AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1342300

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1342300 MtrunA17_Chr1g0205861 50.495 101 50 0 3 103 2 102 9.46e-29 102
Msa1342300 MtrunA17_Chr7g0256011 52.809 89 41 1 1 89 1 88 6.41e-22 85.1
Msa1342300 MtrunA17_Chr1g0206771 48.611 72 37 0 11 82 10 81 3.59e-16 72.0
Msa1342300 MtrunA17_Chr1g0206771 46.269 67 36 0 15 81 93 159 1.10e-12 62.8
Msa1342300 MtrunA17_Chr3g0077891 44.578 83 45 1 11 92 93 175 1.44e-15 70.1
Msa1342300 MtrunA17_Chr5g0415031 41.558 77 45 0 9 85 35 111 1.56e-14 70.1
Msa1342300 MtrunA17_Chr3g0077941 45.122 82 44 1 12 92 93 174 3.17e-14 66.6
Msa1342300 MtrunA17_Chr8g0364231 42.308 78 44 1 8 85 34 110 1.10e-13 67.8
Msa1342300 MtrunA17_Chr1g0206781 39.080 87 52 1 8 93 2 88 2.10e-13 63.2
Msa1342300 MtrunA17_Chr4g0075971 40.187 107 60 2 16 121 88 191 4.44e-13 65.9
Msa1342300 MtrunA17_Chr4g0075971 32.743 113 72 2 20 128 175 287 2.53e-11 60.8
Msa1342300 MtrunA17_Chr3g0077881 42.169 83 47 1 11 92 93 175 1.44e-12 62.4
Msa1342300 MtrunA17_Chr4g0075861 38.318 107 62 2 16 121 88 191 1.63e-12 63.9
Msa1342300 MtrunA17_Chr4g0075861 33.628 113 71 2 20 128 175 287 7.66e-12 62.0
Msa1342300 MtrunA17_Chr1g0205811 50.000 62 31 0 17 78 14 75 4.14e-12 59.7
Msa1342300 MtrunA17_Chr1g0205801 46.875 64 34 0 15 78 10 73 5.38e-12 59.3
Msa1342300 MtrunA17_Chr6g0452001 35.227 88 56 1 13 99 59 146 1.73e-11 61.2
Msa1342300 MtrunA17_Chr1g0205821 45.902 61 33 0 18 78 100 160 2.32e-11 58.9
Msa1342300 MtrunA17_Chr1g0205821 46.774 62 33 0 17 78 13 74 3.81e-11 58.5
Msa1342300 MtrunA17_Chr1g0205831 48.276 58 30 0 21 78 6 63 7.44e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1342300 AT3G01320.2 36.782 87 55 0 13 99 53 139 6.41e-13 65.9
Msa1342300 AT3G01320.1 36.782 87 55 0 13 99 53 139 6.86e-13 65.9
Msa1342300 AT1G70060.2 38.889 90 54 1 5 94 3 91 2.17e-12 64.3
Msa1342300 AT1G70060.1 38.889 90 54 1 5 94 3 91 2.17e-12 64.3
Msa1342300 AT1G24190.3 39.474 76 45 1 5 80 3 77 7.33e-12 62.8
Msa1342300 AT1G24190.2 39.474 76 45 1 5 80 3 77 7.84e-12 62.8
Msa1342300 AT1G24190.1 39.474 76 45 1 5 80 3 77 7.92e-12 62.8
Msa1342300 AT5G15040.1 42.188 64 37 0 15 78 1 64 2.00e-11 57.4
Msa1342300 AT5G15040.3 42.188 64 37 0 15 78 1 64 2.00e-11 57.4
Msa1342300 AT5G15040.2 42.188 64 37 0 15 78 1 64 2.00e-11 57.4
Msa1342300 AT1G27250.1 34.667 75 49 0 6 80 10 84 9.53e-11 57.0

