AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180003035.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180003035.01.T01 MTR_4g120230 83.898 118 10 2 13 128 38 148 7.68e-63 191
MsG0180003035.01.T01 MTR_4g120230 83.898 118 10 2 13 128 38 148 1.88e-62 191
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180003035.01.T01 AT4G15940 66.949 118 28 2 14 128 38 147 2.18e-49 157
MsG0180003035.01.T01 AT3G16700 66.667 117 30 2 14 128 38 147 4.34e-47 150
MsG0180003035.01.T01 AT3G16700 66.667 117 30 2 14 128 38 147 1.68e-46 150
MsG0180003035.01.T01 AT3G16700 76.056 71 17 0 14 84 38 108 8.80e-34 115
MsG0180003035.01.T01 AT3G16700 76.056 71 17 0 14 84 38 108 8.80e-34 115

Find 31 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAAACATCACGAGCTTTCT+TGG 0.224836 1:+55365071 None:intergenic
TGCAGGTCTTCCATGGAATT+TGG 0.249099 1:-55364689 MsG0180003035.01.T01:CDS
CCAAGACAAAGTGGACTAAT+TGG 0.297011 1:+55364643 None:intergenic
GCAGAGAATAAAGTGTCTTT+TGG 0.346698 1:+55364456 None:intergenic
TAGTGAATAATTTGGATCTA+TGG 0.349494 1:-55364479 MsG0180003035.01.T01:CDS
TCTGCCATGGATTACGTTGC+TGG 0.377543 1:-55365042 MsG0180003035.01.T01:intron
GATGTCGGTAGTGAATAATT+TGG 0.414742 1:-55364487 MsG0180003035.01.T01:CDS
TTGTATATCAGGTTATGCTT+TGG 0.449174 1:-55364958 MsG0180003035.01.T01:intron
TTACCTTAGCAGCAGATTGA+AGG 0.449895 1:+55364913 None:intergenic
CCAATTAGTCCACTTTGTCT+TGG 0.450802 1:-55364643 MsG0180003035.01.T01:CDS
CCGCGTTTATCTTTGCCCTC+AGG 0.460797 1:+55365840 None:intergenic
ATGGAATTTGGCAAAAGGCC+AGG 0.471679 1:-55364677 MsG0180003035.01.T01:CDS
TAATTGGTGTGAACGTATCC+TGG 0.475675 1:+55364659 None:intergenic
GTTAGTCTGCAGGTCTTCCA+TGG 0.478081 1:-55364696 MsG0180003035.01.T01:intron
ATCAGGTTATGCTTTGGCAC+TGG 0.495705 1:-55364952 MsG0180003035.01.T01:intron
CTTCCATGGAATTTGGCAAA+AGG 0.503922 1:-55364682 MsG0180003035.01.T01:CDS
GGACCTTCAATCTGCTGCTA+AGG 0.545703 1:-55364916 MsG0180003035.01.T01:intron
TGGCACTGGATATGACTGCT+AGG 0.551295 1:-55364938 MsG0180003035.01.T01:CDS
GGCACTGGATATGACTGCTA+GGG 0.553282 1:-55364937 MsG0180003035.01.T01:CDS
TGTTTCAGAATCCTCTGCCA+TGG 0.561572 1:-55365055 MsG0180003035.01.T01:CDS
TGAAACAATCCAAGACAAAG+TGG 0.569857 1:+55364634 None:intergenic
ATCTGTGGAACTAATGCCTG+AGG 0.598106 1:-55365856 None:intergenic
CGGCGAGTTCGACTTCGTGA+TGG 0.611541 1:+55365103 None:intergenic
TATACCAGCAACGTAATCCA+TGG 0.619737 1:+55365038 None:intergenic
AGCTTTCTTGGCGATGACGA+CGG 0.621696 1:+55365083 None:intergenic
AGCAACGTAATCCATGGCAG+AGG 0.630505 1:+55365044 None:intergenic
TGGAGAGAACTCTCGTTGTG+TGG 0.652048 1:+55365123 None:intergenic
