
AAAGTTGAGGAACTTGAAGG+AGG + chr2.2:4895669-4895688 MS.gene052084:CDS 40.0%
AAGCCAACATGAAGGCAAAA+GGG - chr2.2:4895575-4895594 None:intergenic 40.0%
AAGTTGAGGAACTTGAAGGA+GGG + chr2.2:4895670-4895689 MS.gene052084:CDS 40.0%
ACAGCAAGAAACCTAAACCA+TGG - chr2.2:4896811-4896830 None:intergenic 40.0%
AGAACACCTCAAGAAGAAGA+GGG + chr2.2:4895693-4895712 MS.gene052084:CDS 40.0%
ATTCCAATTCCTACGCCAAT+TGG - chr2.2:4896640-4896659 None:intergenic 40.0%
CAAAGTCACATCTCACAAGT+AGG - chr2.2:4896311-4896330 None:intergenic 40.0%
GCTAAAGTTGAGGAACTTGA+AGG + chr2.2:4895666-4895685 MS.gene052084:CDS 40.0%
GTGACTTTGCATCTCAAGTT+TGG + chr2.2:4896273-4896292 MS.gene052084:intron 40.0%
TTCCAATTCCTACGCCAATT+GGG - chr2.2:4896639-4896658 None:intergenic 40.0%
! AACCATGTTTGGTGATTGTG+TGG + chr2.2:4895611-4895630 MS.gene052084:CDS 40.0%
! AAGAAGCATGGAGGAATTTG+TGG + chr2.2:4896494-4896513 MS.gene052084:CDS 40.0%
! ATCTTCAACATTGGTGACCT+AGG - chr2.2:4895927-4895946 None:intergenic 40.0%
! GGCAAAAGGGTAAGTTTTCT+TGG - chr2.2:4895562-4895581 None:intergenic 40.0%
! TTACCCTTTTGCCTTCATGT+TGG + chr2.2:4895569-4895588 MS.gene052084:CDS 40.0%
! TTTGCTATCTCTAGCCCAAT+TGG + chr2.2:4896622-4896641 MS.gene052084:CDS 40.0%
!! AGGTTTCTTGCTGTGCTTTT+TGG + chr2.2:4896817-4896836 MS.gene052084:CDS 40.0%
!! TAAACCATGGAGTGTCGAAA+CGG - chr2.2:4896798-4896817 None:intergenic 40.0%
AACAACAGAAGGGAGAACAG+CGG + chr2.2:4896672-4896691 MS.gene052084:CDS 45.0%
CAAGCCAACATGAAGGCAAA+AGG - chr2.2:4895576-4895595 None:intergenic 45.0%
CACCACACAATCACCAAACA+TGG - chr2.2:4895616-4895635 None:intergenic 45.0%
CAGGTACTAAGGAAGAAGCA+TGG + chr2.2:4896482-4896501 MS.gene052084:intron 45.0%
GAGAACACCTCAAGAAGAAG+AGG + chr2.2:4895692-4895711 MS.gene052084:CDS 45.0%
GTTTCGACACTCCATGGTTT+AGG + chr2.2:4896797-4896816 MS.gene052084:CDS 45.0%
TCAGAGGGAAGCTAAAGTTG+AGG + chr2.2:4895656-4895675 MS.gene052084:CDS 45.0%
TCCAGAACAAGCCAACATGA+AGG - chr2.2:4895583-4895602 None:intergenic 45.0%
! CATGTTTGGTGATTGTGTGG+TGG + chr2.2:4895614-4895633 MS.gene052084:CDS 45.0%
! GTACTAAGGAAGAAGCATGG+AGG + chr2.2:4896485-4896504 MS.gene052084:CDS 45.0%
AGCCCAATTGGCGTAGGAAT+TGG + chr2.2:4896634-4896653 MS.gene052084:CDS 50.0%
ATCTCTAGCCCAATTGGCGT+AGG + chr2.2:4896628-4896647 MS.gene052084:CDS 50.0%
CCATCGACGCAACAACAGAA+GGG + chr2.2:4896662-4896681 MS.gene052084:CDS 50.0%
CTAAAGGCTTCAAACCGCAG+AGG + chr2.2:4896767-4896786 MS.gene052084:CDS 50.0%
GTCGTTCCCTCTTCTTCTTG+AGG - chr2.2:4895702-4895721 None:intergenic 50.0%
!! GCCTTCATGTTGGCTTGTTC+TGG + chr2.2:4895579-4895598 MS.gene052084:CDS 50.0%
!!! GTTTTTGAAGGCATCGCCGT+TGG + chr2.2:4895816-4895835 MS.gene052084:CDS 50.0%
AGAAGAGGGAACGACCGAGT+TGG + chr2.2:4895707-4895726 MS.gene052084:CDS 55.0%
AGAGCCGTTTCGACACTCCA+TGG + chr2.2:4896791-4896810 MS.gene052084:CDS 55.0%
CAGAAGGGAGAACAGCGGAT+TGG + chr2.2:4896677-4896696 MS.gene052084:CDS 55.0%
CCCTTCTGTTGTTGCGTCGA+TGG - chr2.2:4896665-4896684 None:intergenic 55.0%
GCCATCGACGCAACAACAGA+AGG + chr2.2:4896661-4896680 MS.gene052084:CDS 55.0%
GCTCTCATCCATCGCCAACT+CGG - chr2.2:4895724-4895743 None:intergenic 55.0%
GGCATCGCCGTTGGAATTTC+AGG + chr2.2:4895825-4895844 MS.gene052084:CDS 55.0%
TCGAAACGGCTCTTCCTCTG+CGG - chr2.2:4896784-4896803 None:intergenic 55.0%
! GGGAACGACCGAGTTGGCGA+TGG + chr2.2:4895713-4895732 MS.gene052084:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 4895513 4896876 4895513 ID=MS.gene052084
chr2.2 mRNA 4895513 4896876 4895513 ID=MS.gene052084.t1;Parent=MS.gene052084
chr2.2 exon 4895513 4895846 4895513 ID=MS.gene052084.t1.exon1;Parent=MS.gene052084.t1
chr2.2 CDS 4895513 4895846 4895513 ID=cds.MS.gene052084.t1;Parent=MS.gene052084.t1
chr2.2 exon 4896485 4896876 4896485 ID=MS.gene052084.t1.exon2;Parent=MS.gene052084.t1
chr2.2 CDS 4896485 4896876 4896485 ID=cds.MS.gene052084.t1;Parent=MS.gene052084.t1
Gene Sequence

