AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0644440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0644440 MtrunA17_Chr4g0031001 96.000 150 4 1 1 150 1 148 6.65e-97 275
Msa0644440 MtrunA17_Chr4g0031651 95.333 150 5 1 1 150 1 148 3.60e-96 273
Msa0644440 MtrunA17_Chr2g0327951 89.333 150 14 1 1 150 38 185 1.84e-85 248
Msa0644440 MtrunA17_Chr4g0032301 96.000 150 4 1 1 150 1 148 2.15e-83 241
Msa0644440 MtrunA17_Chr4g0035621 94.079 152 7 1 1 150 1 152 6.39e-83 240
Msa0644440 MtrunA17_Chr4g0031041 93.939 132 7 1 20 150 14 145 2.17e-81 236
Msa0644440 MtrunA17_Chr2g0327931 88.961 154 12 2 1 150 1 153 9.18e-79 230
Msa0644440 MtrunA17_Chr8g0379311 97.727 132 3 0 1 132 1 132 6.30e-76 223
Msa0644440 MtrunA17_Chr7g0272611 79.699 133 26 1 10 142 13 144 1.39e-70 209
Msa0644440 MtrunA17_Chr7g0268831 75.591 127 25 3 4 129 6 127 5.30e-60 182
Msa0644440 MtrunA17_Chr7g0273351 74.803 127 28 1 3 129 2 124 5.80e-60 182
Msa0644440 MtrunA17_Chr7g0259151 73.016 126 31 1 4 129 5 127 2.65e-59 180
Msa0644440 MtrunA17_Chr7g0273331 74.803 127 28 1 3 129 58 180 2.86e-59 182
Msa0644440 MtrunA17_Chr2g0319191 74.790 119 30 0 11 129 3 121 1.38e-58 178
Msa0644440 MtrunA17_Chr2g0319181 73.950 119 31 0 11 129 3 121 1.10e-57 176
Msa0644440 MtrunA17_Chr6g0449661 64.567 127 31 3 24 149 85 198 1.16e-47 152
Msa0644440 MtrunA17_Chr3g0119971 64.286 126 31 3 25 149 81 193 2.88e-47 151
Msa0644440 MtrunA17_Chr4g0031031 75.238 105 21 1 45 149 10 109 1.56e-45 144
Msa0644440 MtrunA17_Chr7g0273341 70.909 110 21 2 23 132 57 155 3.40e-45 145
Msa0644440 MtrunA17_Chr1g0148961 59.292 113 44 2 21 132 23 134 6.46e-36 120
Msa0644440 MtrunA17_Chr1g0148951 59.292 113 44 2 21 132 23 134 6.46e-36 120
Msa0644440 MtrunA17_Chr1g0211651 59.633 109 42 2 21 128 20 127 7.02e-35 118
Msa0644440 MtrunA17_Chr1g0184901 61.538 104 38 2 26 128 28 130 3.37e-34 116
Msa0644440 MtrunA17_Chr1g0183701 58.904 73 30 0 67 139 30 102 7.36e-25 91.7
Msa0644440 MtrunA17_Chr4g0024701 49.524 105 33 2 24 128 26 110 5.91e-22 84.7
Msa0644440 MtrunA17_Chr4g0000531 71.111 45 13 0 85 129 5 49 7.75e-16 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0644440 AT5G02560.1 81.699 153 25 1 1 150 1 153 1.54e-78 229
Msa0644440 AT5G02560.2 70.621 177 25 2 1 150 1 177 1.38e-73 218
Msa0644440 AT5G27670.1 75.658 152 33 3 1 150 1 150 2.46e-73 216
Msa0644440 AT5G59870.1 74.324 148 37 1 4 150 3 150 4.10e-71 211
Msa0644440 AT1G51060.1 71.318 129 37 0 11 139 3 131 9.31e-61 184
Msa0644440 AT4G27230.2 70.543 129 38 0 11 139 3 131 3.91e-60 182
Msa0644440 AT4G27230.1 70.543 129 38 0 11 139 3 131 3.91e-60 182
Msa0644440 AT3G20670.1 71.318 129 37 0 11 139 3 131 8.69e-60 181
Msa0644440 AT1G08880.1 72.222 126 32 1 7 129 2 127 2.20e-58 178