TCTGTGGAACTAATGCCTGA+GGG 0.672004 1:-55365855 None:intergenic
GTTGGTTTCAGAAACAACAC+TGG 0.677277 1:+55365183 None:intergenic
CCTGAGGGCAAAGATAAACG+CGG 0.730351 1:-55365840 MsG0180003035.01.T01:CDS
GAGGGCAAAGATAAACGCGG+TGG 0.734356 1:-55365837 MsG0180003035.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATTATCTTTGTATATC+AGG - Chr1:55365326-55365345 MsG0180003035.01.T01:intron 15.0%
!!! AATCAAATTTGAAATTTGAA+AGG + Chr1:55365290-55365309 None:intergenic 15.0%
! AGGAATGAATTGAATTGATT+TGG + Chr1:55365035-55365054 None:intergenic 25.0%
! CAATCTCATCTTCTTATAAT+GGG - Chr1:55364942-55364961 MsG0180003035.01.T01:CDS 25.0%
! TAGTGAATAATTTGGATCTA+TGG - Chr1:55365816-55365835 MsG0180003035.01.T01:intron 25.0%
! TATTAGATCACGAAAATATC+AGG + Chr1:55365550-55365569 None:intergenic 25.0%
! TCAATCTCATCTTCTTATAA+TGG - Chr1:55364941-55364960 MsG0180003035.01.T01:CDS 25.0%
!! ATTTTTGTTCTTTTCCTTGT+AGG - Chr1:55365775-55365794 MsG0180003035.01.T01:intron 25.0%
!! GGAATGAATTGAATTGATTT+GGG + Chr1:55365034-55365053 None:intergenic 25.0%
!! TAATTGATGCACTAATTTTC+AGG - Chr1:55365087-55365106 MsG0180003035.01.T01:CDS 25.0%
!!! TTTTCTGCTTAGTAGTTTTA+AGG - Chr1:55365515-55365534 MsG0180003035.01.T01:intron 25.0%
AACAATTACACTTGAACTAC+TGG - Chr1:55365429-55365448 MsG0180003035.01.T01:intron 30.0%
AATATTCTAATCTGATCCCA+AGG + Chr1:55365747-55365766 None:intergenic 30.0%
ACATCAAACATTGTTCACAT+CGG - Chr1:55364506-55364525 MsG0180003035.01.T01:intron 30.0%
ACATCGTCTTACTTGAAAAA+TGG - Chr1:55365133-55365152 MsG0180003035.01.T01:CDS 30.0%
ATGAAGAACATTGTAGATCT+AGG + Chr1:55364778-55364797 None:intergenic 30.0%
CAGATTAGGAAATTTGAGAA+AGG + Chr1:55365055-55365074 None:intergenic 30.0%
TGAAGAACATTGTAGATCTA+GGG + Chr1:55364777-55364796 None:intergenic 30.0%
TGGAAAGAAACTCAATTGAA+CGG + Chr1:55364694-55364713 None:intergenic 30.0%
TTGTATATCAGGTTATGCTT+TGG - Chr1:55365337-55365356 MsG0180003035.01.T01:intron 30.0%
! ACAACTTCTTTTACGAAGAA+AGG + Chr1:55364814-55364833 None:intergenic 30.0%
! CTTTCCAATTTTGTTCATCT+GGG - Chr1:55364707-55364726 MsG0180003035.01.T01:intron 30.0%
! TCTTTCCAATTTTGTTCATC+TGG - Chr1:55364706-55364725 MsG0180003035.01.T01:intron 30.0%
!!! TTTTTCAAGTAAGACGATGT+TGG + Chr1:55365133-55365152 None:intergenic 30.0%
AATTGAACGGATATTTGTGG+TGG + Chr1:55364681-55364700 None:intergenic 35.0%
AGTGCATCAATTACAGTACA+CGG + Chr1:55365080-55365099 None:intergenic 35.0%
CATCTTCAAAACAACCTACA+AGG + Chr1:55365792-55365811 None:intergenic 35.0%
CTAACCCAGATGAACAAAAT+TGG + Chr1:55364714-55364733 None:intergenic 35.0%
