AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0733410


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 41 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTCCATGAGTTTGATTTA+TGG 0.165464 5_1:-46662012 None:intergenic
TTCCCTTTCGCTAATCATTA+AGG 0.243915 5_1:+46661389 Msa0733410:five_prime_UTR
TAGAGCCCAGTTGTTGAAAA+AGG 0.264059 5_1:+46661215 None:intergenic
TGGAGCGGCAGCTGCAGATA+TGG 0.376724 5_1:-46661286 None:intergenic
GCAGCTGCAGATATGGATCT+AGG 0.381091 5_1:-46661279 None:intergenic
GGCACTATATAAAACCAGTT+AGG 0.391939 5_1:-46661991 None:intergenic
GCACTATATAAAACCAGTTA+GGG 0.395114 5_1:-46661990 None:intergenic
AGAGAGAGTGTATGTGTGAA+TGG 0.411788 5_1:-46661306 None:intergenic
GGAGGTTATCATAATCTTTG+TGG 0.432763 5_1:+46661874 Msa0733410:CDS
AGAGACTGTTCCTCGGCCAC+TGG 0.440961 5_1:-46661788 None:intergenic
CATTCGCACAGGCAGTTGTC+GGG 0.443831 5_1:+46661903 Msa0733410:CDS
GAGGTTATCATAATCTTTGT+GGG 0.464601 5_1:+46661875 Msa0733410:CDS
ACATTCGCACAGGCAGTTGT+CGG 0.465169 5_1:+46661902 Msa0733410:CDS
AAAATACCACATAAAAGGTC+AGG 0.488134 5_1:-46661932 None:intergenic
TACCTTAATGATTAGCGAAA+GGG 0.488891 5_1:-46661391 None:intergenic
AGAGACTGTTCCTCGGCCAC+TGG 0.495260 5_1:-46661764 None:intergenic
CTCTCTCTCTGAGAGAGACT+CGG 0.506826 5_1:+46661345 Msa0733410:five_prime_UTR
ACAGTCTCTCCCAGTGGCCG+AGG 0.515343 5_1:+46661778 Msa0733410:CDS
TACTTAGTGAGTCCGTCCTA+TGG 0.519882 5_1:+46661955 Msa0733410:exon
AGTGCCATAAATCAAACTCA+TGG 0.545857 5_1:+46662008 Msa0733410:three_prime_UTR
GAGACTGTTCCTCGGCCACT+GGG 0.547422 5_1:-46661787 None:intergenic
TGTTAACGTTCCAGTGGCCG+AGG 0.552882 5_1:+46661754 Msa0733410:CDS
CAGCTGCAGATATGGATCTA+GGG 0.561068 5_1:-46661278 None:intergenic
AGGGAAGGAAGAAACAATGA+TGG 0.569540 5_1:-46661372 None:intergenic
ATACCTTAATGATTAGCGAA+AGG 0.589059 5_1:-46661392 None:intergenic
CACTGGGAGAGACTGTTCCT+CGG 0.589590 5_1:-46661771 None:intergenic
TGCCGTGGAGATTGTCGAGG+AGG 0.607269 5_1:+46661856 Msa0733410:CDS
AACCTCCTCGACAATCTCCA+CGG 0.623848 5_1:-46661858 None:intergenic
GGGAAGGAAGAAACAATGAT+GGG 0.633138 5_1:-46661371 None:intergenic
CCTTGCCGTGGAGATTGTCG+AGG 0.634500 5_1:+46661853 Msa0733410:CDS
TGCCACTGTTAACGTTCCAG+TGG 0.638491 5_1:+46661748 Msa0733410:CDS
CCTCGACAATCTCCACGGCA+AGG 0.648860 5_1:-46661853 None:intergenic
AACTGGAAGAGACTGTTCCT+CGG 0.670113 5_1:-46661795 None:intergenic
ACTATATAAAACCAGTTAGG+GGG 0.674586 5_1:-46661988 None:intergenic
AAGGAAGAAACAATGATGGG+TGG 0.677187 5_1:-46661368 None:intergenic
CACTATATAAAACCAGTTAG+GGG 0.682263 5_1:-46661989 None:intergenic
GGTTAGATACAACCATAGGA+CGG 0.705181 5_1:-46661967 None:intergenic
CGAGGAACAGTCTCTCCCAG+TGG 0.711633 5_1:+46661772 Msa0733410:CDS
TTAATGATTAGCGAAAGGGA+AGG 0.713195 5_1:-46661387 None:intergenic
