AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1410420


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1410420 MtrunA17_Chr4g0071001 92.126 127 2 3 1 123 1 123 8.97e-78 225
Msa1410420 MtrunA17_Chr3g0135901 54.032 124 42 3 1 123 1 110 1.45e-28 100
Msa1410420 MtrunA17_Chr2g0329951 49.587 121 44 5 3 122 2 106 3.83e-28 99.4
Msa1410420 MtrunA17_Chr8g0342841 51.282 117 42 3 3 119 2 103 9.24e-28 98.2
Msa1410420 MtrunA17_Chr8g0342831 51.282 117 42 3 3 119 2 103 9.24e-28 98.2
Msa1410420 MtrunA17_Chr1g0151181 49.600 125 50 5 1 121 1 116 1.41e-19 77.8
Msa1410420 MtrunA17_Chr7g0269811 54.386 57 25 1 67 123 36 91 1.10e-17 72.0
Msa1410420 MtrunA17_Chr1g0195031 51.923 52 25 0 72 123 55 106 2.11e-16 69.3
Msa1410420 MtrunA17_Chr1g0201581 53.333 60 23 2 69 123 29 88 5.15e-11 55.1
Msa1410420 MtrunA17_Chr7g0271701 55.319 47 20 1 73 119 73 118 9.83e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1410420 AT2G19460.1 53.906 128 40 6 1 121 1 116 3.63e-34 115
Msa1410420 AT2G19460.2 53.906 128 40 6 1 121 53 168 8.10e-34 115
Msa1410420 AT5G11970.1 52.419 124 38 6 1 123 1 104 1.06e-30 105
Msa1410420 AT3G13910.1 60.294 68 22 2 52 114 30 97 4.03e-19 76.6
Msa1410420 AT3G13910.2 60.294 68 22 2 52 114 30 97 8.52e-19 75.9
Msa1410420 AT3G05725.1 44.872 78 41 2 46 122 47 123 1.51e-17 73.2
Msa1410420 AT3G62640.1 48.077 52 27 0 71 122 59 110 8.56e-15 65.5
Msa1410420 AT2G47480.1 45.902 61 33 0 61 121 48 108 9.84e-15 65.5
Msa1410420 AT1G72720.1 44.565 92 41 4 33 122 42 125 1.63e-14 65.5
Msa1410420 AT4G09890.1 59.459 37 15 0 79 115 39 75 8.89e-11 54.7

