AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0250780

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0250780 MtrunA17_Chr5g0394601 96.296 108 4 0 1 108 1 108 5.15e-72 213
Msa0250780 MtrunA17_Chr1g0205251 77.647 85 18 1 1 84 1 85 2.03e-42 138
Msa0250780 MtrunA17_Chr5g0394631 77.011 87 18 1 98 182 287 373 8.52e-35 126
Msa0250780 MtrunA17_Chr5g0394631 65.476 84 29 0 99 182 79 162 2.26e-28 108
Msa0250780 MtrunA17_Chr5g0394621 71.951 82 23 0 101 182 81 162 1.76e-32 115
Msa0250780 MtrunA17_Chr8g0344381 48.077 104 46 2 2 97 30 133 1.63e-27 101
Msa0250780 MtrunA17_Chr1g0204951 66.176 68 23 0 115 182 95 162 2.50e-24 94.0
Msa0250780 MtrunA17_Chr1g0204971 63.235 68 25 0 115 182 95 162 6.14e-22 87.8
Msa0250780 MtrunA17_Chr3g0136441 44.304 79 44 0 1 79 10 88 6.93e-22 86.3
Msa0250780 MtrunA17_Chr4g0070371 45.833 72 39 0 1 72 23 94 4.12e-21 84.7
Msa0250780 MtrunA17_Chr3g0140381 35.897 117 65 2 2 114 36 146 1.63e-19 80.5
Msa0250780 MtrunA17_Chr4g0070351 45.946 74 40 0 1 74 29 102 3.65e-19 79.0
Msa0250780 MtrunA17_Chr8g0340421 40.625 96 48 3 2 91 62 154 8.28e-19 79.7
Msa0250780 MtrunA17_Chr2g0331111 40.426 94 51 2 2 91 62 154 9.28e-18 77.0
Msa0250780 MtrunA17_Chr1g0150711 45.312 64 32 1 5 65 19 82 8.26e-15 68.2
Msa0250780 MtrunA17_Chr7g0223351 50.820 61 30 0 122 182 84 144 3.02e-14 67.4
Msa0250780 MtrunA17_Chr7g0223361 52.459 61 29 0 122 182 85 145 3.72e-14 67.0
Msa0250780 MtrunA17_Chr7g0273661 52.459 61 29 0 122 182 86 146 1.56e-13 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0250780 AT3G22540.1 68.519 108 30 3 1 105 1 107 2.41e-42 138
Msa0250780 AT4G14819.1 64.151 106 35 2 1 105 1 104 4.37e-39 129
Msa0250780 AT1G72510.1 47.253 91 43 1 2 87 33 123 5.18e-23 90.5
Msa0250780 AT1G72510.2 47.253 91 43 1 2 87 33 123 5.18e-23 90.5
Msa0250780 AT2G32020.1 68.333 60 19 0 123 182 96 155 2.06e-20 84.0
Msa0250780 AT2G32030.1 68.852 61 19 0 122 182 100 160 3.43e-20 83.6
Msa0250780 AT1G79770.1 42.202 109 58 2 1 105 50 157 4.18e-20 82.8
Msa0250780 AT5G20670.1 38.462 104 53 2 3 95 23 126 7.91e-20 81.6
Msa0250780 AT5G25840.1 37.143 105 57 2 2 97 42 146 4.52e-18 77.8
Msa0250780 AT1G54095.1 44.737 76 39 2 2 74 15 90 5.94e-15 68.9
Msa0250780 AT2G09970.1 38.043 92 51 2 2 87 33 124 1.07e-14 68.6
Msa0250780 AT2G25780.1 39.326 89 47 3 7 89 40 127 1.20e-13 65.5
Msa0250780 AT3G22560.1 39.394 99 51 3 85 182 57 147 2.30e-12 62.8

