AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0958540


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0958540 MtrunA17_Chr6g0485511 62.097 124 13 2 44 135 1 122 3.36e-40 130
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCATTCTCCTGCTGGTT+TGG 0.290743 6_3:-72519576 None:intergenic
TTAGATGTACCTTCTTCATT+TGG 0.332645 6_3:-72519540 None:intergenic
TCAGCCTTCGAAGTTCTTTA+CGG 0.344809 6_3:-72518737 None:intergenic
CTTAAGCTTCATTCTCCTGC+TGG 0.359038 6_3:-72519581 None:intergenic
AAATGAAGAAGGTACATCTA+AGG 0.414920 6_3:+72519542 Msa0958540:CDS
CCACATCTCAAAACCGCAAA+TGG 0.423400 6_3:+72518993 Msa0958540:CDS
GAAGTGGAAGTGGCGGAAGC+CGG 0.426962 6_3:-72519022 None:intergenic
AAGTGGAAGTGGCGGAAGCC+GGG 0.428762 6_3:-72519021 None:intergenic
AAGCCGGGTGGAGCCATTTG+CGG 0.466138 6_3:-72519006 None:intergenic
ATGCTGAAAACTGCGTGGTT+TGG 0.474624 6_3:+72518681 Msa0958540:CDS
TCGTCAATCACACTGCAAAC+AGG 0.488932 6_3:-72519048 None:intergenic
GTATGCAGCGCGGACTGCCC+TGG 0.503284 6_3:+72519398 Msa0958540:intron
AAACAGGAGGGAAGTGGAAG+TGG 0.512473 6_3:-72519032 None:intergenic
CACTGCAAACAGGAGGGAAG+TGG 0.520900 6_3:-72519038 None:intergenic
AGCTGAAGTTCCAAACCAGC+AGG 0.526615 6_3:+72519566 Msa0958540:CDS
GAAAACTGCGTGGTTTGGCA+AGG 0.583493 6_3:+72518686 Msa0958540:CDS
CGAACTTTCTGCAGAACCCA+AGG 0.585785 6_3:+72519068 Msa0958540:CDS
GCTGAAGTTCCAAATGAAGA+AGG 0.589203 6_3:+72519531 Msa0958540:CDS
AAAACTGCGTGGTTTGGCAA+GGG 0.599527 6_3:+72518687 Msa0958540:CDS
TCAATCACACTGCAAACAGG+AGG 0.629072 6_3:-72519045 None:intergenic
CAGGAGGGAAGTGGAAGTGG+CGG 0.629148 6_3:-72519029 None:intergenic
AAACCGCAAATGGCTCCACC+CGG 0.634759 6_3:+72519003 Msa0958540:CDS
TGGAAGTGGCGGAAGCCGGG+TGG 0.646475 6_3:-72519018 None:intergenic
AAAACCGTAAAGAACTTCGA+AGG 0.659678 6_3:+72518733 Msa0958540:CDS
CAATCACACTGCAAACAGGA+GGG 0.665161 6_3:-72519044 None:intergenic
TATTTATGCTGAAAACTGCG+TGG 0.707815 6_3:+72518676 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTAAAGAACTCAAAATA+TGG - chr6_3:72519174-72519193 None:intergenic 15.0%
!! TTATTAAAGAACTCAAAATA+TGG - chr6_3:72519174-72519193 None:intergenic 15.0%
!! AAAGCAAATTAAAAAACATG+AGG + chr6_3:72518761-72518780 Msa0958540:CDS 20.0%
!! TGAAATGTTAACAAAGTTTA+TGG + chr6_3:72519103-72519122 Msa0958540:intron 20.0%
!! GAAATGTTAACAAAGTTTAT+GGG + chr6_3:72519104-72519123 Msa0958540:intron 20.0%
!! AAATGTTAACAAAGTTTATG+GGG + chr6_3:72519105-72519124 Msa0958540:intron 20.0%
