AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0559680

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0559680 MtrunA17_Chr4g0050631 90.116 172 16 1 9 180 212 382 1.85e-106 310
Msa0559680 MtrunA17_Chr4g0050971 72.527 91 22 2 91 178 9 99 1.32e-39 130
Msa0559680 MtrunA17_Chr4g0050651 70.652 92 23 3 91 178 9 100 3.55e-37 124
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 62 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGCTACTTCAGTGGTTTC+AGG 0.236813 4_1:-58845850 None:intergenic
TACCTCAGATTTACTCTTCA+TGG 0.246210 4_1:-58845530 None:intergenic
TTCCGTGGGCAAACTGTAAA+AGG 0.259903 4_1:-58845480 None:intergenic
TCAGCTACTTCAGCGGATTC+AGG 0.301044 4_1:-58845736 None:intergenic
GCATGAGTGCGATGAGGTTC+AGG 0.301934 4_1:-58845805 None:intergenic
TCAGGAACAATGCGGCTATC+CGG 0.378472 4_1:-58845832 None:intergenic
GGAACTCTGTCTGAACCATT+TGG 0.381458 4_1:-58846003 None:intergenic
GAGGTTCAGGGGAAGCTGGC+TGG 0.386384 4_1:-58845792 None:intergenic
CTTTATTGTGTAGGCACAGA+TGG 0.404871 4_1:+58845657 Msa0559680:intron
TCCGCTGAAGTAGCTGAATC+TGG 0.412882 4_1:+58845742 Msa0559680:CDS
CTCTTCATGGAGAGACAACT+TGG 0.416746 4_1:-58845517 None:intergenic
CTGATGGTGTTGGGATTGAC+AGG 0.416902 4_1:-58845940 None:intergenic
GAACTCTGTCTGAACCATTT+GGG 0.424835 4_1:-58846002 None:intergenic
CAGGAACAATGCGGCTATCC+GGG 0.448018 4_1:-58845831 None:intergenic
AACAATGCGGCTATCCGGGC+TGG 0.449752 4_1:-58845827 None:intergenic
AGGTTCAGGGGAAGCTGGCT+GGG 0.458963 4_1:-58845791 None:intergenic
CAGCCTCAATGCCATCATCC+AGG 0.459441 4_1:-58845975 None:intergenic
ATTGAGGCTGTCCTCCCAAA+TGG 0.462042 4_1:+58845988 Msa0559680:CDS
CGATGAGATTGAGGCAAAGT+TGG 0.463226 4_1:-58845913 None:intergenic
TGACCAGTCGCTGATGGTGT+TGG 0.464996 4_1:-58845950 None:intergenic
AGATTGAGGCAAAGTTGGTT+GGG 0.474012 4_1:-58845908 None:intergenic
AGTGTTTGCGGCACTTTGCG+AGG 0.476892 4_1:+58846095 Msa0559680:CDS
GACCAGTCGCTGATGGTGTT+GGG 0.478745 4_1:-58845949 None:intergenic
CGATGAGGTTCAGGGGAAGC+TGG 0.482193 4_1:-58845796 None:intergenic
GTGTTTGCGGCACTTTGCGA+GGG 0.482529 4_1:+58846096 Msa0559680:CDS
GAGATTGAGGCAAAGTTGGT+TGG 0.485001 4_1:-58845909 None:intergenic
AAGAAGACTACCAGTGTTTG+CGG 0.493423 4_1:+58846083 Msa0559680:CDS
GATGAAGCTCTTCTCTTCCG+TGG 0.504434 4_1:-58845495 None:intergenic
CATGAGTGCGATGAGGTTCA+GGG 0.509014 4_1:-58845804 None:intergenic
GACTGGTCACCCCTGGATGA+TGG 0.509897 4_1:+58845964 Msa0559680:CDS
CAGGAACAATGCGACTATCC+AGG 0.512004 4_1:-58845717 None:intergenic
CTTGCAAGTCTTGTGACTAC+AGG 0.513276 4_1:-58845883 None:intergenic
CATCAGCGACTGGTCACCCC+TGG 0.525662 4_1:+58845957 Msa0559680:CDS
CTTGCAAGTCTTGTGACTAA+AGG 0.531988 4_1:-58845766 None:intergenic
ATGAAGCTCTTCTCTTCCGT+GGG 0.538111 4_1:-58845494 None:intergenic
TTTATTGTGTAGGCACAGAT+GGG 0.538263 4_1:+58845658 Msa0559680:intron
GTTCAGACAGAGTTCCCTCT+AGG 0.542921 4_1:+58846010 Msa0559680:CDS
