AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280007336.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280007336.01.T01 MTR_8g064310 82.812 64 11 0 69 132 7 70 4.21e-34 114
MsG0280007336.01.T01 MTR_8g064240 84.127 63 10 0 70 132 26 88 6.15e-34 114
MsG0280007336.01.T01 MTR_8g064320 76.562 64 15 0 70 133 10 73 9.01e-30 104
MsG0280007336.01.T01 MTR_8g064250 72.308 65 18 0 69 133 7 71 9.07e-29 101
MsG0280007336.01.T01 MTR_7g109560 81.633 49 9 0 69 117 699 747 4.12e-24 96.7
MsG0280007336.01.T01 MTR_1g086980 61.224 49 17 1 69 117 569 615 5.13e-13 65.1
MsG0280007336.01.T01 MTR_1g086980 61.224 49 17 1 69 117 697 743 6.62e-13 64.7
MsG0280007336.01.T01 MTR_1g086980 61.224 49 17 1 69 117 718 764 7.46e-13 64.7
MsG0280007336.01.T01 MTR_5g016870 59.184 49 20 0 69 117 801 849 7.91e-13 64.7
MsG0280007336.01.T01 MTR_1g086980 61.224 49 17 1 69 117 749 795 9.35e-13 64.3
MsG0280007336.01.T01 MTR_1g086980 61.224 49 17 1 69 117 769 815 9.37e-13 64.3
MsG0280007336.01.T01 MTR_1g086980 61.224 49 17 1 69 117 759 805 1.04e-12 64.3
MsG0280007336.01.T01 MTR_7g055660 59.184 49 19 1 70 117 670 718 6.52e-12 62.0
MsG0280007336.01.T01 MTR_5g085010 73.810 42 11 0 18 59 783 824 8.86e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280007336.01.T01 AT2G23380 61.224 49 19 0 69 117 612 660 6.51e-13 64.7
MsG0280007336.01.T01 AT2G23380 61.224 49 19 0 69 117 839 887 7.55e-13 64.7
MsG0280007336.01.T01 AT4G02020 59.184 49 18 1 69 117 794 840 5.29e-11 59.3

Find 25 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGTGAGAGCAATGTTTCT+TGG 0.232152 2:+13924789 None:intergenic
CAGAATTCAGCTCAGCAATT+TGG 0.247609 2:+13925997 None:intergenic
ATGTTTGATCATCATCTTCT+TGG 0.251332 2:+13924827 None:intergenic
GAAGCTTGAGGAAGAATTAA+TGG 0.278658 2:-13926030 MsG0280007336.01.T01:CDS
TTGTAGGTTGTGCTTGTTAA+TGG 0.284481 2:-13924972 MsG0280007336.01.T01:intron
TTGTTGTACTGCAGTGTCTT+TGG 0.325940 2:+13925971 None:intergenic
TGTAGGTTGTGCTTGTTAAT+GGG 0.345826 2:-13924971 MsG0280007336.01.T01:intron
CAAAGGAACGTATTGAAGTT+GGG 0.371751 2:-13924926 MsG0280007336.01.T01:CDS
GCAAAGGAACGTATTGAAGT+TGG 0.419225 2:-13924927 MsG0280007336.01.T01:CDS
CTTCATAAACTTATAGATGA+TGG 0.430748 2:-13924852 MsG0280007336.01.T01:CDS
ATATGAAACACCCTCTCAAT+CGG 0.496449 2:-13926097 MsG0280007336.01.T01:CDS
TTATGTCATGCAGGAGTTCA+CGG 0.512323 2:-13926055 MsG0280007336.01.T01:CDS
CCGAGTCATCACTCATGTAA+TGG 0.524250 2:+13925913 None:intergenic
CTCATCATATTATGTCATGC+AGG 0.524762 2:-13926064 MsG0280007336.01.T01:CDS
AGAAACATTGCTCTCACTTG+AGG 0.546978 2:-13924786 None:intergenic
GTAGGTTGTGCTTGTTAATG+GGG 0.554178 2:-13924970 MsG0280007336.01.T01:intron
CCATTACATGAGTGATGACT+CGG 0.557579 2:-13925913 MsG0280007336.01.T01:intron
