AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0582650


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582650 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0582650 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0582650 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0582650 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa0582650 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa0582650 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa0582650 MtrunA17_Chr6g0460191 74.468 94 24 0 154 247 8 101 1.73e-28 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582650 ATCG00150.1 91.165 249 20 1 1 247 1 249 1.75e-151 422

Find 45 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTATACCTGTTATGTTTC+TGG 0.052609 4_2:-1120557 Msa0582650:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 4_2:-1121123 Msa0582650:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 4_2:-1121122 Msa0582650:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 4_2:+1120683 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 4_2:-1120919 Msa0582650:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 4_2:+1120753 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 4_2:-1120556 Msa0582650:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 4_2:-1121083 Msa0582650:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 4_2:+1121032 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 4_2:+1120676 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 4_2:-1120496 Msa0582650:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 4_2:+1120804 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 4_2:-1121082 Msa0582650:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 4_2:+1120805 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 4_2:+1120645 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 4_2:+1120907 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 4_2:-1120940 Msa0582650:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 4_2:+1120550 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 4_2:+1120556 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 4_2:+1121012 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 4_2:-1121131 Msa0582650:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 4_2:-1120485 Msa0582650:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 4_2:+1120968 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 4_2:+1120694 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 4_2:-1121147 Msa0582650:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 4_2:+1120646 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 4_2:-1120952 Msa0582650:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 4_2:+1120698 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 4_2:-1120841 Msa0582650:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 4_2:+1120495 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 4_2:+1120688 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 4_2:-1121012 Msa0582650:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 4_2:+1121000 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 4_2:-1120760 Msa0582650:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 4_2:-1121121 Msa0582650:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 4_2:+1120568 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 4_2:-1120481 Msa0582650:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 4_2:-1120932 Msa0582650:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 4_2:-1120933 Msa0582650:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 4_2:-1120541 Msa0582650:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 4_2:+1120993 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 4_2:+1120916 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 4_2:-1120761 Msa0582650:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 4_2:+1121068 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 4_2:+1120826 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr4_2:1120778-1120797 Msa0582650:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr4_2:1120822-1120841 Msa0582650:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr4_2:1120861-1120880 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr4_2:1120862-1120881 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr4_2:1120990-1121009 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr4_2:1120541-1120560 Msa0582650:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr4_2:1120673-1120692 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr4_2:1120759-1120778 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr4_2:1120819-1120838 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr4_2:1120933-1120952 Msa0582650:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr4_2:1120532-1120551 Msa0582650:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr4_2:1120540-1120559 Msa0582650:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr4_2:1120542-1120561 Msa0582650:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr4_2:1120581-1120600 Msa0582650:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr4_2:1120783-1120802 Msa0582650:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr4_2:1120784-1120803 Msa0582650:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr4_2:1120918-1120937 Msa0582650:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr4_2:1120923-1120942 Msa0582650:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr4_2:1120978-1120997 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr4_2:1120983-1121002 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr4_2:1121020-1121039 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr4_2:1121021-1121040 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr4_2:1121023-1121042 Msa0582650:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr4_2:1121116-1121135 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr4_2:1121122-1121141 Msa0582650:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr4_2:1121182-1121201 Msa0582650:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr4_2:1120580-1120599 Msa0582650:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr4_2:1120634-1120653 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr4_2:1120723-1120742 Msa0582650:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr4_2:1120785-1120804 Msa0582650:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr4_2:1120913-1120932 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr4_2:1121098-1121117 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr4_2:1121106-1121125 Msa0582650:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr4_2:1121107-1121126 Msa0582650:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr4_2:1121157-1121176 Msa0582650:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr4_2:1121178-1121197 Msa0582650:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr4_2:1120516-1120535 Msa0582650:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr4_2:1120598-1120617 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr4_2:1120902-1120921 Msa0582650:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr4_2:1120903-1120922 Msa0582650:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr4_2:1120968-1120987 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr4_2:1120972-1120991 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr4_2:1121110-1121129 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr4_2:1120666-1120685 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr4_2:1120698-1120717 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr4_2:1120710-1120729 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr4_2:1120711-1120730 Msa0582650:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr4_2:1120730-1120749 Msa0582650:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr4_2:1120731-1120750 Msa0582650:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr4_2:1120750-1120769 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr4_2:1121167-1121186 Msa0582650:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr4_2:1121171-1121190 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr4_2:1120654-1120673 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr4_2:1120651-1120670 Msa0582650:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr4_2:1120840-1120859 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr4_2:1120744-1120763 Msa0582650:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr4_2:1120799-1120818 Msa0582650:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 1120471 1121214 1120471 ID=Msa0582650;Name=Msa0582650
chr4_2 mRNA 1120471 1121214 1120471 ID=Msa0582650-mRNA-1;Parent=Msa0582650;Name=Msa0582650-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
chr4_2 exon 1120471 1121214 1120471 ID=Msa0582650-mRNA-1:exon:239;Parent=Msa0582650-mRNA-1
chr4_2 CDS 1120471 1121214 1120471 ID=Msa0582650-mRNA-1:cds;Parent=Msa0582650-mRNA-1
Gene Sequence

>Msa0582650

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa0582650

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*