Find 31 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAATCAAATGTGCAGAAAT+TGG 0.218349 2_2:+39894997 Msa0250780:CDS
TCCTAAGAACTCACTCCTTT+TGG 0.233747 2_2:-39895182 None:intergenic
AGTCAAAATTTGATGGAAAA+TGG 0.285752 2_2:+39894570 Msa0250780:CDS
ATGTTCTAGGCTCTAAATAC+TGG 0.313478 2_2:+39895022 Msa0250780:CDS
GCAGAAATTGGGTATGTTCT+AGG 0.344662 2_2:+39895009 Msa0250780:CDS
GTTAGAGATGAAGCTATTAG+AGG 0.347276 2_2:+39894617 Msa0250780:CDS
GGCTCTAAATACTGGGGTAA+AGG 0.409375 2_2:+39895030 Msa0250780:CDS
CACGTTTGCTGTGAAACAAA+TGG 0.422199 2_2:+39895059 Msa0250780:CDS
CTTGTTGATGTGGATAATGT+TGG 0.439455 2_2:+39895129 Msa0250780:CDS
GCTCTAAATACTGGGGTAAA+GGG 0.442106 2_2:+39895031 Msa0250780:CDS
CAAAGAGTGCTTGAGAAAGT+TGG 0.446874 2_2:+39895156 Msa0250780:CDS
GAATCAAATGTGCAGAAATT+GGG 0.456981 2_2:+39894998 Msa0250780:CDS
GAAGTGAAGTCAAAATTTGA+TGG 0.458617 2_2:+39894563 Msa0250780:CDS
TGCTGTGAAACAAATGGTTA+AGG 0.473285 2_2:+39895065 Msa0250780:CDS
TTTGATGGAAAATGGTTATG+TGG 0.481592 2_2:+39894578 Msa0250780:CDS
TGAGAAAGTTGGTTTCCAAA+AGG 0.498958 2_2:+39895167 Msa0250780:CDS
TGTTCTAGGCTCTAAATACT+GGG 0.526941 2_2:+39895023 Msa0250780:CDS
TTGATGGAAAATGGTTATGT+GGG 0.531455 2_2:+39894579 Msa0250780:CDS
TTGTTGATGTGGATAATGTT+GGG 0.535303 2_2:+39895130 Msa0250780:CDS
TGAGTGTTGCGGCTTAAAAG+AGG 0.545307 2_2:+39894517 Msa0250780:CDS
TTAGAGATGAAGCTATTAGA+GGG 0.554437 2_2:+39894618 Msa0250780:CDS
AACTCTGTTGACCTTCTCCT+AGG 0.571015 2_2:-39894746 None:intergenic
GCTTGAAGCTCTTGTTGATG+TGG 0.580383 2_2:+39895119 Msa0250780:CDS
CCATCAGCAACACAAACTGC+AGG 0.594058 2_2:-39894710 None:intergenic
ATGGTATGAGACAGATACCT+AGG 0.596540 2_2:+39894729 Msa0250780:CDS
CCTGCAGTTTGTGTTGCTGA+TGG 0.605550 2_2:+39894710 Msa0250780:CDS
TGAGACAGATACCTAGGAGA+AGG 0.609498 2_2:+39894735 Msa0250780:CDS
TCAGCTAAGTGTGAGTGTTG+CGG 0.613560 2_2:+39894506 Msa0250780:CDS
CATTTGTTTCACAGCAAACG+TGG 0.659491 2_2:-39895058 None:intergenic
CATCAAACAAACACAGTACG+AGG 0.670845 2_2:+39894774 Msa0250780:CDS
GTTCTAGGCTCTAAATACTG+GGG 0.712321 2_2:+39895024 Msa0250780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTGCTTACTATTTAAAAAA+AGG - chr2_2:39894913-39894932 None:intergenic 15.0%
!!! ATTCATTGTATTTTCATACT+TGG + chr2_2:39895092-39895111 Msa0250780:CDS 20.0%
! AGTCAAAATTTGATGGAAAA+TGG + chr2_2:39894570-39894589 Msa0250780:CDS 25.0%
! TATTTCAACCATACCAAAAA+CGG - chr2_2:39894878-39894897 None:intergenic 25.0%
!! TTGTATTTTCATACTTGGAA+AGG + chr2_2:39895097-39895116 Msa0250780:CDS 25.0%