CTACAATGTTCTTCATCTAC+TGG - Chr1:55364782-55364801 MsG0180003035.01.T01:intron 35.0%
CTCAATTGAACGGATATTTG+TGG + Chr1:55364684-55364703 None:intergenic 35.0%
GATGTCGGTAGTGAATAATT+TGG - Chr1:55365808-55365827 MsG0180003035.01.T01:intron 35.0%
TCGTCTTACTTGAAAAATGG+CGG - Chr1:55365136-55365155 MsG0180003035.01.T01:CDS 35.0%
TGAAACAATCCAAGACAAAG+TGG + Chr1:55365664-55365683 None:intergenic 35.0%
! TCTTTTACGAAGAAAGGAAC+TGG + Chr1:55364808-55364827 None:intergenic 35.0%
!! GCAGAGAATAAAGTGTCTTT+TGG + Chr1:55365842-55365861 None:intergenic 35.0%
!! TTTTGTTCATCTGGGTTAGA+AGG - Chr1:55364715-55364734 MsG0180003035.01.T01:intron 35.0%
!!! GTAGGTTGTTTTGAAGATGT+CGG - Chr1:55365793-55365812 MsG0180003035.01.T01:intron 35.0%
AACGGATATTTGTGGTGGTT+GGG + Chr1:55364676-55364695 None:intergenic 40.0%
ACCTGCAGACTAACAACAAA+AGG + Chr1:55365593-55365612 None:intergenic 40.0%
ATAGCCTTTACAAGGACCTT+GGG - Chr1:55365728-55365747 MsG0180003035.01.T01:intron 40.0%
CCAATTAGTCCACTTTGTCT+TGG - Chr1:55365652-55365671 MsG0180003035.01.T01:intron 40.0%
CCTGCAGACTAACAACAAAA+GGG + Chr1:55365592-55365611 None:intergenic 40.0%
CTTCCATGGAATTTGGCAAA+AGG - Chr1:55365613-55365632 MsG0180003035.01.T01:intron 40.0%
CTTCGTAAAAGAAGTTGTCG+AGG - Chr1:55364816-55364835 MsG0180003035.01.T01:intron 40.0%
TAATTGGTGTGAACGTATCC+TGG + Chr1:55365639-55365658 None:intergenic 40.0%
TACAGTACACGGATCAGATT+AGG + Chr1:55365069-55365088 None:intergenic 40.0%
TATACCAGCAACGTAATCCA+TGG + Chr1:55365260-55365279 None:intergenic 40.0%
TCAAACATTGTTCACATCGG+TGG - Chr1:55364509-55364528 MsG0180003035.01.T01:intron 40.0%
TGAAACATCACGAGCTTTCT+TGG + Chr1:55365227-55365246 None:intergenic 40.0%
TGAGAGAAGACCAGAGATTT+GGG + Chr1:55364924-55364943 None:intergenic 40.0%
TTACCTTAGCAGCAGATTGA+AGG + Chr1:55365385-55365404 None:intergenic 40.0%
TTGAGAGAAGACCAGAGATT+TGG + Chr1:55364925-55364944 None:intergenic 40.0%
! AAGAGTGTGTTTGTGACCTT+GGG + Chr1:55365009-55365028 None:intergenic 40.0%
! AGGGTTTTGCTTCAACTAGA+GGG + Chr1:55364758-55364777 None:intergenic 40.0%
! GAATTTGGGACTGAATTTGG+TGG + Chr1:55364651-55364670 None:intergenic 40.0%
! GACGAATTTGGGACTGAATT+TGG + Chr1:55364654-55364673 None:intergenic 40.0%
! GTTGGTTTCAGAAACAACAC+TGG + Chr1:55365115-55365134 None:intergenic 40.0%
! TAGGGTTTTGCTTCAACTAG+AGG + Chr1:55364759-55364778 None:intergenic 40.0%
! TTCTGAAAACCCCAAATCTC+TGG - Chr1:55364911-55364930 MsG0180003035.01.T01:intron 40.0%
!! AGACGTTGATAGCCTTTACA+AGG - Chr1:55365720-55365739 MsG0180003035.01.T01:intron 40.0%
!! ATTTTGAGGGTTTTGGTGGT+GGG + Chr1:55364623-55364642 None:intergenic 40.0%