TCTATAAGTTTATGAAGCCA+TGG 0.576047 2:+13924858 None:intergenic
AAAGGAACGTATTGAAGTTG+GGG 0.584434 2:-13924925 MsG0280007336.01.T01:CDS
GTTAATGGGGATCATCGAGT+AGG 0.622578 2:-13924957 MsG0280007336.01.T01:CDS
TCGAGTAGGAATATTTGCAA+AGG 0.624767 2:-13924943 MsG0280007336.01.T01:CDS
GAGTTCACGGAAGAAGCTTG+AGG 0.633563 2:-13926042 MsG0280007336.01.T01:CDS
GGAACGTATTGAAGTTGGGG+AGG 0.649243 2:-13924922 MsG0280007336.01.T01:CDS
ATGAAAATAGTCGACCACCA+TGG 0.704208 2:-13924875 MsG0280007336.01.T01:CDS
ATAAGTTTATGAAGCCATGG+TGG 0.735249 2:+13924861 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAACATAATATATGTTTTTA+GGG - Chr2:13925498-13925517 MsG0280007336.01.T01:intron 10.0%
!!! TAACATAATATATGTTTTTA+GGG + Chr2:13925517-13925498 None:intergenic 10.0%
!!! TTAACATAATATATGTTTTT+AGG - Chr2:13925497-13925516 MsG0280007336.01.T01:intron 10.0%
!!! TTAACATAATATATGTTTTT+AGG + Chr2:13925516-13925497 None:intergenic 10.0%
!! TAGATAGTAAAAGACTATAT+AGG + Chr2:13925612-13925631 None:intergenic 20.0%
!!! TATATGTTTTTAGGGATATA+AGG - Chr2:13925506-13925525 MsG0280007336.01.T01:intron 20.0%
!!! TATATGTTTTTAGGGATATA+AGG + Chr2:13925525-13925506 None:intergenic 20.0%
! AAAAGCTAATTGATATGCAA+AGG - Chr2:13925783-13925802 MsG0280007336.01.T01:intron 25.0%
! AAAAGCTAATTGATATGCAA+AGG + Chr2:13925802-13925783 None:intergenic 25.0%
! ACTGAAGAAAAATCATAGTA+AGG + Chr2:13925710-13925729 None:intergenic 25.0%
! AGAAAAAAATCATAGTAAGC+TGG - Chr2:13925473-13925492 MsG0280007336.01.T01:intron 25.0%
! CTTCATAAACTTATAGATGA+TGG - Chr2:13926031-13926050 MsG0280007336.01.T01:CDS 25.0%
! GCTTCATAAACTTCTATTAA+TGG + Chr2:13925146-13925165 None:intergenic 25.0%
AAAGGAACATATTGAAGCAA+GGG + Chr2:13925218-13925237 None:intergenic 30.0%
AACTTCTATTAATGGTTCCA+AGG + Chr2:13925138-13925157 None:intergenic 30.0%
AATAATGTGTCTCCTATTGT+AGG + Chr2:13925281-13925300 None:intergenic 30.0%
AATAATGTGTGTCCTATTGT+AGG - Chr2:13925895-13925914 MsG0280007336.01.T01:intron 30.0%
AATAGAAGTTTATGAAGCCA+TGG - Chr2:13925148-13925167 MsG0280007336.01.T01:intron 30.0%
ATGTTTGATCATCATCTTCT+TGG + Chr2:13926059-13926078 None:intergenic 30.0%
TCTATAAGTTTATGAAGCCA+TGG + Chr2:13926028-13926047 None:intergenic 30.0%
! GATGATCAAACATTTTCTCA+AGG - Chr2:13926066-13926085 MsG0280007336.01.T01:CDS 30.0%
AAAGGAACGTATTGAAGTTG+GGG - Chr2:13925958-13925977 MsG0280007336.01.T01:CDS 35.0%
AGGATGACTTAATGCACAAA+AGG + Chr2:13925657-13925676 None:intergenic 35.0%
ATAAGTTTATGAAGCCATGG+TGG + Chr2:13926025-13926044 None:intergenic 35.0%
ATCCAACATTTCTCAAGGAA+AGG + Chr2:13925106-13925125 None:intergenic 35.0%
CAAAGGAACATATTGAAGCA+AGG + Chr2:13925219-13925238 None:intergenic 35.0%
CAAAGGAACGTATTGAAGTT+GGG - Chr2:13925957-13925976 MsG0280007336.01.T01:CDS 35.0%