!!! ATATGAGCAATAGTAATTTT+AGG - chr6_3:72519230-72519249 None:intergenic 20.0%
!! AAAGCAAATTAAAAAACATG+AGG + chr6_3:72518761-72518780 Msa0958540:CDS 20.0%
!! TGAAATGTTAACAAAGTTTA+TGG + chr6_3:72519103-72519122 Msa0958540:intron 20.0%
!! GAAATGTTAACAAAGTTTAT+GGG + chr6_3:72519104-72519123 Msa0958540:intron 20.0%
!! AAATGTTAACAAAGTTTATG+GGG + chr6_3:72519105-72519124 Msa0958540:intron 20.0%
!!! ATATGAGCAATAGTAATTTT+AGG - chr6_3:72519230-72519249 None:intergenic 20.0%
!!! AGAAAGAAGCTGATTTTAAA+AGG + chr6_3:72519436-72519455 Msa0958540:CDS 25.0%
!!! GAAAGAAGCTGATTTTAAAA+GGG + chr6_3:72519437-72519456 Msa0958540:CDS 25.0%
!!! AGAAAGAAGCTGATTTTAAA+AGG + chr6_3:72519436-72519455 Msa0958540:CDS 25.0%
!!! GAAAGAAGCTGATTTTAAAA+GGG + chr6_3:72519437-72519456 Msa0958540:CDS 25.0%
TCAACTACAATTGATTGAAG+AGG - chr6_3:72518838-72518857 None:intergenic 30.0%
ATTGCTGAGAATAATGTTGT+CGG + chr6_3:72518882-72518901 Msa0958540:intron 30.0%
TTCATGAAAAAACTTGCCTT+GGG - chr6_3:72519087-72519106 None:intergenic 30.0%
TTTCATGAAAAAACTTGCCT+TGG - chr6_3:72519088-72519107 None:intergenic 30.0%
TAAATTTAAAGAACTTGCCG+CGG - chr6_3:72519297-72519316 None:intergenic 30.0%
TTAGATGTACCTTCTTCATT+TGG - chr6_3:72519543-72519562 None:intergenic 30.0%
! AAATGAAGAAGGTACATCTA+AGG + chr6_3:72519542-72519561 Msa0958540:CDS 30.0%
TCAACTACAATTGATTGAAG+AGG - chr6_3:72518838-72518857 None:intergenic 30.0%
ATTGCTGAGAATAATGTTGT+CGG + chr6_3:72518882-72518901 Msa0958540:intron 30.0%
TTCATGAAAAAACTTGCCTT+GGG - chr6_3:72519087-72519106 None:intergenic 30.0%
TTTCATGAAAAAACTTGCCT+TGG - chr6_3:72519088-72519107 None:intergenic 30.0%
TAAATTTAAAGAACTTGCCG+CGG - chr6_3:72519297-72519316 None:intergenic 30.0%
TTAGATGTACCTTCTTCATT+TGG - chr6_3:72519543-72519562 None:intergenic 30.0%
! AAATGAAGAAGGTACATCTA+AGG + chr6_3:72519542-72519561 Msa0958540:CDS 30.0%
! TCGAAGTTCTTTACGGTTTT+TGG - chr6_3:72518733-72518752 None:intergenic 35.0%
AAAACCGTAAAGAACTTCGA+AGG + chr6_3:72518733-72518752 Msa0958540:CDS 35.0%
GATTGAAGAGGAAAACAAGA+AGG - chr6_3:72518826-72518845 None:intergenic 35.0%
AGAATAATGTTGTCGGATTC+AGG + chr6_3:72518889-72518908 Msa0958540:intron 35.0%
GAATAATGTTGTCGGATTCA+GGG + chr6_3:72518890-72518909 Msa0958540:intron 35.0%
AATAATGTTGTCGGATTCAG+GGG + chr6_3:72518891-72518910 Msa0958540:intron 35.0%
! TTTTAGGCTTCAATTTCTGC+TGG - chr6_3:72519214-72519233 None:intergenic 35.0%