Msa0644440 AT5G54640.1 72.000 125 35 0 11 135 3 127 2.74e-58 177
Msa0644440 AT1G54690.1 73.438 128 28 3 3 129 5 127 9.34e-58 177
Msa0644440 AT2G38810.1 60.550 109 41 2 21 128 25 132 5.99e-36 121
Msa0644440 AT2G38810.4 60.550 109 41 2 21 128 25 132 5.99e-36 121
Msa0644440 AT2G38810.3 60.550 109 41 2 21 128 25 132 5.99e-36 121
Msa0644440 AT2G38810.2 60.550 109 41 2 21 128 25 132 5.99e-36 121
Msa0644440 AT1G52740.1 61.905 105 38 2 25 128 27 130 1.40e-34 117
Msa0644440 AT3G54560.1 57.798 109 44 2 25 132 29 136 9.47e-34 115
Msa0644440 AT3G54560.2 57.798 109 44 2 25 132 29 136 9.47e-34 115
Msa0644440 AT4G13570.1 47.826 92 46 2 32 122 28 118 5.87e-20 80.1
Msa0644440 AT4G13570.2 47.253 91 46 2 33 122 35 124 1.61e-19 79.0

Find 44 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACAGATCTAAGCCTTCTT+TGG 0.260065 4_3:-48314801 None:intergenic
CTTGTCACCGACTTCTTCCT+TGG 0.333455 4_3:-48314420 None:intergenic
CGATTCTTCCCACTGGGAAC+TGG 0.359689 4_3:-48314461 None:intergenic
TTCTTTGGCTCTTTGTTAGC+AGG 0.375405 4_3:-48314765 None:intergenic
AGAACTGCTGCTAGGTATAC+TGG 0.389575 4_3:-48314534 None:intergenic
TTTCATTCTTCTTAGGCAAA+AGG 0.417964 4_3:-48314734 None:intergenic
TACGCTCAGCGTGTTGGAAC+CGG 0.422732 4_3:+48314507 Msa0644440:CDS
TGCTGCTGAAGTTCTTGAGT+TGG 0.438702 4_3:+48314566 Msa0644440:CDS
GGCATGTGTTGTTGGCTGTT+AGG 0.442957 4_3:+48314634 Msa0644440:CDS
AAAAGGATAGGGTTAATGTT+TGG 0.446113 4_3:-48314717 None:intergenic
TCCTCCTCCTTTCCTTCCAC+CGG 0.452471 4_3:-48314397 None:intergenic
AACAAAGAGCCAAAGAAGGC+TGG 0.466354 4_3:+48314771 Msa0644440:CDS
AGCACAAAGACAACGAAGAA+AGG 0.469389 4_3:+48314372 Msa0644440:CDS
GCTGAAGTTCTTGAGTTGGC+TGG 0.471187 4_3:+48314570 Msa0644440:CDS
CAGTTCCCAGTGGGAAGAAT+CGG 0.476269 4_3:+48314462 Msa0644440:CDS
AAAGGAGCCGGTGGAAGGAA+AGG 0.476592 4_3:+48314390 Msa0644440:CDS
GCCGGTGGAAGGAAAGGAGG+AGG 0.487329 4_3:+48314396 Msa0644440:CDS
TTCTTCTTAGGCAAAAGGAT+AGG 0.488209 4_3:-48314729 None:intergenic
AATTCCAAGGCATGTGTTGT+TGG 0.490560 4_3:+48314626 Msa0644440:CDS
TCTTCTTAGGCAAAAGGATA+GGG 0.492139 4_3:-48314728 None:intergenic
GAGCTTGGTAAATTACTTGC+TGG 0.499780 4_3:+48314666 Msa0644440:CDS
ACAGCCAACAACACATGCCT+TGG 0.515073 4_3:-48314630 None:intergenic
ATCGGTCGATACTTGAAGAA+AGG 0.519021 4_3:+48314480 Msa0644440:CDS
GGCTGGAAAATCTCCAAAGA+AGG 0.523644 4_3:+48314788 Msa0644440:CDS
GGAAGATACGCTCAGCGTGT+TGG 0.531317 4_3:+48314501 Msa0644440:CDS
TATCGACCGATTCTTCCCAC+TGG 0.544173 4_3:-48314468 None:intergenic
TGCTAACAAAGAGCCAAAGA+AGG 0.544648 4_3:+48314767 Msa0644440:CDS
CGAAGAAAGGAGCCGGTGGA+AGG 0.551864 4_3:+48314385 Msa0644440:CDS
GTTAGGAACGATGAAGAGCT+TGG 0.552797 4_3:+48314651 Msa0644440:CDS
GAAGGAAAGGAGGAGGACCA+AGG 0.555100 4_3:+48314403 Msa0644440:CDS