!! CCAAGACAAAGTGGACTAAT+TGG + Chr1:55365655-55365674 None:intergenic 40.0%
!!! ATTTGGTGGTGGAGATTTTG+AGG + Chr1:55364637-55364656 None:intergenic 40.0%
!!! TTTGGTGGTGGAGATTTTGA+GGG + Chr1:55364636-55364655 None:intergenic 40.0%
ATCAGGTTATGCTTTGGCAC+TGG - Chr1:55365343-55365362 MsG0180003035.01.T01:intron 45.0%
ATGGAATTTGGCAAAAGGCC+AGG - Chr1:55365618-55365637 MsG0180003035.01.T01:intron 45.0%
GAACGGATATTTGTGGTGGT+TGG + Chr1:55364677-55364696 None:intergenic 45.0%
GAGAGAAGACCAGAGATTTG+GGG + Chr1:55364923-55364942 None:intergenic 45.0%
GATAGCCTTTACAAGGACCT+TGG - Chr1:55365727-55365746 MsG0180003035.01.T01:intron 45.0%
TGATCCCAAGGTCCTTGTAA+AGG + Chr1:55365735-55365754 None:intergenic 45.0%
TGCAGGTCTTCCATGGAATT+TGG - Chr1:55365606-55365625 MsG0180003035.01.T01:intron 45.0%
TGTTTCAGAATCCTCTGCCA+TGG - Chr1:55365240-55365259 MsG0180003035.01.T01:intron 45.0%
! CTGGGTTAGAAGGATCGATT+GGG - Chr1:55364725-55364744 MsG0180003035.01.T01:intron 45.0%
! GAAGAGTGTGTTTGTGACCT+TGG + Chr1:55365010-55365029 None:intergenic 45.0%
! GTTTTCAGAAGACGACGAGA+GGG + Chr1:55364901-55364920 None:intergenic 45.0%
! TCTGGGTTAGAAGGATCGAT+TGG - Chr1:55364724-55364743 MsG0180003035.01.T01:intron 45.0%
! TGGCCTTTTGCCAAATTCCA+TGG + Chr1:55365619-55365638 None:intergenic 45.0%
! TTTGGGACTGAATTTGGTGG+TGG + Chr1:55364648-55364667 None:intergenic 45.0%
!! GATTTTGAGGGTTTTGGTGG+TGG + Chr1:55364624-55364643 None:intergenic 45.0%
!! GGAGATTTTGAGGGTTTTGG+TGG + Chr1:55364627-55364646 None:intergenic 45.0%
!! GGTGGAGATTTTGAGGGTTT+TGG + Chr1:55364630-55364649 None:intergenic 45.0%
!!! CCCTTTTGTTGTTAGTCTGC+AGG - Chr1:55365589-55365608 MsG0180003035.01.T01:intron 45.0%
ACTAAGCAACGCTGTTCCCA+AGG - Chr1:55364990-55365009 MsG0180003035.01.T01:intron 50.0%
AGCAACGTAATCCATGGCAG+AGG + Chr1:55365254-55365273 None:intergenic 50.0%
AGCTTTCTTGGCGATGACGA+CGG + Chr1:55365215-55365234 None:intergenic 50.0%
CCTGAGGGCAAAGATAAACG+CGG - Chr1:55364455-55364474 MsG0180003035.01.T01:CDS 50.0%
GGACCTTCAATCTGCTGCTA+AGG - Chr1:55365379-55365398 MsG0180003035.01.T01:intron 50.0%
GGTGGATAGAGTCAGCTGAA+GGG - Chr1:55364527-55364546 MsG0180003035.01.T01:intron 50.0%
GTGGTGGTTGGGACGAATTT+GGG + Chr1:55364665-55364684 None:intergenic 50.0%
TGGAGAGAACTCTCGTTGTG+TGG + Chr1:55365175-55365194 None:intergenic 50.0%
TGTGGTGGTTGGGACGAATT+TGG + Chr1:55364666-55364685 None:intergenic 50.0%
! GGCACTGGATATGACTGCTA+GGG - Chr1:55365358-55365377 MsG0180003035.01.T01:intron 50.0%
! GGTTTTCAGAAGACGACGAG+AGG + Chr1:55364902-55364921 None:intergenic 50.0%