TCATCGCACTCATGCCAGCC+CGG 0.549587 4_1:+58845813 Msa0559680:CDS
AGCTGATTCAGCTACTTCAG+TGG 0.552361 4_1:-58845857 None:intergenic
CAGGGGTGACCAGTCGCTGA+TGG 0.559234 4_1:-58845956 None:intergenic
AGCCTCAATGCCATCATCCA+GGG 0.563569 4_1:-58845974 None:intergenic
TCGCAAAGTGCCGCAAACAC+TGG 0.580686 4_1:-58846093 None:intergenic
TTCAGACAGAGTTCCCTCTA+GGG 0.586505 4_1:+58846011 Msa0559680:CDS
ACAGGGGTACGATGAGATTG+AGG 0.587061 4_1:-58845922 None:intergenic
ACTGAAGTAGCTGAATCAGC+TGG 0.591905 4_1:+58845859 Msa0559680:CDS
ATCCCAACACCATCAGCGAC+TGG 0.592240 4_1:+58845947 Msa0559680:CDS
ACCCCTGGATGATGGCATTG+AGG 0.599820 4_1:+58845972 Msa0559680:CDS
GCATCAACTTCCTCCCTAGA+GGG 0.614358 4_1:-58846024 None:intergenic
CTCTGTCTGAACCATTTGGG+AGG 0.615742 4_1:-58845999 None:intergenic
CTCCATGAAGAGTAAATCTG+AGG 0.616657 4_1:+58845528 Msa0559680:CDS
TGCATCAACTTCCTCCCTAG+AGG 0.621656 4_1:-58846025 None:intergenic
TGTTTGCGGCACTTTGCGAG+GGG 0.624671 4_1:+58846097 Msa0559680:CDS
ATTGTGTAGGCACAGATGGG+CGG 0.625772 4_1:+58845661 Msa0559680:intron
AGGACTGTGCTTGTATGACC+TGG 0.630112 4_1:+58845699 Msa0559680:CDS
TCCAGATTCAGCTACTTCAG+CGG 0.639551 4_1:-58845743 None:intergenic
AGACAGAGTTCCCTCTAGGG+AGG 0.648644 4_1:+58846014 Msa0559680:CDS
GCCTCAATGCCATCATCCAG+GGG 0.652087 4_1:-58845973 None:intergenic
TGATGGTGTTGGGATTGACA+GGG 0.653379 4_1:-58845939 None:intergenic
ATGAGTGCGATGAGGTTCAG+GGG 0.671572 4_1:-58845803 None:intergenic
GGGCTGGCATGAGTGCGATG+AGG 0.673771 4_1:-58845811 None:intergenic
GATGGTGTTGGGATTGACAG+GGG 0.706471 4_1:-58845938 None:intergenic
CAGTGGTTTCAGGAACAATG+CGG 0.725745 4_1:-58845840 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTAGGTGTTTATTATGCTTA+AGG - chr4_1:58845585-58845604 None:intergenic 25.0%
! CATAATAAACACCTAATTAG+CGG + chr4_1:58845589-58845608 Msa0559680:intron 25.0%
GTTTATTATGCTTAAGGACA+AGG - chr4_1:58845579-58845598 None:intergenic 30.0%
GAAATACTTAACCGCTAATT+AGG - chr4_1:58845603-58845622 None:intergenic 30.0%
GCATTTCTTCTTTATTGTGT+AGG + chr4_1:58845648-58845667 Msa0559680:intron 30.0%
!!! GAAGTTGATGCATACATTTT+TGG + chr4_1:58846036-58846055 Msa0559680:CDS 30.0%
TACCTCAGATTTACTCTTCA+TGG - chr4_1:58845533-58845552 None:intergenic 35.0%
TTTATTGTGTAGGCACAGAT+GGG + chr4_1:58845658-58845677 Msa0559680:intron 35.0%
! GGTAGTCTTCTTTTAGTAGT+CGG - chr4_1:58846075-58846094 None:intergenic 35.0%
! ATCCTTTTACAGTTTGCCCA+CGG + chr4_1:58845478-58845497 Msa0559680:CDS 40.0%
CTCCATGAAGAGTAAATCTG+AGG + chr4_1:58845528-58845547 Msa0559680:CDS 40.0%
CTTTATTGTGTAGGCACAGA+TGG + chr4_1:58845657-58845676 Msa0559680:intron 40.0%
! CTTGCAAGTCTTGTGACTAA+AGG - chr4_1:58845769-58845788 None:intergenic 40.0%
! AGATTGAGGCAAAGTTGGTT+GGG - chr4_1:58845911-58845930 None:intergenic 40.0%
GAACTCTGTCTGAACCATTT+GGG - chr4_1:58846005-58846024 None:intergenic 40.0%