GAAGTGAAGTCAAAATTTGA+TGG + chr2_2:39894563-39894582 Msa0250780:CDS 30.0%
TTTGATGGAAAATGGTTATG+TGG + chr2_2:39894578-39894597 Msa0250780:CDS 30.0%
TTGATGGAAAATGGTTATGT+GGG + chr2_2:39894579-39894598 Msa0250780:CDS 30.0%
TTAGAGATGAAGCTATTAGA+GGG + chr2_2:39894618-39894637 Msa0250780:CDS 30.0%
! TTTTTATTCACCACCTACTT+GGG - chr2_2:39894813-39894832 None:intergenic 30.0%
!!! TTTTTTATTCACCACCTACT+TGG - chr2_2:39894814-39894833 None:intergenic 30.0%
GAATAAAAAACAGAGGAGAT+TGG + chr2_2:39894824-39894843 Msa0250780:intron 30.0%
AGAATCAAATGTGCAGAAAT+TGG + chr2_2:39894997-39895016 Msa0250780:CDS 30.0%
GAATCAAATGTGCAGAAATT+GGG + chr2_2:39894998-39895017 Msa0250780:CDS 30.0%
TTGTTGATGTGGATAATGTT+GGG + chr2_2:39895130-39895149 Msa0250780:CDS 30.0%
GTTAGAGATGAAGCTATTAG+AGG + chr2_2:39894617-39894636 Msa0250780:CDS 35.0%
AGGGAAAAAGACATTTGCAA+TGG + chr2_2:39894637-39894656 Msa0250780:CDS 35.0%
AGGTGGTGAATAAAAAACAG+AGG + chr2_2:39894817-39894836 Msa0250780:intron 35.0%
AAAAACAGAGGAGATTGGAA+AGG + chr2_2:39894829-39894848 Msa0250780:intron 35.0%
TGCCATAATGATCATGCTAT+TGG + chr2_2:39894934-39894953 Msa0250780:intron 35.0%
GCCATAATGATCATGCTATT+GGG + chr2_2:39894935-39894954 Msa0250780:intron 35.0%
ACCCAATAGCATGATCATTA+TGG - chr2_2:39894939-39894958 None:intergenic 35.0%
!! ATGTTCTAGGCTCTAAATAC+TGG + chr2_2:39895022-39895041 Msa0250780:CDS 35.0%
!! TGTTCTAGGCTCTAAATACT+GGG + chr2_2:39895023-39895042 Msa0250780:CDS 35.0%
TGCTGTGAAACAAATGGTTA+AGG + chr2_2:39895065-39895084 Msa0250780:CDS 35.0%
CTTGTTGATGTGGATAATGT+TGG + chr2_2:39895129-39895148 Msa0250780:CDS 35.0%
! TGAGAAAGTTGGTTTCCAAA+AGG + chr2_2:39895167-39895186 Msa0250780:CDS 35.0%
ATGGTATGAGACAGATACCT+AGG + chr2_2:39894729-39894748 Msa0250780:CDS 40.0%
CATCAAACAAACACAGTACG+AGG + chr2_2:39894774-39894793 Msa0250780:CDS 40.0%
TCAACTTCAACTTCCCAAGT+AGG + chr2_2:39894797-39894816 Msa0250780:intron 40.0%
GAGATTGGAAAGGTTGGAAT+AGG + chr2_2:39894839-39894858 Msa0250780:intron 40.0%
! ACATACCATCACTCCGTTTT+TGG + chr2_2:39894862-39894881 Msa0250780:intron 40.0%
GCAGAAATTGGGTATGTTCT+AGG + chr2_2:39895009-39895028 Msa0250780:CDS 40.0%
!! GTTCTAGGCTCTAAATACTG+GGG + chr2_2:39895024-39895043 Msa0250780:CDS 40.0%
! GCTCTAAATACTGGGGTAAA+GGG + chr2_2:39895031-39895050 Msa0250780:CDS 40.0%
CATTTGTTTCACAGCAAACG+TGG - chr2_2:39895061-39895080 None:intergenic 40.0%
!! CACGTTTGCTGTGAAACAAA+TGG + chr2_2:39895059-39895078 Msa0250780:CDS 40.0%