GAGTGTATGTGTGAATGGAG+CGG 0.714383 5_1:-46661301 None:intergenic
GGCCACTGGAACGTTAACAG+TGG 0.749520 5_1:-46661750 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTAAAAATACCACATAAA+AGG - chr5_1:46661940-46661959 None:intergenic 20.0%
!! AAGTAAAAATACCACATAAA+AGG - chr5_1:46661940-46661959 None:intergenic 20.0%
!! TGAATGTATGATAATGAAGA+AGG - chr5_1:46661431-46661450 None:intergenic 25.0%
! AACTTGCAATAATCAGAAAT+GGG - chr5_1:46661542-46661561 None:intergenic 25.0%
! AAACTTGCAATAATCAGAAA+TGG - chr5_1:46661543-46661562 None:intergenic 25.0%
!! TGAATGTATGATAATGAAGA+AGG - chr5_1:46661431-46661450 None:intergenic 25.0%
! AACTTGCAATAATCAGAAAT+GGG - chr5_1:46661542-46661561 None:intergenic 25.0%
! AAACTTGCAATAATCAGAAA+TGG - chr5_1:46661543-46661562 None:intergenic 25.0%
TACCTTAATGATTAGCGAAA+GGG - chr5_1:46661394-46661413 None:intergenic 30.0%
ATACCTTAATGATTAGCGAA+AGG - chr5_1:46661395-46661414 None:intergenic 30.0%
!! CATTTTAGTGTTCTGTTAGT+TGG + chr5_1:46661566-46661585 Msa0733410:intron 30.0%
GAGGTTATCATAATCTTTGT+GGG + chr5_1:46661875-46661894 Msa0733410:CDS 30.0%
AAAATACCACATAAAAGGTC+AGG - chr5_1:46661935-46661954 None:intergenic 30.0%
ACTATATAAAACCAGTTAGG+GGG - chr5_1:46661991-46662010 None:intergenic 30.0%
CACTATATAAAACCAGTTAG+GGG - chr5_1:46661992-46662011 None:intergenic 30.0%
GCACTATATAAAACCAGTTA+GGG - chr5_1:46661993-46662012 None:intergenic 30.0%
TACCTTAATGATTAGCGAAA+GGG - chr5_1:46661394-46661413 None:intergenic 30.0%
ATACCTTAATGATTAGCGAA+AGG - chr5_1:46661395-46661414 None:intergenic 30.0%
!! CATTTTAGTGTTCTGTTAGT+TGG + chr5_1:46661566-46661585 Msa0733410:intron 30.0%
GAGGTTATCATAATCTTTGT+GGG + chr5_1:46661875-46661894 Msa0733410:CDS 30.0%
AAAATACCACATAAAAGGTC+AGG - chr5_1:46661935-46661954 None:intergenic 30.0%
ACTATATAAAACCAGTTAGG+GGG - chr5_1:46661991-46662010 None:intergenic 30.0%
CACTATATAAAACCAGTTAG+GGG - chr5_1:46661992-46662011 None:intergenic 30.0%
GCACTATATAAAACCAGTTA+GGG - chr5_1:46661993-46662012 None:intergenic 30.0%
TTAATGATTAGCGAAAGGGA+AGG - chr5_1:46661390-46661409 None:intergenic 35.0%
TTCCCTTTCGCTAATCATTA+AGG + chr5_1:46661389-46661408 Msa0733410:five_prime_UTR 35.0%
TTGCAATAATCAGAAATGGG+TGG - chr5_1:46661539-46661558 None:intergenic 35.0%
!! TTGGATTTGTTGCTGTCTTA+GGG + chr5_1:46661585-46661604 Msa0733410:intron 35.0%
ATTCAGACATTGCTTCACAT+AGG - chr5_1:46661721-46661740 None:intergenic 35.0%
GGAGGTTATCATAATCTTTG+TGG + chr5_1:46661874-46661893 Msa0733410:CDS 35.0%
! CTTTATCCTGACCTTTTATG+TGG + chr5_1:46661926-46661945 Msa0733410:CDS 35.0%
GGCACTATATAAAACCAGTT+AGG - chr5_1:46661994-46662013 None:intergenic 35.0%
AGTGCCATAAATCAAACTCA+TGG + chr5_1:46662008-46662027 Msa0733410:three_prime_UTR 35.0%