AAATTTAAAGAACTTGCCGC+GGG - chr6_3:72519296-72519315 None:intergenic 35.0%
!! CTGCTTTTCAATTTCATCCA+GGG - chr6_3:72519418-72519437 None:intergenic 35.0%
!! TCTGCTTTTCAATTTCATCC+AGG - chr6_3:72519419-72519438 None:intergenic 35.0%
AGATGAAAAAGCTGCATCTA+AGG + chr6_3:72519506-72519525 Msa0958540:CDS 35.0%
! TCGAAGTTCTTTACGGTTTT+TGG - chr6_3:72518733-72518752 None:intergenic 35.0%
AAAACCGTAAAGAACTTCGA+AGG + chr6_3:72518733-72518752 Msa0958540:CDS 35.0%
GATTGAAGAGGAAAACAAGA+AGG - chr6_3:72518826-72518845 None:intergenic 35.0%
AGAATAATGTTGTCGGATTC+AGG + chr6_3:72518889-72518908 Msa0958540:intron 35.0%
GAATAATGTTGTCGGATTCA+GGG + chr6_3:72518890-72518909 Msa0958540:intron 35.0%
AATAATGTTGTCGGATTCAG+GGG + chr6_3:72518891-72518910 Msa0958540:intron 35.0%
! TTTTAGGCTTCAATTTCTGC+TGG - chr6_3:72519214-72519233 None:intergenic 35.0%
AAATTTAAAGAACTTGCCGC+GGG - chr6_3:72519296-72519315 None:intergenic 35.0%
!! CTGCTTTTCAATTTCATCCA+GGG - chr6_3:72519418-72519437 None:intergenic 35.0%
!! TCTGCTTTTCAATTTCATCC+AGG - chr6_3:72519419-72519438 None:intergenic 35.0%
AGATGAAAAAGCTGCATCTA+AGG + chr6_3:72519506-72519525 Msa0958540:CDS 35.0%
TCAGCCTTCGAAGTTCTTTA+CGG - chr6_3:72518740-72518759 None:intergenic 40.0%
TTAACCTCTAAACCAGCAGT+TGG + chr6_3:72519368-72519387 Msa0958540:intron 40.0%
GCTGAAGTTCCAAATGAAGA+AGG + chr6_3:72519531-72519550 Msa0958540:CDS 40.0%
TCAGCCTTCGAAGTTCTTTA+CGG - chr6_3:72518740-72518759 None:intergenic 40.0%
TTAACCTCTAAACCAGCAGT+TGG + chr6_3:72519368-72519387 Msa0958540:intron 40.0%
GCTGAAGTTCCAAATGAAGA+AGG + chr6_3:72519531-72519550 Msa0958540:CDS 40.0%
ATGCTGAAAACTGCGTGGTT+TGG + chr6_3:72518681-72518700 Msa0958540:CDS 45.0%
! AAAACTGCGTGGTTTGGCAA+GGG + chr6_3:72518687-72518706 Msa0958540:CDS 45.0%
TTGTCGGATTCAGGGGTTTA+GGG + chr6_3:72518898-72518917 Msa0958540:intron 45.0%
ATGTGGCAGTTAAACTGCAG+AGG - chr6_3:72518979-72518998 None:intergenic 45.0%
!!! CCATTTGCGGTTTTGAGATG+TGG - chr6_3:72518996-72519015 None:intergenic 45.0%
CCACATCTCAAAACCGCAAA+TGG + chr6_3:72518993-72519012 Msa0958540:CDS 45.0%
CAATCACACTGCAAACAGGA+GGG - chr6_3:72519047-72519066 None:intergenic 45.0%
TCAATCACACTGCAAACAGG+AGG - chr6_3:72519048-72519067 None:intergenic 45.0%
TCGTCAATCACACTGCAAAC+AGG - chr6_3:72519051-72519070 None:intergenic 45.0%
TGTGTCTGATTTACAACCCG+CGG + chr6_3:72519277-72519296 Msa0958540:intron 45.0%
!! AACTCCAACTGCTGGTTTAG+AGG - chr6_3:72519375-72519394 None:intergenic 45.0%