!! CAAAGAGTGCTTGAGAAAGT+TGG + chr2_2:39895156-39895175 Msa0250780:CDS 40.0%
! TCAGCTAAGTGTGAGTGTTG+CGG + chr2_2:39894506-39894525 Msa0250780:CDS 45.0%
! TGAGTGTTGCGGCTTAAAAG+AGG + chr2_2:39894517-39894536 Msa0250780:CDS 45.0%
TGAGACAGATACCTAGGAGA+AGG + chr2_2:39894735-39894754 Msa0250780:CDS 45.0%
AACTCTGTTGACCTTCTCCT+AGG - chr2_2:39894749-39894768 None:intergenic 45.0%
ACTTCAACTTCCCAAGTAGG+TGG + chr2_2:39894800-39894819 Msa0250780:intron 45.0%
ACAGAGGAGATTGGAAAGGT+TGG + chr2_2:39894833-39894852 Msa0250780:intron 45.0%
CCATACCAAAAACGGAGTGA+TGG - chr2_2:39894870-39894889 None:intergenic 45.0%
!!! CCATCACTCCGTTTTTGGTA+TGG + chr2_2:39894867-39894886 Msa0250780:intron 45.0%
!! GGCTCTAAATACTGGGGTAA+AGG + chr2_2:39895030-39895049 Msa0250780:CDS 45.0%
GCTTGAAGCTCTTGTTGATG+TGG + chr2_2:39895119-39895138 Msa0250780:CDS 45.0%
CCATCAGCAACACAAACTGC+AGG - chr2_2:39894713-39894732 None:intergenic 50.0%
! CCTGCAGTTTGTGTTGCTGA+TGG + chr2_2:39894710-39894729 Msa0250780:CDS 50.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 39894494 39895194 39894494 ID=Msa0250780;Name=Msa0250780
chr2_2 mRNA 39894494 39895194 39894494 ID=Msa0250780-mRNA-1;Parent=Msa0250780;Name=Msa0250780-mRNA-1;_AED=0.29;_eAED=0.29;_QI=0|0|0|1|1|1|2|0|182
chr2_2 exon 39894494 39894814 39894494 ID=Msa0250780-mRNA-1:exon:12349;Parent=Msa0250780-mRNA-1
chr2_2 exon 39894967 39895194 39894967 ID=Msa0250780-mRNA-1:exon:12350;Parent=Msa0250780-mRNA-1
chr2_2 CDS 39894494 39894814 39894494 ID=Msa0250780-mRNA-1:cds;Parent=Msa0250780-mRNA-1
chr2_2 CDS 39894967 39895194 39894967 ID=Msa0250780-mRNA-1:cds;Parent=Msa0250780-mRNA-1
Gene Sequence

>Msa0250780

ATGGAAATCGAATCAGCTAAGTGTGAGTGTTGCGGCTTAAAAGAGGATTGCACTCAAGACTACATCAGTGAAGTGAAGTCAAAATTTGATGGAAAATGGTTATGTGGGTTGTGTTCAGAAGTTGTTAGAGATGAAGCTATTAGAGGGAAAAAGACATTTGCAATGGAAGAAGCAATAAAAGCTCACATGTTGTTCTGTTGTAAGATTAAATCAAATCCTGCAGTTTGTGTTGCTGATGGTATGAGACAGATACCTAGGAGAAGGTCAACAGAGTTGTCTTCATCAAACAAACACAGTACGAGGTCAACTTCAACTTCCCAATTGTTCTCGAGTTCACGTCATGATCTAAGCAGAATCAAATGTGCAGAAATTGGGTATGTTCTAGGCTCTAAATACTGGGGTAAAGGGATTACCACGTTTGCTGTGAAACAAATGGTTAAGGTTGCATTCATTGTATTTTCATACTTGGAAAGGCTTGAAGCTCTTGTTGATGTGGATAATGTTGGGTCGCAAAGAGTGCTTGAGAAAGTTGGTTTCCAAAAGGAGTGA
Protein sequence

>Msa0250780

MEIESAKCECCGLKEDCTQDYISEVKSKFDGKWLCGLCSEVVRDEAIRGKKTFAMEEAIKAHMLFCCKIKSNPAVCVADGMRQIPRRRSTELSSSNKHSTRSTSTSQLFSSSRHDLSRIKCAEIGYVLGSKYWGKGITTFAVKQMVKVAFIVFSYLERLEALVDVDNVGSQRVLEKVGFQKE*