! CTCTCCATGAGTTTGATTTA+TGG - chr5_1:46662015-46662034 None:intergenic 35.0%
TTAATGATTAGCGAAAGGGA+AGG - chr5_1:46661390-46661409 None:intergenic 35.0%
TTCCCTTTCGCTAATCATTA+AGG + chr5_1:46661389-46661408 Msa0733410:five_prime_UTR 35.0%
TTGCAATAATCAGAAATGGG+TGG - chr5_1:46661539-46661558 None:intergenic 35.0%
!! TTGGATTTGTTGCTGTCTTA+GGG + chr5_1:46661585-46661604 Msa0733410:intron 35.0%
ATTCAGACATTGCTTCACAT+AGG - chr5_1:46661721-46661740 None:intergenic 35.0%
GGAGGTTATCATAATCTTTG+TGG + chr5_1:46661874-46661893 Msa0733410:CDS 35.0%
! CTTTATCCTGACCTTTTATG+TGG + chr5_1:46661926-46661945 Msa0733410:CDS 35.0%
GGCACTATATAAAACCAGTT+AGG - chr5_1:46661994-46662013 None:intergenic 35.0%
AGTGCCATAAATCAAACTCA+TGG + chr5_1:46662008-46662027 Msa0733410:three_prime_UTR 35.0%
! CTCTCCATGAGTTTGATTTA+TGG - chr5_1:46662015-46662034 None:intergenic 35.0%
! AGAGAGAGTGTATGTGTGAA+TGG - chr5_1:46661309-46661328 None:intergenic 40.0%
! AAGGAAGAAACAATGATGGG+TGG - chr5_1:46661371-46661390 None:intergenic 40.0%
GGGAAGGAAGAAACAATGAT+GGG - chr5_1:46661374-46661393 None:intergenic 40.0%
AGGGAAGGAAGAAACAATGA+TGG - chr5_1:46661375-46661394 None:intergenic 40.0%
!! GTTGGATTTGTTGCTGTCTT+AGG + chr5_1:46661584-46661603 Msa0733410:intron 40.0%
TTCACATAGGCAGAAGCAAA+GGG - chr5_1:46661708-46661727 None:intergenic 40.0%
!! TTCGCCTACAAGTTTTTGGA+AGG + chr5_1:46661816-46661835 Msa0733410:CDS 40.0%
!! GTTTTTGGAAGGCGTGTTTT+TGG + chr5_1:46661827-46661846 Msa0733410:CDS 40.0%
GGTTAGATACAACCATAGGA+CGG - chr5_1:46661970-46661989 None:intergenic 40.0%
! AGAGAGAGTGTATGTGTGAA+TGG - chr5_1:46661309-46661328 None:intergenic 40.0%
! AAGGAAGAAACAATGATGGG+TGG - chr5_1:46661371-46661390 None:intergenic 40.0%
GGGAAGGAAGAAACAATGAT+GGG - chr5_1:46661374-46661393 None:intergenic 40.0%
AGGGAAGGAAGAAACAATGA+TGG - chr5_1:46661375-46661394 None:intergenic 40.0%
!! GTTGGATTTGTTGCTGTCTT+AGG + chr5_1:46661584-46661603 Msa0733410:intron 40.0%
TTCACATAGGCAGAAGCAAA+GGG - chr5_1:46661708-46661727 None:intergenic 40.0%
!! TTCGCCTACAAGTTTTTGGA+AGG + chr5_1:46661816-46661835 Msa0733410:CDS 40.0%
!! GTTTTTGGAAGGCGTGTTTT+TGG + chr5_1:46661827-46661846 Msa0733410:CDS 40.0%
GGTTAGATACAACCATAGGA+CGG - chr5_1:46661970-46661989 None:intergenic 40.0%
CAGCTGCAGATATGGATCTA+GGG - chr5_1:46661281-46661300 None:intergenic 45.0%
GAGTGTATGTGTGAATGGAG+CGG - chr5_1:46661304-46661323 None:intergenic 45.0%
TTGCTGTCTTAGGGTCTGTT+TGG + chr5_1:46661594-46661613 Msa0733410:intron 45.0%
CTTCACATAGGCAGAAGCAA+AGG - chr5_1:46661709-46661728 None:intergenic 45.0%
AACTGGAAGAGACTGTTCCT+CGG - chr5_1:46661798-46661817 None:intergenic 45.0%
CCAAAAACTTGTAGGCGAAC+TGG - chr5_1:46661815-46661834 None:intergenic 45.0%