! GTTAGTCTGCAGGTCTTCCA+TGG - Chr1:55365599-55365618 MsG0180003035.01.T01:intron 50.0%
! TCTGCCATGGATTACGTTGC+TGG - Chr1:55365253-55365272 MsG0180003035.01.T01:intron 50.0%
! TGGCACTGGATATGACTGCT+AGG - Chr1:55365357-55365376 MsG0180003035.01.T01:intron 50.0%
CCGCGTTTATCTTTGCCCTC+AGG + Chr1:55364458-55364477 None:intergenic 55.0%
CGGTGGATAGAGTCAGCTGA+AGG - Chr1:55364526-55364545 MsG0180003035.01.T01:intron 55.0%
GAGGGCAAAGATAAACGCGG+TGG - Chr1:55364458-55364477 MsG0180003035.01.T01:CDS 55.0%
! AGAAGACGACGAGAGGGCAT+CGG + Chr1:55364895-55364914 None:intergenic 55.0%
CGGCGAGTTCGACTTCGTGA+TGG + Chr1:55365195-55365214 None:intergenic 60.0%
!! ACGACGAGAGGGCATCGGAG+AGG + Chr1:55364890-55364909 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr1 gene 55364452 55365865 55364452 ID=MsG0180003035.01;Name=MsG0180003035.01
Chr1 mRNA 55364452 55365865 55364452 ID=MsG0180003035.01.T01;Parent=MsG0180003035.01;Name=MsG0180003035.01.T01;_AED=0.49;_eAED=0.49;_QI=0|0|0|0.6|0.75|0.6|5|0|135
Chr1 exon 55365830 55365865 55365830 ID=MsG0180003035.01.T01:exon:3003;Parent=MsG0180003035.01.T01
Chr1 exon 55365043 55365208 55365043 ID=MsG0180003035.01.T01:exon:3002;Parent=MsG0180003035.01.T01
Chr1 exon 55364917 55364969 55364917 ID=MsG0180003035.01.T01:exon:3001;Parent=MsG0180003035.01.T01
Chr1 exon 55364633 55364713 55364633 ID=MsG0180003035.01.T01:exon:3000;Parent=MsG0180003035.01.T01
Chr1 exon 55364452 55364520 55364452 ID=MsG0180003035.01.T01:exon:2999;Parent=MsG0180003035.01.T01
Chr1 CDS 55365830 55365865 55365830 ID=MsG0180003035.01.T01:cds;Parent=MsG0180003035.01.T01
Chr1 CDS 55365043 55365208 55365043 ID=MsG0180003035.01.T01:cds;Parent=MsG0180003035.01.T01
Chr1 CDS 55364917 55364969 55364917 ID=MsG0180003035.01.T01:cds;Parent=MsG0180003035.01.T01
Chr1 CDS 55364633 55364713 55364633 ID=MsG0180003035.01.T01:cds;Parent=MsG0180003035.01.T01
Chr1 CDS 55364452 55364520 55364452 ID=MsG0180003035.01.T01:cds;Parent=MsG0180003035.01.T01
Gene Sequence

>MsG0180003035.01.T01

ATGCCTGAGGGCAAAGATAAACGCGGTGGCAATTTCGCACCAGTGTTGTTTCTGAAACCAACATCGTCTTACTTGAAAAATGGCGGAACAATCGAAATTCCACACAACGAGAGTTCTCTCCATCACGAAGTCGAACTCGCCGTCGTCATCGCCAAGAAAGCTCGTGATGTTTCAGAATCCTCTGCCATGGATTACGTTGCTGGTTATGCTTTGGCACTGGATATGACTGCTAGGGACCTTCAATCTGCTGCTAAGTCTGCAGGTCTTCCATGGAATTTGGCAAAAGGCCAGGATACGTTCACACCAATTAGTCCACTTTGTCTTGGATTGTTTCAAGTTGTTTTGAAGATGTCGGTAGTGAATAATTTGGATCTATGGCCAAAAGACACTTTATTCTCTGCAGCG
Protein sequence

>MsG0180003035.01.T01

MPEGKDKRGGNFAPVLFLKPTSSYLKNGGTIEIPHNESSLHHEVELAVVIAKKARDVSESSAMDYVAGYALALDMTARDLQSAAKSAGLPWNLAKGQDTFTPISPLCLGLFQVVLKMSVVNNLDLWPKDTLFSAA