CTCATCATATTATGTCATGC+AGG - Chr2:13924819-13924838 MsG0280007336.01.T01:CDS 35.0%
GAAGCTTGAGGAAGAATTAA+TGG - Chr2:13924853-13924872 MsG0280007336.01.T01:CDS 35.0%
GATTACGGGTATGATGAAAA+TGG + Chr2:13926014-13925995 None:intergenic 35.0%
GGATGACTTAATGCATGAAA+AGG - Chr2:13925527-13925546 MsG0280007336.01.T01:intron 35.0%
TAACAAGCACAACCTACAAT+AGG - Chr2:13925266-13925285 MsG0280007336.01.T01:intron 35.0%
TAACAAGCACAACCTACAAT+AGG + Chr2:13925285-13925266 None:intergenic 35.0%
TCGAGTAGGAATATTTGCAA+AGG - Chr2:13925940-13925959 MsG0280007336.01.T01:CDS 35.0%
TGATGATCCAACATTTCTCA+AGG + Chr2:13925111-13925130 None:intergenic 35.0%
TTCTTGATGCTTATCGCAAA+GGG + Chr2:13925445-13925464 None:intergenic 35.0%
TTTCTTGATGCTTATCGCAA+AGG + Chr2:13925446-13925465 None:intergenic 35.0%
! AGGAGCTTTTCTTTGATTAC+GGG - Chr2:13925981-13926000 MsG0280007336.01.T01:CDS 35.0%
! AGGAGCTTTTCTTTGATTAC+GGG + Chr2:13926000-13925981 None:intergenic 35.0%
! GAGGAGCTTTTCTTTGATTA+CGG - Chr2:13925980-13925999 MsG0280007336.01.T01:CDS 35.0%
! GAGGAGCTTTTCTTTGATTA+CGG + Chr2:13925999-13925980 None:intergenic 35.0%
! TGTAGGTTGTGCTTGTTAAT+GGG - Chr2:13925912-13925931 MsG0280007336.01.T01:intron 35.0%
! TGTAGGTTGTGCTTGTTAAT+GGG + Chr2:13925931-13925912 None:intergenic 35.0%
! TTGTAGGTTGTGCTTGTTAA+TGG - Chr2:13925911-13925930 MsG0280007336.01.T01:intron 35.0%
! TTGTAGGTTGTGCTTGTTAA+TGG + Chr2:13925930-13925911 None:intergenic 35.0%
!! TAGAGTAGGAGTATTTGCAA+AGG + Chr2:13925236-13925255 None:intergenic 35.0%
ATGAAAATAGTCGACCACCA+TGG - Chr2:13926008-13926027 MsG0280007336.01.T01:CDS 40.0%
ATGAAAATGGTCGATCACCA+TGG + Chr2:13925168-13925187 None:intergenic 40.0%
CAAGTGAGAGCAATGTTTCT+TGG + Chr2:13926097-13926116 None:intergenic 40.0%
CAGAATTCAGCTCAGCAATT+TGG + Chr2:13924889-13924908 None:intergenic 40.0%
CCATTACATGAGTGATGACT+CGG - Chr2:13924970-13924989 MsG0280007336.01.T01:intron 40.0%
GCAAAGGAACGTATTGAAGT+TGG - Chr2:13925956-13925975 MsG0280007336.01.T01:CDS 40.0%
GTCTTGATGCTTATCGCAAA+GGG - Chr2:13925733-13925752 MsG0280007336.01.T01:intron 40.0%
GTTAATGGGGATCATAGAGT+AGG + Chr2:13925250-13925269 None:intergenic 40.0%
TGATATGCAAAGGAGAGTCT+AGG + Chr2:13925383-13925402 None:intergenic 40.0%
TGTCTTGATGCTTATCGCAA+AGG - Chr2:13925732-13925751 MsG0280007336.01.T01:intron 40.0%
TGTTGGATCATCATCTTCCT+TGG - Chr2:13925118-13925137 MsG0280007336.01.T01:intron 40.0%
TTATGTCATGCAGGAGTTCA+CGG - Chr2:13924828-13924847 MsG0280007336.01.T01:CDS 40.0%
TTGTTGTACTGCAGTGTCTT+TGG + Chr2:13924915-13924934 None:intergenic 40.0%
! GTAGGTTGTGCTTGTTAATG+GGG - Chr2:13925913-13925932 MsG0280007336.01.T01:intron 40.0%
! GTAGGTTGTGCTTGTTAATG+GGG + Chr2:13925932-13925913 None:intergenic 40.0%