! CCAGTTCGCCTACAAGTTTT+TGG + chr5_1:46661812-46661831 Msa0733410:CDS 45.0%
CACGCCTTCCAAAAACTTGT+AGG - chr5_1:46661823-46661842 None:intergenic 45.0%
! TGTGGGTTTTACATTCGCAC+AGG + chr5_1:46661892-46661911 Msa0733410:CDS 45.0%
TACTTAGTGAGTCCGTCCTA+TGG + chr5_1:46661955-46661974 Msa0733410:exon 45.0%
AGGGGGTTAGATACAACCAT+AGG - chr5_1:46661974-46661993 None:intergenic 45.0%
GTTGTATCTAACCCCCTAAC+TGG + chr5_1:46661977-46661996 Msa0733410:three_prime_UTR 45.0%
CAGCTGCAGATATGGATCTA+GGG - chr5_1:46661281-46661300 None:intergenic 45.0%
GAGTGTATGTGTGAATGGAG+CGG - chr5_1:46661304-46661323 None:intergenic 45.0%
TTGCTGTCTTAGGGTCTGTT+TGG + chr5_1:46661594-46661613 Msa0733410:intron 45.0%
CTTCACATAGGCAGAAGCAA+AGG - chr5_1:46661709-46661728 None:intergenic 45.0%
AACTGGAAGAGACTGTTCCT+CGG - chr5_1:46661798-46661817 None:intergenic 45.0%
CCAAAAACTTGTAGGCGAAC+TGG - chr5_1:46661815-46661834 None:intergenic 45.0%
! CCAGTTCGCCTACAAGTTTT+TGG + chr5_1:46661812-46661831 Msa0733410:CDS 45.0%
CACGCCTTCCAAAAACTTGT+AGG - chr5_1:46661823-46661842 None:intergenic 45.0%
! TGTGGGTTTTACATTCGCAC+AGG + chr5_1:46661892-46661911 Msa0733410:CDS 45.0%
TACTTAGTGAGTCCGTCCTA+TGG + chr5_1:46661955-46661974 Msa0733410:exon 45.0%
AGGGGGTTAGATACAACCAT+AGG - chr5_1:46661974-46661993 None:intergenic 45.0%
GTTGTATCTAACCCCCTAAC+TGG + chr5_1:46661977-46661996 Msa0733410:three_prime_UTR 45.0%
GCAGCTGCAGATATGGATCT+AGG - chr5_1:46661282-46661301 None:intergenic 50.0%
! CTCTCTCTCTGAGAGAGACT+CGG + chr5_1:46661345-46661364 Msa0733410:five_prime_UTR 50.0%
TGCCACTGTTAACGTTCCAG+TGG + chr5_1:46661748-46661767 Msa0733410:CDS 50.0%
!!! TGTTTTTGGTTGCCTTGCCG+TGG + chr5_1:46661841-46661860 Msa0733410:CDS 50.0%
AACCTCCTCGACAATCTCCA+CGG - chr5_1:46661861-46661880 None:intergenic 50.0%
ACATTCGCACAGGCAGTTGT+CGG + chr5_1:46661902-46661921 Msa0733410:CDS 50.0%
GCAGCTGCAGATATGGATCT+AGG - chr5_1:46661282-46661301 None:intergenic 50.0%
! CTCTCTCTCTGAGAGAGACT+CGG + chr5_1:46661345-46661364 Msa0733410:five_prime_UTR 50.0%
TGCCACTGTTAACGTTCCAG+TGG + chr5_1:46661748-46661767 Msa0733410:CDS 50.0%
!!! TGTTTTTGGTTGCCTTGCCG+TGG + chr5_1:46661841-46661860 Msa0733410:CDS 50.0%
AACCTCCTCGACAATCTCCA+CGG - chr5_1:46661861-46661880 None:intergenic 50.0%
ACATTCGCACAGGCAGTTGT+CGG + chr5_1:46661902-46661921 Msa0733410:CDS 50.0%
GGCCACTGGAACGTTAACAG+TGG - chr5_1:46661753-46661772 None:intergenic 55.0%
TGTTAACGTTCCAGTGGCCG+AGG + chr5_1:46661754-46661773 Msa0733410:CDS 55.0%
CACTGGGAGAGACTGTTCCT+CGG - chr5_1:46661774-46661793 None:intergenic 55.0%
CATTCGCACAGGCAGTTGTC+GGG + chr5_1:46661903-46661922 Msa0733410:CDS 55.0%
GGCCACTGGAACGTTAACAG+TGG - chr5_1:46661753-46661772 None:intergenic 55.0%