>MS.gene052084

ATGATGCATTTCTTGAGTGACTCAAATGAAACTTTTGAAGATCTTACCAAGAAAACTTACCCTTTTGCCTTCATGTTGGCTTGTTCTGGATATCTTTTAACCATGTTTGGTGATTGTGTGGTGGTTTATGTAACAAGTAATAATCAGAGGGAAGCTAAAGTTGAGGAACTTGAAGGAGGGAGAACACCTCAAGAAGAAGAGGGAACGACCGAGTTGGCGATGGATGAGAGCAACGTTGCATTCATGAAGACTACTAATCTTGGAGATACAATTTTGCTTATTCTTGCACTTTGTTTTCATTCGGTTTTTGAAGGCATCGCCGTTGGAATTTCAGGTTATTTCACACTCCATCGTTTATTTCATCCTTTCTTGATAGTCTTTTTCTTTTTTCGGGAGTGTTAAAGTATCAAACCTAGGTCACCAATGTTGAAGATCAAATTTTCTATCAAGATACTATATGAAGACCAACATCATTTCTTGGTAGTCTATTGTTAGAAGAGAAGTTTTAACAAGAAACGCAATATATTAAGTGCTAGCATGTATAACACTTGCAAACAATAATCATCATTCTCCCATATATACGAATAGTTAAAATTTGATTAGTTAAATATCATATTTTTATGCATTCTTCTCTTTCTTGGATAGATATTTCGAAACAAATAGCAAATTTTTATATTTTAAATAGCATCAAAGTGGGAAGCTGTATATATGATGTGTTTTAGGGTGACTGTTATGTTACTGTATTGGCTAGCTATGAGATGTGACTTTGCATCTCAAGTTTGAATCTCTTCTTCACCTACTTGTGAGATGTGACTTTGCATCTCAAGTTTGGCATGTGATTTTTAGGTGAGTGAAACCATATAGTCCATCCCTTTCAATATGAAAATGCATATGATGTTATTTTGAAGCAAATTGATACATTTCATAACTTAATTTGTTTAAACTAATGCTAATATACAAATTAATGATCAGGTACTAAGGAAGAAGCATGGAGGAATTTGTGGACAATATCATTACACAAGATATTTGCTGCAATAGCAATGGGAATCGCGTTGCTAAGAATGTTACCAAAAAGACCATTAATAACAACAGCAGGATATTCATTTGCATTTGCTATCTCTAGCCCAATTGGCGTAGGAATTGGAATTGCCATCGACGCAACAACAGAAGGGAGAACAGCGGATTGGATGTATGCAATATCAATGGGTATTGCTTGTGGTGTTTTTGTTTATGTTGCTATCAATCATTTAATCTCTAAAGGCTTCAAACCGCAGAGGAAGAGCCGTTTCGACACTCCATGGTTTAGGTTTCTTGCTGTGCTTTTTGGTGTTGCTGTAATTGCAGTTGTCATGATTTGGGATTGA
Protein sequence

>MS.gene052084.t1

MMHFLSDSNETFEDLTKKTYPFAFMLACSGYLLTMFGDCVVVYVTSNNQREAKVEELEGGRTPQEEEGTTELAMDESNVAFMKTTNLGDTILLILALCFHSVFEGIAVGISGTKEEAWRNLWTISLHKIFAAIAMGIALLRMLPKRPLITTAGYSFAFAISSPIGVGIGIAIDATTEGRTADWMYAISMGIACGVFVYVAINHLISKGFKPQRKSRFDTPWFRFLAVLFGVAVIAVVMIWD