AAGAAGACTACCAGTGTTTG+CGG + chr4_1:58846083-58846102 Msa0559680:CDS 40.0%
TTCCGTGGGCAAACTGTAAA+AGG - chr4_1:58845483-58845502 None:intergenic 45.0%
ATGAAGCTCTTCTCTTCCGT+GGG - chr4_1:58845497-58845516 None:intergenic 45.0%
CTCTTCATGGAGAGACAACT+TGG - chr4_1:58845520-58845539 None:intergenic 45.0%
TCCAGATTCAGCTACTTCAG+CGG - chr4_1:58845746-58845765 None:intergenic 45.0%
CAGTGGTTTCAGGAACAATG+CGG - chr4_1:58845843-58845862 None:intergenic 45.0%
TCAGCTACTTCAGTGGTTTC+AGG - chr4_1:58845853-58845872 None:intergenic 45.0%
! AGCTGATTCAGCTACTTCAG+TGG - chr4_1:58845860-58845879 None:intergenic 45.0%
ACTGAAGTAGCTGAATCAGC+TGG + chr4_1:58845859-58845878 Msa0559680:CDS 45.0%
! CTTGCAAGTCTTGTGACTAC+AGG - chr4_1:58845886-58845905 None:intergenic 45.0%
! GAGATTGAGGCAAAGTTGGT+TGG - chr4_1:58845912-58845931 None:intergenic 45.0%
CGATGAGATTGAGGCAAAGT+TGG - chr4_1:58845916-58845935 None:intergenic 45.0%
! TGATGGTGTTGGGATTGACA+GGG - chr4_1:58845942-58845961 None:intergenic 45.0%
GGAACTCTGTCTGAACCATT+TGG - chr4_1:58846006-58846025 None:intergenic 45.0%
TTCAGACAGAGTTCCCTCTA+GGG + chr4_1:58846011-58846030 Msa0559680:CDS 45.0%
GATGAAGCTCTTCTCTTCCG+TGG - chr4_1:58845498-58845517 None:intergenic 50.0%
ATTGTGTAGGCACAGATGGG+CGG + chr4_1:58845661-58845680 Msa0559680:intron 50.0%
!! GGCGGATTTTCTATGAGAGC+AGG + chr4_1:58845679-58845698 Msa0559680:CDS 50.0%
AGGACTGTGCTTGTATGACC+TGG + chr4_1:58845699-58845718 Msa0559680:CDS 50.0%
CAGGAACAATGCGACTATCC+AGG - chr4_1:58845720-58845739 None:intergenic 50.0%
! TCAGCTACTTCAGCGGATTC+AGG - chr4_1:58845739-58845758 None:intergenic 50.0%
TCCGCTGAAGTAGCTGAATC+TGG + chr4_1:58845742-58845761 Msa0559680:CDS 50.0%
ATGAGTGCGATGAGGTTCAG+GGG - chr4_1:58845806-58845825 None:intergenic 50.0%
CATGAGTGCGATGAGGTTCA+GGG - chr4_1:58845807-58845826 None:intergenic 50.0%
TCAGGAACAATGCGGCTATC+CGG - chr4_1:58845835-58845854 None:intergenic 50.0%
! ACAGGGGTACGATGAGATTG+AGG - chr4_1:58845925-58845944 None:intergenic 50.0%
! GATGGTGTTGGGATTGACAG+GGG - chr4_1:58845941-58845960 None:intergenic 50.0%
! CTGATGGTGTTGGGATTGAC+AGG - chr4_1:58845943-58845962 None:intergenic 50.0%
AGCCTCAATGCCATCATCCA+GGG - chr4_1:58845977-58845996 None:intergenic 50.0%
ATTGAGGCTGTCCTCCCAAA+TGG + chr4_1:58845988-58846007 Msa0559680:CDS 50.0%
CTCTGTCTGAACCATTTGGG+AGG - chr4_1:58846002-58846021 None:intergenic 50.0%
GTTCAGACAGAGTTCCCTCT+AGG + chr4_1:58846010-58846029 Msa0559680:CDS 50.0%
GCATCAACTTCCTCCCTAGA+GGG - chr4_1:58846027-58846046 None:intergenic 50.0%
TGCATCAACTTCCTCCCTAG+AGG - chr4_1:58846028-58846047 None:intergenic 50.0%
GCATGAGTGCGATGAGGTTC+AGG - chr4_1:58845808-58845827 None:intergenic 55.0%
CAGGAACAATGCGGCTATCC+GGG - chr4_1:58845834-58845853 None:intergenic 55.0%
ATCCCAACACCATCAGCGAC+TGG + chr4_1:58845947-58845966 Msa0559680:CDS 55.0%
! GACCAGTCGCTGATGGTGTT+GGG - chr4_1:58845952-58845971 None:intergenic 55.0%