TGTTAACGTTCCAGTGGCCG+AGG + chr5_1:46661754-46661773 Msa0733410:CDS 55.0%
CACTGGGAGAGACTGTTCCT+CGG - chr5_1:46661774-46661793 None:intergenic 55.0%
CATTCGCACAGGCAGTTGTC+GGG + chr5_1:46661903-46661922 Msa0733410:CDS 55.0%
TGGAGCGGCAGCTGCAGATA+TGG - chr5_1:46661289-46661308 None:intergenic 60.0%
AGAGACTGTTCCTCGGCCAC+TGG - chr5_1:46661767-46661786 None:intergenic 60.0%
CGAGGAACAGTCTCTCCCAG+TGG + chr5_1:46661772-46661791 Msa0733410:CDS 60.0%
GAGACTGTTCCTCGGCCACT+GGG - chr5_1:46661766-46661785 None:intergenic 60.0%
AGAGACTGTTCCTCGGCCAC+TGG - chr5_1:46661767-46661786 None:intergenic 60.0%
CCTCGACAATCTCCACGGCA+AGG - chr5_1:46661856-46661875 None:intergenic 60.0%
CCTTGCCGTGGAGATTGTCG+AGG + chr5_1:46661853-46661872 Msa0733410:CDS 60.0%
TGCCGTGGAGATTGTCGAGG+AGG + chr5_1:46661856-46661875 Msa0733410:CDS 60.0%
TGGAGCGGCAGCTGCAGATA+TGG - chr5_1:46661289-46661308 None:intergenic 60.0%
AGAGACTGTTCCTCGGCCAC+TGG - chr5_1:46661767-46661786 None:intergenic 60.0%
CGAGGAACAGTCTCTCCCAG+TGG + chr5_1:46661772-46661791 Msa0733410:CDS 60.0%
GAGACTGTTCCTCGGCCACT+GGG - chr5_1:46661766-46661785 None:intergenic 60.0%
AGAGACTGTTCCTCGGCCAC+TGG - chr5_1:46661767-46661786 None:intergenic 60.0%
CCTCGACAATCTCCACGGCA+AGG - chr5_1:46661856-46661875 None:intergenic 60.0%
CCTTGCCGTGGAGATTGTCG+AGG + chr5_1:46661853-46661872 Msa0733410:CDS 60.0%
TGCCGTGGAGATTGTCGAGG+AGG + chr5_1:46661856-46661875 Msa0733410:CDS 60.0%
ACAGTCTCTCCCAGTGGCCG+AGG + chr5_1:46661778-46661797 Msa0733410:CDS 65.0%
ACAGTCTCTCCCAGTGGCCG+AGG + chr5_1:46661778-46661797 Msa0733410:CDS 65.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 46661230 46662109 46661230 ID=Msa0733410;Name=Msa0733410
chr5_1 mRNA 46661230 46662109 46661230 ID=Msa0733410-mRNA-1;Parent=Msa0733410;Name=Msa0733410-mRNA-1;_AED=0.00;_eAED=0.00;_QI=181|0|0.5|1|0|0.5|2|148|76
chr5_1 exon 46661230 46661410 46661230 ID=Msa0733410-mRNA-1:exon:13275;Parent=Msa0733410-mRNA-1
chr5_1 exon 46661731 46662109 46661731 ID=Msa0733410-mRNA-1:exon:13276;Parent=Msa0733410-mRNA-1
chr5_1 five_prime_UTR 46661230 46661410 46661230 ID=Msa0733410-mRNA-1:five_prime_utr;Parent=Msa0733410-mRNA-1
chr5_1 CDS 46661731 46661961 46661731 ID=Msa0733410-mRNA-1:cds;Parent=Msa0733410-mRNA-1
chr5_1 three_prime_UTR 46661962 46662109 46661962 ID=Msa0733410-mRNA-1:three_prime_utr;Parent=Msa0733410-mRNA-1
Gene Sequence

>Msa0733410

ATGTCTGAATCTGTAGCTGCCACTGTTAACGTTCCAGTGGCCGAGGAACAGTCTCTCCCAGTGGCCGAGGAACAGTCTCTTCCAGTTCGCCTACAAGTTTTTGGAAGGCGTGTTTTTGGTTGCCTTGCCGTGGAGATTGTCGAGGAGGTTATCATAATCTTTGTGGGTTTTACATTCGCACAGGCAGTTGTCGGGCTTTATCCTGACCTTTTATGTGGTATTTTTACTTAG

Protein sequence

>Msa0733410

MSESVAATVNVPVAEEQSLPVAEEQSLPVRLQVFGRRVFGCLAVEIVEEVIIIFVGFTFAQAVVGLYPDLLCGIFT*