CATACAACAACTCCAACTGC+TGG - chr6_3:72519383-72519402 None:intergenic 45.0%
!! GCTGATTTTAAAAGGGCTGC+AGG + chr6_3:72519444-72519463 Msa0958540:CDS 45.0%
ATGCTGAAAACTGCGTGGTT+TGG + chr6_3:72518681-72518700 Msa0958540:CDS 45.0%
! AAAACTGCGTGGTTTGGCAA+GGG + chr6_3:72518687-72518706 Msa0958540:CDS 45.0%
TTGTCGGATTCAGGGGTTTA+GGG + chr6_3:72518898-72518917 Msa0958540:intron 45.0%
ATGTGGCAGTTAAACTGCAG+AGG - chr6_3:72518979-72518998 None:intergenic 45.0%
!!! CCATTTGCGGTTTTGAGATG+TGG - chr6_3:72518996-72519015 None:intergenic 45.0%
CCACATCTCAAAACCGCAAA+TGG + chr6_3:72518993-72519012 Msa0958540:CDS 45.0%
CAATCACACTGCAAACAGGA+GGG - chr6_3:72519047-72519066 None:intergenic 45.0%
TCAATCACACTGCAAACAGG+AGG - chr6_3:72519048-72519067 None:intergenic 45.0%
TCGTCAATCACACTGCAAAC+AGG - chr6_3:72519051-72519070 None:intergenic 45.0%
TGTGTCTGATTTACAACCCG+CGG + chr6_3:72519277-72519296 Msa0958540:intron 45.0%
!! AACTCCAACTGCTGGTTTAG+AGG - chr6_3:72519375-72519394 None:intergenic 45.0%
CATACAACAACTCCAACTGC+TGG - chr6_3:72519383-72519402 None:intergenic 45.0%
!! GCTGATTTTAAAAGGGCTGC+AGG + chr6_3:72519444-72519463 Msa0958540:CDS 45.0%
! GAAAACTGCGTGGTTTGGCA+AGG + chr6_3:72518686-72518705 Msa0958540:CDS 50.0%
GTTGTCGGATTCAGGGGTTT+AGG + chr6_3:72518897-72518916 Msa0958540:intron 50.0%
AAACAGGAGGGAAGTGGAAG+TGG - chr6_3:72519035-72519054 None:intergenic 50.0%
CGAACTTTCTGCAGAACCCA+AGG + chr6_3:72519068-72519087 Msa0958540:CDS 50.0%
TGGAGTTGTTGTATGCAGCG+CGG + chr6_3:72519388-72519407 Msa0958540:intron 50.0%
AGCTGAAGTTCCAAACCAGC+AGG + chr6_3:72519566-72519585 Msa0958540:CDS 50.0%
! GCTTCATTCTCCTGCTGGTT+TGG - chr6_3:72519579-72519598 None:intergenic 50.0%
! GAAAACTGCGTGGTTTGGCA+AGG + chr6_3:72518686-72518705 Msa0958540:CDS 50.0%
GTTGTCGGATTCAGGGGTTT+AGG + chr6_3:72518897-72518916 Msa0958540:intron 50.0%
AAACAGGAGGGAAGTGGAAG+TGG - chr6_3:72519035-72519054 None:intergenic 50.0%
CGAACTTTCTGCAGAACCCA+AGG + chr6_3:72519068-72519087 Msa0958540:CDS 50.0%
TGGAGTTGTTGTATGCAGCG+CGG + chr6_3:72519388-72519407 Msa0958540:intron 50.0%
AGCTGAAGTTCCAAACCAGC+AGG + chr6_3:72519566-72519585 Msa0958540:CDS 50.0%
! GCTTCATTCTCCTGCTGGTT+TGG - chr6_3:72519579-72519598 None:intergenic 50.0%
AAACCGCAAATGGCTCCACC+CGG + chr6_3:72519003-72519022 Msa0958540:CDS 55.0%
CACTGCAAACAGGAGGGAAG+TGG - chr6_3:72519041-72519060 None:intergenic 55.0%
AAACCGCAAATGGCTCCACC+CGG + chr6_3:72519003-72519022 Msa0958540:CDS 55.0%