! TGACCAGTCGCTGATGGTGT+TGG - chr4_1:58845953-58845972 None:intergenic 55.0%
! ACCCCTGGATGATGGCATTG+AGG + chr4_1:58845972-58845991 Msa0559680:CDS 55.0%
GCCTCAATGCCATCATCCAG+GGG - chr4_1:58845976-58845995 None:intergenic 55.0%
CAGCCTCAATGCCATCATCC+AGG - chr4_1:58845978-58845997 None:intergenic 55.0%
! AGACAGAGTTCCCTCTAGGG+AGG + chr4_1:58846014-58846033 Msa0559680:CDS 55.0%
!! TCGCAAAGTGCCGCAAACAC+TGG - chr4_1:58846096-58846115 None:intergenic 55.0%
AGTGTTTGCGGCACTTTGCG+AGG + chr4_1:58846095-58846114 Msa0559680:CDS 55.0%
GTGTTTGCGGCACTTTGCGA+GGG + chr4_1:58846096-58846115 Msa0559680:CDS 55.0%
TGTTTGCGGCACTTTGCGAG+GGG + chr4_1:58846097-58846116 Msa0559680:CDS 55.0%
AGGTTCAGGGGAAGCTGGCT+GGG - chr4_1:58845794-58845813 None:intergenic 60.0%
CGATGAGGTTCAGGGGAAGC+TGG - chr4_1:58845799-58845818 None:intergenic 60.0%
TCATCGCACTCATGCCAGCC+CGG + chr4_1:58845813-58845832 Msa0559680:CDS 60.0%
AACAATGCGGCTATCCGGGC+TGG - chr4_1:58845830-58845849 None:intergenic 60.0%
! GACTGGTCACCCCTGGATGA+TGG + chr4_1:58845964-58845983 Msa0559680:CDS 60.0%
GAGGTTCAGGGGAAGCTGGC+TGG - chr4_1:58845795-58845814 None:intergenic 65.0%
! GGGCTGGCATGAGTGCGATG+AGG - chr4_1:58845814-58845833 None:intergenic 65.0%
CAGGGGTGACCAGTCGCTGA+TGG - chr4_1:58845959-58845978 None:intergenic 65.0%
! CATCAGCGACTGGTCACCCC+TGG + chr4_1:58845957-58845976 Msa0559680:CDS 65.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 58845463 58846125 58845463 ID=Msa0559680;Name=Msa0559680
chr4_1 mRNA 58845463 58846125 58845463 ID=Msa0559680-mRNA-1;Parent=Msa0559680;Name=Msa0559680-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|1|0|1|1|1|2|0|180
chr4_1 exon 58845463 58845549 58845463 ID=Msa0559680-mRNA-1:exon:18043;Parent=Msa0559680-mRNA-1
chr4_1 exon 58845670 58846125 58845670 ID=Msa0559680-mRNA-1:exon:18044;Parent=Msa0559680-mRNA-1
chr4_1 CDS 58845463 58845549 58845463 ID=Msa0559680-mRNA-1:cds;Parent=Msa0559680-mRNA-1
chr4_1 CDS 58845670 58846125 58845670 ID=Msa0559680-mRNA-1:cds;Parent=Msa0559680-mRNA-1
Gene Sequence

>Msa0559680

ATGCTTGACACTATCATCCTTTTACAGTTTGCCCACGGAAGAGAAGAGCTTCATCCAAGTTGTCTCTCCATGAAGAGTAAATCTGAGGCACAGATGGGCGGATTTTCTATGAGAGCAGGACTGTGCTTGTATGACCTGGATAGTCGCATTGTTCCTGAATCCGCTGAAGTAGCTGAATCTGGACCTTTAGTCACAAGACTTGCAAGATCCCAGCCAGCTTCCCCTGAACCTCATCGCACTCATGCCAGCCCGGATAGCCGCATTGTTCCTGAAACCACTGAAGTAGCTGAATCAGCTGGACCTGTAGTCACAAGACTTGCAAGATCCCAACCAACTTTGCCTCAATCTCATCGTACCCCTGTCAATCCCAACACCATCAGCGACTGGTCACCCCTGGATGATGGCATTGAGGCTGTCCTCCCAAATGGTTCAGACAGAGTTCCCTCTAGGGAGGAAGTTGATGCATACATTTTTGGCATTCTCAATCAGCCGACTACTAAAAGAAGACTACCAGTGTTTGCGGCACTTTGCGAGGGGCAGTAA
Protein sequence

>Msa0559680

MLDTIILLQFAHGREELHPSCLSMKSKSEAQMGGFSMRAGLCLYDLDSRIVPESAEVAESGPLVTRLARSQPASPEPHRTHASPDSRIVPETTEVAESAGPVVTRLARSQPTLPQSHRTPVNPNTISDWSPLDDGIEAVLPNGSDRVPSREEVDAYIFGILNQPTTKRRLPVFAALCEGQ*