GCTGGTGTCACAATTGCTCA+TGG 0.556477 4_3:+48314684 Msa0644440:CDS
TCCCACTGGGAACTGGAGAC+CGG 0.556836 4_3:-48314454 None:intergenic
GGAGCCGGTGGAAGGAAAGG+AGG 0.561766 4_3:+48314393 Msa0644440:CDS
TGCTAGGTATACTGGTGCAC+CGG 0.591842 4_3:-48314526 None:intergenic
GATATTCAAGAACTGCTGCT+AGG 0.592671 4_3:-48314542 None:intergenic
AAGACAACGAAGAAAGGAGC+CGG 0.594835 4_3:+48314378 Msa0644440:CDS
GTGACAAGATCAATCAGAGC+CGG 0.601599 4_3:+48314435 Msa0644440:CDS
AGGAGGACCAAGGAAGAAGT+CGG 0.610829 4_3:+48314413 Msa0644440:CDS
GCCGGTCTCCAGTTCCCAGT+GGG 0.615696 4_3:+48314453 Msa0644440:CDS
AGAAGAATAGAATAATTCCA+AGG 0.617592 4_3:+48314613 Msa0644440:CDS
ATCGACCGATTCTTCCCACT+GGG 0.626884 4_3:-48314467 None:intergenic
ACAACGAAGAAAGGAGCCGG+TGG 0.637849 4_3:+48314381 Msa0644440:CDS
AGCCGGTCTCCAGTTCCCAG+TGG 0.691656 4_3:+48314452 Msa0644440:CDS
GGTGTCACAATTGCTCATGG+TGG 0.701079 4_3:+48314687 Msa0644440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAAGAATAGAATAATTCCA+AGG + chr4_3:48314613-48314632 Msa0644440:CDS 25.0%
AAAAGGATAGGGTTAATGTT+TGG - chr4_3:48314720-48314739 None:intergenic 30.0%
TTTCATTCTTCTTAGGCAAA+AGG - chr4_3:48314737-48314756 None:intergenic 30.0%
TCTTCTTAGGCAAAAGGATA+GGG - chr4_3:48314731-48314750 None:intergenic 35.0%
TTCTTCTTAGGCAAAAGGAT+AGG - chr4_3:48314732-48314751 None:intergenic 35.0%
!!! GCAGCTTTTTCATTCTTCTT+AGG - chr4_3:48314744-48314763 None:intergenic 35.0%
AGCACAAAGACAACGAAGAA+AGG + chr4_3:48314372-48314391 Msa0644440:CDS 40.0%
ATCGGTCGATACTTGAAGAA+AGG + chr4_3:48314480-48314499 Msa0644440:CDS 40.0%
GATATTCAAGAACTGCTGCT+AGG - chr4_3:48314545-48314564 None:intergenic 40.0%
AATTCCAAGGCATGTGTTGT+TGG + chr4_3:48314626-48314645 Msa0644440:CDS 40.0%
GAGCTTGGTAAATTACTTGC+TGG + chr4_3:48314666-48314685 Msa0644440:CDS 40.0%
!! TTCTTTGGCTCTTTGTTAGC+AGG - chr4_3:48314768-48314787 None:intergenic 40.0%
TGCTAACAAAGAGCCAAAGA+AGG + chr4_3:48314767-48314786 Msa0644440:CDS 40.0%
AAGACAACGAAGAAAGGAGC+CGG + chr4_3:48314378-48314397 Msa0644440:CDS 45.0%
GTGACAAGATCAATCAGAGC+CGG + chr4_3:48314435-48314454 Msa0644440:CDS 45.0%
AGAACTGCTGCTAGGTATAC+TGG - chr4_3:48314537-48314556 None:intergenic 45.0%
TGCTGCTGAAGTTCTTGAGT+TGG + chr4_3:48314566-48314585 Msa0644440:CDS 45.0%
GTTAGGAACGATGAAGAGCT+TGG + chr4_3:48314651-48314670 Msa0644440:CDS 45.0%
AACAAAGAGCCAAAGAAGGC+TGG + chr4_3:48314771-48314790 Msa0644440:CDS 45.0%
! GGAGATTTTCCAGCCTTCTT+TGG - chr4_3:48314783-48314802 None:intergenic 45.0%
GGCTGGAAAATCTCCAAAGA+AGG + chr4_3:48314788-48314807 Msa0644440:CDS 45.0%
AGGAGGACCAAGGAAGAAGT+CGG + chr4_3:48314413-48314432 Msa0644440:CDS 50.0%
!! CTTGTCACCGACTTCTTCCT+TGG - chr4_3:48314423-48314442 None:intergenic 50.0%
CAGTTCCCAGTGGGAAGAAT+CGG + chr4_3:48314462-48314481 Msa0644440:CDS 50.0%