!! CATTTTTGAGCCGATTGAGA+GGG + Chr2:13924799-13924818 None:intergenic 40.0%
AAGCGAGGAGCAATGTTTCT+TGG - Chr2:13925080-13925099 MsG0280007336.01.T01:intron 45.0%
ACGAACATCACTCTGTCCAA+AGG - Chr2:13925010-13925029 MsG0280007336.01.T01:intron 45.0%
CCGAGTCATCACTCATGTAA+TGG + Chr2:13924973-13924992 None:intergenic 45.0%
CGAACATCACTCTGTCCAAA+GGG - Chr2:13925011-13925030 MsG0280007336.01.T01:intron 45.0%
GGAACATATTGAAGCAAGGG+AGG + Chr2:13925215-13925234 None:intergenic 45.0%
GGCCTTTCCTTGAGAAATGT+TGG - Chr2:13925101-13925120 MsG0280007336.01.T01:intron 45.0%
GTTAATGGGGATCATCGAGT+AGG - Chr2:13925926-13925945 MsG0280007336.01.T01:CDS 45.0%
TGTCCAAATTTCCTCAAGCG+AGG - Chr2:13925065-13925084 MsG0280007336.01.T01:intron 45.0%
TTCCACAGACAGGACATTTG+CGG - Chr2:13925036-13925055 MsG0280007336.01.T01:intron 45.0%
!! GCATTTTTGAGCCGATTGAG+AGG + Chr2:13924800-13924819 None:intergenic 45.0%
GAAACATTGCTCCTCGCTTG+AGG + Chr2:13925079-13925098 None:intergenic 50.0%
GAGTTCACGGAAGAAGCTTG+AGG - Chr2:13924841-13924860 MsG0280007336.01.T01:CDS 50.0%
GCTCCTCGCTTGAGGAAATT+TGG + Chr2:13925071-13925090 None:intergenic 50.0%
GGAACGTATTGAAGTTGGGG+AGG - Chr2:13925961-13925980 MsG0280007336.01.T01:CDS 50.0%
CACCGCAAATGTCCTGTCTG+TGG + Chr2:13925041-13925060 None:intergenic 55.0%
CCTGTCTGTGGAACACCCTT+TGG + Chr2:13925029-13925048 None:intergenic 55.0%
!! CCAAAGGGTGTTCCACAGAC+AGG - Chr2:13925026-13925045 MsG0280007336.01.T01:intron 55.0%
Chromosome Type Strat End Strand Name
Chr2 gene 13924788 13926117 13924788 ID=MsG0280007336.01;Name=MsG0280007336.01
Chr2 mRNA 13924788 13926117 13924788 ID=MsG0280007336.01.T01;Parent=MsG0280007336.01;Name=MsG0280007336.01.T01;_AED=0.34;_eAED=0.45;_QI=0|0|0|1|1|1|2|0|134
Chr2 exon 13925914 13926117 13925914 ID=MsG0280007336.01.T01:exon:9410;Parent=MsG0280007336.01.T01
Chr2 exon 13924788 13924988 13924788 ID=MsG0280007336.01.T01:exon:9411;Parent=MsG0280007336.01.T01
Chr2 CDS 13925914 13926117 13925914 ID=MsG0280007336.01.T01:cds;Parent=MsG0280007336.01.T01
Chr2 CDS 13924788 13924988 13924788 ID=MsG0280007336.01.T01:cds;Parent=MsG0280007336.01.T01
Gene Sequence

>MsG0280007336.01.T01

ATGAAACACCCTCTCAATCGGCTCAAAAATGCTCATCATATTATGTCATGCAGGAGTTCACGGAAGAAGCTTGAGGAAGAATTAATGGAAGTGAATAACCAAATTGCTGAGCTGAATTCTGAAGCCAAAGACACTGCAGTACAACAACAAGAATTTTTCTTTAACTTATTATCGAACAATTACCATTACATGAGTGATGACTCGGTTGTGCTTGTTAATGGGGATCATCGAGTAGGAATATTTGCAAAGGAACGTATTGAAGTTGGGGAGGAGCTTTTCTTTGATTACGGGTATGATGAAAATAGTCGACCACCATGGCTTCATAAACTTATAGATGATGGTTCCAAGAAGATGATGATCAAACATTTTCTCAAGGAAAAGCCAAGAAACATTGCTCTCACTTGA
Protein sequence

>MsG0280007336.01.T01

MKHPLNRLKNAHHIMSCRSSRKKLEEELMEVNNQIAELNSEAKDTAVQQQEFFFNLLSNNYHYMSDDSVVLVNGDHRVGIFAKERIEVGEELFFDYGYDENSRPPWLHKLIDDGSKKMMIKHFLKEKPRNIALT*