Find 15 sgRNAs with CRISPR-Local

Find 18 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTCAAGCATTTGATTAAAT+TGG 0.233339 tig0005338:-7357 None:intergenic
TAGAGATCTCTTTAGCATTA+AGG 0.235668 tig0005338:-7257 None:intergenic
TGACCCTATTTGATCGAGTT+TGG 0.318141 tig0005338:-7410 None:intergenic
ATTGCCAAACTCGATCAAAT+AGG 0.324623 tig0005338:+7406 Msa1342300:CDS
AGTTGTGTTTCAAGATAAGA+TGG 0.435039 tig0005338:+7108 Msa1342300:CDS
AAGCAAAACAGCACATCAAA+CGG 0.452640 tig0005338:+7308 Msa1342300:CDS
TTGCCAAACTCGATCAAATA+GGG 0.483923 tig0005338:+7407 Msa1342300:CDS
AGCAAAACAGCACATCAAAC+GGG 0.507498 tig0005338:+7309 Msa1342300:CDS
CAAACGGGATCGATTCAAGT+TGG 0.545140 tig0005338:+7324 Msa1342300:CDS
AAGGATTACAGTGGTGATGC+TGG 0.561781 tig0005338:+7034 Msa1342300:CDS
ACGGGATCGATTCAAGTTGG+AGG 0.593315 tig0005338:+7327 Msa1342300:CDS
AAAATGGAGGAGTTGTTCGA+TGG 0.597043 tig0005338:+7205 Msa1342300:CDS
TCAGAAACTACTAAGCATGA+AGG 0.638522 tig0005338:+7057 Msa1342300:CDS
GCAGAGAACATGAAGAAGCG+AGG 0.677188 tig0005338:+7469 Msa1342300:CDS
CGACTGATGAAGGATTACAG+TGG 0.795711 tig0005338:+7025 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAAAGTTTTGTATGATTTCA+AGG + tig0005338:7150-7169 Msa1342300:CDS 25.0%
! TGTCAAGCATTTGATTAAAT+TGG - tig0005338:7360-7379 None:intergenic 25.0%
AGTTGTGTTTCAAGATAAGA+TGG + tig0005338:7108-7127 Msa1342300:CDS 30.0%
TAGAGATCTCTTTAGCATTA+AGG - tig0005338:7260-7279 None:intergenic 30.0%
TCAGAAACTACTAAGCATGA+AGG + tig0005338:7057-7076 Msa1342300:CDS 35.0%
AAGCAAAACAGCACATCAAA+CGG + tig0005338:7308-7327 Msa1342300:CDS 35.0%
ATTGCCAAACTCGATCAAAT+AGG + tig0005338:7406-7425 Msa1342300:CDS 35.0%
TTGCCAAACTCGATCAAATA+GGG + tig0005338:7407-7426 Msa1342300:CDS 35.0%
!! AGAAAGTGCCACAGCAAAAA+TGG + tig0005338:7189-7208 Msa1342300:CDS 40.0%
AAAATGGAGGAGTTGTTCGA+TGG + tig0005338:7205-7224 Msa1342300:CDS 40.0%
AGCAAAACAGCACATCAAAC+GGG + tig0005338:7309-7328 Msa1342300:CDS 40.0%
TGACCCTATTTGATCGAGTT+TGG - tig0005338:7413-7432 None:intergenic 40.0%
! AAGGATTACAGTGGTGATGC+TGG + tig0005338:7034-7053 Msa1342300:CDS 45.0%
AAGTGCCACAGCAAAAATGG+AGG + tig0005338:7192-7211 Msa1342300:CDS 45.0%
!! CAACTCCTCCATTTTTGCTG+TGG - tig0005338:7200-7219 None:intergenic 45.0%
! CAAACGGGATCGATTCAAGT+TGG + tig0005338:7324-7343 Msa1342300:CDS 45.0%
!! ACGGGATCGATTCAAGTTGG+AGG + tig0005338:7327-7346 Msa1342300:CDS 50.0%
GCAGAGAACATGAAGAAGCG+AGG + tig0005338:7469-7488 Msa1342300:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0005338 gene 7031 7516 7031 ID=Msa1342300;Name=Msa1342300
tig0005338 mRNA 7031 7516 7031 ID=Msa1342300-mRNA-1;Parent=Msa1342300;Name=Msa1342300-mRNA-1;_AED=0.13;_eAED=0.15;_QI=0|-1|0|1|-1|1|1|0|161
tig0005338 exon 7031 7516 7031 ID=Msa1342300-mRNA-1:exon:3540;Parent=Msa1342300-mRNA-1
tig0005338 CDS 7031 7516 7031 ID=Msa1342300-mRNA-1:cds;Parent=Msa1342300-mRNA-1
Gene Sequence

>Msa1342300

ATGAAGGATTACAGTGGTGATGCTGGTCAGAAACTACTAAGCATGAAGGAAGCATCAGCGTTTGTAAATGATGTAAAAGTTGTGTTTCAAGATAAGATGGAAAAGTATGATGAGTTTGTGAAAGTTTTGTATGATTTCAAGGCTATGAGAATTGATCAAGAAAGTGCCACAGCAAAAATGGAGGAGTTGTTCGATGGACATTCAGATTTGATTATGAAATTAAACTCCTTAATGCTAAAGAGATCTCTAATGACTAACAATGATCATAATGACACTGAAGCAAAACAGCACATCAAACGGGATCGATTCAAGTTGGAGGTAATTGACCAATTTAATCAAATGCTTGACAAACTAGAGAAATTTGAGTTGAAAGTGATTGCCAAACTCGATCAAATAGGGTCAAGTGCTCAACATTCAACTAAAGCAATATTAGACATTGCAGAGAACATGAAGAAGCGAGGCGTGACAAACGTGAGTCAAAAGTGA
Protein sequence

>Msa1342300

MKDYSGDAGQKLLSMKEASAFVNDVKVVFQDKMEKYDEFVKVLYDFKAMRIDQESATAKMEELFDGHSDLIMKLNSLMLKRSLMTNNDHNDTEAKQHIKRDRFKLEVIDQFNQMLDKLEKFELKVIAKLDQIGSSAQHSTKAILDIAENMKKRGVTNVSQK*