! ATCGACCGATTCTTCCCACT+GGG - chr4_3:48314470-48314489 None:intergenic 50.0%
! TATCGACCGATTCTTCCCAC+TGG - chr4_3:48314471-48314490 None:intergenic 50.0%
TGCTAGGTATACTGGTGCAC+CGG - chr4_3:48314529-48314548 None:intergenic 50.0%
!! GCTGAAGTTCTTGAGTTGGC+TGG + chr4_3:48314570-48314589 Msa0644440:CDS 50.0%
ACAGCCAACAACACATGCCT+TGG - chr4_3:48314633-48314652 None:intergenic 50.0%
! GGCATGTGTTGTTGGCTGTT+AGG + chr4_3:48314634-48314653 Msa0644440:CDS 50.0%
!! GCTGGTGTCACAATTGCTCA+TGG + chr4_3:48314684-48314703 Msa0644440:CDS 50.0%
! GGTGTCACAATTGCTCATGG+TGG + chr4_3:48314687-48314706 Msa0644440:CDS 50.0%
ACAACGAAGAAAGGAGCCGG+TGG + chr4_3:48314381-48314400 Msa0644440:CDS 55.0%
AAAGGAGCCGGTGGAAGGAA+AGG + chr4_3:48314390-48314409 Msa0644440:CDS 55.0%
TCCTCCTCCTTTCCTTCCAC+CGG - chr4_3:48314400-48314419 None:intergenic 55.0%
GAAGGAAAGGAGGAGGACCA+AGG + chr4_3:48314403-48314422 Msa0644440:CDS 55.0%
CGATTCTTCCCACTGGGAAC+TGG - chr4_3:48314464-48314483 None:intergenic 55.0%
GGAAGATACGCTCAGCGTGT+TGG + chr4_3:48314501-48314520 Msa0644440:CDS 55.0%
TACGCTCAGCGTGTTGGAAC+CGG + chr4_3:48314507-48314526 Msa0644440:CDS 55.0%
CGAAGAAAGGAGCCGGTGGA+AGG + chr4_3:48314385-48314404 Msa0644440:CDS 60.0%
TCCCACTGGGAACTGGAGAC+CGG - chr4_3:48314457-48314476 None:intergenic 60.0%
GGAGCCGGTGGAAGGAAAGG+AGG + chr4_3:48314393-48314412 Msa0644440:CDS 65.0%
GCCGGTGGAAGGAAAGGAGG+AGG + chr4_3:48314396-48314415 Msa0644440:CDS 65.0%
AGCCGGTCTCCAGTTCCCAG+TGG + chr4_3:48314452-48314471 Msa0644440:CDS 65.0%
GCCGGTCTCCAGTTCCCAGT+GGG + chr4_3:48314453-48314472 Msa0644440:CDS 65.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 48314363 48314815 48314363 ID=Msa0644440;Name=Msa0644440
chr4_3 mRNA 48314363 48314815 48314363 ID=Msa0644440-mRNA-1;Parent=Msa0644440;Name=Msa0644440-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|-1|0|1|-1|1|1|0|150
chr4_3 exon 48314363 48314815 48314363 ID=Msa0644440-mRNA-1:exon:11473;Parent=Msa0644440-mRNA-1
chr4_3 CDS 48314363 48314815 48314363 ID=Msa0644440-mRNA-1:cds;Parent=Msa0644440-mRNA-1
Gene Sequence

>Msa0644440

ATGGACGCAAGCACAAAGACAACGAAGAAAGGAGCCGGTGGAAGGAAAGGAGGAGGACCAAGGAAGAAGTCGGTGACAAGATCAATCAGAGCCGGTCTCCAGTTCCCAGTGGGAAGAATCGGTCGATACTTGAAGAAAGGAAGATACGCTCAGCGTGTTGGAACCGGTGCACCAGTATACCTAGCAGCAGTTCTTGAATATCTTGCTGCTGAAGTTCTTGAGTTGGCTGGAAATGCAGCACGTGATAACAAGAAGAATAGAATAATTCCAAGGCATGTGTTGTTGGCTGTTAGGAACGATGAAGAGCTTGGTAAATTACTTGCTGGTGTCACAATTGCTCATGGTGGTGTTCTTCCAAACATTAACCCTATCCTTTTGCCTAAGAAGAATGAAAAAGCTGCTCCTGCTAACAAAGAGCCAAAGAAGGCTGGAAAATCTCCAAAGAAGGCTTAG
Protein sequence

>Msa0644440

MDASTKTTKKGAGGRKGGGPRKKSVTRSIRAGLQFPVGRIGRYLKKGRYAQRVGTGAPVYLAAVLEYLAAEVLELAGNAARDNKKNRIIPRHVLLAVRNDEELGKLLAGVTIAHGGVLPNINPILLPKKNEKAAPANKEPKKAGKSPKKA*