CACTGCAAACAGGAGGGAAG+TGG - chr6_3:72519041-72519060 None:intergenic 55.0%
AAGCCGGGTGGAGCCATTTG+CGG - chr6_3:72519009-72519028 None:intergenic 60.0%
! AAGTGGAAGTGGCGGAAGCC+GGG - chr6_3:72519024-72519043 None:intergenic 60.0%
! GAAGTGGAAGTGGCGGAAGC+CGG - chr6_3:72519025-72519044 None:intergenic 60.0%
CAGGAGGGAAGTGGAAGTGG+CGG - chr6_3:72519032-72519051 None:intergenic 60.0%
AAGCCGGGTGGAGCCATTTG+CGG - chr6_3:72519009-72519028 None:intergenic 60.0%
! AAGTGGAAGTGGCGGAAGCC+GGG - chr6_3:72519024-72519043 None:intergenic 60.0%
! GAAGTGGAAGTGGCGGAAGC+CGG - chr6_3:72519025-72519044 None:intergenic 60.0%
CAGGAGGGAAGTGGAAGTGG+CGG - chr6_3:72519032-72519051 None:intergenic 60.0%
! TGGAAGTGGCGGAAGCCGGG+TGG - chr6_3:72519021-72519040 None:intergenic 70.0%
! GTATGCAGCGCGGACTGCCC+TGG + chr6_3:72519398-72519417 Msa0958540:intron 70.0%
! TGGAAGTGGCGGAAGCCGGG+TGG - chr6_3:72519021-72519040 None:intergenic 70.0%
! GTATGCAGCGCGGACTGCCC+TGG + chr6_3:72519398-72519417 Msa0958540:intron 70.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 72518681 72519602 72518681 ID=Msa0958540;Name=Msa0958540
chr6_3 mRNA 72518681 72519602 72518681 ID=Msa0958540-mRNA-1;Parent=Msa0958540;Name=Msa0958540-mRNA-1;_AED=0.43;_eAED=0.43;_QI=0|0|0|1|1|1|3|0|135
chr6_3 exon 72518681 72518782 72518681 ID=Msa0958540-mRNA-1:exon:13223;Parent=Msa0958540-mRNA-1
chr6_3 exon 72518985 72519093 72518985 ID=Msa0958540-mRNA-1:exon:13224;Parent=Msa0958540-mRNA-1
chr6_3 exon 72519406 72519602 72519406 ID=Msa0958540-mRNA-1:exon:13225;Parent=Msa0958540-mRNA-1
chr6_3 CDS 72518681 72518782 72518681 ID=Msa0958540-mRNA-1:cds;Parent=Msa0958540-mRNA-1
chr6_3 CDS 72518985 72519093 72518985 ID=Msa0958540-mRNA-1:cds;Parent=Msa0958540-mRNA-1
chr6_3 CDS 72519406 72519602 72519406 ID=Msa0958540-mRNA-1:cds;Parent=Msa0958540-mRNA-1
Gene Sequence

>Msa0958540

ATGCTGAAAACTGCGTGGTTTGGCAAGGGTCATTATAGAGATTATGTTGCCAAAAACCGTAAAGAACTTCGAAGGCTGAAAAAGCAAATTAAAAAACATGAGTTTAACTGCCACATCTCAAAACCGCAAATGGCTCCACCCGGCTTCCGCCACTTCCACTTCCCTCCTGTTTGCAGTGTGATTGACGAACTTTCTGCAGAACCCAAGGCAACGCGGACTGCCCTGGATGAAATTGAAAAGCAGAAAGAAGCTGATTTTAAAAGGGCTGCAGGTGAAATTAAGAAACTGAGAGTTCAAATTCAAAAGAAGATAGATGAAAAAGCTGCATCTAAGGCAGCTGAAGTTCCAAATGAAGAAGGTACATCTAAGGCAGCTGAAGTTCCAAACCAGCAGGAGAATGAAGCTTAA

Protein sequence

>Msa0958540

MLKTAWFGKGHYRDYVAKNRKELRRLKKQIKKHEFNCHISKPQMAPPGFRHFHFPPVCSVIDELSAEPKATRTALDEIEKQKEADFKRAAGEIKKLRVQIQKKIDEKAASKAAEVPNEEGTSKAAEVPNQQENEA*