Find 22 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTGTTACCAATCTGGTTT+TGG 0.243522 tig0023654:+64478 None:intergenic
CCTTCCATCAGCGTAGGATT+TGG 0.309332 tig0023654:+64602 None:intergenic
TGTTGTTGTTGTTACCAATC+TGG 0.354115 tig0023654:+64472 None:intergenic
GTAAACTCAAAGGCTCTCTT+AGG 0.367994 tig0023654:-64323 Msa1410420:CDS
AAGAAAGGTAAATCCACAAA+TGG 0.395506 tig0023654:-64432 Msa1410420:CDS
TACAAGGTTTATTCTGTTGA+AGG 0.413127 tig0023654:-64345 Msa1410420:CDS
TTTGAAGAAGGTGCAGAGTA+AGG 0.455372 tig0023654:+64564 None:intergenic
TACTCTGCACCTTCTTCAAA+CGG 0.463760 tig0023654:-64561 Msa1410420:CDS
AGATGCAACAGAGTTGTTCA+TGG 0.485910 tig0023654:-64276 Msa1410420:CDS
AACGATGTTAAGTTCAAGAA+AGG 0.501790 tig0023654:-64447 Msa1410420:CDS
CATCCAACCCAAAACCAGAT+TGG 0.504703 tig0023654:-64486 Msa1410420:CDS
ATGCCTCCTCCGTTTGAAGA+AGG 0.518627 tig0023654:+64552 None:intergenic
AGAAAGGTAAATCCACAAAT+GGG 0.520575 tig0023654:-64431 Msa1410420:CDS
CTGCATCCTTCCATCAGCGT+AGG 0.527015 tig0023654:+64596 None:intergenic
GCAACAGAGTTGTTCATGGC+TGG 0.536888 tig0023654:-64272 Msa1410420:CDS
TTTGGATCTGAAATCTTCCA+TGG 0.557041 tig0023654:+64620 None:intergenic
AGATCCAAATCCTACGCTGA+TGG 0.558533 tig0023654:-64606 Msa1410420:CDS
TCTGTTGAAGGTAAACTCAA+AGG 0.562516 tig0023654:-64333 Msa1410420:CDS
GCACCTTCTTCAAACGGAGG+AGG 0.581419 tig0023654:-64555 Msa1410420:CDS
CCAAATCCTACGCTGATGGA+AGG 0.584749 tig0023654:-64602 Msa1410420:CDS
TCAGTGATCCTGAATTGCAG+AGG 0.668157 tig0023654:-64386 Msa1410420:CDS
TCTGCACCTTCTTCAAACGG+AGG 0.687076 tig0023654:-64558 Msa1410420:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AACGATGTTAAGTTCAAGAA+AGG - tig0023654:64440-64459 Msa1410420:CDS 30.0%
AAGAAAGGTAAATCCACAAA+TGG - tig0023654:64455-64474 Msa1410420:CDS 30.0%
AGAAAGGTAAATCCACAAAT+GGG - tig0023654:64456-64475 Msa1410420:CDS 30.0%
AAAAAGAGTTGCTAGTTACA+AGG - tig0023654:64526-64545 Msa1410420:CDS 30.0%
TACAAGGTTTATTCTGTTGA+AGG - tig0023654:64542-64561 Msa1410420:CDS 30.0%
!!! GTTGTTACCAATCTGGTTTT+GGG + tig0023654:64411-64430 None:intergenic 35.0%
!! TGTTGTTACCAATCTGGTTT+TGG + tig0023654:64412-64431 None:intergenic 35.0%
! TGTTGTTGTTGTTACCAATC+TGG + tig0023654:64418-64437 None:intergenic 35.0%
!!! TTTTGAAGTTGACCCATTTG+TGG + tig0023654:64471-64490 None:intergenic 35.0%
ATGGGTCAACTTCAAAAAGT+TGG - tig0023654:64474-64493 Msa1410420:CDS 35.0%
!!! CTTTTTTTCCTCTGCAATTC+AGG + tig0023654:64512-64531 None:intergenic 35.0%
TCTGTTGAAGGTAAACTCAA+AGG - tig0023654:64554-64573 Msa1410420:CDS 35.0%
!!! CTCTTAGGAAGAGTTTTAAG+TGG - tig0023654:64579-64598 Msa1410420:CDS 35.0%
! TTTGAAGAAGGTGCAGAGTA+AGG + tig0023654:64326-64345 None:intergenic 40.0%
TACTCTGCACCTTCTTCAAA+CGG - tig0023654:64326-64345 Msa1410420:CDS 40.0%
!!! TTACCAATCTGGTTTTGGGT+TGG + tig0023654:64407-64426 None:intergenic 40.0%
GTAAACTCAAAGGCTCTCTT+AGG - tig0023654:64564-64583 Msa1410420:CDS 40.0%
AGATGCAACAGAGTTGTTCA+TGG - tig0023654:64611-64630 Msa1410420:CDS 40.0%
AGATCCAAATCCTACGCTGA+TGG - tig0023654:64281-64300 Msa1410420:CDS 45.0%
!!! GTTTTGGGTTGGATGAACAG+AGG + tig0023654:64396-64415 None:intergenic 45.0%
CATCCAACCCAAAACCAGAT+TGG - tig0023654:64401-64420 Msa1410420:CDS 45.0%
TCAGTGATCCTGAATTGCAG+AGG - tig0023654:64501-64520 Msa1410420:CDS 45.0%
CCTTCCATCAGCGTAGGATT+TGG + tig0023654:64288-64307 None:intergenic 50.0%
CCAAATCCTACGCTGATGGA+AGG - tig0023654:64285-64304 Msa1410420:CDS 50.0%
TCTGCACCTTCTTCAAACGG+AGG - tig0023654:64329-64348 Msa1410420:CDS 50.0%
ATGCCTCCTCCGTTTGAAGA+AGG + tig0023654:64338-64357 None:intergenic 50.0%
GCAACAGAGTTGTTCATGGC+TGG - tig0023654:64615-64634 Msa1410420:CDS 50.0%
CTGCATCCTTCCATCAGCGT+AGG + tig0023654:64294-64313 None:intergenic 55.0%
GCACCTTCTTCAAACGGAGG+AGG - tig0023654:64332-64351 Msa1410420:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0023654 gene 64269 64640 64269 ID=Msa1410420;Name=Msa1410420
tig0023654 mRNA 64269 64640 64269 ID=Msa1410420-mRNA-1;Parent=Msa1410420;Name=Msa1410420-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|123
tig0023654 exon 64269 64640 64269 ID=Msa1410420-mRNA-1:exon:26539;Parent=Msa1410420-mRNA-1
tig0023654 CDS 64269 64640 64269 ID=Msa1410420-mRNA-1:cds;Parent=Msa1410420-mRNA-1
Gene Sequence

>Msa1410420

ATGGAAGATTTCAGATCCAAATCCTACGCTGATGGAAGGATGCAGCAAATTGAACCTTACTCTGCACCTTCTTCAAACGGAGGAGGCATGCAAGATCTACGTTGTTACAGCGCTTCTTATGCTTCCTCTGTTCATCCAACCCAAAACCAGATTGGTAACAACAACAACAACAACGATGTTAAGTTCAAGAAAGGTAAATCCACAAATGGGTCAACTTCAAAAAGTTGGAGCTTCAGTGATCCTGAATTGCAGAGGAAAAAAAGAGTTGCTAGTTACAAGGTTTATTCTGTTGAAGGTAAACTCAAAGGCTCTCTTAGGAAGAGTTTTAAGTGGATTAAAGATAGATGCAACAGAGTTGTTCATGGCTGGTAG

Protein sequence

>Msa1410420

MEDFRSKSYADGRMQQIEPYSAPSSNGGGMQDLRCYSASYASSVHPTQNQIGNNNNNNDVKFKKGKSTNGSTSKSWSFSDPELQRKKRVASYKVYSVEGKLKGSLRKSFKWIKDRCNRVVHGW*